Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold85
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1350895
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.21
Warning! 487514 characters in sequence are not A, C, G, or T
File 4 of 6
Found at i:590794 original size:50 final size:48
Alignment explanation
Indices: 590645--590809 Score: 188
Period size: 50 Copynumber: 3.3 Consensus size: 48
590635 CGGGAATGAT
*
590645 GGGGTTGGAGTATCCTCGATTATGAAAAATTAATTTTTTAGAAATAAAGCC
1 GGGGTTGGAGTATCC-CG-TTATGAAAAATTAATGTTTTAGAAATAAA-CC
* * *
590696 GGGGTTGGAGTATCCC-TGATGAAAATTTCATGTTTTAGAAATAAAACC
1 GGGGTTGGAGTATCCCGTTATGAAAAATTAATGTTTTAGAAAT-AAACC
* * * *
590744 GGGGTTGGAGTATCCCGGTTAAGAAAAATTGATGTTTTGGAAATGGAACC
1 GGGGTTGGAGTATCCC-GTTATGAAAAATTAATGTTTTAGAAAT-AAACC
*
590794 GGGATTGGAGTATCCC
1 GGGGTTGGAGTATCCC
590810 CGAGATGAAA
Statistics
Matches: 99, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
48 40 0.40
49 3 0.03
50 41 0.41
51 15 0.15
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.30
Consensus pattern (48 bp):
GGGGTTGGAGTATCCCGTTATGAAAAATTAATGTTTTAGAAATAAACC
Found at i:593143 original size:20 final size:20
Alignment explanation
Indices: 593120--593193 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
593110 TTCATTGTAA
593120 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAGC
*
593140 AATGTATCGATACAATAAGC
1 AATGTATCGATACAATGAGC
* * *
593160 TATGTATTGATACAATGCA-A
1 AATGTATCGATACAATG-AGC
593180 AATGTATCGATACA
1 AATGTATCGATACA
593194 TCTAGGTAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
20 45 0.98
21 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (20 bp):
AATGTATCGATACAATGAGC
Found at i:593898 original size:41 final size:40
Alignment explanation
Indices: 593799--594010 Score: 145
Period size: 41 Copynumber: 5.3 Consensus size: 40
593789 GTCCCACTTT
* * *
593799 TTGAGGACAAAGG-AAAAGAGAATGAAA-TAAGTCTTGCTCC
1 TTGAGGACAAAGGAAAAAGAAAAAGAAAGT--GTCTTGCTTC
*
593839 TTGAGGACAAAGGAAAAAAGAAAAAGAAAGTGTCCTGCTTC
1 TTGAGGACAAAGG-AAAAAGAAAAAGAAAGTGTCTTGCTTC
* * * *
593880 TTGAGGACAAAGTGAAAAAG----AG-TA-CGTCCTGCTTT
1 TTGAGGACAAAG-GAAAAAGAAAAAGAAAGTGTCTTGCTTC
* * *
593915 TTGAGGACAAAGGAAAAAAGGAAAACGAAATGCGTCTTGCTTT
1 TTGAGGACAAAGG-AAAAA-GAAAAAGAAA-GTGTCTTGCTTC
* * *
593958 TTGAGGACAAAAGAAAGAGAAAAATAAAGTGCATCTTGC-TC
1 TTGAGGACAAAGGAAAAAGAAAAAGAAAGTG--TCTTGCTTC
593999 TTTGAGGACAAA
1 -TTGAGGACAAA
594011 AAAGAAAAGA
Statistics
Matches: 140, Mismatches: 16, Indels: 30
0.75 0.09 0.16
Matches are distributed among these distances:
34 1 0.01
35 26 0.19
36 2 0.01
37 2 0.01
40 16 0.11
41 36 0.26
42 34 0.24
43 23 0.16
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.21
Consensus pattern (40 bp):
TTGAGGACAAAGGAAAAAGAAAAAGAAAGTGTCTTGCTTC
Found at i:594008 original size:42 final size:41
Alignment explanation
Indices: 593798--594069 Score: 127
Period size: 43 Copynumber: 6.6 Consensus size: 41
593788 TGTCCCACTT
* * **
593798 TTTGAGGACAAAGGAAAAG-AGAATGAAA-TAAGTCTTGCTC
1 TTTGAGGACAAAAGAAAAGAAAAAT-AAAGTGCGTCTTGCTC
* * * *
593838 CTTGAGGACAAAGGAAAAAAGAAAAAGAAAGT--GTCCTGCT-
1 TTTGAGGACAAA--AGAAAAGAAAAATAAAGTGCGTCTTGCTC
* * * * *
593878 TCTTGAGGAC-AAAG---TG-AAAA-AGAGTACGTCCTGCTT
1 T-TTGAGGACAAAAGAAAAGAAAAATAAAGTGCGTCTTGCTC
* ** *
593914 TTTGAGGACAAAGGAAAAAAGGAAAACGAAA-TGCGTCTTGCTT
1 TTTGAGGACAAA--AGAAAA-GAAAAATAAAGTGCGTCTTGCTC
*
593957 TTTGAGGACAAAAGAAAGAGAAAAATAAAGTGCATCTTGCTC
1 TTTGAGGACAAAAGAAA-AGAAAAATAAAGTGCGTCTTGCTC
* * *
593999 TTTGAGGACAAAAAAGAAAAGAAGAGAATGAAGTGTGTCCTGCTC
1 TTTGAGGAC--AAAAGAAAAGAA-A-AATAAAGTGCGTCTTGCTC
* *
594044 TTTAAGGACAAAGAAGAAAAGGAAAA
1 TTTGAGGAC-AA-AAGAAAAGAAAAA
594070 GACGTCCTGC
Statistics
Matches: 181, Mismatches: 27, Indels: 45
0.72 0.11 0.18
Matches are distributed among these distances:
33 4 0.02
34 4 0.02
35 17 0.09
36 3 0.02
38 2 0.01
40 13 0.07
41 27 0.15
42 29 0.16
43 35 0.19
44 15 0.08
45 32 0.18
ACGTcount: A:0.44, C:0.11, G:0.25, T:0.20
Consensus pattern (41 bp):
TTTGAGGACAAAAGAAAAGAAAAATAAAGTGCGTCTTGCTC
Found at i:594043 original size:45 final size:42
Alignment explanation
Indices: 593904--594095 Score: 146
Period size: 42 Copynumber: 4.5 Consensus size: 42
593894 AAAAAGAGTA
* * * *
593904 CGTCCTGCTTTTTGAGGACAAAGGAAAA-AAGGAAAACGAAATG
1 CGTCCTGCTCTTTGAGGACAAAAGAAAAGAA-G-AAATGAAGTG
* * *
593947 CGTCTTGCTTTTTGAGGACAAAAGAAAGAGAA-AAATAAAGTG
1 CGTCCTGCTCTTTGAGGACAAAAGAAA-AGAAGAAATGAAGTG
* *
593989 CATCTTGCTCTTTGAGGACAAAAAAGAAAAGAAGAGAATGAAGTG
1 CGTCCTGCTCTTTGAGGAC--AAAAGAAAAGAAGA-AATGAAGTG
* * * *
594034 TGTCCTGCTCTTTAAGGAC-AAAGAAGAA-AAGGAA--AAG-A
1 CGTCCTGCTCTTTGAGGACAAAAGAA-AAGAAGAAATGAAGTG
594072 CGTCCTGCTCTTTGAGGACTAAAA
1 CGTCCTGCTCTTTGAGGAC-AAAA
594096 AGTGCCACCA
Statistics
Matches: 124, Mismatches: 16, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
38 17 0.14
39 3 0.02
40 3 0.02
41 2 0.02
42 33 0.27
43 31 0.25
44 10 0.08
45 25 0.20
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (42 bp):
CGTCCTGCTCTTTGAGGACAAAAGAAAAGAAGAAATGAAGTG
Found at i:594239 original size:27 final size:27
Alignment explanation
Indices: 594154--594239 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
594144 TGAGGACTGG
594154 AAAATGCCACCAACTTGTGTGGGCTTT
1 AAAATGCCACCAACTTGTGTGGGCTTT
* ** ** * *
594181 AAAAGGCGTCCTGCTCT-T-TGAGGATTGA
1 AAAATGCCACCAACT-TGTGTG-GGCTT-T
594209 AAAATGCCACCAACTTGTGTGGGCTTT
1 AAAATGCCACCAACTTGTGTGGGCTTT
594236 AAAA
1 AAAA
594240 AGAAAAGGCA
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
26 2 0.05
27 20 0.50
28 16 0.40
29 2 0.05
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (27 bp):
AAAATGCCACCAACTTGTGTGGGCTTT
Found at i:594239 original size:28 final size:28
Alignment explanation
Indices: 594154--594240 Score: 72
Period size: 28 Copynumber: 3.1 Consensus size: 28
594144 TGAGGACTGG
594154 AAAATGCCACCAACTTGTGTGGGCTTT-
1 AAAATGCCACCAACTTGTGTGGGCTTTA
* ** ** * *
594181 AAAAGGCGTCCTGCTCT-T-TGAGGATTGA
1 AAAATGCCACCAACT-TGTGTG-GGCTTTA
594209 AAAATGCCACCAACTTGTGTGGGCTTTA
1 AAAATGCCACCAACTTGTGTGGGCTTTA
594237 AAAA
1 AAAA
594241 GAAAAGGCAT
Statistics
Matches: 41, Mismatches: 14, Indels: 9
0.64 0.22 0.14
Matches are distributed among these distances:
26 2 0.05
27 16 0.39
28 21 0.51
29 2 0.05
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (28 bp):
AAAATGCCACCAACTTGTGTGGGCTTTA
Found at i:594276 original size:61 final size:59
Alignment explanation
Indices: 594065--594612 Score: 622
Period size: 55 Copynumber: 9.5 Consensus size: 59
594055 AGAAGAAAAG
* *
594065 GAAAAGACGTCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTCGTGTGGGCTTTGAAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTT-AAA
* * *
594125 -AGAAAGGTGTCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT---
1 GA-AAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAA
*
594181 -AAAAGGCGTCCTGCTCTTTGAGGA-TTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTAG-AAAATGCCACCAACTTGTGTGGGCTTT--AAA
* * *
594241 GAAAAGGCATCCTGCTCTTTAAGGACTAGAAAATGCCACCAACTTGTATGGGCTTT---
1 GAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAA
594297 G-AAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT--AAA
* *
594357 GAAAAGGCGTTCTGCTTTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT-AAA
* * * * *
594417 GGAAAAGGTGTCCTACTCTTTGAGGACTGGAAAGTGCCACCAACCTGTGTGGGCTTT---
1 -GAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAA
* * *
594474 -AAAAGGCGTCCTACTCTTTGAGGACTAAAAAAAATGCCACCAACTTGTGTAGGCTTT---
1 GAAAAGGCGTCCTGCTCTTTGAGGACT--AGAAAATGCCACCAACTTGTGTGGGCTTTAAA
* *
594531 G-AAAGGCATCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT---
1 GAAAAGGCGTCCTGCTCTTTGAGGACTAGAAA-ATGCCACCAACTTGTGTGGGCTTTAAA
594586 G-AAAGGCGTCCTGCTCTTTGAGGACTA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTA
594613 AAAGGTGAAA
Statistics
Matches: 430, Mismatches: 36, Indels: 48
0.84 0.07 0.09
Matches are distributed among these distances:
54 5 0.01
55 171 0.40
56 2 0.00
57 47 0.11
59 1 0.00
60 49 0.11
61 153 0.36
62 2 0.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.26
Consensus pattern (59 bp):
GAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAA
Found at i:594296 original size:116 final size:116
Alignment explanation
Indices: 594066--594612 Score: 665
Period size: 116 Copynumber: 4.8 Consensus size: 116
594056 GAAGAAAAGG
* * *
594066 AAAAGACGTCCTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAG-AA
1 AAAAGGCGTCCTGCTCTTTGAGGACTGAAAAA-TGCCACCAACTTGTGTGGGCTTTAAAAAGAAA
* *
594129 AGGTGTCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT
65 AGGCGTCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
*
594181 AAAAGGCGTCCTGCTCTTTGAGGATTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAA
1 AAAAGGCGTCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAA
* * * *
594246 GGCATCCTGCTCTTTAAGGACTAGAAAATGCCACCAACTTGTATGGGCTTT
66 GGCGTCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
*
594297 GAAAGGCGTCCTGCTCTTTGAGGACT-AGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAA
1 AAAAGGCGTCCTGCTCTTTGAGGACTGA-AAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAA
* * *
594361 AGGCGTTCTGCTTTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
65 AGGCGTCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
* * * * *
594413 AAAAGGAAAAGGTGTCCTACTCTTTGAGGACTGGAAAGTGCCACCAACCTGTGTGGGCTTT----
1 ------AAAAGGCGTCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAA
* *
594474 --AAAAGGCGTCCTACTCTTTGAGGACTAAAAAAAATGCCACCAACTTGTGTAGGCTTT
60 AGAAAAGGCGTCCTACTCTTTGAGGACT--AGAAAATGCCACCAACTTGTGTGGGCTTT
* * **
594531 GAAAGGCATCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-----G-AAA
1 AAAAGGCGTCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAA
*
594590 GGCGTCCTGCTCTTTGAGGACTA
66 GGCGTCCTACTCTTTGAGGACTA
594613 AAAGGTGAAA
Statistics
Matches: 383, Mismatches: 36, Indels: 31
0.85 0.08 0.07
Matches are distributed among these distances:
110 1 0.00
112 72 0.19
115 52 0.14
116 183 0.48
118 27 0.07
122 48 0.13
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (116 bp):
AAAAGGCGTCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAA
GGCGTCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
Found at i:594700 original size:94 final size:94
Alignment explanation
Indices: 594539--594821 Score: 451
Period size: 94 Copynumber: 2.9 Consensus size: 94
594529 TTGAAAGGCA
*
594539 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTT
594604 TGAGGACTAAAAGGTGAAAGGAGAGAGCG
66 TGAGGACTAAAAGGTGAAAGGAGAGAGCG
594633 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTT
*
594698 TGAGGACTGAAAGGTGAAAGGAGAGAGCG
66 TGAGGACTAAAAGGTGAAAGGAGAGAGCG
* * *
594727 TCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCTT
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCGTCCT
594792 GCTCTTTGAGGACTGAAAA-GTGAAAGGAGA
60 GCTCTTTGAGGACT-AAAAGGTGAAAGGAGA
594822 AAGTTTAAAA
Statistics
Matches: 176, Mismatches: 6, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
94 138 0.78
99 1 0.01
100 34 0.19
101 3 0.02
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (94 bp):
TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTT
TGAGGACTAAAAGGTGAAAGGAGAGAGCG
Found at i:595807 original size:10 final size:9
Alignment explanation
Indices: 595806--595859 Score: 65
Period size: 10 Copynumber: 5.7 Consensus size: 9
595796 TTTCTTTGTT
595806 TTTTTTTTG
1 TTTTTTTTG
595815 TTATTTTTTG
1 TT-TTTTTTG
595825 TTTTTTTTTG
1 -TTTTTTTTG
595835 TTCTTTTGTTG
1 TT-TTTT-TTG
595846 -TTTTTTTG
1 TTTTTTTTG
595854 TTTTTT
1 TTTTTT
595860 GGAAAGGAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
8 3 0.08
9 13 0.32
10 19 0.47
11 5 0.12
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.85
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:595814 original size:11 final size:11
Alignment explanation
Indices: 595794--595852 Score: 68
Period size: 11 Copynumber: 5.5 Consensus size: 11
595784 CTTTTCTCTC
*
595794 TTTTTCTTTGT
1 TTTTTTTTTGT
595805 TTTTTTTTTG-
1 TTTTTTTTTGT
*
595815 TTATTTTTTG-
1 TTTTTTTTTGT
595825 TTTTTTTTTGT
1 TTTTTTTTTGT
* *
595836 TCTTTTGTTGT
1 TTTTTTTTTGT
595847 TTTTTT
1 TTTTTT
595853 GTTTTTTGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
10 18 0.44
11 23 0.56
ACGTcount: A:0.02, C:0.03, G:0.10, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:595824 original size:21 final size:21
Alignment explanation
Indices: 595800--595852 Score: 81
Period size: 20 Copynumber: 2.5 Consensus size: 21
595790 TCTCTTTTTC
595800 TTTGTTTTTTTTTTGTTATTT
1 TTTGTTTTTTTTTTGTTATTT
*
595821 TTTG-TTTTTTTTTGTTCTTT
1 TTTGTTTTTTTTTTGTTATTT
595841 TGTTGTTTTTTT
1 T-TTGTTTTTTT
595853 GTTTTTTGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 16 0.55
21 7 0.24
22 6 0.21
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.85
Consensus pattern (21 bp):
TTTGTTTTTTTTTTGTTATTT
Found at i:595855 original size:11 final size:10
Alignment explanation
Indices: 595794--595852 Score: 73
Period size: 10 Copynumber: 5.7 Consensus size: 10
595784 CTTTTCTCTC
*
595794 TTTTTCTTTG
1 TTTTTTTTTG
595804 TTTTTTTTTTG
1 -TTTTTTTTTG
*
595815 TTATTTTTTG
1 TTTTTTTTTG
595825 TTTTTTTTTG
1 TTTTTTTTTG
*
595835 TTCTTTTGTTG
1 TT-TTTTTTTG
595846 TTTTTTT
1 TTTTTTT
595853 GTTTTTTGGA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
10 24 0.57
11 18 0.43
ACGTcount: A:0.02, C:0.03, G:0.10, T:0.85
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:606167 original size:4 final size:4
Alignment explanation
Indices: 606151--606183 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
606141 AAAACAAAAC
*
606151 AAAT AAAT CAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
606184 CCTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:607734 original size:14 final size:14
Alignment explanation
Indices: 607715--607743 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
