Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 133 of 143
Found at i:39290394 original size:11 final size:11
Alignment explanation
Indices: 39290312--39290395 Score: 50
Period size: 11 Copynumber: 7.8 Consensus size: 11
39290302 GAAAATAACA
*
39290312 ACCAAAACAGT
1 ACCAAAACAGC
* *
39290323 A-AAAAAAAGC
1 ACCAAAACAGC
*
39290333 ACCAAAACAGT
1 ACCAAAACAGC
*
39290344 A--AAAA-AAC
1 ACCAAAACAGC
* *
39290352 ACAAAAATAGC
1 ACCAAAACAGC
*
39290363 AACCAAAACAGTA
1 -ACCAAAACAG-C
39290376 ACCAAAACAGC
1 ACCAAAACAGC
39290387 ACCAAAACA
1 ACCAAAACA
39290396 AAAATATAAT
Statistics
Matches: 54, Mismatches: 13, Indels: 12
0.68 0.16 0.15
Matches are distributed among these distances:
8 2 0.04
9 4 0.07
10 11 0.20
11 19 0.35
12 18 0.33
ACGTcount: A:0.64, C:0.24, G:0.07, T:0.05
Consensus pattern (11 bp):
ACCAAAACAGC
Found at i:39291103 original size:21 final size:21
Alignment explanation
Indices: 39291077--39291118 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39291067 CCATGATTCC
39291077 AAGGAA-CACAACATAAGCAAA
1 AAGGAAGCA-AACATAAGCAAA
*
39291098 AAGGAAGTAAACATAAGCAAA
1 AAGGAAGCAAACATAAGCAAA
39291119 CTCGTTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.62, C:0.14, G:0.17, T:0.07
Consensus pattern (21 bp):
AAGGAAGCAAACATAAGCAAA
Found at i:39309644 original size:2 final size:2
Alignment explanation
Indices: 39309637--39309677 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
39309627 ATTTATGAAT
39309637 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39309678 TAATATTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39319982 original size:24 final size:24
Alignment explanation
Indices: 39319955--39320000 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
39319945 TGACGCTGAA
*
39319955 ATTAATTTAATATATAATTTTTTT
1 ATTAATTTAATATATAAATTTTTT
*
39319979 ATTAATTTAATATTTAAATTTT
1 ATTAATTTAATATATAAATTTT
39320001 AAGAGTCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTAATTTAATATATAAATTTTTT
Found at i:39323675 original size:6 final size:6
Alignment explanation
Indices: 39323650--39323688 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
39323640 ACAATTCATA
* * *
39323650 TCACTT TCAATT TTAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
39323689 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (6 bp):
TCACTT
Found at i:39323843 original size:15 final size:15
Alignment explanation
Indices: 39323811--39323850 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
39323801 TATAATTAAC
39323811 CACATA-ATATTTCA
1 CACATATATATTTCA
* *
39323825 CACATATATTTTTCT
1 CACATATATATTTCA
39323840 CACATATATAT
1 CACATATATAT
39323851 CATTATATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (15 bp):
CACATATATATTTCA
Found at i:39337187 original size:21 final size:21
Alignment explanation
Indices: 39337161--39337203 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39337151 AATTTTATAA
*
39337161 AAAATATATTTAAATTTTTTT
1 AAAATATATTTAAACTTTTTT
* *
39337182 AAAATATCTTTACACTTTTTT
1 AAAATATATTTAAACTTTTTT
39337203 A
1 A
39337204 TAATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (21 bp):
AAAATATATTTAAACTTTTTT
Found at i:39337214 original size:21 final size:20
Alignment explanation
Indices: 39337176--39337231 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
39337166 ATATTTAAAT
39337176 TTTTTTAAAATATCTTTACAC
1 TTTTTTAAAATATCTTTAC-C
* * *
39337197 TTTTTTATAATTTTTTTACC
1 TTTTTTAAAATATCTTTACC
39337217 TTTTTGTAATAATAT
1 TTTTT-TAA-AATAT
39337232 TATTAATTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 6 0.21
21 18 0.64
22 4 0.14
ACGTcount: A:0.29, C:0.09, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTTTTAAAATATCTTTACC
Found at i:39338140 original size:13 final size:13
Alignment explanation
Indices: 39338122--39338157 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
39338112 TTAATTTGAT
*
39338122 ATTTGATTTTTTA
1 ATTTGATTTTTAA
*
39338135 ATTTGATATTTAA
1 ATTTGATTTTTAA
39338148 ATTTGATTTT
1 ATTTGATTTT
39338158 AATATTCAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
ATTTGATTTTTAA
Found at i:39343044 original size:12 final size:14
Alignment explanation
Indices: 39343022--39343055 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
39343012 ACCACCTTTC
*
39343022 TTTTTTATTATAAAT
1 TTTTTTA-TATACAT
39343037 TTTTTTATATACAT
1 TTTTTTATATACAT
39343051 TTTTT
1 TTTTT
39343056 AAAACTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTTATATACAT
Found at i:39347436 original size:19 final size:20
Alignment explanation
Indices: 39347398--39347438 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
39347388 TTCAAAGCTT
* *
39347398 AATTTTTAAAATATTATTAA
1 AATTTATAAAATAATATTAA
39347418 AATTTATAAAA-AATATTAA
1 AATTTATAAAATAATATTAA
39347437 AA
1 AA
39347439 AAATAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTTATAAAATAATATTAA
Found at i:39358510 original size:31 final size:31
Alignment explanation
Indices: 39358457--39358528 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
39358447 ACGTTTAAGC
* *
39358457 ACCAACTTAAGAAAAAGAGTCAAATTTAGGT
1 ACCAAATTAGGAAAAAGAGTCAAATTTAGGT
** * * *
39358488 GTCAAATTAGGAAAAAGTGTCAAGTTTGGGT
1 ACCAAATTAGGAAAAAGAGTCAAATTTAGGT
39358519 ACCAAATTAG
1 ACCAAATTAG
39358529 ACCAAAAACA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (31 bp):
ACCAAATTAGGAAAAAGAGTCAAATTTAGGT
Found at i:39361918 original size:25 final size:26
Alignment explanation
Indices: 39361878--39361926 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
39361868 TTCGTTAAAC
39361878 AAAAATATGAAAGATTGAAAACTTTTG
1 AAAAATATGAAAGATTG-AAACTTTTG
39361905 AAAAA-AT-AAAGATTGAAACTTT
1 AAAAATATGAAAGATTGAAACTTT
39361927 GAATTTGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 7 0.32
25 8 0.36
26 2 0.09
27 5 0.23
ACGTcount: A:0.55, C:0.04, G:0.12, T:0.29
Consensus pattern (26 bp):
AAAAATATGAAAGATTGAAACTTTTG
Found at i:39366420 original size:27 final size:28
Alignment explanation
Indices: 39366371--39366425 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
39366361 CCAATATTTT
39366371 AAAATTTATCAATATTTAAATAATCAAA
1 AAAATTTATCAATATTTAAATAATCAAA
*
39366399 AAAATTGT-TCAATA-TTATATAATCAAA
1 AAAATT-TATCAATATTTAAATAATCAAA
39366426 TTTGAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 12 0.48
28 12 0.48
29 1 0.04
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (28 bp):
AAAATTTATCAATATTTAAATAATCAAA
Found at i:39367214 original size:11 final size:11
Alignment explanation
Indices: 39367194--39367268 Score: 69
Period size: 11 Copynumber: 6.5 Consensus size: 11
39367184 AAGCCTCTTA
*
39367194 TCTTTCCTTTC
1 TCTTTTCTTTC
*
39367205 TCTTTTCTTTT
1 TCTTTTCTTTC
*
39367216 TCTCATTCATTTC
1 TCT-TTTC-TTTC
*
39367229 TTTTTTCTTTC
1 TCTTTTCTTTC
39367240 TCTTTTCTTTTC
1 TCTTTTC-TTTC
* *
39367252 TATTTTCTTCC
1 TCTTTTCTTTC
39367263 TCTTTT
1 TCTTTT
39367269 AATCACACTT
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
11 30 0.59
12 16 0.31
13 5 0.10
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.71
Consensus pattern (11 bp):
TCTTTTCTTTC
Found at i:39367251 original size:12 final size:12
Alignment explanation
Indices: 39367196--39367260 Score: 62
Period size: 12 Copynumber: 5.5 Consensus size: 12
39367186 GCCTCTTATC
*
39367196 TTTCCTTTCTCT
1 TTTCTTTTCTCT
39367208 TTTCTTTT-TCT
1 TTTCTTTTCTCT
* * *
39367219 CATTCATTTCTTT
1 -TTTCTTTTCTCT
39367232 TTTC-TTTCTCT
1 TTTCTTTTCTCT
*
39367243 TTTCTTTTCTAT
1 TTTCTTTTCTCT
39367255 TTTCTT
1 TTTCTT
39367261 CCTCTTTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
11 13 0.30
12 28 0.65
13 2 0.05
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTCTTTTCTCT
Found at i:39367674 original size:21 final size:21
Alignment explanation
Indices: 39367638--39367705 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
39367628 ACCCATTAAG
*
39367638 CCCAAATCCTATTTAAACCAAA
1 CCCAAATGC-ATTTAAACCAAA
**
39367660 CCCTCATGCATTTAAACCAAA
1 CCCAAATGCATTTAAACCAAA
*
39367681 CCCAAATTCATTTAAACCAAA
1 CCCAAATGCATTTAAACCAAA
39367702 CCCA
1 CCCA
39367706 TTTGAACCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
21 34 0.85
22 6 0.15
ACGTcount: A:0.43, C:0.34, G:0.01, T:0.22
Consensus pattern (21 bp):
CCCAAATGCATTTAAACCAAA
Found at i:39367707 original size:15 final size:15
Alignment explanation
Indices: 39367689--39367718 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39367679 AACCCAAATT
39367689 CATTTAAACCAAACC
1 CATTTAAACCAAACC
*
39367704 CATTTGAACCAAACC
1 CATTTAAACCAAACC
39367719 AAATGAACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (15 bp):
CATTTAAACCAAACC
Found at i:39367799 original size:11 final size:10
Alignment explanation
Indices: 39367755--39367802 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
39367745 AGTCAAACCA
*
39367755 TTGACCGATG
1 TTGACCGACG
* *
39367765 TTGACTGGCG
1 TTGACCGACG
*
39367775 TTGATCGACG
1 TTGACCGACG
39367785 TTGACCGACCG
1 TTGACCGA-CG
39367796 TTGACCG
1 TTGACCG
39367803 GTGTTGATTG
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
10 21 0.70
11 9 0.30
ACGTcount: A:0.17, C:0.25, G:0.31, T:0.27
Consensus pattern (10 bp):
TTGACCGACG
Found at i:39367808 original size:21 final size:21
Alignment explanation
Indices: 39367784--39367823 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
39367774 GTTGATCGAC
39367784 GTTGACCGACCGTTGACCGGT
1 GTTGACCGACCGTTGACCGGT
** *
39367805 GTTGATTGATCGTTGACCG
1 GTTGACCGACCGTTGACCG
39367824 TTGATCGTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.15, C:0.23, G:0.33, T:0.30
Consensus pattern (21 bp):
GTTGACCGACCGTTGACCGGT
Found at i:39367820 original size:7 final size:7
Alignment explanation
Indices: 39367810--39367854 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
39367800 CCGGTGTTGA
39367810 TTGATCG
1 TTGATCG
*
39367817 TTGACCG
1 TTGATCG
39367824 TTGATCG
1 TTGATCG
*
39367831 TTGA-CT
1 TTGATCG
39367837 TTGATCG
1 TTGATCG
*
39367844 TTGACCG
1 TTGATCG
39367851 TTGA
1 TTGA
39367855 CTTTTTCGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.16, C:0.18, G:0.27, T:0.40
Consensus pattern (7 bp):
TTGATCG
Found at i:39367827 original size:14 final size:14
Alignment explanation
Indices: 39367810--39367854 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
39367800 CCGGTGTTGA
39367810 TTGATCGTTGACCG
1 TTGATCGTTGACCG
*
39367824 TTGATCGTTGA-CT
1 TTGATCGTTGACCG
39367837 TTGATCGTTGACCG
1 TTGATCGTTGACCG
39367851 TTGA
1 TTGA
39367855 CTTTTTCGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 12 0.43
14 16 0.57
ACGTcount: A:0.16, C:0.18, G:0.27, T:0.40
Consensus pattern (14 bp):
TTGATCGTTGACCG
Found at i:39367845 original size:20 final size:20
Alignment explanation
Indices: 39367817--39367858 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
39367807 TGATTGATCG
*
39367817 TTGACCGTTGATCGTTGACT
1 TTGACCGTTGACCGTTGACT
*
39367837 TTGATCGTTGACCGTTGACT
1 TTGACCGTTGACCGTTGACT
39367857 TT
1 TT
39367859 TTCGAAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.19, G:0.24, T:0.43
Consensus pattern (20 bp):
TTGACCGTTGACCGTTGACT
Found at i:39368916 original size:3 final size:3
Alignment explanation
Indices: 39368904--39368935 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
39368894 TATTCTATTC
39368904 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39368936 GGGATGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:39374594 original size:7 final size:7
Alignment explanation
Indices: 39374582--39374624 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
39374572 AAAACATGAT
39374582 ATTTATA
1 ATTTATA
*
39374589 ATTTATT
1 ATTTATA
39374596 ATTTATA
1 ATTTATA
*
39374603 ATCTATA
1 ATTTATA
*
39374610 ATTTGTA
1 ATTTATA
*
39374617 ATATATA
1 ATTTATA
39374624 A
1 A
39374625 AAGCAAATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (7 bp):
ATTTATA
Found at i:39374786 original size:19 final size:21
Alignment explanation
Indices: 39374758--39374797 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
39374748 AAATTCTTGC
39374758 AATTTATTTT-G-TTATATAT
1 AATTTATTTTAGATTATATAT
*
39374777 AATTTTTTTTAGATTATATAT
1 AATTTATTTTAGATTATATAT
39374798 TTTTTTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 1 0.06
21 8 0.44
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (21 bp):
AATTTATTTTAGATTATATAT
Found at i:39376547 original size:24 final size:24
Alignment explanation
Indices: 39376416--39376542 Score: 184
Period size: 24 Copynumber: 5.3 Consensus size: 24
39376406 CTAAGTCTTT
* *
39376416 CAGAATGGTTACCTCTTACGAG-T
1 CAGAATGGTTAGCTCTTACGAGCC
*
39376439 CAGAATGGTTAGCTCTTACGAGTC
1 CAGAATGGTTAGCTCTTACGAGCC
39376463 CAGAATGGTTAGCTCTTACGAGCC
1 CAGAATGGTTAGCTCTTACGAGCC
* *
39376487 CAGAATGGTTAGCTCTTATGAACC
1 CAGAATGGTTAGCTCTTACGAGCC
*