607705 CCTCTAATGT
607715 ATGAAATTTTGTGA
1 ATGAAATTTTGTGA
607729 ATGAAATTTTGTGA
1 ATGAAATTTTGTGA
607743 A
1 A
607744 AACTACAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (14 bp):
ATGAAATTTTGTGA
Found at i:608472 original size:130 final size:128
Alignment explanation
Indices: 608257--608558 Score: 324
Period size: 130 Copynumber: 2.3 Consensus size: 128
608247 GAGATAATAA
* * * *
608257 CGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGA
1 CGGGGTTGGAGTATCCCCT-AAAAATAATGGGGTTGGAGTATCCCCAATTATGAAAAATCAATGA
* ** *
608322 TTTAGAAATAAGGCAAGGGTTAAAGTGT-CCTAGATTAT-AGAAAATGGATGTTTCAAAAACAAA
65 TTTAGAAATAAGGCAAGGGTTAAAGTATCCCT-GATTATGAG-AAATCAATATTTCAAAAA-AAA
*
608385 AT
127 AG
* * *
608387 CGGGATTGGAGTATCCCCGTAAAAATAATGGGGTTGGAGTGTCCCCAATTATGAGAAATCAAT-A
1 CGGGGTTGGAGTATCCCC-TAAAAATAATGGGGTTGGAGTATCCCCAATTATGAAAAATCAATGA
* * * *** *
608451 TTTTAGAAATAAGGTC-GGGGTTGAAGTATCCCTGATTGTGAGAAATCAATATTTTGGAAATAAA
65 -TTTAGAAATAAGG-CAAGGGTTAAAGTATCCCTGATTATGAGAAATCAATATTTCAAAAAAAAA
608515 G
128 G
*
608516 CGGGGTTGGAGTATCCCCTTGAAAATAATGGGGTTGGAGTATC
1 CGGGGTTGGAGTATCCCC-TAAAAATAATGGGGTTGGAGTATC
608559 TCCGATGAAA
Statistics
Matches: 144, Mismatches: 23, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
129 43 0.30
130 94 0.65
131 7 0.05
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.27
Consensus pattern (128 bp):
CGGGGTTGGAGTATCCCCTAAAAATAATGGGGTTGGAGTATCCCCAATTATGAAAAATCAATGAT
TTAGAAATAAGGCAAGGGTTAAAGTATCCCTGATTATGAGAAATCAATATTTCAAAAAAAAAG
Found at i:608591 original size:28 final size:29
Alignment explanation
Indices: 608517--608592 Score: 120
Period size: 28 Copynumber: 2.7 Consensus size: 29
608507 GAAATAAAGC
*
608517 GGGGTTGGAGTATCCCC-TTGAAAATAAT
1 GGGGTTGGAGTATCCCCGATGAAAATAAT
*
608545 GGGGTTGGAGTATCTCCGATG-AAATAAT
1 GGGGTTGGAGTATCCCCGATGAAAATAAT
608573 GGGGTTGGAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
608593 TGTGAAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
28 42 0.95
29 2 0.05
ACGTcount: A:0.25, C:0.14, G:0.33, T:0.28
Consensus pattern (29 bp):
GGGGTTGGAGTATCCCCGATGAAAATAAT
Found at i:608596 original size:106 final size:107
Alignment explanation
Indices: 608467--608671 Score: 259
Period size: 107 Copynumber: 1.9 Consensus size: 107
608457 AAATAAGGTC
* * * * *
608467 GGGGTTGAAGTATCCCTGATTGTGAGAAATCAATATTTTGGAAAT-AAAGCGGGGTTGGAGTATC
1 GGGGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTGGAAATAAAAGCAGAGTTGGAATATC
* * *
608531 CCCTTGAAAATAATGGGGTTGGAGTATCTCCGATGAAATAAT
66 CCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAATAAT
* * * * **
608573 GGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTCTTTTGGAAATAAAATTAGAGTTGGAATATC
1 GGGGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTGGAAATAAAAGCAGAGTTGGAATATC
* *
608638 CCCTCGGAAATAACGGGGTTGGGGTATCCCCGAT
66 CCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
608672 TATGAAAAAT
Statistics
Matches: 82, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
106 39 0.48
107 43 0.52
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.29
Consensus pattern (107 bp):
GGGGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTGGAAATAAAAGCAGAGTTGGAATATC
CCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAATAAT
Found at i:608679 original size:79 final size:79
Alignment explanation
Indices: 608546--608874 Score: 373
Period size: 79 Copynumber: 4.2 Consensus size: 79
608536 GAAAATAATG
* *** * * *
608546 GGGTTGGAGTATCTCCGATGAAATAATGGGGTTGGAGTATCCCCGATTGTGAAAAATT-AGTCTT
1 GGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGA-TGTT
* **
608610 TTGGAAATAAAATTA
65 TTAGAAATAAAACCA
* * *
608625 GAGTTGGAATATCCCCTCGGAAATAACGGGGTTGGGGTATCCCCGATTATGAAAAATTGATGTTT
1 GGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTT
*
608690 TAGAAATAAAACCG
66 TAGAAATAAAACCA
* * * * * *
608704 GGGTTAGAGTATCCCCTCAGG-AATGACGGGGTTAGAGTATCCCCGATTATGAGAAATTAATTTT
1 GGGTTGGAGTATCCCCTC-GGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTT
* *
608768 TTAGAAATAAAGCCG
65 TTAGAAATAAAACCA
*
608783 GGGTTGGAGTATCCCCTC-GAGAATGACGGGGTTGGAGTATCCCCG---ATGAAAAATTGATGTT
1 GGGTTGGAGTATCCCCTCGGA-AATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTT
*
608844 TTAGAAATAAAACTA
65 TTAGAAATAAAACCA
608859 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
608875 GATTAAGAAA
Statistics
Matches: 214, Mismatches: 32, Indels: 11
0.83 0.12 0.04
Matches are distributed among these distances:
76 41 0.19
77 1 0.00
79 169 0.79
80 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (79 bp):
GGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTT
TAGAAATAAAACCA
Found at i:608902 original size:51 final size:47
Alignment explanation
Indices: 608811--608937 Score: 146
Period size: 51 Copynumber: 2.6 Consensus size: 47
608801 GAGAATGACG
*
608811 GGGTTGGAGTATCCCCGATGAAAAATTGATGTTTTAGAAATAAAACTA
1 GGGTTGGAGTATCCCCGATGAAAAATTGACGTTTTAGAAATAAAAC-A
* ** *
608859 GGGTTGGAGTATCCCCGATTAAGAAAAATTGACGTTTTGGAAATGGAACC
1 GGGTTGGAGTATCCCCGA-T--GAAAAATTGACGTTTTAGAAATAAAACA
608909 GGGATTGGAGTATCCCCGAGATGAAAAAT
1 GGG-TTGGAGTATCCCC--GATGAAAAAT
608938 CTAGAAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
48 18 0.26
49 1 0.01
50 10 0.15
51 36 0.53
52 1 0.01
53 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.27, T:0.26
Consensus pattern (47 bp):
GGGTTGGAGTATCCCCGATGAAAAATTGACGTTTTAGAAATAAAACA
Found at i:611185 original size:13 final size:13
Alignment explanation
Indices: 611169--611199 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
611159 ATACAATGAG
*
611169 CAATGTATCGATA
1 CAATGTAACGATA
611182 CAATGTAACGATA
1 CAATGTAACGATA
611195 CAATG
1 CAATG
611200 AGCCATGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (13 bp):
CAATGTAACGATA
Found at i:611194 original size:33 final size:33
Alignment explanation
Indices: 611150--611216 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
611140 AAAATGCTTG
*
611150 AATGTATCGATACAATGAGCAATGTATCGATAC
1 AATGTAACGATACAATGAGCAATGTATCGATAC
*
611183 AATGTAACGATACAATGAGCCATGTATCGATAC
1 AATGTAACGATACAATGAGCAATGTATCGATAC
611216 A
1 A
611217 TTTGATACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.25
Consensus pattern (33 bp):
AATGTAACGATACAATGAGCAATGTATCGATAC
Found at i:611266 original size:20 final size:20
Alignment explanation
Indices: 611241--611311 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
611231 GTAAACCCAA
611241 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATGAAC
*
611261 AATGTATCGATACAATGAAG
1 AATGTATCGATACAATGAAC
*
611281 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAAC
611301 AATGTATCGAT
1 AATGTATCGAT
611312 TCAAATTGTG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAATGAAC
Found at i:611802 original size:31 final size:30
Alignment explanation
Indices: 611613--612166 Score: 546
Period size: 30 Copynumber: 17.9 Consensus size: 30
611603 GAGGTGTCTA
* *
611613 CAAAGTCCATGACTTAGTGGCATCTTTTCT
1 CAAAGTCCACGACTCAGTGGCATCTTTTCT
611643 CAAAGTCCACGACTCAGTGGCATCTTTTC-
1 CAAAGTCCACGACTCAGTGGCATCTTTTCT
**
611672 CAAAAGTCCACGACTCAGTGGTGT-TTCTTC-
1 C-AAAGTCCACGACTCAGTGGCATCTT-TTCT
* **
611702 CTAAAGTCCACAACTCAGTGGCATATCTCCTCT
1 C-AAAGTCCACGACTCAGTGGC--ATCTTTTCT
*
611735 CAAAGTCCATGACTCAGTGGCATCTTTTCT
1 CAAAGTCCACGACTCAGTGGCATCTTTTCT
611765 CAAAGTCCACGACTCAGTGGCATCTTTTCTT
1 CAAAGTCCACGACTCAGTGGCATCTTTTC-T
* *
611796 CAAAGTCCAC-AGCTTAGTGGCATATCTCTTCT
1 CAAAGTCCACGA-CTCAGTGGC--ATCTTTTCT
* *
611828 CAAAGTCAATGACTCAGTGGCATCTTTTCT
1 CAAAGTCCACGACTCAGTGGCATCTTTTCT
* *
611858 CAAAGTCCACAACTCAATGGCATCTTTTTCCTT
1 CAAAGTCCACGACTCAGTGGCATC-TTTT-C-T
* *
611891 CAAAGTCCACGACTCAATGGCAATCTCTTCT
1 CAAAGTCCACGACTCAGTGGC-ATCTTTTCT
** **
611922 CAAAGTCCTTGACTCAGTGGCAATCTCCTCT
1 CAAAGTCCACGACTCAGTGGC-ATCTTTTCT
*
611953 CAAAGTCCACGACTCAGTGGCAT-TTTGTCC
1 CAAAGTCCACGACTCAGTGGCATCTTT-TCT
* *
611983 CAAAGTCCATGACTTAGTGGCATCTTTTCTT
1 CAAAGTCCACGACTCAGTGGCATCTTTTC-T
* *
612014 CAAAGTCCACAACTCAATGGCATCTTTTTTCTT
1 CAAAGTCCACGACTCAGTGGCATC--TTTTC-T
* *
612047 CAAAGTCTATGACTCAGTGGCATCTTTTCTT
1 CAAAGTCCACGACTCAGTGGCATCTTTTC-T
* * *
612078 CAAAGTCCATGACTTAGTGGCAATCTCTTCT
1 CAAAGTCCACGACTCAGTGGC-ATCTTTTCT
* * *
612109 CAAAGTCCGCGACTTAATGGCATCTCTTTC-
1 CAAAGTCCACGACTCAGTGGCATCT-TTTCT
*
612139 CAAAGTCCACGACTCTA-TGGCACCTTTT
1 CAAAGTCCACGACTC-AGTGGCATCTTTT
612167 TCCTTTAAGT
Statistics
Matches: 444, Mismatches: 57, Indels: 47
0.81 0.10 0.09
Matches are distributed among these distances:
29 7 0.02
30 184 0.41
31 142 0.32
32 47 0.11
33 61 0.14
34 3 0.01
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (30 bp):
CAAAGTCCACGACTCAGTGGCATCTTTTCT
Found at i:612034 original size:156 final size:155
Alignment explanation
Indices: 611613--612166 Score: 664
Period size: 156 Copynumber: 3.6 Consensus size: 155
611603 GAGGTGTCTA
* * *
611613 CAAAGTCCATGACTTAGTGGCATCTTTTCTCAAAGTCCACGACTCAGTGGCATCT-TTTCCAAAA
1 CAAAGTCCATGACTCAGTGGCATCTCTTCTCAAAGTCCACGACTCAGTGGCATCTCTTTCCCAAA
* * * *
611677 GTCCACGACTCAGTGG--T-GTTTCTTCCTAAAGTCCACAACTCAGTGGCA--TATCTCCTCTCA
66 GTCCACGACTCAGTGGCATCTTTTCTT-C-AAAGTCCACAACTCAATGGCATCTTTTTCCT-TCA
611737 AAGTCCATGACTCAGTGGCATCTTTTCT
128 AAGTCCATGACTCAGTGGCATCTTTTCT
* * * * *
611765 CAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCAC-AGCTTAGTGGCATATCTCTTCTC
1 CAAAGTCCATGACTCAGTGGCATCTCTTC-TCAAAGTCCACGA-CTCAGTGGCATCTCT-TTCCC
* *
611829 AAAGTCAATGACTCAGTGGCATCTTTTC-TCAAAGTCCACAACTCAATGGCATCTTTTTCCTTCA
63 AAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAATGGCATCTTTTTCCTTCA
* * *
611893 AAGTCCACGACTCAATGGCAATCTCTTCT
128 AAGTCCATGACTCAGTGGC-ATCTTTTCT
* *
611922 CAAAGTCCTTGACTCAGTGGCAATCTCCTCTCAAAGTCCACGACTCAGTGGCAT-T-TTGTCCCA
1 CAAAGTCCATGACTCAGTGGC-ATCTCTTCTCAAAGTCCACGACTCAGTGGCATCTCTT-TCCCA
* * *
611985 AAGTCCATGACTTAGTGGCATCTTTTCTTCAAAGTCCACAACTCAATGGCATCTTTTTTCTTCAA
64 AAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAATGGCATCTTTTTCCTTCAA
*
612050 AGTCTATGACTCAGTGGCATCTTTTCTT
129 AGTCCATGACTCAGTGGCATCTTTTC-T
* * * *
612078 CAAAGTCCATGACTTAGTGGCAATCTCTTCTCAAAGTCCGCGACTTAATGGCATCTCTTT-CCAA
1 CAAAGTCCATGACTCAGTGGC-ATCTCTTCTCAAAGTCCACGACTCAGTGGCATCTCTTTCCCAA
*
612142 AGTCCACGACTCTA-TGGCACCTTTT
65 AGTCCACGACTC-AGTGGCATCTTTT
612167 TCCTTTAAGT
Statistics
Matches: 347, Mismatches: 37, Indels: 32
0.83 0.09 0.08
Matches are distributed among these distances:
152 28 0.08
153 22 0.06
154 2 0.01
155 77 0.22
156 146 0.42
157 59 0.17
158 13 0.04
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (155 bp):
CAAAGTCCATGACTCAGTGGCATCTCTTCTCAAAGTCCACGACTCAGTGGCATCTCTTTCCCAAA
GTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAATGGCATCTTTTTCCTTCAAAG
TCCATGACTCAGTGGCATCTTTTCT
Found at i:612199 original size:125 final size:123
Alignment explanation
Indices: 611613--612192 Score: 538
Period size: 125 Copynumber: 4.7 Consensus size: 123
611603 GAGGTGTCTA
* * * *
611613 CAAAGTCCATGACTTAGTGGCATCTTTTCTCAAAGTCCACGACTCAGTGGCATC-TTTTC--CAA
1 CAAAGTCCACGACTCAATGGCATCTTTTCTCAAAGTCCACGACTCAATGGCATCTTTTTCTTC-A
** ** * *
611675 AAGTCCACGACTCAGTGG-TGT-TTCTTC-CTAAAGTCCACAACTCAGTGGCATATCTCCTCT
65 AAGTCCATAACTCAGTGGCAATCTT-TTCTC-AAAGTCCACGACTCAGTGGC--ATCTCTTCT
* * *
611735 CAAAGTCCATGACTCAGTGGCATCTTTTCTCAAAGTCCACGACTCAGTGGCATC-TTTTCTTCAA
1 CAAAGTCCACGACTCAATGGCATCTTTTCTCAAAGTCCACGACTCAATGGCATCTTTTTCTTCAA
* * * * * * *
611799 AGTCCACAGCTTAGTGGCATATCTCTTCTCAAAGTCAATGACTCAGTGGCATCTTTTCT
66 AGTCCATAACTCAGTGGCA-ATCTTTTCTCAAAGTCCACGACTCAGTGGCATCTCTTCT
* *
611858 CAAAGTCCACAACTCAATGGCATCTTTTTCCTTCAAAGTCCACGACTCAATGGCAATC-TCTTC-
1 CAAAGTCCACGACTCAATGGCATC-TTTT-C-TCAAAGTCCACGACTCAATGGC-ATCTTTTTCT
* * ** * *
611921 TCAAAGTCCTTGACTCAGTGGCAATCTCCTCTCAAAGTCCACGACTCAGTGGCAT-TTTGTCC
62 TCAAAGTCCATAACTCAGTGGCAATCTTTTCTCAAAGTCCACGACTCAGTGGCATCTCT-TCT
* * * *
611983 CAAAGTCCATGACTTAGTGGCATCTTTTCTTCAAAGTCCACAACTCAATGGCATCTTTTTTCTTC
1 CAAAGTCCACGACTCAATGGCATCTTTTC-TCAAAGTCCACGACTCAATGGCATC-TTTTTCTTC
* * * *
612048 AAAGTCTATGACTCAGTGGC-ATCTTTTCTTCAAAGTCCATGACTTAGTGGCAATCTCTTCT
64 AAAGTCCATAACTCAGTGGCAATCTTTTC-TCAAAGTCCACGACTCAGTGGC-ATCTCTTCT
* * * *
612109 CAAAGTCCGCGACTTAATGGCATCTCTTTC-CAAAGTCCACGACTCTATGGCACCTTTTTCCTT-
1 CAAAGTCCACGACTCAATGGCATCT-TTTCTCAAAGTCCACGACTCAATGGCATCTTTTT-CTTC
* *
612172 TAAGTCCATAACTCCGTGGCA
64 AAAGTCCATAACTCAGTGGCA
612193 CCCTTTTAAG
Statistics
Matches: 388, Mismatches: 50, Indels: 37
0.82 0.11 0.08
Matches are distributed among these distances:
122 61 0.16
123 67 0.17
124 43 0.11
125 137 0.35
126 67 0.17
127 13 0.03
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (123 bp):
CAAAGTCCACGACTCAATGGCATCTTTTCTCAAAGTCCACGACTCAATGGCATCTTTTTCTTCAA
AGTCCATAACTCAGTGGCAATCTTTTCTCAAAGTCCACGACTCAGTGGCATCTCTTCT
Found at i:612332 original size:34 final size:33
Alignment explanation
Indices: 612141--612390 Score: 239
Period size: 33 Copynumber: 7.8 Consensus size: 33
612131 TCTCTTTCCA
* *
612141 AAGTCCACGACTCTATGGCACCTTTTTCC-TTT
1 AAGTCCACAACTCTGTGGCACCTTTTTCCTTTT
* *
612173 AAGTCCATAACTCCGTGGCA-C-----CCTTTT
1 AAGTCCACAACTCTGTGGCACCTTTTTCCTTTT
** *
612200 AAGTCCACAACTCCATGGCATCTTTTTCCTTTT
1 AAGTCCACAACTCTGTGGCACCTTTTTCCTTTT
* *
612233 AAGTCCACAACTTTGTGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCTGTGGCACCTTTTTCCTTTT
* * * *
612266 AAGTTCATAACTCTATGGCACC-TTTTCTTTTT
1 AAGTCCACAACTCTGTGGCACCTTTTTCCTTTT
* *
612298 AAGTCCACGACTCCGTGGCACCTTTTTCCCTTTT
1 AAGTCCACAACTCTGTGGCACCTTTTT-CCTTTT
* * * *
612332 AAGCCCACACCTTTGTGGCATCCTTTTTTCC-TAT
1 AAGTCCACAACTCTGTGGCA-CC-TTTTTCCTTTT
612366 AAGTCCACAACTCTGTGGCACCTTT
1 AAGTCCACAACTCTGTGGCACCTTT
612391 AAGTCAATAT
Statistics
Matches: 175, Mismatches: 32, Indels: 22
0.76 0.14 0.10
Matches are distributed among these distances:
26 2 0.01
27 21 0.12
28 1 0.01
31 1 0.01
32 44 0.25
33 58 0.33
34 39 0.22
35 4 0.02
36 5 0.03
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (33 bp):