39376511 CAGAATGGTTAACTCTTACGAGCC
1 CAGAATGGTTAGCTCTTACGAGCC
*
39376535 CAAAATGG
1 CAGAATGG
39376543 CTAACCAGTA
Statistics
Matches: 94, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
23 21 0.22
24 73 0.78
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
CAGAATGGTTAGCTCTTACGAGCC
Found at i:39381432 original size:20 final size:21
Alignment explanation
Indices: 39381395--39381433 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
39381385 TTTATGTATA
39381395 ATTATATTAAATTATTTAAAT
1 ATTATATTAAATTATTTAAAT
* *
39381416 ATTAT-TTAATTTTTTTAA
1 ATTATATTAAATTATTTAA
39381434 TTTCTAGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTATATTAAATTATTTAAAT
Found at i:39383349 original size:7 final size:7
Alignment explanation
Indices: 39383337--39383364 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
39383327 CAGTGAAGCC
39383337 GGAAAAG
1 GGAAAAG
39383344 GGAAAAG
1 GGAAAAG
39383351 GGAAAAG
1 GGAAAAG
39383358 GGAAAAG
1 GGAAAAG
39383365 TGTAAACGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (7 bp):
GGAAAAG
Found at i:39393091 original size:67 final size:67
Alignment explanation
Indices: 39392983--39393117 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
39392973 CCCAACCTAG
39392983 AGAAGGTAATTTGCTGTGCCTGTGACAGAAATTAACAATTTTGGGTTAATAGATTTACATAGCTC
1 AGAAGGTAATTTGCTGTGCCTGTGACAGAAATTAACAATTTTGGGTTAATAGATTTACATAGCTC
39393048 TT
66 TT
39393050 AGAAGGTAATTTGCTGTGCCTGTGACAGAAATTAACAATTTTGGGTTAATAGATTTACATAGCTC
1 AGAAGGTAATTTGCTGTGCCTGTGACAGAAATTAACAATTTTGGGTTAATAGATTTACATAGCTC
39393115 TT
66 TT
39393117 A
1 A
39393118 ATGTTGGTTC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.36
Consensus pattern (67 bp):
AGAAGGTAATTTGCTGTGCCTGTGACAGAAATTAACAATTTTGGGTTAATAGATTTACATAGCTC
TT
Found at i:39402560 original size:16 final size:16
Alignment explanation
Indices: 39402539--39402575 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
39402529 TTGTGTGGGA
39402539 GGAAATCTAATTTCTT
1 GGAAATCTAATTTCTT
39402555 GGAAATCTAATTTCTT
1 GGAAATCTAATTTCTT
39402571 GGAAA
1 GGAAA
39402576 AGCAAGAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (16 bp):
GGAAATCTAATTTCTT
Found at i:39405143 original size:78 final size:78
Alignment explanation
Indices: 39405014--39405248 Score: 353
Period size: 78 Copynumber: 3.0 Consensus size: 78
39405004 AAATAATTAC
* * *
39405014 CATAATCATTCCATACCCACTATCCAGAAGAAAAAATCCACCTCGCACCGCATCCATTTTTCAAA
1 CATAATCATTCCATACCCACTATCCAAAAGAAAAAATCCACCCCGCCCCGCATCCATTTTTCAAA
*
39405079 GAAAAAAACTGCT
66 GAAAAAATCTGCT
* * *
39405092 CATAACCATTCCATACCCACAATCCAAAAGAAAAAATTCACCCCGCCCCGCATCCATTTTTCAAA
1 CATAATCATTCCATACCCACTATCCAAAAGAAAAAATCCACCCCGCCCCGCATCCATTTTTCAAA
**
39405157 GAAAAAATCCACT
66 GAAAAAATCTGCT
* * * *
39405170 CATAATTATTTCATACCCACTATCCAAAAGAAAAAATCCACCCCACCCCACATCCATTTTTCAAA
1 CATAATCATTCCATACCCACTATCCAAAAGAAAAAATCCACCCCGCCCCGCATCCATTTTTCAAA
39405235 GAAAAAATCTGCT
66 GAAAAAATCTGCT
39405248 C
1 C
39405249 CATTTGAAGC
Statistics
Matches: 139, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 139 1.00
ACGTcount: A:0.40, C:0.32, G:0.06, T:0.22
Consensus pattern (78 bp):
CATAATCATTCCATACCCACTATCCAAAAGAAAAAATCCACCCCGCCCCGCATCCATTTTTCAAA
GAAAAAATCTGCT
Found at i:39415303 original size:15 final size:16
Alignment explanation
Indices: 39415283--39415315 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
39415273 TACATATTTC
*
39415283 TTTCATT-CTTTTAAT
1 TTTCATTGCTTTGAAT
39415298 TTTCATTGCTTTGAAT
1 TTTCATTGCTTTGAAT
39415314 TT
1 TT
39415316 GCAGGTAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.64
Consensus pattern (16 bp):
TTTCATTGCTTTGAAT
Found at i:39418489 original size:11 final size:11
Alignment explanation
Indices: 39418473--39418525 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
39418463 TATTACATGG
39418473 TAAAATTTAAA
1 TAAAATTTAAA
39418484 TAAAATTTAAA
1 TAAAATTTAAA
39418495 T---ATTT-AA
1 TAAAATTTAAA
*
39418502 TACATATTTAAA
1 TA-AAATTTAAA
*
39418514 TTAAATTTAAA
1 TAAAATTTAAA
39418525 T
1 T
39418526 TGATAGTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
7 3 0.09
8 4 0.11
11 25 0.71
12 3 0.09
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (11 bp):
TAAAATTTAAA
Found at i:39418501 original size:19 final size:19
Alignment explanation
Indices: 39418473--39418514 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
39418463 TATTACATGG
39418473 TAAA-ATTTAAATA-AAATT
1 TAAATATTT-AATACAAATT
*
39418491 TAAATATTTAATACATATT
1 TAAATATTTAATACAAATT
39418510 TAAAT
1 TAAAT
39418515 TAAATTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TAAATATTTAATACAAATT
Found at i:39424112 original size:19 final size:18
Alignment explanation
Indices: 39424076--39424116 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
39424066 GTTTATAAAG
*
39424076 TTAAAAATCTCCAATATA
1 TTAAAAATATCCAATATA
*
39424094 TTAAACAATATCCATTATA
1 TTAAA-AATATCCAATATA
39424113 TTAA
1 TTAA
39424117 GGAGGTAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.37
Consensus pattern (18 bp):
TTAAAAATATCCAATATA
Found at i:39429676 original size:183 final size:182
Alignment explanation
Indices: 39429368--39429906 Score: 821
Period size: 183 Copynumber: 2.9 Consensus size: 182
39429358 ACAAATGTCG
* * * * * *
39429368 GTAATGAGACGGTTCACGATGATAAGATCTTCGAAGGGAAAAACATAGATACTGATGTTATAACA
1 GTAATGAGACAGCTCATGATGATGAGATCTTCGAAGGGGAAGACATAGATACTGATGTTATAACA
*
39429433 GAAGCAGATGTGGGGTTGAATAAATCTTCTACATTCGATGAAGGTACCAAAGTTCGGAAGGAGTC
66 GAAGCAGATGTGGGGTTGAATAAATCTTCTACATTCGATGAAGGTA-CAAAGCTCGGAAGGAGTC
39429498 TTCGACTGCTGAACCGGTAGAGTTAAATAAGAATTCAACAGTGGACAGCGCCA
130 TTCGACTGCTGAACCGGTAGAGTTAAATAAGAATTCAACAGTGGACAGCGCCA
39429551 GTAATGAGACAGCTCATGATGATGAGATCTTCGAAGGGGAAGACATAGATACTGATGTTATAACA
1 GTAATGAGACAGCTCATGATGATGAGATCTTCGAAGGGGAAGACATAGATACTGATGTTATAACA
*
39429616 GAGGCAGATGTGGGGTTGAATAAATCTTCTACATTCGATGAAGGTACAAAAGCTCGGAAGGAGTC
66 GAAGCAGATGTGGGGTTGAATAAATCTTCTACATTCGATGAAGGTAC-AAAGCTCGGAAGGAGTC
* *
39429681 TTCGACTGCTGAACCAGTAGAGTTAAATAAGAATTCAACAGTGGACAGCGCCG
130 TTCGACTGCTGAACCGGTAGAGTTAAATAAGAATTCAACAGTGGACAGCGCCA
*
39429734 GTAATGAGACAGCTCATGATGATGAGATCTTTGAA-GGGAGAGACATAGATACTGAT-TTAATAA
1 GTAATGAGACAGCTCATGATGATGAGATCTTCGAAGGGGA-AGACATAGATACTGATGTT-ATAA
* ** * * * * *
39429797 CAGAAACAGATGTGGACTTGAATAAATCTTCAACATTCAATGAAGGTATCGATGCTCCGAAGGAG
64 CAGAAGCAGATGTGGGGTTGAATAAATCTTCTACATTCGATGAAGGTA-CAAAGCTCGGAAGGAG
* * *
39429862 TCTTCAACTGCTGAACTGGTAGACTTAAATAAGAATTCAACAGTG
128 TCTTCGACTGCTGAACCGGTAGAGTTAAATAAGAATTCAACAGTG
39429907 AACAATGCTG
Statistics
Matches: 328, Mismatches: 24, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
182 7 0.02
183 320 0.98
184 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (182 bp):
GTAATGAGACAGCTCATGATGATGAGATCTTCGAAGGGGAAGACATAGATACTGATGTTATAACA
GAAGCAGATGTGGGGTTGAATAAATCTTCTACATTCGATGAAGGTACAAAGCTCGGAAGGAGTCT
TCGACTGCTGAACCGGTAGAGTTAAATAAGAATTCAACAGTGGACAGCGCCA
Found at i:39432340 original size:18 final size:18
Alignment explanation
Indices: 39432319--39432356 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
39432309 TTCAATTCTC
39432319 TACAAAGAGAAAAAATTG
1 TACAAAGAGAAAAAATTG
39432337 TACAAAGAGAAAAAATTG
1 TACAAAGAGAAAAAATTG
39432355 TA
1 TA
39432357 TGAAACTGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.61, C:0.05, G:0.16, T:0.18
Consensus pattern (18 bp):
TACAAAGAGAAAAAATTG
Found at i:39437530 original size:22 final size:21
Alignment explanation
Indices: 39437505--39437546 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39437495 AACATTATCC
* *
39437505 TTTAAATATTTTACTTTTAAAA
1 TTTAAA-AATTTACATTTAAAA
39437527 TTTAAAAATTTACATTTAAA
1 TTTAAAAATTTACATTTAAA
39437547 TTCAATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTAAAAATTTACATTTAAAA
Found at i:39441061 original size:33 final size:33
Alignment explanation
Indices: 39441024--39441092 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
39441014 TCGTTTTAGG
*
39441024 TATAAAGCAATTTTAAAATTCGTAATCAACATT
1 TATAAAGCAATTTTAAAATTCGTAACCAACATT
* *
39441057 TATAAAGCAATTTTAAAATTTGTAGCCAACATT
1 TATAAAGCAATTTTAAAATTCGTAACCAACATT
39441090 TAT
1 TAT
39441093 CTATTAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (33 bp):
TATAAAGCAATTTTAAAATTCGTAACCAACATT
Found at i:39441711 original size:18 final size:18
Alignment explanation
Indices: 39441690--39441741 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
39441680 AAATAATAGC
39441690 AAAATTAATAATAAAACA
1 AAAATTAATAATAAAACA
* **
39441708 AAAATTATACAAT-ATCCA
1 AAAATTA-ATAATAAAACA
*
39441726 AATATTAATAATAAAA
1 AAAATTAATAATAAAA
39441742 TAATAGCAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 4
0.69 0.19 0.11
Matches are distributed among these distances:
17 4 0.16
18 17 0.68
19 4 0.16
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAATTAATAATAAAACA
Found at i:39445550 original size:61 final size:62
Alignment explanation
Indices: 39445413--39445550 Score: 176
Period size: 61 Copynumber: 2.3 Consensus size: 62
39445403 ATATCAGAGA
* * * *
39445413 TTAACTTAGACAAAAATAAAAATTTAGGCTCCAATGTAAAAATAATTGTTAAGTTCAGTGTC
1 TTAACTTAGACAAAAATAAAAATTCAGGCTCCAACGTAAAAATAATTGTCAAGTTCAGTGAC
* *
39445475 -TAACTT-GAATAAAAATAAAAATTCAGGCTCCAACGT-AAGATCAATTGTCAAGTTCA-TGAC
1 TTAACTTAG-ACAAAAATAAAAATTCAGGCTCCAACGTAAAAAT-AATTGTCAAGTTCAGTGAC
39445535 TTAACTTAGACAAAAA
1 TTAACTTAGACAAAAA
39445551 AAATTAAACC
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
60 8 0.12
61 56 0.86
62 1 0.02
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (62 bp):
TTAACTTAGACAAAAATAAAAATTCAGGCTCCAACGTAAAAATAATTGTCAAGTTCAGTGAC
Found at i:39446378 original size:22 final size:21
Alignment explanation
Indices: 39446347--39446387 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
39446337 CATTTTTTAA
39446347 TAATACAAATAGATAAATTTTT
1 TAATACAAAT-GATAAATTTTT
* *
39446369 TAATAGAAATGATCAATTT
1 TAATACAAATGATAAATTT
39446388 ATTATTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (21 bp):
TAATACAAATGATAAATTTTT
Found at i:39455301 original size:136 final size:136
Alignment explanation
Indices: 39455057--39455309 Score: 325
Period size: 136 Copynumber: 1.9 Consensus size: 136
39455047 TGTAGGAAGC
* * * **
39455057 TTTCCATACTGAGAAATCTGAATATATGTAATAATTCCATAGCACCTTTGGTTCTGCAATTTAGA
1 TTTCCATACTGAGAAACCTGAATATATGTAAAAATTCCATAGCACCTCTGGTTCTGCAATCAAGA
* * * *
39455122 CACCATAATTTGGACCAGGATTTCTGAAACTATTCATTCATAAAGACAACTACTAATGATAATAT
66 CACCATAATTTGGACCAGAATTTCTAAAACAATTCATTCATAAAGAAAACTACTAATGATAATAT
39455187 CACATG
131 CACATG
* *
39455193 TTTCCATACTGAGAAACCTGAA-AGTATGTAAAAATTCCATATCACCATCT-GTTGTAG-AATCA
1 TTTCCATACTGAGAAACCTGAATA-TATGTAAAAATTCCATAGCACC-TCTGGTTCT-GCAATCA
* *
39455255 AGACACCATGATTTGGAGCTA-AATTTCTAAAACAATTCATTCATAAAGAAAACTA
63 AGACACCATAATTTGGA-CCAGAATTTCTAAAACAATTCATTCATAAAGAAAACTA
39455310 ATATTTTGAT
Statistics
Matches: 100, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
135 1 0.01
136 94 0.94
137 5 0.05
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.31
Consensus pattern (136 bp):
TTTCCATACTGAGAAACCTGAATATATGTAAAAATTCCATAGCACCTCTGGTTCTGCAATCAAGA
CACCATAATTTGGACCAGAATTTCTAAAACAATTCATTCATAAAGAAAACTACTAATGATAATAT
CACATG
Found at i:39475681 original size:29 final size:31
Alignment explanation
Indices: 39475626--39475692 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 31
39475616 TGTATTTTTT
* *
39475626 AATTTTATTATTTTTAAATGGA-TTAAATA-
1 AATTTTATTATATTTAAATGGAGTAAAATAC
*
39475655 AATTTTTTTATATTTAAGA-GGAGTAAAATAC
1 AATTTTATTATATTTAA-ATGGAGTAAAATAC
39475686 AATTTTA
1 AATTTTA
39475693 CCATAATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 18 0.58
30 7 0.23
31 6 0.19
ACGTcount: A:0.42, C:0.01, G:0.09, T:0.48
Consensus pattern (31 bp):
AATTTTATTATATTTAAATGGAGTAAAATAC
Found at i:39476605 original size:19 final size:19
Alignment explanation
Indices: 39476580--39476626 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
39476570 ATAAAAAACA
*
39476580 ATAAAAAATTAACT-AAAT
1 ATAAAAAATAAACTAAAAT
*
39476598 ATTAAAAAATAAATTAAAAT
1 A-TAAAAAATAAACTAAAAT
39476618 ATAAAAAAT
1 ATAAAAAAT
39476627 CTTATCTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 1 0.04
19 19 0.76
20 5 0.20
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (19 bp):
ATAAAAAATAAACTAAAAT
Found at i:39477342 original size:29 final size:29
Alignment explanation
Indices: 39477308--39477364 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
39477298 TTTGATTATT
39477308 TTTAATAATACAAGGACTAAATTGATCAA
1 TTTAATAATACAAGGACTAAATTGATCAA
* * * *
39477337 TTTAATAGTAGAGGGACTAATTTGATCA
1 TTTAATAATACAAGGACTAAATTGATCA
39477365 TGTACCTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (29 bp):
TTTAATAATACAAGGACTAAATTGATCAA