AAGTCCACAACTCTGTGGCACCTTTTTCCTTTT
Found at i:612721 original size:191 final size:189
Alignment explanation
Indices: 612387--613228 Score: 830
Period size: 191 Copynumber: 4.5 Consensus size: 189
612377 TCTGTGGCAC
* * * * *
612387 CTTTAAG-TCAATATCGCTAGCCTTGAATCAGCATATTGTCACCTTTACCATCTTAAGTCTAATA
1 CTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTT--CATCTTAAGTCCAATA
* * * * *
612451 TTGCTGGCTTTGAATTAGCATATTAGCACCTTGTCTTTAAAACCAATGTCACTGGCCTTGAATCA
64 TTGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCA
* *
612516 ACACATTGGCACCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
129 GCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * *
612577 CTTGAAGCCCGATATCGCTGGCCTTGAATCAACATATTGGCACATTTACCATCTTAAGTCCAATA
1 CTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTT--CATCTTAAGTCCAATA
*
612642 TTGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACTAATGTCGCTGGCCTTGAATCA
64 TTGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCA
612707 GCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
129 GCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * *
612768 CTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTC-T-TTAAGACCAATGT
1 CTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATT-TCATCTTAAGTCCAATAT
* * *
612831 TGCTGGCCTTGAATCAGCACATTGGCA-C---T-TTTAAGTCCAATATCGCTGGCCTTGAATCAG
65 TGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCAG
* * * * *
612891 CATATTGGCAACTTCATCTTTAAGCCCGATATCGTTGGCCTTGAATCAGCATATTGGCACCTT-G
130 CACATTGGC-A---C--CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
612955 T
189 T
* * * * * * *
612956 CTTTAAGACTAATA-CACTGGCCTTGAATCAGCACATTGG----------CGTAAGCCCAATATC
1 CTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTCATCTTAAGTCCAATATT
* ** * *
613010 GCTGGCCTTGAATCATCATATTGGCACCTCATCTTTAAGACCAATGTCGTTGGCCTTAAATCAGC
66 GCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGC
*** * * * *
613075 ACATTGGCACCTTCATCTTTAAGTTTGATATCGTTGGCCTTGAATCAGCATATTGGCATCTTTAA
131 ACATTGGCA----C--CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * ** * * *
613140 CATTCCTAAGCCCAATGTCACTGGCCTTGTCTCAGCACATTGG--CA-TTCTTCTTCAAGTCTAA
1 C-TT--TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTCATCTT-AAGTCCAA
* * *
613202 TGTTGCTGGCCATGAATCAGCACATTG
62 TATTGCTGGCCTTGAATCAGCATATTG
613229 TCGTTCTTCG
Statistics
Matches: 559, Mismatches: 65, Indels: 50
0.83 0.10 0.07
Matches are distributed among these distances:
178 34 0.06
179 1 0.00
182 2 0.00
183 119 0.21
184 3 0.01
185 2 0.00
187 33 0.06
188 73 0.13
189 44 0.08
190 7 0.01
191 210 0.38
192 1 0.00
195 2 0.00
196 28 0.05
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (189 bp):
CTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTCATCTTAAGTCCAATATT
GCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGC
ACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
Found at i:612813 original size:140 final size:140
Alignment explanation
Indices: 612439--613139 Score: 816
Period size: 140 Copynumber: 5.0 Consensus size: 140
612429 CTTTACCATC
* * * * * * * * *
612439 TTAAGTCTAATATTGCTGGCTTTGAATTAGCATATTAGCACCTT-GTCTTTAAAACCAATGTCAC
1 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATATCGC
* * * * *
612503 TGGCCTTGAATCAACACATTGGCA-C----CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCAT
66 TGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACTAATGTCGCTGGCCTTGAATCAGCAC
612563 ATTGGCACCTTCAT
131 ATTGGCA-C--C-T
* * * * *
612577 CTTGAAGCCCGATATCGCTGGCCTTGAATCAACATATTGGCACATTTACCATC-TTAAGTCCAAT
1 -TT-AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC-CTT--CATCTTTAAGACCAAT
*
612641 ATTGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACTAATGTCGCTGGCCTTGAATC
61 ATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACTAATGTCGCTGGCCTTGAATC
612706 AGCACATTGGCACCT
126 AGCACATTGGCACCT
*
612721 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGCCCAATATCGC
1 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATATCGC
* *
612786 TGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTTGCTGGCCTTGAATCAGCAC
66 TGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACTAATGTCGCTGGCCTTGAATCAGCAC
*
612851 ATTGGCACTT
131 ATTGGCACCT
* * * *
612861 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTCATCTTTAAGCCCGATATCGT
1 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATATCGC
* *
612926 TGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACTAAT-ACACTGGCCTTGAATCAGCAC
66 TGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACTAATGTCGCTGGCCTTGAATCAGCAC
612990 ATTGG---C-
131 ATTGGCACCT
* * * * *
612996 GTAAGCCCAATATCGCTGGCCTTGAATCATCATATTGGCACC-TCATCTTTAAGACCAATGTCGT
1 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATATCGC
* * * ** * * *
613060 TGGCCTTAAATCAGCACATTGGCACCTTCATCTTTAAGTTTGATATCGTTGGCCTTGAATCAGCA
66 TGGCCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGACTAATGTCGCTGGCCTTGAATCAGCA
* *
613125 TATTGGCATCT
130 CATTGGCACCT
613136 TTAA
1 TTAA
613140 CATTCCTAAG
Statistics
Matches: 490, Mismatches: 55, Indels: 33
0.85 0.10 0.06
Matches are distributed among these distances:
134 45 0.09
135 49 0.10
136 22 0.04
139 30 0.06
140 224 0.46
141 4 0.01
142 36 0.07
143 35 0.07
144 4 0.01
145 1 0.00
147 1 0.00
148 39 0.08
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (140 bp):
TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATATCGC
TGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACTAATGTCGCTGGCCTTGAATCAGCAC
ATTGGCACCT
Found at i:612840 original size:331 final size:318
Alignment explanation
Indices: 612381--613132 Score: 952
Period size: 331 Copynumber: 2.3 Consensus size: 318
612371 CACAACTCTG
* *
612381 TGGCACCTTTAAGT-CAATATCGCTAGCCTTGAATCAGCATATTGTCACCTTTACCATC-TTAAG
1 TGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT--CATCTTTAAG
* * * *
612444 TCTAATATTGCTGGCTTTGAATTAGCATATTAGCACCTTGTCTTTAAAACCAATGTCACTGGCCT
63 TCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAAACCAATGTCACTGGCCT
* *
612509 TGAATCAACACATTGGCACCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTT
128 TGAATCAACACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTT
*
612574 CATCTTGAAGCCCGATATCGCTGGCCTTGAATCAACATATTGGCACATT-TACCATCTTAAGTCC
193 CATCTTGAAGCCCGATATCGCTGGCCTTGAATCAACATATTGGCACATTGT--C-T-TTAAGACC
** * * *
612638 AATATTGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACTAATGTCGCTGGCCTTGA
254 AATA-CACTGGCCTTGAATCAGCACATTGG---C--G----TAAGACCAATATCGCTGGCCTTGA
612703 ATCAGCACAT
309 ATCAGCACAT
* *
612713 TGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGCCC
1 TGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCT
* **
612778 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTTGCTGGCCTTGA
66 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAAACCAATGTCACTGGCCTTGA
* *
612843 ATCAGCACATTGGCACTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTCAT
131 ATCAACACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTCAT
* * * * *
612908 CTTTAAGCCCGATATCGTTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACTAATACAC
196 CTTGAAGCCCGATATCGCTGGCCTTGAATCAACATATTGGCACATTGTCTTTAAGACCAATACAC
* * *
612973 TGGCCTTGAATCAGCACATTGGCGTAAGCCCAATATCGCTGGCCTTGAATCATCATAT
261 TGGCCTTGAATCAGCACATTGGCGTAAGACCAATATCGCTGGCCTTGAATCAGCACAT
* * * * *
613031 TGGCACCTCATCTTTAAGACCAATGTCGTTGGCCTTAAATCAGCACATTGGCACCTTCATCTTTA
1 TGGCA---C--CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTA
* * *
613096 AGTTTGATATCGTTGGCCTTGAATCAGCATATTGGCA
61 AGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCA
613133 TCTTTAACAT
Statistics
Matches: 373, Mismatches: 39, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
318 34 0.09
321 1 0.00
322 1 0.00
323 81 0.22
324 1 0.00
327 22 0.06
328 10 0.03
329 1 0.00
330 5 0.01
331 167 0.45
332 17 0.05
333 33 0.09
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (318 bp):
TGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCT
AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAAACCAATGTCACTGGCCTTGA
ATCAACACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTCAT
CTTGAAGCCCGATATCGCTGGCCTTGAATCAACATATTGGCACATTGTCTTTAAGACCAATACAC
TGGCCTTGAATCAGCACATTGGCGTAAGACCAATATCGCTGGCCTTGAATCAGCACAT
Found at i:612898 original size:91 final size:95
Alignment explanation
Indices: 612387--613132 Score: 571
Period size: 91 Copynumber: 8.0 Consensus size: 95
612377 TCTGTGGCAC
* * * * * *
612387 CTTTAAG-TCAATATCGCTAGCCTTGAATCAGCATATTGTCACCTTTACCATC-TTAAGTCTAAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCAAC-TT--CATCTTTAAGACCAAT
* * * * *
612450 ATTGCTGGCTTTGAATTAGCATATTAGCACCTTGT
63 ATCGCTGGCCTTGAATCAGCACATTGGCACC-T-T
* * * * * * *
612485 CTTTAAAACCAATGTCACTGGCCTTGAATCAACACATTGGC-A---C--CTTTAAGTCCAATGTC
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTCATCTTTAAGACCAATATC
*
612544 GCTGGCCTTGAATCAGCATATTGGCACCTT
66 GCTGGCCTTGAATCAGCACATTGGCACCTT
* * * * *
612574 CATCTTGAAGCCCGATATCGCTGGCCTTGAATCAACATATTGGCACATTTACCATC-TTAAGTCC
1 C-T-TT-AAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCA-ACTT--CATCTTTAAGACC
* *
612638 AATATTGCTGGCCTTGAATCAGCATATTGGCACCTTGT
60 AATATCGCTGGCCTTGAATCAGCACATTGGCACC-T-T
* * * *
612676 CTTTAAGACTAATGTCGCTGGCCTTGAATCAGCACATTGGC-A---C--CTTTAAGTCCAATATC
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTCATCTTTAAGACCAATATC
*
612735 GCTGGCCTTGAATCAGCATATTGGCACCTTCAT
66 GCTGGCCTTGAATCAGCACATTGGCACC-T--T
* * * * *
612768 CTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGACCAATGTT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTCATCTTTAAGACCAATATC
612832 GCTGGCCTTGAATCAGCACATTGGCA-C-T
66 GCTGGCCTTGAATCAGCACATTGGCACCTT
* * *
612860 -TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTCATCTTTAAGCCCGATATC
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTCATCTTTAAGACCAATATC
* *
612924 GTTGGCCTTGAATCAGCATATTGGCACCTTGT
66 GCTGGCCTTGAATCAGCACATTGGCACC-T-T
* * * * *
612956 CTTTAAGACTAATA-CACTGGCCTTGAATCAGCACATTGG---------C-GTAAGCCCAATATC
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTCATCTTTAAGACCAATATC
* *
613010 GCTGGCCTTGAATCATCATATTGGCACCTCAT
66 GCTGGCCTTGAATCAGCACATTGGCACCT--T
* * * * * ****
613042 CTTTAAGACCAATGTCGTTGGCCTTAAATCAGCACATTGGCACCTTCATCTTTAAGTTTGATATC
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTCATCTTTAAGACCAATATC
* *
613107 GTTGGCCTTGAATCAGCATATTGGCA
66 GCTGGCCTTGAATCAGCACATTGGCA
613133 TCTTTAACAT
Statistics
Matches: 536, Mismatches: 70, Indels: 85
0.78 0.10 0.12
Matches are distributed among these distances:
85 1 0.00
86 51 0.10
87 23 0.04
89 2 0.00
90 4 0.01
91 124 0.23
92 109 0.20
93 1 0.00
94 1 0.00
96 26 0.05
97 83 0.15
98 6 0.01
99 58 0.11
100 42 0.08
101 3 0.01
102 2 0.00
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (95 bp):
CTTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTCATCTTTAAGACCAATATC
GCTGGCCTTGAATCAGCACATTGGCACCTT
Found at i:613022 original size:86 final size:87
Alignment explanation
Indices: 612911--613082 Score: 247
Period size: 86 Copynumber: 2.0 Consensus size: 87
612901 ACTTCATCTT
* * ** *
612911 TAAGCCCGATATCGTTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACTAAT-ACACTG
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATCTTTAAGACCAATGACACTG
*
612975 GCCTTGAATCAGCACATTGGCG
66 GCCTTAAATCAGCACATTGGCG
* * **
612997 TAAGCCCAATATCGCTGGCCTTGAATCATCATATTGGCACCTCATCTTTAAGACCAATGTCGTTG
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATCTTTAAGACCAATGACACTG
613062 GCCTTAAATCAGCACATTGGC
66 GCCTTAAATCAGCACATTGGC
613083 ACCTTCATCT
Statistics
Matches: 75, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
86 52 0.69
87 23 0.31
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (87 bp):
TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATCTTTAAGACCAATGACACTG
GCCTTAAATCAGCACATTGGCG
Found at i:613184 original size:101 final size:97
Alignment explanation
Indices: 613005--613228 Score: 227
Period size: 99 Copynumber: 2.3 Consensus size: 97
612995 CGTAAGCCCA
* * **
613005 ATATCGCTGGCCTTGAATCATCATATTGGCACCTCATCTTTAAGACCAATGTCGTTGGCCTTAAA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTCAACTTTAAGACCAATGTCACTGGCCTTAAA
613070 TCAGCACATTGGCACCTTCATCTTTAAGTTTG
66 TCAGCACATTGGCACCTTCATCTTTAAGTTTG
* * * *
613102 ATATCGTTGGCCTTGAATCAGCATATTGGCATCTTTAACATTCCTAAGCCCAATGTCACTGGCCT
1 ATATCGCTGGCCTTGAATCAGCATATTGGCA-CCTCAAC-TT--TAAGACCAATGTCACTGGCCT
*** * * * *
613167 TGTCTCAGCACATTGGCA--TTCTTCTTCAAGTCTA
62 TAAATCAGCACATTGGCACCTTCATCTTTAAGTTTG
* * * *
613201 ATGTTGCTGGCCATGAATCAGCACATTG
1 ATATCGCTGGCCTTGAATCAGCATATTG
613229 TCGTTCTTCG
Statistics
Matches: 103, Mismatches: 20, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
97 29 0.28
98 4 0.04
99 37 0.36
101 33 0.32
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.33
Consensus pattern (97 bp):
ATATCGCTGGCCTTGAATCAGCATATTGGCACCTCAACTTTAAGACCAATGTCACTGGCCTTAAA
TCAGCACATTGGCACCTTCATCTTTAAGTTTG
Found at i:613212 original size:331 final size:325
Alignment explanation
Indices: 612381--613228 Score: 946
Period size: 331 Copynumber: 2.6 Consensus size: 325
612371 CACAACTCTG
* * * * *
612381 TGGCACCTTTAAG-TCAATATCGCTAGCCTTGAATCAGCATATTGTCACCTTTACCATC-TTAAG
1 TGGCACCTTTAAGACCAATATCGCTGGCCTTAAATCAGCACATTGGCACC-TT--CATCTTTAAG
* * * * * * *
612444 TCTAATATTGCTGGCTTTGAATTAGCATATTAGCACCTTGTCTTTAAAACCAATGTCACTGGCCT
63 CCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCACTGGCCT
* * *
612509 TGAATCAACACATTGGCACCT-TTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCT
128 TGAATCAGCACATTGGCACTTCTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCAACT
*
612573 TCATCTTGAAGCCCGATATCGCTGGCCTTGAATCAACATATTGGCACATTTACCATCTTAAGTCC
193 TCATCTTGAAGCCCGATATCGCTGGCCTTGAATCAACATATTGGCACATTTA-CATCTTAAGACC
** * * *
612638 AATATTGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACTAATGTCGCTGGCCTTGA
257 AATATCACTGGCCTTGAATCAGCACATTGG--CC-TG---TTAAGACCAATATCGCTGGCCTTGA
612703 ATCAGCACAT
316 ATCAGCACAT
* * *
612713 TGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGCCC
1 TGGCACCTTTAAGACCAATATCGCTGGCCTTAAATCAGCACATTGGCACCTTCATCTTTAAGCCC
**
612778 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTTGCTGGCCTTGA
66 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCACTGGCCTTGA
*
612843 ATCAGCACATTGGCACTT-TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTCA
131 ATCAGCACATTGGCACTTCTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCAACTTCA
* * * * *
612907 TCTTTAAGCCCGATATCGTTGGCCTTGAATCAGCATATTGGCACCTTGT-C-T-TTAAGACTAAT
196 TCTTGAAGCCCGATATCGCTGGCCTTGAATCAACATATTGGCACATT-TACATCTTAAGACCAAT
* * *
612969 A-CACTGGCCTTGAATCAGCACATTGG-C-G-TAAGCCCAATATCGCTGGCCTTGAATCATCATA
260 ATCACTGGCCTTGAATCAGCACATTGGCCTGTTAAGACCAATATCGCTGGCCTTGAATCAGCACA
613030 T
325 T
* *
613031 TGGCACCTCATCTTTAAGACCAATGTCGTTGGCCTTAAATCAGCACATTGGCACCTTCATCTTTA
1 TGGCA---C--CTTTAAGACCAATATCGCTGGCCTTAAATCAGCACATTGGCACCTTCATCTTTA
**** * * *
613096 AGTTTGATATCGTTGGCCTTGAATCAGCATATTGGCATCTT-TAACATTCCTAAGCCCAATGTCA
61 AGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT--C-TT--TAAGACCAATGTCA
** * * * *
613160 CTGGCCTTGTCTCAGCACATTGGCATTCTTCTTCAAGTCTAATGTTGCTGGCCATGAATCAGCAC
121 CTGGCCTTGAATCAGCACATTGGCA--CTTCTT-AAGTCCAATGTCGCTGGCCTTGAATCAGCAT
613225 ATTG
183 ATTG
613229 TCGTTCTTCG
Statistics
Matches: 448, Mismatches: 51, Indels: 35
0.84 0.10 0.07
Matches are distributed among these distances:
318 34 0.08
321 1 0.00
322 2 0.00
323 84 0.19
324 2 0.00
325 2 0.00
327 56 0.12
328 10 0.02
329 4 0.01
330 7 0.02
331 197 0.44
332 16 0.04
333 33 0.07
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (325 bp):
TGGCACCTTTAAGACCAATATCGCTGGCCTTAAATCAGCACATTGGCACCTTCATCTTTAAGCCC
AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCACTGGCCTTGA
ATCAGCACATTGGCACTTCTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCAACTTCA
TCTTGAAGCCCGATATCGCTGGCCTTGAATCAACATATTGGCACATTTACATCTTAAGACCAATA
TCACTGGCCTTGAATCAGCACATTGGCCTGTTAAGACCAATATCGCTGGCCTTGAATCAGCACAT
Found at i:616987 original size:21 final size:20
Alignment explanation
Indices: 616943--616996 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
616933 ACAATTCAAA
** *
616943 GTATCGATACATGTTACAAT
1 GTATCGATACATGAAAAAAT
616963 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGAAAAA-AT
*
616984 GTATCAATACATG
1 GTATCGATACATG
616997 TCATTGGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.30
Consensus pattern (20 bp):
GTATCGATACATGAAAAAAT
Found at i:617051 original size:19 final size:18
Alignment explanation
Indices: 617027--617111 Score: 81
Period size: 20 Copynumber: 4.7 Consensus size: 18
617017 TAGCCAAACT
617027 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAA-A
617046 TGTATCGAT--AC---AA
1 TGTATCGATACACAAAAA
617059 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC--AAAA-A
617080 TGTATCGATACATCAAAAA
1 TGTATCGATACA-CAAAAA
617099 TTGTATCGATACA
1 -TGTATCGATACA
617112 TTCACACGGG
Statistics
Matches: 56, Mismatches: 0, Indels: 19
0.75 0.00 0.25
Matches are distributed among these distances:
13 10 0.18
14 1 0.02
15 2 0.04
17 2 0.04
19 10 0.18
20 17 0.30
21 13 0.23
22 1 0.02
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (18 bp):
TGTATCGATACACAAAAA
Found at i:617063 original size:13 final size:13
Alignment explanation
Indices: 617045--617070 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
617035 TACACAAAAT
617045 ATGTATCGATACA
1 ATGTATCGATACA
617058 ATGTATCGATACA
1 ATGTATCGATACA
617071 CAAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:617068 original size:32 final size:33
Alignment explanation
Indices: 617027--617091 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
617017 TAGCCAAACT
617027 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
617059 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACAC-AAAAATATGTATCGATACA
617092 TCAAAAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
34 18 0.58
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:617103 original size:20 final size:22
Alignment explanation
Indices: 617058--617112 Score: 89
Period size: 21 Copynumber: 2.6 Consensus size: 22
617048 TATCGATACA
617058 ATGTATCGATACA-CAAAAAAT
1 ATGTATCGATACATCAAAAAAT
617079 ATGTATCGATACATC-AAAAAT
1 ATGTATCGATACATCAAAAAAT
617100 -TGTATCGATACAT
1 ATGTATCGATACAT
617113 TCACACGGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
20 13 0.39
21 19 0.58
22 1 0.03
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (22 bp):
ATGTATCGATACATCAAAAAAT
Found at i:619273 original size:21 final size:21
Alignment explanation
Indices: 619240--619289 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
619230 TTGCAAGTTG
*
619240 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
619262 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
619283 AAATAAA
1 AAATAAA
619290 AATTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:621107 original size:15 final size:15
Alignment explanation
Indices: 621087--621117 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
621077 TAAAAATGTC
*
621087 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
621102 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
621117 C
1 C
621118 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:623216 original size:13 final size:13
Alignment explanation
Indices: 623198--623222 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
623188 CATTTTTCTT
623198 TGTATCGATACAC
1 TGTATCGATACAC
623211 TGTATCGATACA
1 TGTATCGATACA
623223 GGGGGATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:623377 original size:20 final size:20
Alignment explanation
Indices: 623334--623379 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
623324 AAATCTTTTG
623334 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
623355 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
623375 CAAAA
1 CAAAA
623380 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:961344 original size:9 final size:9
Alignment explanation
Indices: 961332--961390 Score: 52
Period size: 9 Copynumber: 6.9 Consensus size: 9
961322 CTCTATTATC
961332 TCTCTCCTA
1 TCTCTCCTA
961341 TCTCTCCT-
1 TCTCTCCTA
* *
961349 CCTAT-C-A
1 TCTCTCCTA
*
961356 TCCCTCCTA
1 TCTCTCCTA
*
961365 TCTCTACTA
1 TCTCTCCTA
961374 TCTCTCCTA
1 TCTCTCCTA
*
961383 TATCTCCT
1 TCTCTCCT
961391 CCTATCATCC
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
7 3 0.08
8 4 0.11
9 31 0.82
ACGTcount: A:0.14, C:0.44, G:0.00, T:0.42
Consensus pattern (9 bp):
TCTCTCCTA
Found at i:961352 original size:12 final size:12
Alignment explanation
Indices: 961328--961369 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
961318 CTCTCTCTAT
961328 TATCTCT-CTCC
1 TATCTCTCCTCC
961339 TATCTCTCCTCC
1 TATCTCTCCTCC
961351 TATCATC-CCTCC
1 TATC-TCTCCTCC
961363 TATCTCT
1 TATCTCT
961370 ACTATCTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 9 0.32
12 17 0.61
13 2 0.07
ACGTcount: A:0.12, C:0.45, G:0.00, T:0.43
Consensus pattern (12 bp):
TATCTCTCCTCC
Found at i:961391 original size:42 final size:42
Alignment explanation
Indices: 961314--961418 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 42
961304 CTGTCATCAA
* * *
961314 CCTCCTCTCTCTATTATCTCTCTCCTATCTCTCCTCCTATCATC
1 CCTCCTATCTCTACTA--TCTCTCCTATATCTCCTCCTATCATC
961358 CCTCCTATCTCTACTATCTCTCCTATATCTCCTCCTATCATC
1 CCTCCTATCTCTACTATCTCTCCTATATCTCCTCCTATCATC
*
961400 CC-CCTATCTCTTCT-TCTCT
1 CCTCCTATCTCTACTATCTCT
961419 TTGAGGGCTA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
40 5 0.09
41 11 0.19
42 27 0.47
44 14 0.25
ACGTcount: A:0.12, C:0.45, G:0.00, T:0.43
Consensus pattern (42 bp):
CCTCCTATCTCTACTATCTCTCCTATATCTCCTCCTATCATC
Found at i:961394 original size:12 final size:12
Alignment explanation
Indices: 961328--961395 Score: 51
Period size: 12 Copynumber: 6.1 Consensus size: 12
961318 CTCTCTCTAT
961328 TATCTCTCTCCTA
1 TATCTC-CTCCTA
*
961341 TCTCTCCTCCTA
1 TATCTCCTCCTA
961353 TCATC-CCTCC--
1 T-ATCTCCTCCTA
*
961363 TATCT-CTAC--
1 TATCTCCTCCTA
961372 TATCT-CTCCTA
1 TATCTCCTCCTA
961383 TATCTCCTCCTA
1 TATCTCCTCCTA
961395 T
1 T
961396 CATCCCCCTA
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
9 14 0.30
10 1 0.02
11 5 0.11
12 19 0.41
13 7 0.15
ACGTcount: A:0.15, C:0.43, G:0.00, T:0.43
Consensus pattern (12 bp):
TATCTCCTCCTA
Found at i:962160 original size:20 final size:19
Alignment explanation
Indices: 962132--962174 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
962122 AATCAAATGC
*
962132 TGTTTTTTCTCTTTCTTTTG
1 TGTTCTTTCT-TTTCTTTTG
* *
962152 TGTTCTTTCTTTTTTTTTT
1 TGTTCTTTCTTTTCTTTTG
962171 TGTT
1 TGTT
962175 TCGAAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.00, C:0.12, G:0.09, T:0.79
Consensus pattern (19 bp):
TGTTCTTTCTTTTCTTTTG
Found at i:966990 original size:12 final size:11
Alignment explanation
Indices: 966971--967057 Score: 76
Period size: 12 Copynumber: 8.0 Consensus size: 11
966961 AGAGAAAGAA
966971 GAGATAGGAGG
1 GAGATAGGAGG
966982 GATGATAGGAGG
1 GA-GATAGGAGG
966994 AGAGATAGGA--
1 -GAGATAGGAGG
*
967004 GAGATAGTA--
1 GAGATAGGAGG
967013 GAGATAGGAGG
1 GAGATAGGAGG
967024 GATGATAGGA-G
1 GA-GATAGGAGG
*
967035 GAGAGAGGAGG
1 GAGATAGGAGG
*
967046 GATGACAGGAGG
1 GA-GATAGGAGG
967058 AGAAGAGAAG
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
9 16 0.25
10 6 0.09
11 10 0.15
12 31 0.48
13 2 0.03
ACGTcount: A:0.38, C:0.01, G:0.49, T:0.11
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:967005 original size:9 final size:9
Alignment explanation
Indices: 966991--967022 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
966981 GGATGATAGG
966991 AGGAGAGAT
1 AGGAGAGAT
967000 AGGAGAGAT
1 AGGAGAGAT
*
967009 AGTAGAGAT
1 AGGAGAGAT
967018 AGGAG
1 AGGAG
967023 GGATGATAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.12
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:967020 original size:42 final size:42
Alignment explanation
Indices: 966961--967040 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
966951 TAGCCCTCAA
966961 AGAGAAAGAAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
1 AGAGAAAGAAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
* *
967003 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGA
1 AGAGAAAGAAGAGATAGGAGGGATGATAGGAGGAGAGA
967041 GGAGGGATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.44, C:0.00, G:0.45, T:0.11
Consensus pattern (42 bp):
AGAGAAAGAAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
Found at i:967065 original size:25 final size:22
Alignment explanation
Indices: 966971--967060 Score: 87
Period size: 22 Copynumber: 4.2 Consensus size: 22
966961 AGAGAAAGAA
* *
966971 GAGATAGGAGGGATGATAGGAG
1 GAGAGAGGAGGGATGACAGGAG
* * *
966993 GAGAGA-TAGGAGA-GATAGTA-
1 GAGAGAGGAGG-GATGACAGGAG
* *
967013 GAGATAGGAGGGATGATAGGAG
1 GAGAGAGGAGGGATGACAGGAG
967035 GAGAGAGGAGGGATGACAGGAG
1 GAGAGAGGAGGGATGACAGGAG
967057 GAGA
1 GAGA
967061 AGAGAAGAAG
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
20 7 0.12
21 18 0.32
22 31 0.55
ACGTcount: A:0.39, C:0.01, G:0.49, T:0.11
Consensus pattern (22 bp):
GAGAGAGGAGGGATGACAGGAG
Found at i:972811 original size:18 final size:20
Alignment explanation
Indices: 972769--972818 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 20
972759 TCCATCTTCT
972769 TCTCTCCTC-CTC-ATGTCA
1 TCTCTCCTCTCTCTATGTCA
*
972787 TCCCTCCTCTCTCTAT-T-A
1 TCTCTCCTCTCTCTATGTCA
*
972805 TCTCTCCTATCTCT
1 TCTCTCCTCTCTCT
972819 CCTCCTATCC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 21 0.78
19 4 0.15
20 2 0.07
ACGTcount: A:0.10, C:0.44, G:0.02, T:0.44
Consensus pattern (20 bp):
TCTCTCCTCTCTCTATGTCA
Found at i:972834 original size:10 final size:12
Alignment explanation
Indices: 972808--972882 Score: 57
Period size: 12 Copynumber: 5.9 Consensus size: 12
972798 TCTATTATCT
972808 CTCCTATCTCTC
1 CTCCTATCTCTC
972820 CTCCTATC-C-C
1 CTCCTATCTCTC
972830 CTCCTATCTCTACTC
1 CTCCTA--TCT-CTC
972845 TCTATCCTATCTCTC
1 -C--TCCTATCTCTC
972860 CTCCTATCATC-C
1 CTCCTATC-TCTC
*
972872 CTCCTGTCTCT
1 CTCCTATCTCT
972883 TTTTTCTCTT
Statistics
Matches: 52, Mismatches: 1, Indels: 20
0.71 0.01 0.27
Matches are distributed among these distances:
10 7 0.13
11 3 0.06
12 25 0.48
13 2 0.04
14 2 0.04
15 4 0.08
16 4 0.08
18 5 0.10
ACGTcount: A:0.11, C:0.48, G:0.01, T:0.40
Consensus pattern (12 bp):
CTCCTATCTCTC
Found at i:972840 original size:40 final size:41
Alignment explanation
Indices: 972769--972891 Score: 131
Period size: 40 Copynumber: 2.9 Consensus size: 41
972759 TCCATCTTCT
*
972769 TCTCTCCTCCTCATGTCATCCCTCCTCTCTCTATTATCTCTCCTA
1 TCTCTCCTCCT-A--TCA-CCCTCCTATCTCTATTATCTCTCCTA
* * *
972814 TCTCTCCTCCTATC-CCCTCCTATCTCTACTCTCTATCCTA
1 TCTCTCCTCCTATCACCCTCCTATCTCTATTATCTCTCCTA
* * *
972854 TCTCTCCTCCTATCATCCCTCCTGTCTCTTTTTTCTCT
1 TCTCTCCTCCTATCA-CCCTCCTATCTCTATTATCTCT
972892 TTGAGGGCTA
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
40 36 0.54
42 19 0.28
44 1 0.01
45 11 0.16
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.44
Consensus pattern (41 bp):
TCTCTCCTCCTATCACCCTCCTATCTCTATTATCTCTCCTA
Found at i:972854 original size:18 final size:17
Alignment explanation
Indices: 972831--972867 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
972821 TCCTATCCCC
972831 TCCTATCTCTACTCTCTA
1 TCCTATCTCTACTC-CTA
*
972849 TCCTATCTCTCCTCCTA
1 TCCTATCTCTACTCCTA
972866 TC
1 TC
972868 ATCCCTCCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.14, C:0.43, G:0.00, T:0.43
Consensus pattern (17 bp):
TCCTATCTCTACTCCTA
Found at i:977902 original size:9 final size:9
Alignment explanation
Indices: 977890--977950 Score: 65
Period size: 9 Copynumber: 7.1 Consensus size: 9
977880 CTCTCTCTAT
977890 TATCTCTCC
1 TATCTCTCC
977899 TATCTCTCC
1 TATCTCTCC
* *