Found at i:39486537 original size:9 final size:9
Alignment explanation
Indices: 39486507--39486546 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
39486497 CGCAGCAGTT
39486507 GCTGCTGCA
1 GCTGCTGCA
* *
39486516 GCTGCGGCG
1 GCTGCTGCA
39486525 GCTGCTGCA
1 GCTGCTGCA
*
39486534 GCTGATGCA
1 GCTGCTGCA
39486543 GCTG
1 GCTG
39486547 GACTAGAACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.10, C:0.30, G:0.40, T:0.20
Consensus pattern (9 bp):
GCTGCTGCA
Found at i:39492551 original size:30 final size:28
Alignment explanation
Indices: 39492488--39492588 Score: 79
Period size: 27 Copynumber: 3.6 Consensus size: 28
39492478 AGATCTGCCC
* *
39492488 ATATTATTATTATT-ATTTTTAAAAATATT
1 ATATT-TTATT-TTAATATTTAAAAATTTT
39492517 -TATTTTATTTTAATATTTAATAAATTTAT
1 ATATTTTATTTTAATATTTAA-AAATTT-T
39492546 ATATTTT-TTTT--TA-TTAAAAATTTT
1 ATATTTTATTTTAATATTTAAAAATTTT
* *
39492570 ATATAGTTATCTTAATATT
1 ATAT-TTTATTTTAATATT
39492589 ATTTTAATGT
Statistics
Matches: 59, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
24 5 0.08
25 8 0.14
26 9 0.15
27 14 0.24
28 11 0.19
29 6 0.10
30 6 0.10
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (28 bp):
ATATTTTATTTTAATATTTAAAAATTTT
Found at i:39500974 original size:20 final size:21
Alignment explanation
Indices: 39500928--39500974 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
39500918 AAACAGAGTG
* *
39500928 AGAAATAGAAAAAAATAGAGA
1 AGAAAGAGAAAAAAATAGAAA
*
39500949 ACAAAGAGAAAAAAA-AGAAA
1 AGAAAGAGAAAAAAATAGAAA
39500969 AGAAAG
1 AGAAAG
39500975 TTAACAAAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.04
Consensus pattern (21 bp):
AGAAAGAGAAAAAAATAGAAA
Found at i:39501574 original size:2 final size:2
Alignment explanation
Indices: 39501567--39501594 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39501557 ATTGTCCTTT
39501567 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39501595 AATGTCCTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39505016 original size:15 final size:15
Alignment explanation
Indices: 39504996--39505027 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
39504986 AATTTATTAT
39504996 TATTATTATTAGTAG
1 TATTATTATTAGTAG
39505011 TATTATTATTAGTAG
1 TATTATTATTAGTAG
39505026 TA
1 TA
39505028 GTAGTAGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
TATTATTATTAGTAG
Found at i:39505016 original size:18 final size:18
Alignment explanation
Indices: 39504993--39505030 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
39504983 TCCAATTTAT
*
39504993 TATTATTATTATTAGTAG
1 TATTATTATTAGTAGTAG
39505011 TATTATTATTAGTAGTAG
1 TATTATTATTAGTAGTAG
39505029 TA
1 TA
39505031 GTAGTAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (18 bp):
TATTATTATTAGTAGTAG
Found at i:39505023 original size:12 final size:12
Alignment explanation
Indices: 39504989--39505024 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
39504979 TGGATCCAAT
*
39504989 TTATTATTATTA
1 TTATTATTAGTA
*
39505001 TTATTAGTAGTA
1 TTATTATTAGTA
39505013 TTATTATTAGTA
1 TTATTATTAGTA
39505025 GTAGTAGTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (12 bp):
TTATTATTAGTA
Found at i:39506639 original size:9 final size:9
Alignment explanation
Indices: 39506619--39506653 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
39506609 AATATTAATT
39506619 ATTAAGTTCG
1 ATTAA-TTCG
39506629 ATTAATTCG
1 ATTAATTCG
39506638 ATTAATTCG
1 ATTAATTCG
*
39506647 ACTAATT
1 ATTAATT
39506654 ACCCGATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 19 0.79
10 5 0.21
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (9 bp):
ATTAATTCG
Found at i:39510851 original size:29 final size:30
Alignment explanation
Indices: 39510766--39510858 Score: 102
Period size: 29 Copynumber: 3.1 Consensus size: 30
39510756 GATCAAATTA
*
39510766 TTCAAAACGATTAAATAAGGATTATAA-CTT
1 TTCAAAATGATTAAATAAGGATTA-AACCTT
* * *
39510796 TTCGAAAGTG-TTCAAATAAGAACTAAACCTT
1 TTC-AAAATGATT-AAATAAGGATTAAACCTT
39510827 TT-AAAATGATTAAATAAGGATTAAACCTT
1 TTCAAAATGATTAAATAAGGATTAAACCTT
39510856 TTC
1 TTC
39510859 GAATATGCTT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
29 23 0.45
30 9 0.18
31 19 0.37
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (30 bp):
TTCAAAATGATTAAATAAGGATTAAACCTT
Found at i:39511742 original size:30 final size:31
Alignment explanation
Indices: 39511683--39511744 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
39511673 TTTATCATTA
*
39511683 TTAATTTAAAATTTTATAAATTGTAAAGGAT
1 TTAAATTAAAATTTTATAAATTGTAAAGGAT
* *
39511714 TTAAATTAAAATTTTAT-CATTTTAAAGGAT
1 TTAAATTAAAATTTTATAAATTGTAAAGGAT
39511744 T
1 T
39511745 ATAATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 12 0.43
31 16 0.57
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (31 bp):
TTAAATTAAAATTTTATAAATTGTAAAGGAT
Found at i:39529278 original size:16 final size:16
Alignment explanation
Indices: 39529233--39529304 Score: 51
Period size: 16 Copynumber: 4.6 Consensus size: 16
39529223 CCCGTCCATA
*
39529233 TTATT-TTTTAATTTT
1 TTATTATTTTAATATT
**
39529248 TTAAAATATTT-ATATT
1 TTATTAT-TTTAATATT
39529264 TTATTATTTTAATATT
1 TTATTATTTTAATATT
* * *
39529280 TAATAATTTTATACATT
1 TTATTATTTTA-ATATT
39529297 TT-TTATTT
1 TTATTATTT
39529305 ATTGAAATTT
Statistics
Matches: 43, Mismatches: 10, Indels: 7
0.72 0.17 0.12
Matches are distributed among these distances:
15 6 0.14
16 29 0.67
17 8 0.19
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTATTTTAATATT
Found at i:39529282 original size:31 final size:31
Alignment explanation
Indices: 39529233--39529292 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
39529223 CCCGTCCATA
*
39529233 TTATTTTTTAATTTTTTAA-AATATTTATATT
1 TTATTTTTTAATTATTTAATAAT-TTTATATT
39529264 TTATTATTTTAA-TATTTAATAATTTTATA
1 TTATT-TTTTAATTATTTAATAATTTTATA
39529293 CATTTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (31 bp):
TTATTTTTTAATTATTTAATAATTTTATATT
Found at i:39534446 original size:36 final size:36
Alignment explanation
Indices: 39534406--39534480 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
39534396 CCTATCTCCA
39534406 TATGTATTTGATATGGGTACTGTTAAATATTCAATT
1 TATGTATTTGATATGGGTACTGTTAAATATTCAATT
39534442 TATGTATTTGATATGGGTACTGTTAAATATTCAATT
1 TATGTATTTGATATGGGTACTGTTAAATATTCAATT
39534478 TAT
1 TAT
39534481 TTTATATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.48
Consensus pattern (36 bp):
TATGTATTTGATATGGGTACTGTTAAATATTCAATT
Found at i:39535268 original size:21 final size:21
Alignment explanation
Indices: 39535242--39535281 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
39535232 TCAATTAAAA
*
39535242 AATATTAAAAATTTAAAATAT
1 AATATTAAAAATTAAAAATAT
39535263 AATATTAAAAATTAAAAAT
1 AATATTAAAAATTAAAAAT
39535282 TCGATTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AATATTAAAAATTAAAAATAT
Found at i:39536212 original size:27 final size:28
Alignment explanation
Indices: 39536159--39536212 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
39536149 AATTGAATCA
* *
39536159 AAATCAAAACTTTATATATAATTTTATT
1 AAATCAAAAATTTATATATAATATTATT
39536187 AAAT-AAAAATTTATATATCAA-ATTAT
1 AAATCAAAAATTTATATAT-AATATTAT
39536213 GTCTTTGCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.43
Consensus pattern (28 bp):
AAATCAAAAATTTATATATAATATTATT
Found at i:39538560 original size:16 final size:17
Alignment explanation
Indices: 39538529--39538561 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
39538519 TATTTAGGTC
39538529 TTTTATAATTAATAATA
1 TTTTATAATTAATAATA
*
39538546 TTTTA-AATTAGTAATA
1 TTTTATAATTAATAATA
39538562 GTAAACTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
TTTTATAATTAATAATA
Found at i:39539109 original size:15 final size:16
Alignment explanation
Indices: 39539084--39539117 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
39539074 TGCATATCAT
39539084 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
*
39539100 TTTA-TATTTTTATAA
1 TTTATTATTTTAATAA
39539115 TTT
1 TTT
39539118 TTAAAAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:39539142 original size:31 final size:31
Alignment explanation
Indices: 39539106--39539169 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
39539096 ATAATTTATA
39539106 TTTTTATAATTTTTAAAAGATTAAA-T-TAATT
1 TTTTTATAATTTTT--AAGATTAAAGTATAATT
*
39539137 TTTTTATTATTTTTAAGATTAAAGTATAATT
1 TTTTTATAATTTTTAAGATTAAAGTATAATT
39539168 TT
1 TT
39539170 ATCATTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 9 0.30
30 1 0.03
31 20 0.67
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (31 bp):
TTTTTATAATTTTTAAGATTAAAGTATAATT
Found at i:39550071 original size:3 final size:3
Alignment explanation
Indices: 39550065--39550113 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
39550055 TAATAATAAC
* * *
39550065 TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT CAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39550113 T
1 T
39550114 CGAATCTAGC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:39550389 original size:1 final size:1
Alignment explanation
Indices: 39550383--39550411 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
39550373 CCAGCTCCCT
39550383 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
39550412 AAAAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:39555526 original size:26 final size:26
Alignment explanation
Indices: 39555497--39555548 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
39555487 CAGCTCACCT
39555497 TATTTTAAT-TTTTTAAATATTCATAC
1 TATTTTAATATTTTTAAATA-TCATAC
39555523 TATTTTAATATTTTTAAATATCATAC
1 TATTTTAATATTTTTAAATATCATAC
39555549 GAATTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.56
Consensus pattern (26 bp):
TATTTTAATATTTTTAAATATCATAC
Found at i:39561345 original size:2 final size:2
Alignment explanation
Indices: 39561338--39561363 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39561328 AAATAAATTT
39561338 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
39561364 ATTGCTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39561504 original size:20 final size:20
Alignment explanation
Indices: 39561479--39561519 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
39561469 TCAATTTGAT
*
39561479 TATTAAAGTATTAAATTAAA
1 TATTAAAGTATTAAAATAAA
**
39561499 TATTAATTTATTAAAATAAA
1 TATTAAAGTATTAAAATAAA
39561519 T
1 T
39561520 TTGAATTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TATTAAAGTATTAAAATAAA
Found at i:39568714 original size:15 final size:15
Alignment explanation
Indices: 39568696--39568742 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
39568686 AAATTTGAAA
39568696 TTTAATTTTTATATT
1 TTTAATTTTTATATT
* *
39568711 TTTAATTTTAAAATT
1 TTTAATTTTTATATT
* *
39568726 TTAAATTTTTTTATT
1 TTTAATTTTTATATT
39568741 TT
1 TT
39568743 GTTTTATTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTAATTTTTATATT
Found at i:39568824 original size:34 final size:34
Alignment explanation
Indices: 39568785--39568858 Score: 112
Period size: 34 Copynumber: 2.2 Consensus size: 34
39568775 ATTATTTTAC
* *
39568785 TAAATTTAAGTTTATTATAATATTAATTTTTAAT
1 TAAATTCAAATTTATTATAATATTAATTTTTAAT
* *
39568819 TAAATTCAAATTTATTATGATATTATTTTTTAAT
1 TAAATTCAAATTTATTATAATATTAATTTTTAAT
39568853 TAAATT
1 TAAATT
39568859 ATTATTAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (34 bp):
TAAATTCAAATTTATTATAATATTAATTTTTAAT
Found at i:39569911 original size:6 final size:6
Alignment explanation
Indices: 39569865--39569910 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
39569855 TTGCTATGTT
* * *
39569865 AATCCG AATCTG AATTCG AATCCG AATCCG AATCCG AATCTG AATC
1 AATCCG AATCCG AATCCG AATCCG AATCCG AATCCG AATCCG AATC
39569911 TTCATTTTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (6 bp):
AATCCG
Found at i:39587978 original size:11 final size:11
Alignment explanation
Indices: 39587960--39587997 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
39587950 ATAATAACAA
39587960 TAAAATAATAG
1 TAAAATAATAG
*
39587971 TAACATAATAG
1 TAAAATAATAG
*
39587982 TAAAATGATAG
1 TAAAATAATAG
39587993 TAAAA
1 TAAAA
39587998 CTGTGATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.61, C:0.03, G:0.11, T:0.26
Consensus pattern (11 bp):
TAAAATAATAG
Found at i:39587978 original size:22 final size:22
Alignment explanation
Indices: 39587953--39587995 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
39587943 TATCTAAATA
39587953 ATAACAATAAAATAATAGTAAC
1 ATAACAATAAAATAATAGTAAC
* * *
39587975 ATAATAGTAAAATGATAGTAA
1 ATAACAATAAAATAATAGTAA
39587996 AACTGTGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.05, G:0.09, T:0.26
Consensus pattern (22 bp):
ATAACAATAAAATAATAGTAAC
Found at i:39605525 original size:6 final size:6
Alignment explanation