977908 T-CCTATCC
1 TATCTCTCC
*
977916 --TCCCTCC
1 TATCTCTCC
*
977923 TATCTCTAC
1 TATCTCTCC
977932 TATCTCTCC
1 TATCTCTCC
977941 TATCTCTCC
1 TATCTCTCC
977950 T
1 T
977951 CCTATCATCC
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
7 4 0.10
8 5 0.12
9 33 0.79
ACGTcount: A:0.11, C:0.46, G:0.00, T:0.43
Consensus pattern (9 bp):
TATCTCTCC
Found at i:977908 original size:42 final size:42
Alignment explanation
Indices: 977861--977980 Score: 186
Period size: 42 Copynumber: 2.9 Consensus size: 42
977851 CTTCTTCTCT
* * *
977861 TCTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTATC
1 TCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATC
*
977903 TCTCCTCCTATCCTCCCTCCTATCTCTACTATCTCTCCTATC
1 TCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATC
* *
977945 TCTCCTCCTATCATCCCTCCTATCTCTTCTTTCTCT
1 TCTCCTCCTATCATCCCTCCTATCTCTACTATCTCT
977981 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.10, C:0.46, G:0.01, T:0.43
Consensus pattern (42 bp):
TCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATC
Found at i:977910 original size:12 final size:12
Alignment explanation
Indices: 977895--977971 Score: 71
Period size: 12 Copynumber: 6.9 Consensus size: 12
977885 TCTATTATCT
977895 CTCCTATCTCTC
1 CTCCTATCTCTC
977907 CTCCTATC-CTCC
1 CTCCTATCTCT-C
977919 CTCCTA--TCT-
1 CTCCTATCTCTC
*
977928 CTACTA--TCT-
1 CTCCTATCTCTC
977937 CTCCTATCTCTC
1 CTCCTATCTCTC
977949 CTCCTATCATC-C
1 CTCCTATC-TCTC
977961 CTCCTATCTCT
1 CTCCTATCTCT
977972 TCTTTCTCTT
Statistics
Matches: 56, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
9 13 0.23
11 9 0.16
12 32 0.57
13 2 0.04
ACGTcount: A:0.12, C:0.48, G:0.00, T:0.40
Consensus pattern (12 bp):
CTCCTATCTCTC
Found at i:985239 original size:12 final size:11
Alignment explanation
Indices: 985217--985323 Score: 70
Period size: 12 Copynumber: 10.0 Consensus size: 11
985207 AGAGAAAGAA
*
985217 GAGATAAGAGG
1 GAGATAGGAGG
985228 GATGATAGGAGG
1 GA-GATAGGAGG
985240 AGAGATAGGA--
1 -GAGATAGGAGG
*
985250 GAGATAGTA--
1 GAGATAGGAGG
985259 GAGATAGGAGG
1 GAGATAGGAGG
*
985270 GATGATAGAAGG
1 GA-GATAGGAGG
985282 AGAGATAGGA--
1 -GAGATAGGAGG
985292 GAGATAAGG-GG
1 GAGAT-AGGAGG
985303 GAG--AGGAGG
1 GAGATAGGAGG
985312 GATGATAGGAGG
1 GA-GATAGGAGG
985324 AAGAGAGAAG
Statistics
Matches: 78, Mismatches: 5, Indels: 25
0.72 0.05 0.23
Matches are distributed among these distances:
8 3 0.04
9 25 0.32
10 4 0.05
11 7 0.09
12 35 0.45
13 4 0.05
ACGTcount: A:0.40, C:0.00, G:0.48, T:0.12
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:985262 original size:11 final size:9
Alignment explanation
Indices: 985237--985297 Score: 74
Period size: 9 Copynumber: 7.1 Consensus size: 9
985227 GGATGATAGG
985237 AGGAGAGAT
1 AGGAGAGAT
985246 AGGAGAGAT
1 AGGAGAGAT
*
985255 AGTAGAGAT
1 AGGAGAGAT
*
985264 AGGAGGGAT
1 AGGAGAGAT
*
985273 --GATAGA-
1 AGGAGAGAT
985279 AGGAGAGAT
1 AGGAGAGAT
985288 AGGAGAGAT
1 AGGAGAGAT
985297 A
1 A
985298 AGGGGGAGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
7 4 0.09
8 5 0.12
9 34 0.79
ACGTcount: A:0.44, C:0.00, G:0.43, T:0.13
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:985270 original size:42 final size:41
Alignment explanation
Indices: 985207--985329 Score: 156
Period size: 42 Copynumber: 2.9 Consensus size: 41
985197 TAGCCCTTAA
* *
985207 AGAGAAAGAAGAGATAAGAGGGATGATAGGAGGAGAGATAGG
1 AGAGATAG-AGAGATAGGAGGGATGATAGGAGGAGAGATAGG
*
985249 AGAGATAGTAGAGATAGGAGGGATGATAGAAGGAGAGATAGG
1 AGAGATAG-AGAGATAGGAGGGATGATAGGAGGAGAGATAGG
* * *
985291 AGAGATAAGGGGGAGAGGAGGGATGATAGGAGGAAGAGA
1 AGAGAT-AGAGAGATAGGAGGGATGATAGGAGG-AGAGA
985330 GAAGAAGATG
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
42 64 0.90
43 7 0.10
ACGTcount: A:0.44, C:0.00, G:0.46, T:0.11
Consensus pattern (41 bp):
AGAGATAGAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
Found at i:991139 original size:12 final size:11
Alignment explanation
Indices: 991120--991191 Score: 62
Period size: 12 Copynumber: 6.5 Consensus size: 11
991110 AGAGAAAGAA
991120 GAGATAGGAGG
1 GAGATAGGAGG
991131 GATGATAGGAGG
1 GA-GATAGGAGG
991143 AGAGATAGGA--
1 -GAGATAGGAGG
*
991153 GAGATAGTA--
1 GAGATAGGAGG
991162 GAGATAGGAGG
1 GAGATAGGAGG
*
991173 GATGATAGAAGG
1 GA-GATAGGAGG
991185 AGAGATA
1 -GAGATA
991192 AGAGAGATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
9 16 0.31
11 4 0.08
12 28 0.54
13 4 0.08
ACGTcount: A:0.42, C:0.00, G:0.44, T:0.14
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:991154 original size:9 final size:9
Alignment explanation
Indices: 991140--991200 Score: 65
Period size: 9 Copynumber: 7.1 Consensus size: 9
991130 GGATGATAGG
991140 AGGAGAGAT
1 AGGAGAGAT
991149 AGGAGAGAT
1 AGGAGAGAT
*
991158 AGTAGAGAT
1 AGGAGAGAT
*
991167 AGGAGGGAT
1 AGGAGAGAT
*
991176 --GATAGA-
1 AGGAGAGAT
991182 AGGAGAGAT
1 AGGAGAGAT
*
991191 AAGAGAGAT
1 AGGAGAGAT
991200 A
1 A
991201 ATAGAGAGAG
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
7 4 0.10
8 5 0.12
9 33 0.79
ACGTcount: A:0.46, C:0.00, G:0.41, T:0.13
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:991169 original size:42 final size:42
Alignment explanation
Indices: 991110--991241 Score: 185
Period size: 42 Copynumber: 3.1 Consensus size: 42
991100 TAGCTCTCAA
* * * *
991110 AGAGAAAGAAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
1 AGAGATAGTAGAGATAGGAGGGATGATAGAAGGAGAGATAAG
991152 AGAGATAGTAGAGATAGGAGGGATGATAGAAGGAGAGATAAG
1 AGAGATAGTAGAGATAGGAGGGATGATAGAAGGAGAGATAAG
* * *
991194 AGAGATAATAGAGAGAGGAGGGATGATAGAAGGAGGAGAGAAG
1 AGAGATAGTAGAGATAGGAGGGATGATAGAAGGA-GAGATAAG
991237 A-AGAT
1 AGAGAT
991242 GGAAGAGTGA
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
42 74 0.90
43 8 0.10
ACGTcount: A:0.46, C:0.00, G:0.42, T:0.11
Consensus pattern (42 bp):
AGAGATAGTAGAGATAGGAGGGATGATAGAAGGAGAGATAAG
Found at i:991229 original size:18 final size:18
Alignment explanation
Indices: 991167--991231 Score: 51
Period size: 18 Copynumber: 3.3 Consensus size: 18
991157 TAGTAGAGAT
991167 AGGAGGGATGATAGAAGG
1 AGGAGGGATGATAGAAGG
*
991185 AGAGATAAGAGAGATAATAG-AGAG
1 AG-G---AG-G-GATGATAGAAG-G
991209 AGGAGGGATGATAGAAGG
1 AGGAGGGATGATAGAAGG
991227 AGGAG
1 AGGAG
991232 AGAAGAAGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 16
0.67 0.04 0.29
Matches are distributed among these distances:
18 15 0.41
19 4 0.11
20 2 0.05
22 2 0.05
23 4 0.11
24 10 0.27
ACGTcount: A:0.45, C:0.00, G:0.45, T:0.11
Consensus pattern (18 bp):
AGGAGGGATGATAGAAGG
Found at i:991666 original size:20 final size:20
Alignment explanation
Indices: 991641--991678 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
991631 CCATGATATC
991641 CGTGACATAGTGGAACTCGA
1 CGTGACATAGTGGAACTCGA
991661 CGTGACATAGTGGAACTC
1 CGTGACATAGTGGAACTC
991679 CATCCCTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (20 bp):
CGTGACATAGTGGAACTCGA
Found at i:991881 original size:18 final size:18
Alignment explanation
Indices: 991858--991917 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
991848 AGAAATCCTA
991858 CTAATGCTTCTACTTCTT
1 CTAATGCTTCTACTTCTT
* *
991876 CTAATGCTTCTTTTAATTCTA
1 CTAATGCTTC---TACTTCTT
*
991897 CAAATGCTTCTACTTCTT
1 CTAATGCTTCTACTTCTT
991915 CTA
1 CTA
991918 CTTCTAGGCA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
18 18 0.55
21 15 0.45
ACGTcount: A:0.22, C:0.25, G:0.05, T:0.48
Consensus pattern (18 bp):
CTAATGCTTCTACTTCTT
Found at i:991916 original size:21 final size:20
Alignment explanation
Indices: 991855--991918 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
991845 GTAAGAAATC
991855 CTACTAATGCTTCTACTTCTT
1 CTAC-AATGCTTCTACTTCTT
* *
991876 CT--AATGCTTCT-TTTAATT
1 CTACAATGCTTCTACTT-CTT
991894 CTACAAATGCTTCTACTTCTT
1 CTAC-AATGCTTCTACTTCTT
991915 CTAC
1 CTAC
991919 TTCTAGGCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 2 0.06
18 13 0.38
21 17 0.50
22 2 0.06
ACGTcount: A:0.22, C:0.27, G:0.05, T:0.47
Consensus pattern (20 bp):
CTACAATGCTTCTACTTCTT
Found at i:996842 original size:49 final size:49
Alignment explanation
Indices: 996770--996867 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
996760 GGAACTGCCC
996770 TTACACTTCAATTGCCTTTCTACCTTGATAGCTTTATACAACAATTCCT
1 TTACACTTCAATTGCCTTTCTACCTTGATAGCTTTATACAACAATTCCT
996819 TTACACTTCAATTGCCTTTCTACCTTGATAGCTTTATACAACAATTCCT
1 TTACACTTCAATTGCCTTTCTACCTTGATAGCTTTATACAACAATTCCT
996868 CCATCTCCAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.27, C:0.27, G:0.06, T:0.41
Consensus pattern (49 bp):
TTACACTTCAATTGCCTTTCTACCTTGATAGCTTTATACAACAATTCCT
Found at i:997839 original size:28 final size:28
Alignment explanation
Indices: 997789--997874 Score: 84
Period size: 28 Copynumber: 3.1 Consensus size: 28
997779 AACTTTGATT
* *
997789 AATAAATAAGAAAGATC-AAGGAAGTGA
1 AATAAACAAGAAATATCAAAGGAAGTGA
* ** *
997816 AATCAACAAGAAATATGGAAGGAAATGA
1 AATAAACAAGAAATATCAAAGGAAGTGA
* * *
997844 AATAAAGAAGAACTATCAAAGGAAGAGA
1 AATAAACAAGAAATATCAAAGGAAGTGA
997872 AAT
1 AAT
997875 TAATGAAGAG
Statistics
Matches: 46, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
27 13 0.28
28 33 0.72
ACGTcount: A:0.59, C:0.06, G:0.21, T:0.14
Consensus pattern (28 bp):
AATAAACAAGAAATATCAAAGGAAGTGA
Found at i:999328 original size:39 final size:39
Alignment explanation
Indices: 999222--999345 Score: 121
Period size: 39 Copynumber: 3.2 Consensus size: 39
999212 GCTTACTTCA
* *
999222 TTGCAAACTAAATTACTTGGTTTTGAGTTTATTAGAGGT
1 TTGCAAACTAAATTACTTGGTTTTGAGTTCATTAGAGAT
* *** * *
999261 TTGTATGTTAATGATGTA-TT-G-TTAGAGTTGATTAGAGAT
1 TTGCAAACTAA--AT-TACTTGGTTTTGAGTTCATTAGAGAT
999300 TTGCAAACTAAATTACTTGGTTTTGAGTTCATTAGAGAT
1 TTGCAAACTAAATTACTTGGTTTTGAGTTCATTAGAGAT
999339 TT-CAAAC
1 TTGCAAAC
999346 AAGTATGGAA
Statistics
Matches: 66, Mismatches: 13, Indels: 13
0.72 0.14 0.14
Matches are distributed among these distances:
36 2 0.03
37 4 0.06
38 6 0.09
39 47 0.71
40 1 0.02
41 4 0.06
42 2 0.03
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (39 bp):
TTGCAAACTAAATTACTTGGTTTTGAGTTCATTAGAGAT
Found at i:1001098 original size:51 final size:51
Alignment explanation
Indices: 1001043--1001170 Score: 211
Period size: 51 Copynumber: 2.5 Consensus size: 51
1001033 ACCATAGGGA
*
1001043 TATGATTAGGATTGTCCTTGTTTAGTCAAGATTATTGATTATTGTTAGGAC
1 TATGATTAGGATTGTCCTTGTTTAGTCAAGATTATTGATTAATGTTAGGAC
* * *
1001094 TATGATTATGATTGTCGTTATTTAGTCAAGATTATTGATTAATGTTAGGAC
1 TATGATTAGGATTGTCCTTGTTTAGTCAAGATTATTGATTAATGTTAGGAC
*
1001145 TATGATTAGTATTGTCCTTGTTTAGT
1 TATGATTAGGATTGTCCTTGTTTAGT
1001171 TAGACTATAG
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 69 1.00
ACGTcount: A:0.26, C:0.07, G:0.20, T:0.47
Consensus pattern (51 bp):
TATGATTAGGATTGTCCTTGTTTAGTCAAGATTATTGATTAATGTTAGGAC
Found at i:1002473 original size:317 final size:312
Alignment explanation
Indices: 1001799--1002508 Score: 702
Period size: 317 Copynumber: 2.2 Consensus size: 312
1001789 AAGGAAAATA
**
1001799 AACTTTGATTCTAAGGAAAATAATGGGAGGAAAAGCTTTCTCAT-AAAGGCAAAGCATCGATATC
1 AACTTTGATTCTAAGGAAAATAATGGGA-GAAAAGCTTTCTTGTGAAA--CAAAGCATCGATATC
* * *
1001863 ATCTATCCCAATTAGGAGAATATGCTTTTGTTACCCAATGATGAAAAAAATAGATTAATAAAATA
63 ATCTATCCCAATGAGGAAAATATGCTTTTGTTACCCAATGATGAAAAAAATAGATTAATAAAAGA
* *
1001928 ATCCATGTTTATCTTGTTTGAGGGACATACCTTGATTCTAAGGAAATTGATGAGAAGAAAAGCTT
128 ATCCATGTTTATCTTGTTTGAGGGACAAACCTTGATTCTAAGGAAAATGATGAGAAGAAAAGCTT
* ** ** * *
1001993 TTCTTGTTAAACCCAGGCATCAATACATGTATATGAATAGGAAGAACTTGTTTTGACTGGCAAAA
193 TTCTTGTGAAACCCAGGCATCAATACATGTATACCAATAAAAAGAACTTGCTTTAACTGGCAAAA
* *
1002058 CACAAAAAGAATGGAGATTATTAGGAAAATCCATGTTTATCTTATTTGAAGGATG
258 CACAAAAAGAATGGAGATTATTAGGAAAATCCATGTTTATCTCATTTGAAGGACG
* * * *
1002113 AATTTTGATTCTAAGGAAAATGATAGGGAGAAAAGCCTTTCTTGTGAAATCAAAGTATCGATATT
1 AACTTTGATTCTAAGGAAAATAAT-GGGAGAAAAG-CTTTCTTGTGAAA-CAAAGCATCGATATC
* * ** * * *
1002178 GTGTATCCCAATGAGGAAAACT-TGCTTTT-TTACTGAATTATGAAAAGAATGGTGATT-ATAAC
63 ATCTATCCCAATGAGGAAAA-TATGCTTTTGTTACCCAATGATGAAAAAAAT--AGATTAATAA-
* * * * * * * *
1002240 AAGGATGCATGTTGGTTTC-T-TTTGATGGACAAACTTTTATTCTAAGGAAAATGATGGGATGAA
124 AAGAATCCATGTT--TATCTTGTTTGAGGGACAAACCTTGATTCTAAGGAAAATGATGAGAAGAA
* * *
1002303 AAGCTTTTCTTGTGAAA-CTAGGGCATCAATATCATGTATCCCACTAAAAAGAA-TGTGCTTTAA
187 AAGCTTTTCTTGTGAAACCCA-GGCATCAATA-CATGTATACCAATAAAAAGAACT-TGCTTTAA
* * * * * ** * * *
1002366 TTGTCTAATCACAAAAAGAGTGGA-AGTTATTTTGAGAATCTATGTTTCTCTCATTT-AAGGAAC
249 CTGGCAAAACACAAAAAGAATGGAGA-TTATTAGGAAAATCCATGTTTATCTCATTTGAAGG-AC
1002429 G
312 G
* **
1002430 AACTTTGATTCTAAGGAAAATAATGGGCAGAAAAAGTTTTCTTGTGAAACAAAAGCATTAATATC
1 AACTTTGATTCTAAGGAAAATAATGGG-AG-AAAAGCTTTCTTGTGAAAC-AAAGCATCGATATC
*
1002495 ATGTATCCCAATGA
63 ATCTATCCCAATGA
1002509 AGAGAACATT
Statistics
Matches: 322, Mismatches: 57, Indels: 31
0.79 0.14 0.08
Matches are distributed among these distances:
314 45 0.14
315 53 0.16
316 90 0.28
317 126 0.39
318 8 0.02
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (312 bp):
AACTTTGATTCTAAGGAAAATAATGGGAGAAAAGCTTTCTTGTGAAACAAAGCATCGATATCATC
TATCCCAATGAGGAAAATATGCTTTTGTTACCCAATGATGAAAAAAATAGATTAATAAAAGAATC
CATGTTTATCTTGTTTGAGGGACAAACCTTGATTCTAAGGAAAATGATGAGAAGAAAAGCTTTTC
TTGTGAAACCCAGGCATCAATACATGTATACCAATAAAAAGAACTTGCTTTAACTGGCAAAACAC
AAAAAGAATGGAGATTATTAGGAAAATCCATGTTTATCTCATTTGAAGGACG
Found at i:1002555 original size:159 final size:154
Alignment explanation
Indices: 1002271--1002779 Score: 396
Period size: 159 Copynumber: 3.2 Consensus size: 154
1002261 TTGATGGACA
* * * ** *
1002271 AACTTTTATTCTAAGGAAAATGATGGGATGAAAAGCTTTTCTTGTGAAACTAGGGCATCAATATC
1 AACTTTGATTCTAAGGAAAAT-A--GGAAGAAAAGCTTTTCTTGTGAAACAAAAGCATTAATATC
* ** * * * * * *
1002336 ATGTATCCCACT-AAAAAGAATGTGCTTTAATTGTCTAATCACA-AAAAGAGTGGA-AGTTATTT
63 ATGTATCCCAATGAGGAA-AATGT-ATTTGATTGCCGAATCA-AGAAAACAATGGAGA-TTATTT
*
1002398 TGAGAATCTATGTTTCTCTCATTTAAGGAAC
124 TGAGAATCTATGTTTGTCTCATTTAAGGAAC
*
1002429 GAACTTTGATTCTAAGGAAAATAATGGGCAGAAAAAG-TTTTCTTGTGAAACAAAAGCATTAATA