Indices: 39605514--39605546 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
39605504 TATAGAGTTG
*
39605514 AGTTCA AGTTCA AGTTCA AGTTTA AGTTCA AGT
1 AGTTCA AGTTCA AGTTCA AGTTCA AGTTCA AGT
39605547 AGCTCAAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (6 bp):
AGTTCA
Found at i:39611177 original size:19 final size:19
Alignment explanation
Indices: 39611153--39611190 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
39611143 GGCGTAGCTT
*
39611153 AAAATGAAAATTTTAAAGA
1 AAAATGAAAATTGTAAAGA
*
39611172 AAAATGAATATTGTAAAGA
1 AAAATGAAAATTGTAAAGA
39611191 TAATGTTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (19 bp):
AAAATGAAAATTGTAAAGA
Found at i:39612127 original size:12 final size:11
Alignment explanation
Indices: 39612108--39612138 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
39612098 TGTATAACTC
39612108 TTATTTTATTA
1 TTATTTTATTA
39612119 TTAATTTTATTA
1 TT-ATTTTATTA
39612131 TTATTTTA
1 TTATTTTA
39612139 GAGACATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:39612518 original size:22 final size:23
Alignment explanation
Indices: 39612469--39612521 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
39612459 ATTCTTATAC
39612469 TTTT-ATTTTTAAGAATTTAATA
1 TTTTAATTTTTAAGAATTTAATA
*
39612491 TTTTAATTTTTTA-AATTTCAA-A
1 TTTTAATTTTTAAGAATTT-AATA
39612513 TTTTAATTT
1 TTTTAATTT
39612522 AAATTATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTTAATTTTTAAGAATTTAATA
Found at i:39620859 original size:23 final size:24
Alignment explanation
Indices: 39620810--39620861 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
39620800 ATTTTATATT
*
39620810 TTATATAAATTTTGATATCTTAACA
1 TTATATAAATTTTGATAGCTT-ACA
39620835 TTATATAAATTTTGA-AGCATT-CA
1 TTATATAAATTTTGATAGC-TTACA
39620858 TTAT
1 TTAT
39620862 CTTGGTTCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 6 0.24
24 2 0.08
25 17 0.68
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (24 bp):
TTATATAAATTTTGATAGCTTACA
Found at i:39629792 original size:27 final size:27
Alignment explanation
Indices: 39629745--39629798 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
39629735 ATGACTTAAA
*
39629745 TAAAAACTTATAAACAGTTTAATGACT
1 TAAAAACTTATAAACAATTTAATGACT
* * *
39629772 TAAAAACTTTTAAATAATTTAGTGACT
1 TAAAAACTTATAAACAATTTAATGACT
39629799 AAATTATAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.37
Consensus pattern (27 bp):
TAAAAACTTATAAACAATTTAATGACT
Found at i:39632694 original size:30 final size:29
Alignment explanation
Indices: 39632658--39632715 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
39632648 AATAGTTTCA
39632658 AAAATATTTA-AATTGGTTTTTTAAAAATTC
1 AAAATATTTATAATT--TTTTTTAAAAATTC
39632688 AAAATATTTATAATTTTTTTTAAAAATT
1 AAAATATTTATAATTTTTTTTAAAAATT
39632716 TATAAAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 13 0.48
30 10 0.37
31 4 0.15
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (29 bp):
AAAATATTTATAATTTTTTTTAAAAATTC
Found at i:39635375 original size:12 final size:12
Alignment explanation
Indices: 39635355--39635387 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
39635345 TACGAACAAG
39635355 CTCGTTTATTAA
1 CTCGTTTATTAA
*
39635367 CTTGTTTA-TAA
1 CTCGTTTATTAA
39635378 CTCGTTTATT
1 CTCGTTTATT
39635388 TATTAATGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.21, C:0.15, G:0.09, T:0.55
Consensus pattern (12 bp):
CTCGTTTATTAA
Found at i:39635500 original size:24 final size:23
Alignment explanation
Indices: 39635473--39635542 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
39635463 TCATGAACAT
*
39635473 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCGATTA-A
* *
39635497 TGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
*
39635520 TATTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
39635543 GTTAAATGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 21 0.52
24 19 0.47
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:39635511 original size:12 final size:12
Alignment explanation
Indices: 39635462--39635513 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
39635452 TTGTTTATTA
39635462 TTCATGAACATTG
1 TTCATGAACA-TG
*
39635475 TTCGTGAACATG
1 TTCATGAACATG
* *
39635487 TTCAAT-TATATG
1 TTC-ATGAACATG
39635499 TTCATGAACATG
1 TTCATGAACATG
39635511 TTC
1 TTC
39635514 GTTTAATATT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
11 2 0.06
12 19 0.61
13 10 0.32
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (12 bp):
TTCATGAACATG
Found at i:39650675 original size:2 final size:2
Alignment explanation
Indices: 39650668--39650702 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
39650658 ATCAATCCAA
39650668 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39650703 AATTTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39652022 original size:14 final size:14
Alignment explanation
Indices: 39652003--39652029 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39651993 TTGAAATTAA
39652003 AATAAATTGGTTTC
1 AATAAATTGGTTTC
39652017 AATAAATTGGTTT
1 AATAAATTGGTTT
39652030 TATATTACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (14 bp):
AATAAATTGGTTTC
Found at i:39654025 original size:19 final size:21
Alignment explanation
Indices: 39653987--39654025 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
39653977 AAAAAATAGG
*
39653987 TTAATCATATTCTTTATTTTT
1 TTAATCATATTCTATATTTTT
39654008 TTAATCA-A-TCTATATTTT
1 TTAATCATATTCTATATTTT
39654026 ATAATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 1 0.06
21 7 0.41
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (21 bp):
TTAATCATATTCTATATTTTT
Found at i:39656677 original size:14 final size:14
Alignment explanation
Indices: 39656653--39656708 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 14
39656643 CTAGGTATTG
39656653 TATAA-AAAAAATA
1 TATAATAAAAAATA
* *
39656666 TATGATAAAAAATC
1 TATAATAAAAAATA
*
39656680 TATAAT-AAAATTA
1 TATAATAAAAAATA
*
39656693 -ATATTAAAAAATA
1 TATAATAAAAAATA
39656706 TAT
1 TAT
39656709 TTAAAATTCA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
12 4 0.12
13 15 0.45
14 14 0.42
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (14 bp):
TATAATAAAAAATA
Found at i:39660214 original size:18 final size:18
Alignment explanation
Indices: 39660191--39660238 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
39660181 TTATTTGTGT
39660191 TATAAATTACATAATATA