1 -AACTTTGATTCTAAGGAAAAT-A--GGAAG-AAAAGCTTTTCTTGTGAAACAAAAGCATTAATA
* * * *
1002493 TCATGTATCCCAATGAAGAGAACAT-T-TTCTGATTGCCGAATTATGAAAACAATGGATATTATT
61 TCATGTATCCCAATG-AG-GAAAATGTATT-TGATTGCCGAATCAAGAAAACAATGGAGATTATT
* *
1002556 ATGAGAATCCT-TGATTGTCTCATTTCAAGGATA-
123 TTGAGAAT-CTATGTTTGTCTCATTT-AAGGA-AC
* * *
1002589 AACTTTGATTCTAAGG----TAGGAAGTAAAGCTTTTCTTGTGAAACCAAAGCGTTAATATCATG
1 AACTTTGATTCTAAGGAAAATAGGAAGAAAAGCTTTTCTTGTGAAACAAAAGCATTAATATCATG
* * * **
1002650 TATCCCAATGAGGAAAATGTATTTTATTGTCTAATCAAGAAAGGAATGGAGATTATTTTGAGAAT
66 TATCCCAATGAGGAAAATGTATTTGATTGCCGAATCAAGAAAACAATGGAGATTATTTTGAGAAT
* * *
1002715 -TGATGTTTGTATGATCTTAAGGGAC
131 CT-ATGTTTGTCTCAT-TTAAGGAAC
*
1002740 AAACTTTGATTCTAAGAAAAATGATAGGAAGAAAAGCTTT
1 -AACTTTGATTCTAAG-GAAA--ATAGGAAGAAAAGCTTT
1002780 CTTTGCGAAA
Statistics
Matches: 283, Mismatches: 42, Indels: 50
0.75 0.11 0.13
Matches are distributed among these distances:
149 1 0.00
150 6 0.02
151 53 0.19
152 63 0.22
154 1 0.00
155 1 0.00
158 2 0.01
159 136 0.48
160 14 0.05
161 4 0.01
162 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (154 bp):
AACTTTGATTCTAAGGAAAATAGGAAGAAAAGCTTTTCTTGTGAAACAAAAGCATTAATATCATG
TATCCCAATGAGGAAAATGTATTTGATTGCCGAATCAAGAAAACAATGGAGATTATTTTGAGAAT
CTATGTTTGTCTCATTTAAGGAAC
Found at i:1002744 original size:152 final size:151
Alignment explanation
Indices: 1002462--1002755 Score: 344
Period size: 152 Copynumber: 1.9 Consensus size: 151
1002452 ATGGGCAGAA
*
1002462 AAAGTTTTCTTGTGAAACAAAAGCATTAATATCATGTATCCCAATGAAGAGAACATTTTCTGATT
1 AAAGTTTTCTTGTGAAACAAAAGCATTAATATCATGTATCCCAATGAAGAGAAAATTTTCTGATT
* * * * * *
1002527 GCCGAATTATGAAAACAATGGATATTATTATGAGAATCCTTGATTGTCTCATTTCAAGGATAAAC
66 GCCGAATCAAGAAAACAATGGAGATTATTATGAGAATCCATGATTGTATCATTTCAAGGACAAAC
1002592 TTTGATTCTAAGGTAGGAAGT
131 TTTGATTCTAAGGTAGGAAGT
* * *
1002613 AAAGCTTTTCTTGTGAAACCAAAGCGTTAATATCATGTATCCCAATG-AG-GAAAATGTATT-TT
1 AAAG-TTTTCTTGTGAAACAAAAGCATTAATATCATGTATCCCAATGAAGAGAAAAT-T-TTCTG
* * ** * ** * *
1002675 ATTGTCTAATCAAGAAAGGAATGGAGATTATTTTGAGAATTGATGTTTGTATGATCTT-AAGGGA
63 ATTGCCGAATCAAGAAAACAATGGAGATTATTATGAGAATCCATGATTGTATCAT-TTCAA-GGA
1002739 CAAACTTTGATTCTAAG
126 CAAACTTTGATTCTAAG
1002756 AAAAATGATA
Statistics
Matches: 119, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
150 5 0.04
151 51 0.43
152 63 0.53
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (151 bp):
AAAGTTTTCTTGTGAAACAAAAGCATTAATATCATGTATCCCAATGAAGAGAAAATTTTCTGATT
GCCGAATCAAGAAAACAATGGAGATTATTATGAGAATCCATGATTGTATCATTTCAAGGACAAAC
TTTGATTCTAAGGTAGGAAGT
Found at i:1002930 original size:13 final size:13
Alignment explanation
Indices: 1002912--1002938 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1002902 ATAGAGATTG
1002912 TGGGAAGAAATGA
1 TGGGAAGAAATGA
1002925 TGGGAAGAAATGA
1 TGGGAAGAAATGA
1002938 T
1 T
1002939 TTTCCTCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.37, T:0.19
Consensus pattern (13 bp):
TGGGAAGAAATGA
Found at i:1004801 original size:307 final size:304
Alignment explanation
Indices: 1004403--1004980 Score: 675
Period size: 307 Copynumber: 1.9 Consensus size: 304
1004393 ACAAACATTG
* *
1004403 ATTCTAAGAAAATTAATAAGAAGAAAAGCTTTTCTTGTAAAACCAAAGAATCAACATCTTGTATC
1 ATTCTAAGAAAATTAATAAGAAGAAAAGCTTTTCTTGTAAAACAAAAGAATCAACATCATGTATC
* * * * *
1004468 CTAAAGAAGCAAACATGTTTTTATTGCCCAATCATGGAAAGAAT-GAAAATTACTTGGA-GAATC
66 CCAAAGAAGCAAACATCTTCTTATTGCCCAATCATGAAAAAAATAG-AAATTA-TT--ATGAATC
*
1004531 CATGTTTGTCTCAGTTGAAGGACGAACATTGACTCTAATGAAAATAATGGGAAGAAAAGCATTTC
127 CATGTTTGTCTCAGTTGAAGGACGAACATTGACTCTAAGGAAAATAATGGGAA-AAAAGCATTTC
* * * *
1004596 TTGTGAAGCCAAAAG-ATCAATATCATATATCCTAAT-AAAGAGAATGTG-TTTTGATTGCCCAA
191 TTGTGAA-ACAAAAGCATCAATATCATATATCCAAATGAAA-AGAAAGTGATTTTG-TTGCCAAA
*
1004658 TCAT-GAAAAGAATGGAGATCTTATGAGAGTCTTTTTTATGGGTTGAACTTTT
253 TCATAG-AAAGAATAGAGATCTTATGAGAGTCTTTTTTATGGGTTGAACTTTT
** * * * * *
1004710 ATTCTAAGGAAAA-TAATTGGAGGAAAAGCTTTTCTTGTGAAAGAAAAGTATCAATATCATGTAT
1 ATTCTAA-GAAAATTAATAAGAAGAAAAGCTTTTCTTGTAAAACAAAAGAATCAACATCATGTAT
* ** * * *
1004774 CCCAATGAAGGGAACGTCTTCTTATTGCCCAATCATGAAAAAAATAGAGATTATTATGAATCTAT
65 CCCAAAGAAGCAAACATCTTCTTATTGCCCAATCATGAAAAAAATAGAAATTATTATGAATCCAT
* * ** ** * * *
1004839 GTTTGTCTCATTTGAGGGATTAATTTTGATTCTAAGGAAAATGATGGGAAAAAAGCTTTTCTTGT
130 GTTTGTCTCAGTTGAAGGACGAACATTGACTCTAAGGAAAATAATGGGAAAAAAGCATTTCTTGT
* * *
1004904 GAAACTAAAGCATGAATATCATGTATCCAAATGAAAAGAAAGTGATTTTGTTGCCAAATCATAGA
195 GAAACAAAAGCATCAATATCATATATCCAAATGAAAAGAAAGTGATTTTGTTGCCAAATCATAGA
1004969 AAGAATAGAGAT
260 AAGAATAGAGAT
1004981 TATTACGAAA
Statistics
Matches: 226, Mismatches: 38, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
303 5 0.02
304 66 0.29
305 57 0.25
306 2 0.01
307 90 0.40
308 6 0.03
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (304 bp):
ATTCTAAGAAAATTAATAAGAAGAAAAGCTTTTCTTGTAAAACAAAAGAATCAACATCATGTATC
CCAAAGAAGCAAACATCTTCTTATTGCCCAATCATGAAAAAAATAGAAATTATTATGAATCCATG
TTTGTCTCAGTTGAAGGACGAACATTGACTCTAAGGAAAATAATGGGAAAAAAGCATTTCTTGTG
AAACAAAAGCATCAATATCATATATCCAAATGAAAAGAAAGTGATTTTGTTGCCAAATCATAGAA
AGAATAGAGATCTTATGAGAGTCTTTTTTATGGGTTGAACTTTT
Found at i:1004925 original size:156 final size:157
Alignment explanation
Indices: 1004706--1005065 Score: 426
Period size: 156 Copynumber: 2.3 Consensus size: 157
1004696 TGGGTTGAAC
* * * *
1004706 TTTTATTCTAAGGAAAATAATTGGAGGAAAAGCTTTTCTTGTGAAAGAAAAGTATCAATATCATG
1 TTTTATTCTAAGGAAAATGATGGGAGGAAAAGCTTTTCTTGTGAAACAAAAGCATCAATATCATG
* ** * * * *
1004771 TATCCCAATGAAGGGAACGT-CTTCTTATTGCCCAATCAT-GAAAAAAATAGAGATTATTATG-A
66 TATCCAAATGAAAAGAAAGTGATT-TTATTGCCAAATCATAG-AAAAAATAGAGATTATTACGAA
* * **
1004833 ATCTATGTTTGTCTCATTTGAGGGATTAA
129 ATCCATGTTTCTCTCATTTGAGGGACAAA
* * *
1004862 TTTTGATTCTAAGGAAAATGATGGGA-AAAAAGCTTTTCTTGTGAAACTAAAGCATGAATATCAT
1 TTTT-ATTCTAAGGAAAATGATGGGAGGAAAAGCTTTTCTTGTGAAACAAAAGCATCAATATCAT
* *
1004926 GTATCCAAATGAAAAGAAAGTGATTTTGTTGCCAAATCATAGAAAGAATAGAGATTATTACGAAA
65 GTATCCAAATGAAAAGAAAGTGATTTTATTGCCAAATCATAGAAAAAATAGAGATTATTACG-AA
* *
1004991 ATCCATGTTTCTCTTATTTGATGGACAAA
129 ATCCATGTTTCTCTCATTTGAGGGACAAA
*
1005020 TTTTATTCTAA--AACAATGATGGGAGGAAAAGCTTTTCTTATGAAAC
1 TTTTATTCTAAGGAA-AATGATGGGAGGAAAAGCTTTTCTTGTGAAAC
1005066 CAATAAAAAG
Statistics
Matches: 173, Mismatches: 24, Indels: 13
0.82 0.11 0.06
Matches are distributed among these distances:
155 2 0.01
156 95 0.55
157 48 0.28
158 28 0.16
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (157 bp):
TTTTATTCTAAGGAAAATGATGGGAGGAAAAGCTTTTCTTGTGAAACAAAAGCATCAATATCATG
TATCCAAATGAAAAGAAAGTGATTTTATTGCCAAATCATAGAAAAAATAGAGATTATTACGAAAT
CCATGTTTCTCTCATTTGAGGGACAAA
Found at i:1005385 original size:155 final size:151
Alignment explanation
Indices: 1005074--1005499 Score: 387
Period size: 155 Copynumber: 2.7 Consensus size: 151
1005064 ACCAATAAAA
1005074 AGAACATGCTTTGATTGCCCAATCATGAAAAGAATGGATGTTATTAC-G-ACATGTTTTTCTCAT
1 AGAACATGCTTTGATTGCCCAATCATGAAAAGAATGGATGTTATTACAGAACATGTTTTTCTC--
* * * * * * *
1005137 TTAAAGG-TCTAAC-TTGGTTTTGAGGAAAATGATGGGAAGAAAAGCTTTTCTTATGAAACCATA
64 ---AAGGAT-GAACATTGATTCTAAGGAAAATGATGGGAAGAAAAGCTTTTCTTAAGAAAACAAA
* *
1005200 GTATAAATATCATGTATCCCAATGAGG
125 GCATAAATATCATGTATCACAATGAGG
* *
1005227 AGAACGTGCTTTGATTGCCCACTCATGAAAAGAATGGATGTTATTACTAGAATCTATGTTTTTCT
1 AGAACATGCTTTGATTGCCCAATCATGAAAAGAATGGATGTTATTAC-AGAA-C-ATGTTTTTCT
* *
1005292 CGAGGGATGAACATTGATTCTAAGGAAAATGATTGGAAGAAAAGCTTTTCTTAAGAAAACAAAGC
63 C-AAGGATGAACATTGATTCTAAGGAAAATGATGGGAAGAAAAGCTTTTCTTAAGAAAACAAAGC
* ** * * * *
1005357 ATTAATATTGTGTCTTACAATTATG
127 ATAAATATCATGTATCACAATGAGG
* * * *
1005382 AGAACATG-TTTCGATTGCCTAATTATGAAAAGAATGGA-GATTTTTACAAAAACCCATGATTGT
1 AGAACATGCTTT-GATTGCCCAATCATGAAAAGAATGGATG-TTATTAC-AGAA--CATG-TT-T
* * *
1005445 CTCATTTCAAGAATGAACATTGATTCTAAGGAAAATAATGGGAAGAAAAGCTTTT
59 -T--TCTCAAGGATGAACATTGATTCTAAGGAAAATGATGGGAAGAAAAGCTTTT
1005500 TTTGTGAAAC
Statistics
Matches: 224, Mismatches: 34, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
153 45 0.20
154 10 0.04
155 105 0.47
156 4 0.02
157 2 0.01
158 12 0.05
159 43 0.19
160 3 0.01
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (151 bp):
AGAACATGCTTTGATTGCCCAATCATGAAAAGAATGGATGTTATTACAGAACATGTTTTTCTCAA
GGATGAACATTGATTCTAAGGAAAATGATGGGAAGAAAAGCTTTTCTTAAGAAAACAAAGCATAA
ATATCATGTATCACAATGAGG
Found at i:1007317 original size:12 final size:11
Alignment explanation
Indices: 1007298--1007415 Score: 108
Period size: 12 Copynumber: 10.9 Consensus size: 11
1007288 AGAAAAAGAA
1007298 GAGATAGGAGG
1 GAGATAGGAGG
1007309 GATGATAGGAGG
1 GA-GATAGGAGG
1007321 AGAGATAGGA--
1 -GAGATAGGAGG
*
1007331 GAGATAGTA--
1 GAGATAGGAGG
1007340 GAGATAGGAGG
1 GAGATAGGAGG
1007351 GATGATAGGAGG
1 GA-GATAGGAGG
1007363 AGAGATAGGA--
1 -GAGATAGGAGG
*
1007373 GAGATAGTA--
1 GAGATAGGAGG
1007382 GAGATAGGAGG
1 GAGATAGGAGG
1007393 GATGATAGGAGG
1 GA-GATAGGAGG
1007405 AGAGATAGGAG
1 -GAGATAGGAG
1007416 AGATAATAGA
Statistics
Matches: 93, Mismatches: 4, Indels: 19
0.80 0.03 0.16
Matches are distributed among these distances:
9 32 0.34
11 6 0.06
12 49 0.53
13 6 0.06
ACGTcount: A:0.40, C:0.00, G:0.47, T:0.14
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1007332 original size:9 final size:9
Alignment explanation
Indices: 1007318--1007420 Score: 92
Period size: 9 Copynumber: 12.1 Consensus size: 9
1007308 GGATGATAGG
1007318 AGGAGAGAT
1 AGGAGAGAT
1007327 AGGAGAGAT
1 AGGAGAGAT
*
1007336 AGTAGAGAT
1 AGGAGAGAT
*
1007345 AGGAGGGAT
1 AGGAGAGAT
* *
1007354 --GATAG-G
1 AGGAGAGAT
1007360 AGGAGAGAT
1 AGGAGAGAT
1007369 AGGAGAGAT
1 AGGAGAGAT
*
1007378 AGTAGAGAT
1 AGGAGAGAT
*
1007387 AGGAGGGAT
1 AGGAGAGAT
* *
1007396 --GATAG-G
1 AGGAGAGAT
1007402 AGGAGAGAT
1 AGGAGAGAT
1007411 AGGAGAGAT
1 AGGAGAGAT
1007420 A
1 A
1007421 ATAGAGAGAC
Statistics
Matches: 72, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
7 6 0.08
8 8 0.11
9 58 0.81
ACGTcount: A:0.42, C:0.00, G:0.45, T:0.14
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:1007356 original size:42 final size:42
Alignment explanation
Indices: 1007297--1007448 Score: 259
Period size: 42 Copynumber: 3.6 Consensus size: 42
1007287 AAGAAAAAGA
1007297 AGAGATAGGAGGGATGATAGGAGGAGAGATAGGAGAGATAGT
1 AGAGATAGGAGGGATGATAGGAGGAGAGATAGGAGAGATAGT
1007339 AGAGATAGGAGGGATGATAGGAGGAGAGATAGGAGAGATAGT
1 AGAGATAGGAGGGATGATAGGAGGAGAGATAGGAGAGATAGT
*
1007381 AGAGATAGGAGGGATGATAGGAGGAGAGATAGGAGAGATAAT
1 AGAGATAGGAGGGATGATAGGAGGAGAGATAGGAGAGATAGT
* * **
1007423 AGAGAGACGAGGGATGGCAGGAGGAG
1 AGAGATAGGAGGGATGATAGGAGGAG
1007449 GAGAGAAGAA
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 105 1.00
ACGTcount: A:0.40, C:0.01, G:0.46, T:0.12
Consensus pattern (42 bp):
AGAGATAGGAGGGATGATAGGAGGAGAGATAGGAGAGATAGT
Found at i:1007424 original size:12 final size:12
Alignment explanation
Indices: 1007300--1007429 Score: 67
Period size: 12 Copynumber: 11.9 Consensus size: 12
1007290 AAAAAGAAGA
*
1007300 GATAGGAGGGAT
1 GATAGGAGAGAT
1007312 GATAGGAGGAGA-
1 GATAGGA-GAGAT
1007324 GATA-G-GAGA-
1 GATAGGAGAGAT
*
1007333 GATA-G-TAGA-
1 GATAGGAGAGAT
*
1007342 GATAGGAGGGAT
1 GATAGGAGAGAT
1007354 GATAGGAGGAGA-
1 GATAGGA-GAGAT
1007366 GATA-G-GAGA-
1 GATAGGAGAGAT
*
1007375 GATA-G-TAGA-
1 GATAGGAGAGAT
*
1007384 GATAGGAGGGAT
1 GATAGGAGAGAT
1007396 GATAGGAGGAGA-
1 GATAGGA-GAGAT
1007408 GATAGGAGAGAT
1 GATAGGAGAGAT
*
1007420 AATA-GAGAGA
1 GATAGGAGAGA
1007430 CGAGGGATGG
Statistics
Matches: 98, Mismatches: 10, Indels: 21
0.76 0.08 0.16
Matches are distributed among these distances:
9 32 0.33
10 2 0.02
11 16 0.16
12 39 0.40
13 9 0.09
ACGTcount: A:0.42, C:0.00, G:0.45, T:0.14
Consensus pattern (12 bp):
GATAGGAGAGAT
Found at i:1013280 original size:42 final size:42
Alignment explanation
Indices: 1013233--1013350 Score: 200
Period size: 42 Copynumber: 2.8 Consensus size: 42
1013223 TCTTCTCTGA
*
1013233 TCCTCCTATCATCCCTCCTCTCTCTATTATCTCTCCTGTCTC
1 TCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCTC
*
1013275 TCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCTC
1 TCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCTC
* *
1013317 TCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 TCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
1013351 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.09, C:0.46, G:0.02, T:0.43
Consensus pattern (42 bp):
TCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCTC
Found at i:1013291 original size:12 final size:11
Alignment explanation
Indices: 1013265--1013340 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1013255 TCTATTATCT
*
1013265 CTCCTGTCTCTC
1 CTCCTATCTC-C
1013277 CTCCTATCATCC
1 CTCCTATC-TCC
1013289 CTCCTATCT--
1 CTCCTATCTCC
*
1013298 CTACTATCT--
1 CTCCTATCTCC
*
1013307 CTCCTGTCTCTC
1 CTCCTATCTC-C
1013319 CTCCTATCATCC
1 CTCCTATC-TCC
*
1013331 CTCCTCTCTC
1 CTCCTATCTC
1013341 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:1013316 original size:18 final size:18
Alignment explanation
Indices: 1013247--1013317 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
1013237 CCTATCATCC
* *
1013247 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
1013265 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
1013287 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
1013307 CTCCTGTCTCT
1 CTCCTGTCTCT
1013318 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:1019515 original size:158 final size:160
Alignment explanation
Indices: 1019186--1019522 Score: 355
Period size: 158 Copynumber: 2.1 Consensus size: 160
1019176 GGGATGAACC
* * * *
1019186 TTGATTCTATGGAAAATGATAGGAAGAAAAGCTTTTCTTGTGATACCAAAGCATAAGTATCATGT
1 TTGATTCTAAGGAAAATGATAGGAAGAAAAGCTTTTCTTGTGATACCAAAACATAACTATCATGC
* **
1019251 ATCCCTAATAGGGAGAACTTATTTTGATTGGCCAAAACAAAAAAAAATGGAGATTATTAGGAAAA
66 ATCCCTAATAGGGAGAACTCATTTTGATTGGCCAAAACAAAAAAAAATAAAGATTATTAGGAAAA
* * *
1019316 ACCATGTTTGTCACATTTAAGGGATAAACT
131 ACCATGTTTGTCACATGTAAGGAACAAACT
*
1019346 TTGATTCTAAGGAAAATGATAGGAA-AAAAGCTTTTCTTGT-ATAACCAAAACATTACTATCATG
1 TTGATTCTAAGGAAAATGATAGGAAGAAAAGCTTTTCTTGTGAT-ACCAAAACATAACTATCATG
* * ** * *
1019409 CATCCC-AAT-GAGTAGAA-TGCAGTTTT-ATTGGCCAATTA-TGAAAAGAATAAAGATTATTAT
65 CATCCCTAATAG-GGAGAACT-CA-TTTTGATTGGCCAA-AACAAAAAAAAATAAAGATTATTAG
* * * * * *
1019469 GAGAATCCATGTTTGTCTCCTGTAATGAACAAAGT
126 GAAAAACCATGTTTGTCACATGTAAGGAACAAACT
* *
1019504 TTTATTTTAAGGAAAATGA
1 TTGATTCTAAGGAAAATGA
1019523 CGAATCACAT
Statistics
Matches: 147, Mismatches: 25, Indels: 12
0.80 0.14 0.07
Matches are distributed among these distances:
157 2 0.01
158 79 0.54
159 42 0.29
160 24 0.16
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (160 bp):
TTGATTCTAAGGAAAATGATAGGAAGAAAAGCTTTTCTTGTGATACCAAAACATAACTATCATGC
ATCCCTAATAGGGAGAACTCATTTTGATTGGCCAAAACAAAAAAAAATAAAGATTATTAGGAAAA
ACCATGTTTGTCACATGTAAGGAACAAACT
Found at i:1028688 original size:42 final size:42
Alignment explanation
Indices: 1028633--1028751 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
1028623 TTCTTCTCTC
* *
1028633 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
1028675 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
1028717 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
1028752 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:1028692 original size:12 final size:11
Alignment explanation
Indices: 1028666--1028741 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1028656 TCTATTATCT
*
1028666 CTCCTGTCTCTC
1 CTCCTATCTC-C
1028678 CTCCTATCATCC
1 CTCCTATC-TCC
1028690 CTCCTATCT--
1 CTCCTATCTCC
*
1028699 CTACTATCT--
1 CTCCTATCTCC
*
1028708 CTCCTGTCTCTC
1 CTCCTATCTC-C
1028720 CTCCTATCATCC
1 CTCCTATC-TCC
*
1028732 CTCCTCTCTC
1 CTCCTATCTC
1028742 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:1028693 original size:24 final size:24
Alignment explanation
Indices: 1028657--1028742 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1028647 CCTCCTCTCT
* *
1028657 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
1028681 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
1028702 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
1028723 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
1028743 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:1028717 original size:18 final size:18
Alignment explanation
Indices: 1028648--1028718 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
1028638 CCTGTCATCC
* *
1028648 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
1028666 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
1028688 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
1028708 CTCCTGTCTCT
1 CTCCTGTCTCT
1028719 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:1030721 original size:158 final size:156
Alignment explanation
Indices: 1030371--1031148 Score: 493
Period size: 158 Copynumber: 4.9 Consensus size: 156
1030361 CAAGAAACCT
* * ** * * * **
1030371 AAGCATCAATATCATGTATCCCT-ATAAGTAGAATGTGTTTTTATTGCCTAATCATGAAATGAAT
1 AAGCATCAATATCATGTAT-CCTAATGAGAAGAACATGTTTCTATTGCCCAATCAGGAAAACAAT
* * * ** ** * * * *
1030435 GGATATTGTTACAAGAATCTATGTTTGTCTCAATTAAGGGATGAACATTGATTTTAA-G-TAATG
65 GGAGATTATTA-AAGAATCCATGTTCATCTCTTTTAA-GGATAAACTTTGATTCTAAGGAAAATG
* *
1030498 ATGGGAAGAAAAGTTTTTCCTAT-GAAA-CCA
128 AT-GGAAGAAAAGCTTTT-CT-TCCAAAGCCA
* * ** * *** * * * *
1030528 ATGCTTCAATATCATGTATCCCGATAAGGTTAACATGTTTTTTTTGCCAAATCA-CAAAACCAAT
1 AAGCATCAATATCATGTATCCTAATGAGAAGAACATGTTTCTATTGCCCAATCAGGAAAA-CAAT
* * *
1030592 GGAGATTATTGAAAGAATCCATGTTTATCTCTTTTGAGAATAAACTTTGATTCTAAGGAAAATGA
65 GGAGATTATT-AAAGAATCCATGTTCATCTCTTTTAAGGATAAACTTTGATTCTAAGGAAAATGA
*
1030657 TGAGAAGAAAAGCTTTTCTTCCAAATCCA
129 TG-GAAGAAAAGCTTTTCTTCCAAAGCCA
* * *
1030686 AAGCATCAATATTATGTATCTTAATGAGAAGAACATGTTCCTATTGCCCAATCAGGAAAA-AATG
1 AAGCATCAATATCATGTATCCTAATGAGAAGAACATGTTTCTATTGCCCAATCAGGAAAACAATG
* * ** * * *
1030750 GAGATTATTAGAATAATCAACATTCATCTCTTTTCAAGGATGAACCTTGATTCTAAGGAAAATGT
66 GAGATTATTA-AAGAATCCATGTTCATCTCTTTT-AAGGATAAACTTTGATTCTAAGGAAAATGA
*** *
1030815 TGGGAAGAAAAAGCTTTTCTTGTGAGGCCA
129 T-GGAAG-AAAAGCTTTTCTTCCAAAGCCA
* * * * ** * * *
1030845 AAGTATTAATATCATGTATCCTAATGAGGATAATGTGTTTCTGTTGCCCAATCATGAAAACAATA
1 AAGCATCAATATCATGTATCCTAATGAGAAGAACATGTTTCTATTGCCCAATCAGGAAAACAATG
* *
1030910 GAGATTATTAAAAGAATCCATGTTCAACTCTTGTAAGGGATAAA-TCTTGATTCTAAGGAAAATG
66 GAGATTATT-AAAGAATCCATGTTCATCTCTTTTAA-GGATAAACT-TTGATTCTAAGGAAAATG
** *
1030974 ATGGAA-ATAAATGCTTTTCTTGTGAAA-CGA
128 ATGGAAGA-AAA-GCTTTTCTT-CCAAAGCCA
* * * * * ** * * * *
1031004 AA-CACCAATATCATGTGTTGC-AAAGAGGAGAAGTTGTTTTTGTTGCCCAATCATGAAAACAAA
1 AAGCATCAATATCATGT-ATCCTAATGAGAAGAACATGTTTCTATTGCCCAATCAGGAAAACAAT
* * * ** * *
1031067 GGATATTGTTAAAAGAATCCATATTTGTCTCTTTTAAGGGATGAACTTTGATTATAAGGAAAAT-
65 GGAGATTATT-AAAGAATCCATGTTCATCTCTTTTAA-GGATAAACTTTGATTCTAAGGAAAATG
1031131 AGTAGGAAGAAAAGCTTT
128 A-T-GGAAGAAAAGCTTT
1031149 CTTTGCAAAA
Statistics
Matches: 492, Mismatches: 104, Indels: 49
0.76 0.16 0.08
Matches are distributed among these distances:
156 22 0.04
157 112 0.23
158 201 0.41
159 100 0.20
160 56 0.11
161 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.33
Consensus pattern (156 bp):
AAGCATCAATATCATGTATCCTAATGAGAAGAACATGTTTCTATTGCCCAATCAGGAAAACAATG
GAGATTATTAAAGAATCCATGTTCATCTCTTTTAAGGATAAACTTTGATTCTAAGGAAAATGATG
GAAGAAAAGCTTTTCTTCCAAAGCCA
Found at i:1036969 original size:12 final size:11
Alignment explanation
Indices: 1036947--1037022 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1036937 AGAGAAAGAA
*
1036947 GAGAGAGGAGG
1 GAGATAGGAGG
1036958 GATGATAGGAGG
1 GA-GATAGGAGG
*
1036970 AGAGACAGGA--
1 -GAGATAGGAGG
*
1036980 GAGATAGTA--
1 GAGATAGGAGG
1036989 GAGATAGGAGG
1 GAGATAGGAGG
1037000 GATGATAGGAGG
1 GA-GATAGGAGG
*
1037012 AGAGACAGGAG
1 -GAGATAGGAG
1037023 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1036979 original size:24 final size:24
Alignment explanation
Indices: 1036946--1037031 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1036936 AAGAGAAAGA
*
1036946 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
1036970 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
1036988 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
1037012 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
1037032 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:1036998 original size:42 final size:42
Alignment explanation
Indices: 1036937--1037055 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
1036927 TAGCCCTCAA
* *
1036937 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
1036979 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
1037021 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
1037056 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:1047988 original size:153 final size:151
Alignment explanation
Indices: 1047732--1048237 Score: 539
Period size: 154 Copynumber: 3.3 Consensus size: 151
1047722 TCGACTCTAG
* * * * * ** * *
1047732 AAATTATGAAAATGCCCTAG-GGATATCTTCGACATAGAAGTACCCGATACCTATAAAGTACTCA
1 AAATTATAAAAATGCCCTAGAGGATACCCTCGACTTAAAAGTACCCGATACCCCTAAAGGACTTA
*** *
1047796 AAAAGGATTATAGATGGGATGAACCTATCCTAAATACCCACCTTCAACATAAAAGCAAATCCAGT
66 AAAAGG-TTATAGATGGGATGAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGAA-CCAGT
1047861 GACAACCTAGGAATCAATTTTAA
129 GACAACCTAGGAATCAATTTTAA
* * **** *
1047884 AAATTATGAAAATGCCCCTAGAGGATACCTTCGACTTAAAAGTGTTTGACACCCCTAAAGGACTT
1 AAATTATAAAAATG-CCCTAGAGGATACCCTCGACTTAAAAGTACCCGATACCCCTAAAGGACTT
* * *
1047949 AAAAAGGTTATAGATGGGATGAACCTATCCTAAACACCCACCTTTGGCATAAAAACGGACCCAGT
65 AAAAAGGTTATAGATGGGATGAACCTATCCTAAATACCCACCTTTGGCATAAAAGC-GAACCAGT
1048014 GACAACCTAGGAATCAATTTTAGA
129 GACAACCTAGGAATCAATTTTA-A
* * * * *
1048038 AAATTACAAAAATAGCCCTA-AGAGATACCCTCAACTTTAAAGTACCCAATAGCCCTAAAGGACT
1 AAATTATAAAAAT-GCCCTAGAG-GATACCCTCGACTTAAAAGTACCCGATACCCCTAAAGGACT
* * * * * *
1048102 TAAAAAAGATATAGATGAGATGAACCTATCCTGAATACCCATCTTTGGCATAAAAGTGAACCTAG
64 TAAAAAGGTTATAGATGGGATGAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGAACC-AG
* *
1048167 TGACAACCTAGGAATCGATTCTAAA
128 TGACAACCTAGGAATCAATT-TTAA
* * * * *
1048192 AAATTAAAAAAATACCCCGAGAGGATACCCTCGTCTTAGAAGTACC
1 AAATTATAAAAAT-GCCCTAGAGGATACCCTCGACTTAAAAGTACC
1048238 AAGCGATCCT
Statistics
Matches: 296, Mismatches: 49, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
152 14 0.05
153 83 0.28
154 194 0.66
155 5 0.02
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (151 bp):
AAATTATAAAAATGCCCTAGAGGATACCCTCGACTTAAAAGTACCCGATACCCCTAAAGGACTTA
AAAAGGTTATAGATGGGATGAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGAACCAGTGA
CAACCTAGGAATCAATTTTAA
Found at i:1049695 original size:12 final size:12
Alignment explanation
Indices: 1049654--1049700 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
1049644 TTGATTTTTC
*
1049654 CTTTTTTACTCT
1 CTTTTTTTCTCT
1049666 CTTTTTGCTT-TCT
1 CTTTTT--TTCTCT
*
1049679 TTTTTTTTCTCT
1 CTTTTTTTCTCT
1049691 CTTTTTTTCT
1 CTTTTTTTCT
1049701 TACTTGCCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
11 2 0.07
12 18 0.62
13 8 0.28
14 1 0.03
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (12 bp):
CTTTTTTTCTCT
Found at i:1050551 original size:165 final size:165
Alignment explanation
Indices: 1050342--1050746 Score: 442
Period size: 165 Copynumber: 2.4 Consensus size: 165
1050332 GGCAAGGAAA
* ** *
1050342 AATGATAAATGAATGAATTTTTCAAAACCGATTTACTATGAATTAAATGATGATATTTTATGAAT
1 AATGA-AAATAAATGAATTTTTCAAAACTAATTTAATATGAATTAAATGATGATATTTTATGAAT
* ** *
1050407 GTTAAAAATTATAAACTGAGAAACCTCC-CCTCAAAA-ATGTTATAAAATAGAAAACTCAGTCTT
65 TTTAAAAATTATAAACTGAGAAAAATCCTCCTCAAAACAT-TAATAAAATAGAAAACTCA-T-TT
*
1050470 TTAGAAAA-AGAAAAATTTTAAGAAAAAAATGAAAAACT
127 TTAGAAAATAGAAAAATTTCAAGAAAAAAATGAAAAACT
* * * *
1050508 CATGAAAATAAATAAATTTTTCAAAAATAATTTAATATGAATTAAATGATGATATTTGATGAATT
1 AATGAAAATAAATGAATTTTTCAAAACTAATTTAATATGAATTAAATGATGATATTTTATGAATT
* * * * * * *
1050573 TTAAAAATTTTGAACTGAGAAAAATCCTCGTGAAAACCTTAATAGAATAGAAAACTCATTTTTTG
66 TTAAAAATTATAAACTGAGAAAAATCCTCCTCAAAACATTAATAAAATAGAAAACTCATTTTTAG
* * *
1050638 AAAATAGGAAAATTTCAAGGAAAAAATGAAAAATT
131 AAAATAGAAAAATTTCAAGAAAAAAATGAAAAACT
** ** * * * *
1050673 AATG-AAATAAATGGAATTTTTTGAAACTAATTTCTTGTGAGTTAAAT-AGTAATATTTTAGGAA
1 AATGAAAATAAAT-GAATTTTTCAAAACTAATTTAATATGAATTAAATGA-TGATATTTTATGAA
1050736 TTTTAAAAATT
64 TTTTAAAAATT
1050747 TTGGATTAGT
Statistics
Matches: 199, Mismatches: 35, Indels: 11
0.81 0.14 0.04
Matches are distributed among these distances:
164 18 0.09
165 153 0.77
166 27 0.14
167 1 0.01
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.33
Consensus pattern (165 bp):
AATGAAAATAAATGAATTTTTCAAAACTAATTTAATATGAATTAAATGATGATATTTTATGAATT
TTAAAAATTATAAACTGAGAAAAATCCTCCTCAAAACATTAATAAAATAGAAAACTCATTTTTAG
AAAATAGAAAAATTTCAAGAAAAAAATGAAAAACT
Found at i:1053517 original size:657 final size:658
Alignment explanation
Indices: 1052263--1053558 Score: 2443
Period size: 657 Copynumber: 2.0 Consensus size: 658
1052253 TGGTTCATGG
1052263 TTGTCATCAATTGGTATCAAAGCTTTGGTTTGGAGTTGGATTAAATTCATTATCACTATCAGGTT
1 TTGTCATCAATTGGTATCAAAGCTTTGGTTTGGAGTTGGATTAAATTCATTATCACTATCAGGTT
*
1052328 CATGTTTGCTGTTCATCAAACTGTTTCTATTAGTTTTGAATCTTGAACTCATTTGATCTTGTTGC
66 CATGTTTACTGTTCATCAAACTGTTTCTATTAGTTTTGAATCTTGAACTCATTTGATCTTGTTGC
1052393 TGTTATTTTTTTTCAAGAATACAAAAAAAAAAAGAAAGAATACAAAAAGAGAGGAAAAAACCAGC
131 TGTTATTTTTTTTCAAGAATACAAAAAAAAAAAGAAAGAATACAAAAAGAGAGGAAAAAACCAGC
1052458 ATTTGATTCTGATCATTCATGTGTCAAGATTAAATCTTTATTTGAGTTAATTCTGATCATTGTTA
196 ATTTGATTCTGATCATTCATGTGTCAAGATTAAATCTTTATTTGAGTTAATTCTGATCATTGTTA
1052523 CAGCTTTAATTCCCAGATCAGAAATTCTGGTTGTGTCATTAGTTTTCAAATCCCTACTCCATCAT
261 CAGCTTTAATTCCCAGATCAGAAATTCTGGTTGTGTCATTAGTTTTCAAATCCCTACTCCATCAT
*
1052588 TAAAATTCCTTAATGCCAGACTATATTTTATTATCTATAATCTGTTCTTAATTCTAGGGTCTTGT
326 TAAAATTCCTTAATGCCAGACTATATTTTATTATCTATAATCTATTCTTAATTCTAGGGTCTTGT
*
1052653 CTTGTTACTTTCCTACTTAAGTGTGCTTTATCTTTCTTGTTAGCTTTTCTTGATTGTCTTATTGG
391 CTTGTTACTTTCCTACTTAAGTGTGCTTTATCTTTCATGTTAGCTTTTCTTGATTGTCTTATTGG
*
1052718 ATTTCTTAGTTTTGTTTTAGTGTTTTCTTTGTTGGCCTCACTTAGTTGATTGTCACTTGGTTGTG
456 ATTTCTTAGTTTTGTTTTAGTGTTTTCTTTGTTGGCCTCACTTAGTTGATTATCACTTGGTTGTG
* *
1052783 GTTGATTGTGTGGACTGGAGGTTGACTTCCTTAAGAACTGTTGAGAAGACTTGAGAGGAAAAAGG
521 GTTGATTGTGTGGACTGGAGGTTGACTTCCTTAAGAACTATTGAGAAGACTTGAGAGGAAAAAGC
1052848 CAAGAGTGAAATCAGTACACAAAAGCCAATTTTGAGT-AAACACGAGTGAACATTCCTTTTGGCT
586 CAAGAGTGAAATCAGTACACAAAAGCCAATTTTGAGTGAAACACGAGTGAACATTCCTTTTGGCT
1052912 TATCAATC
651 TATCAATC
* *
1052920 TTGTCATCAATTGGTATCAGAGCTTTGGTTTGGAGTTGGATTCAATTCATTATCACTATCAGGTT
1 TTGTCATCAATTGGTATCAAAGCTTTGGTTTGGAGTTGGATTAAATTCATTATCACTATCAGGTT
* *
1052985 CGTGTTTACTGTTCATCATACTGTTTCTATTAGTTTTGAATCTTGAACTCATTTGATCTTGTTGC
66 CATGTTTACTGTTCATCAAACTGTTTCTATTAGTTTTGAATCTTGAACTCATTTGATCTTGTTGC
1053050 TGTTATTTTTTTTTCAAGAATAC-AAAAAAAAAAGAAAGAATACAAAAAGAGAGGAAAAAACCAG
131 TGTTA-TTTTTTTTCAAGAATACAAAAAAAAAAAGAAAGAATACAAAAAGAGAGGAAAAAACCAG
1053114 CATTTGATTCTGATCATTCATGTGTCAAGATTAAATCTTTATTTGAGTTAATTCTGATCATTGTT
195 CATTTGATTCTGATCATTCATGTGTCAAGATTAAATCTTTATTTGAGTTAATTCTGATCATTGTT
1053179 ACAGCTTTAATTCCCAGATCAGAAATTCTGGTTGTGTCATTAGTTTTCAAATCCCTACTCCATCA
260 ACAGCTTTAATTCCCAGATCAGAAATTCTGGTTGTGTCATTAGTTTTCAAATCCCTACTCCATCA
1053244 TTAAAATTCCTTAATGCCAGACTATATTTTATTATCTATAATCTATTCTTAATTCTAGGGTCTTG
325 TTAAAATTCCTTAATGCCAGACTATATTTTATTATCTATAATCTATTCTTAATTCTAGGGTCTTG
*
1053309 TCTTGTTACTTTCCTACTTGAGTGTGCTTTATCTTTCATGTTAGCTTTTCTTGATTGTCTTATTG
390 TCTTGTTACTTTCCTACTTAAGTGTGCTTTATCTTTCATGTTAGCTTTTCTTGATTGTCTTATTG
*
1053374 GATTTCTTAGTTTTTTTTTAGTGTTTTCTTTGTTGGCCTCACTTAGTTGATTATCACTTGGTTGT
455 GATTTCTTAGTTTTGTTTTAGTGTTTTCTTTGTTGGCCTCACTTAGTTGATTATCACTTGGTTGT
*
1053439 GGTTGATTGTGTGGACTGGTGGTTGACTTCCTTAAGAACTATTGAGAAGACTTGAGAGGAAAAAG
520 GGTTGATTGTGTGGACTGGAGGTTGACTTCCTTAAGAACTATTGAGAAGACTTGAGAGGAAAAAG
*
1053504 CCAAGAGTGAAATCAGTACACAAAAGCCAATTTTGAGTGAAACATGAGTGAACAT
585 CCAAGAGTGAAATCAGTACACAAAAGCCAATTTTGAGTGAAACACGAGTGAACAT
1053559 CTATTGAGTG
Statistics
Matches: 623, Mismatches: 14, Indels: 3
0.97 0.02 0.00
Matches are distributed among these distances:
657 591 0.95
658 32 0.05
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.41
Consensus pattern (658 bp):
TTGTCATCAATTGGTATCAAAGCTTTGGTTTGGAGTTGGATTAAATTCATTATCACTATCAGGTT
CATGTTTACTGTTCATCAAACTGTTTCTATTAGTTTTGAATCTTGAACTCATTTGATCTTGTTGC
TGTTATTTTTTTTCAAGAATACAAAAAAAAAAAGAAAGAATACAAAAAGAGAGGAAAAAACCAGC
ATTTGATTCTGATCATTCATGTGTCAAGATTAAATCTTTATTTGAGTTAATTCTGATCATTGTTA
CAGCTTTAATTCCCAGATCAGAAATTCTGGTTGTGTCATTAGTTTTCAAATCCCTACTCCATCAT
TAAAATTCCTTAATGCCAGACTATATTTTATTATCTATAATCTATTCTTAATTCTAGGGTCTTGT
CTTGTTACTTTCCTACTTAAGTGTGCTTTATCTTTCATGTTAGCTTTTCTTGATTGTCTTATTGG
ATTTCTTAGTTTTGTTTTAGTGTTTTCTTTGTTGGCCTCACTTAGTTGATTATCACTTGGTTGTG
GTTGATTGTGTGGACTGGAGGTTGACTTCCTTAAGAACTATTGAGAAGACTTGAGAGGAAAAAGC
CAAGAGTGAAATCAGTACACAAAAGCCAATTTTGAGTGAAACACGAGTGAACATTCCTTTTGGCT
TATCAATC
Found at i:1053875 original size:12 final size:12
Alignment explanation
Indices: 1053855--1053889 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1053845 AAGAGAAAGA
1053855 AGAGATAGGAGG
1 AGAGATAGGAGG
1053867 -GATGATAGGAGG
1 AGA-GATAGGAGG
1053879 AGAGATAGGAG
1 AGAGATAGGAG
1053890 AGATAGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.40, C:0.00, G:0.49, T:0.11
Consensus pattern (12 bp):
AGAGATAGGAGG
Found at i:1053886 original size:24 final size:23
Alignment explanation
Indices: 1053855--1053946 Score: 88
Period size: 24 Copynumber: 4.2 Consensus size: 23
1053845 AAGAGAAAGA
1053855 AGAGATAGGAGGGATGATAGGAGG
1 AGAGATAGGAGGGATGATA-GAGG
*
1053879 AGAGATAGGA--GA-GAT--AGT
1 AGAGATAGGAGGGATGATAGAGG
*
1053897 AGAGATAGGAAGGATGATAGAAGG
1 AGAGATAGGAGGGATGATAG-AGG
* *
1053921 AGAGATAGGAGAGATAATAGA-G
1 AGAGATAGGAGGGATGATAGAGG
1053943 AGAG
1 AGAG
1053947 GAGGGATGAG
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
18 12 0.21
20 2 0.04
21 6 0.11
22 7 0.12
23 1 0.02
24 29 0.51
ACGTcount: A:0.45, C:0.00, G:0.42, T:0.13
Consensus pattern (23 bp):
AGAGATAGGAGGGATGATAGAGG
Found at i:1053890 original size:9 final size:9
Alignment explanation
Indices: 1053876--1053936 Score: 67
Period size: 9 Copynumber: 7.1 Consensus size: 9
1053866 GGATGATAGG
1053876 AGGAGAGAT
1 AGGAGAGAT
1053885 AGGAGAGAT
1 AGGAGAGAT
*
1053894 AGTAGAGAT
1 AGGAGAGAT
1053903 AGGA-AGGAT
1 AGGAGA-GAT
*
1053912 --GATAGA-
1 AGGAGAGAT
1053918 AGGAGAGAT
1 AGGAGAGAT
1053927 AGGAGAGAT
1 AGGAGAGAT
1053936 A
1 A
1053937 ATAGAGAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
7 4 0.09
8 7 0.16
9 33 0.75
ACGTcount: A:0.46, C:0.00, G:0.41, T:0.13
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:1053905 original size:42 final size:42
Alignment explanation
Indices: 1053846--1053965 Score: 177
Period size: 42 Copynumber: 2.9 Consensus size: 42
1053836 TAGCCCTAAA
* *
1053846 AGAGAAAGAAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
1 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
* *
1053888 AGAGATAGTAGAGATAGGAAGGATGATAGAAGGAGAGATAGG
1 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
* * *
1053930 AGAGATAATAGAGAGAGGAGGGATGAGAGGAGGAGA
1 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGA
1053966 AGAGAAGAAG
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.45, C:0.00, G:0.44, T:0.11
Consensus pattern (42 bp):
AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
Found at i:1060783 original size:29 final size:29
Alignment explanation
Indices: 1060751--1060834 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
1060741 TAAAAGAGGA
1060751 TGCCACTAACTTGTGGACTTTTGAAAGAG
1 TGCCACTAACTTGTGGACTTTTGAAAGAG
* *
1060780 TGCCACTAACTTGTGGCCTTTTGAAAGGG
1 TGCCACTAACTTGTGGACTTTTGAAAGAG
* * * *
1060809 TGCTACTGATTTGTGGGC-TTTGAAAG
1 TGCCACTAACTTGTGGACTTTTGAAAG
1060835 GATTCAACTC
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
28 8 0.16
29 41 0.84
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (29 bp):
TGCCACTAACTTGTGGACTTTTGAAAGAG
Found at i:1060985 original size:30 final size:30
Alignment explanation
Indices: 1060944--1061011 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
1060934 CCGATTCATG
*
1060944 GGCTTT-AAAAGGGTGACA-CTAACTTGTGT
1 GGCTTTGAAAAGGGTGACAGC-AACTCGTGT
* *
1060973 GGCTTTGAAAAGGTTGCCAGCAACTCGTGT
1 GGCTTTGAAAAGGGTGACAGCAACTCGTGT
1061003 GGACTTTGA
1 GG-CTTTGA
1061012 CTGAGGTGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 6 0.18
30 20 0.61
31 7 0.21
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (30 bp):
GGCTTTGAAAAGGGTGACAGCAACTCGTGT
Found at i:1061028 original size:31 final size:32
Alignment explanation
Indices: 1060987--1061174 Score: 130
Period size: 31 Copynumber: 5.8 Consensus size: 32
1060977 TTGAAAAGGT
* * *
1060987 TGCCAGCAACTCGTGTGGACTTTGACTGA-GG
1 TGCCACCAACTCGTGTGGACTTTAAATGATGG
* * * *
1061018 TGTCACCAACTTGTGTGGACTTTAAAAAAGATTG
1 TGCCACCAACTCGTGTGGACTTT--AAATGATGG
** * * *
1061052 TGCCACTGACTTGTGTGGACTTTCAATG-GGG
1 TGCCACCAACTCGTGTGGACTTTAAATGATGG
* * *
1061083 TTCCACCAACTCATGTGGACTTTAACT-ATGG
1 TGCCACCAACTCGTGTGGACTTTAAATGATGG
* * *
1061114 TGCCACCAGCTCGTGTGGACTTTGAAAAGGTTTGG
1 TGCCACCAACTCGTGTGGACTTT--AAATG-ATGG
*
1061149 TTGCCACCAACTTGTGTGGACTTTAA
1 -TGCCACCAACTCGTGTGGACTTTAA
1061175 GAATGGTTTG
Statistics
Matches: 118, Mismatches: 30, Indels: 15
0.72 0.18 0.09
Matches are distributed among these distances:
31 63 0.53
32 3 0.03
33 5 0.04
34 23 0.19
35 3 0.03
36 21 0.18
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.31
Consensus pattern (32 bp):
TGCCACCAACTCGTGTGGACTTTAAATGATGG
Found at i:1061100 original size:96 final size:99
Alignment explanation
Indices: 1060984--1061172 Score: 242
Period size: 96 Copynumber: 1.9 Consensus size: 99
1060974 GCTTTGAAAA
* * * * *
1060984 GGTTGCCAGCAACTCGTGTGGACTTTGACTGA-GGTGTCACCAACTTGTGTGGACTTTAAAAAAG
1 GGTTGCCACCAACTCATGTGGACTTTAACT-ATGGTGCCACCAACTCGTGTGGACTTTAAAAAAG
**
1061048 ATT-G-TGCCACTGACTTGTGTGGACTTTCAATGG
65 ATTGGTTGCCACCAACTTGTGTGGACTTTCAATGG
* * * *
1061081 GGTT-CCACCAACTCATGTGGACTTTAACTATGGTGCCACCAGCTCGTGTGGACTTTGAAAAGGT
1 GGTTGCCACCAACTCATGTGGACTTTAACTATGGTGCCACCAACTCGTGTGGACTTTAAAAAAGA
1061145 TTGGTTGCCACCAACTTGTGTGGACTTT
66 TTGGTTGCCACCAACTTGTGTGGACTTT
1061173 AAGAATGGTT
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
95 1 0.01
96 51 0.65
97 5 0.06
98 21 0.27
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (99 bp):
GGTTGCCACCAACTCATGTGGACTTTAACTATGGTGCCACCAACTCGTGTGGACTTTAAAAAAGA
TTGGTTGCCACCAACTTGTGTGGACTTTCAATGG
Found at i:1061192 original size:37 final size:36
Alignment explanation
Indices: 1061021--1061212 Score: 140
Period size: 31 Copynumber: 5.6 Consensus size: 36
1061011 ACTGAGGTGT
* * *
1061021 CACCAACTTGTGTGGACTTTAAAAAAGATT-G-TGC
1 CACCAACTTGTGTGGACTTTAAGAAGGTTTGGTTGC
** * *
1061055 CACTGACTTGTGTGGACTTTCA-ATGG---GGTT-C
1 CACCAACTTGTGTGGACTTTAAGAAGGTTTGGTTGC
** * *
1061086 CACCAACTCATGTGGACTTT---AA-CTATGG-TGC
1 CACCAACTTGTGTGGACTTTAAGAAGGTTTGGTTGC
* *
1061117 CACCAGCTCGTGTGGACTTTGAA-AAGGTTTGGTTGC
1 CACCAACTTGTGTGGACTTT-AAGAAGGTTTGGTTGC
1061153 CACCAACTTGTGTGGACTTTAAGAATGGTTTGGTTGC
1 CACCAACTTGTGTGGACTTTAAGAA-GGTTTGGTTGC
* *
1061190 CACCGACTTGTGTGCACTTTAAG
1 CACCAACTTGTGTGGACTTTAAG
1061213 TGCTGCCAGC
Statistics
Matches: 126, Mismatches: 19, Indels: 23
0.75 0.11 0.14
Matches are distributed among these distances:
29 1 0.01
30 1 0.01
31 39 0.31
32 1 0.01
33 2 0.02
34 21 0.17
35 6 0.05
36 23 0.18
37 32 0.25
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (36 bp):
CACCAACTTGTGTGGACTTTAAGAAGGTTTGGTTGC
Found at i:1061421 original size:55 final size:55
Alignment explanation
Indices: 1061350--1061512 Score: 215
Period size: 55 Copynumber: 3.0 Consensus size: 55
1061340 TTGACACGAG
* * *
1061350 TGTCGATGTGTTGATTCAAGGCTAGC-AGCATCAAACTTAAAGATTTTGACAAAGA
1 TGTCAATGTGCTGATTCAAGGCTAGCGA-CATCAGACTTAAAGATTTTGACAAAGA
*
1061405 TGTCAATGTGCTGATTCAAGGCTAGCGACAAT-AGACTTAAAGGTTTTGACAAAGA
1 TGTCAATGTGCTGATTCAAGGCTAGCGAC-ATCAGACTTAAAGATTTTGACAAAGA
* * *
1061460 TGTCAATGTGCTAATTCAAGGCCAGTGACA-CTAGACTTAAAGATTTTGACAAA
1 TGTCAATGTGCTGATTCAAGGCTAGCGACATC-AGACTTAAAGATTTTGACAAA
1061513 TTTTGACAAA
Statistics
Matches: 96, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
54 1 0.01
55 92 0.96
56 3 0.03
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.28
Consensus pattern (55 bp):
TGTCAATGTGCTGATTCAAGGCTAGCGACATCAGACTTAAAGATTTTGACAAAGA
Found at i:1062565 original size:33 final size:33
Alignment explanation
Indices: 1062496--1062565 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
1062486 GGCCTGCTTG
* * **
1062496 ACAAGAAAGGTGATATAGTTTGATTTATTTTTA
1 ACAAGAAAGGTGATATAGTTTCATTCATTTCCA
1062529 ACAAGAAAGGTGATA-AGATTTCATTCATTTCCA
1 ACAAGAAAGGTGATATAG-TTTCATTCATTTCCA
1062562 ACAA
1 ACAA
1062566 AATGGTCTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 2 0.06
33 30 0.94
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (33 bp):
ACAAGAAAGGTGATATAGTTTCATTCATTTCCA
Found at i:1072170 original size:18 final size:18
Alignment explanation
Indices: 1072149--1072228 Score: 67
Period size: 18 Copynumber: 4.6 Consensus size: 18
1072139 CCTGTCATCC
*
1072149 CTCCTCTCTCTATTATCT
1 CTCCTATCTCTATTATCT
* *
1072167 CTCCTATCTCTCTTGTCT
1 CTCCTATCTCTATTATCT
* *
1072185 CTCC--TC-CTATCATCC
1 CTCCTATCTCTATTATCT
* *
1072200 CCCCTATCTCTACTATCT
1 CTCCTATCTCTATTATCT
*
1072218 CTCCTGTCTCT
1 CTCCTATCTCT
1072229 CCTCCTATCA
Statistics
Matches: 46, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
15 8 0.17
16 2 0.04
17 2 0.04
18 34 0.74
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTATCTCTATTATCT
Found at i:1072193 original size:21 final size:21
Alignment explanation
Indices: 1072167--1072237 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
1072157 TCTATTATCT
*
1072167 CTCCTATCTCTCTTGTCTCTC
1 CTCCTATCTCTCCTGTCTCTC
* ** *
1072188 CTCCTATCATCCCCCCTATCT-
1 CTCCTATC-TCTCCTGTCTCTC
*
1072209 CTACTATCTCTCCTGTCTCTC
1 CTCCTATCTCTCCTGTCTCTC
1072230 CTCCTATC
1 CTCCTATC
1072238 ATCCCTCCTC
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
20 8 0.22
21 22 0.59
22 7 0.19
ACGTcount: A:0.10, C:0.46, G:0.03, T:0.41
Consensus pattern (21 bp):
CTCCTATCTCTCCTGTCTCTC
Found at i:1072209 original size:42 final size:42
Alignment explanation
Indices: 1072162--1072261 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 42
1072152 CTCTCTCTAT
* *
1072162 TATCTCTCCTATCTCTCTTGTCTCTCCTCCTATCATCCCCCC
1 TATCTCTACTATCTCTCCTGTCTCTCCTCCTATCATCCCCCC
*
1072204 TATCTCTACTATCTCTCCTGTCTCTCCTCCTATCATCCCTCC
1 TATCTCTACTATCTCTCCTGTCTCTCCTCCTATCATCCCCCC
* * *
1072246 TCTCTCTTCTTTCTCT
1 TATCTCTACTATCTCT
1072262 TTGAGGGCTA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.09, C:0.45, G:0.02, T:0.44
Consensus pattern (42 bp):
TATCTCTACTATCTCTCCTGTCTCTCCTCCTATCATCCCCCC
Found at i:1072210 original size:51 final size:52
Alignment explanation
Indices: 1072121--1072229 Score: 150
Period size: 51 Copynumber: 2.1 Consensus size: 52
1072111 TCACTCTTCC
* * * *
1072121 ATCT-TCTTCTCTCCTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCT
1 ATCTCTCTTCTCTCCTCCTCCTATCATCCCCCCTATCTCTACTATCTCTCCT
*
1072172 ATCTCTCTTGTCT-CTCCTCCTATCATCCCCCCTATCTCTACTATCTCTCCT
1 ATCTCTCTTCTCTCCTCCTCCTATCATCCCCCCTATCTCTACTATCTCTCCT
*
1072223 GTCTCTC
1 ATCTCTC
1072230 CTCCTATCAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
51 44 0.86
52 7 0.14
ACGTcount: A:0.09, C:0.45, G:0.03, T:0.43
Consensus pattern (52 bp):
ATCTCTCTTCTCTCCTCCTCCTATCATCCCCCCTATCTCTACTATCTCTCCT
Found at i:1073029 original size:24 final size:24
Alignment explanation
Indices: 1073002--1073047 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1072992 CTGGCTTTTT
1073002 TTTCCTCTCTTTTTGTATTCTTTC
1 TTTCCTCTCTTTTTGTATTCTTTC
* * *
1073026 TTTCTTTTTTTTTTGTATTCTT
1 TTTCCTCTCTTTTTGTATTCTT
1073048 GAAAAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.74
Consensus pattern (24 bp):
TTTCCTCTCTTTTTGTATTCTTTC
Found at i:1075288 original size:9 final size:9
Alignment explanation
Indices: 1075264--1075337 Score: 73
Period size: 9 Copynumber: 8.6 Consensus size: 9
1075254 CCTGTCATCC
*
1075264 CTCCTCTCT
1 CTCCTATCT
*
1075273 CTACTATCT
1 CTCCTATCT
1075282 CTCCTATCT
1 CTCCTATCT
*
1075291 CTCCT-CCT
1 CTCCTATCT
* *
1075299 AT-C-ATCC
1 CTCCTATCT
1075306 CTCCTATCT
1 CTCCTATCT
*
1075315 CTACTATCT
1 CTCCTATCT
1075324 CTCCTATCT
1 CTCCTATCT
1075333 CTCCT
1 CTCCT
1075338 TTTATCATCC
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
7 3 0.06
8 4 0.08
9 44 0.86
ACGTcount: A:0.12, C:0.46, G:0.00, T:0.42
Consensus pattern (9 bp):
CTCCTATCT
Found at i:1075299 original size:12 final size:12
Alignment explanation
Indices: 1075282--1075316 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1075272 TCTACTATCT
1075282 CTCCTATCTCTC
1 CTCCTATCTCTC
1075294 CTCCTATCATC-C
1 CTCCTATC-TCTC
1075306 CTCCTATCTCT
1 CTCCTATCTCT
1075317 ACTATCTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.11, C:0.49, G:0.00, T:0.40
Consensus pattern (12 bp):
CTCCTATCTCTC
Found at i:1075367 original size:42 final size:42
Alignment explanation
Indices: 1075249--1075358 Score: 175
Period size: 42 Copynumber: 2.6 Consensus size: 42
1075239 TTCTTCTCTC
* *
1075249 CTCCTCCTGTCATCCCTCCTCTCTCTACTATCTCTCCTATCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
1075291 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
** *
1075333 CTCCTTTTATCATCCCTCTTATCTCT
1 CTCCTCCTATCATCCCTCCTATCTCT
1075359 TTTTTCTCTT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.12, C:0.45, G:0.01, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
Done.