1 TATAAATTACATAATATA
*
39660209 TATAAAAATAACATAATATA
1 TAT--AAATTACATAATATA
*
39660229 -AGAAATTACA
1 TATAAATTACA
39660239 AACTCATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 7 0.28
18 3 0.12
19 1 0.04
20 14 0.56
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.31
Consensus pattern (18 bp):
TATAAATTACATAATATA
Found at i:39665291 original size:14 final size:12
Alignment explanation
Indices: 39665261--39665309 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
39665251 CACTGCCAAG
39665261 TAATTTTTTTTT
1 TAATTTTTTTTT
39665273 TAATTTTTGTTTT
1 TAATTTTT-TTTT
*
39665286 TAAATTTTTAATTT
1 T-AATTTTT-TTTT
39665300 T-ATTTTTTTT
1 TAATTTTTTTT
39665310 CCTCCTAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
11 2 0.06
12 14 0.44
13 5 0.16
14 11 0.34
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (12 bp):
TAATTTTTTTTT
Found at i:39665393 original size:11 final size:10
Alignment explanation
Indices: 39665367--39665391 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
39665357 ACAGAAACAA
39665367 TTTTTATTTT
1 TTTTTATTTT
39665377 TTTTTATTTT
1 TTTTTATTTT
39665387 TTTTT
1 TTTTT
39665392 TAAAAACGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:39668858 original size:30 final size:30
Alignment explanation
Indices: 39668838--39669053 Score: 221
Period size: 30 Copynumber: 7.3 Consensus size: 30
39668828 TCATATCTTG
*
39668838 ACCCTTAAACTTTTCTAAAATTACATTTTT
1 ACCCTTAAACTTTTCTAAAATTACATTTTA
** *
39668868 ACCC-CGAACTTTT-TCAAAATTATATTTTA
1 ACCCTTAAACTTTTCT-AAAATTACATTTTA
* * * *
39668897 A-CCTCAAAATTTTCCAAAATTATATTTTTA
1 ACCCTTAAACTTTTCTAAAATTACA-TTTTA
*
39668927 ACCCTTAAACTTTTCCAAAATTACATTTTA
1 ACCCTTAAACTTTTCTAAAATTACATTTTA
** * *
39668957 ACCCCCAAACTTCTCTAAAATCACATTTTA
1 ACCCTTAAACTTTTCTAAAATTACATTTTA
39668987 ACCC-TAAAC-TTTCTTAAAATTACAATTTT-
1 ACCCTTAAACTTTTC-TAAAATTAC-ATTTTA
39669016 ACCCTTAAACTTTT-TCAAAATTACATTTTA
1 ACCCTTAAACTTTTCT-AAAATTACATTTTA
39669046 ACCCTTAA
1 ACCCTTAA
39669054 CTCTCTGAAA
Statistics
Matches: 157, Mismatches: 18, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
28 6 0.04
29 58 0.37
30 70 0.45
31 23 0.15
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (30 bp):
ACCCTTAAACTTTTCTAAAATTACATTTTA
Found at i:39668880 original size:29 final size:29
Alignment explanation
Indices: 39668844--39669049 Score: 195
Period size: 29 Copynumber: 7.0 Consensus size: 29
39668834 CTTGACCCTT
*
39668844 AAACTTTTCTAAAATTACATTTTTACCCC
1 AAACTTTTCTAAAATTACATTTTAACCCC
* * *
39668873 GAACTTTT-TCAAAATTATATTTTAACCTC
1 AAACTTTTCT-AAAATTACATTTTAACCCC
* * * *
39668902 AAAATTTTCCAAAATTATATTTTTAACCCTT
1 AAACTTTTCTAAAATTACA-TTTTAACCC-C
*
39668933 AAACTTTTCCAAAATTACATTTTAACCCCC
1 AAACTTTTCTAAAATTACATTTTAA-CCCC
* * *
39668963 AAACTTCTCTAAAATCACATTTTAACCCT
1 AAACTTTTCTAAAATTACATTTTAACCCC
*
39668992 AAAC-TTTCTTAAAATTACAATTTT-ACCCTT
1 AAACTTTTC-TAAAATTAC-ATTTTAACCC-C
39669022 AAACTTTT-TCAAAATTACATTTTAACCC
1 AAACTTTTCT-AAAATTACATTTTAACCC
39669050 TTAACTCTCT
Statistics
Matches: 148, Mismatches: 18, Indels: 21
0.79 0.10 0.11
Matches are distributed among these distances:
28 4 0.03
29 63 0.43
30 58 0.39
31 23 0.16
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.40
Consensus pattern (29 bp):
AAACTTTTCTAAAATTACATTTTAACCCC
Found at i:39669020 original size:89 final size:90
Alignment explanation
Indices: 39668814--39669049 Score: 275
Period size: 89 Copynumber: 2.6 Consensus size: 90
39668804 TAGGTCCCCT
* * * * * *
39668814 AAACTTTCCAAAAAT-CATATCTTGACCCTTAAACTTTTCTAAAATTACATTTTTA-CCCCGAAC
1 AAACTTTCCAAAATTACA-ATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCCCCAAAC
* * *
39668877 TTTTTCAAAATTATATTTTAACCTCA
65 TTTCTCAAAATCACATTTTAACCTCA
* * *
39668903 AAATTTTCCAAAATTATATTTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCCCCAAAC-
1 AAACTTTCCAAAATTACAATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCCCCAAACT
*
39668967 TTCTCTAAAATCACATTTTAACC-CT
66 TTCTC-AAAATCACATTTTAACCTCA
* *
39668992 AAACTTTCTTAAAATTACAATTTT-ACCCTTAAACTTTTTCAAAATTACATTTTAACCC
1 AAACTTTC-CAAAATTACAATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCC
39669050 TTAACTCTCT
Statistics
Matches: 125, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
89 90 0.72
90 35 0.28
ACGTcount: A:0.37, C:0.23, G:0.01, T:0.39
Consensus pattern (90 bp):
AAACTTTCCAAAATTACAATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCCCCAAACT
TTCTCAAAATCACATTTTAACCTCA
Found at i:39677178 original size:85 final size:85
Alignment explanation
Indices: 39677030--39677196 Score: 228
Period size: 85 Copynumber: 2.0 Consensus size: 85
39677020 TCAAACCTCA
* * * * * *
39677030 TCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGGTCATCTTCTTGATGAGATAC
1 TCTTCCTGATGAGATACAGAAAAGTGGATCAAAACAATAAAGAGGTCATCTTCCTAATAAGATAC
39677095 AGAGAAGT-GAACCAAATCCG
66 AGAGAAGTAG-ACCAAATCCG
* * * *
39677115 TCTTCCTGATGAGATACAGAAAAGTGTATTAAAACAATGAAGCGGTCATCTTCCTAATAAGATAC
1 TCTTCCTGATGAGATACAGAAAAGTGGATCAAAACAATAAAGAGGTCATCTTCCTAATAAGATAC
39677180 AGAGAAGTAGACCAAAT
66 AGAGAAGTAGACCAAAT
39677197 TCATGAAGCG
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
85 70 0.99
86 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (85 bp):
TCTTCCTGATGAGATACAGAAAAGTGGATCAAAACAATAAAGAGGTCATCTTCCTAATAAGATAC
AGAGAAGTAGACCAAATCCG
Found at i:39677561 original size:125 final size:124
Alignment explanation
Indices: 39677323--39677655 Score: 402
Period size: 125 Copynumber: 2.7 Consensus size: 124
39677313 ACCAAATCCG
* *
39677323 TCTT-TTTGATGAGATACAGAGAAGC-AGATTAAAACAAGTGATGCGGTCATCTTCTTGATAAGA
1 TCTTCTTT-ATGAGATACAGAGAAGCGA-ATTAAAAC-AGTGATGCGGTCATCTTCCTGATGAGA
* *
39677386 TACAGAAAAGTAGACCAAATCAATTAAGCGAAGCTCAATGTCAGTAAAACTTCAAACCCCCA
63 TACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGTCAGTAAAACTTCAAACCCCCA
39677448 TCTTCTTTATGAGATACAGAGAAGCGAATTAAAACAGGTGATGCGGTCATCTTCCTGATGAGATA
1 TCTTCTTTATGAGATACAGAGAAGCGAATTAAAACA-GTGATGCGGTCATCTTCCTGATGAGATA
* * *
39677513 CAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATG-CGAGTGAAACTTCAAACCCTCA
65 CAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGTC-AGTAAAACTTCAAACCCCCA
* * * * * * * * * * * * * *
39677573 TTTTCCTGATGAGATACTGAGAAGTGAGTCAAAGCAATAAAGCGATCGTTTTCCTGATGAGATAC
1 TCTTCTTTATGAGATACAGAGAAGCGAATTAAAACAGTGATGCGGTCATCTTCCTGATGAGATAC
*
39677638 AGAGAAGTGGACCAAATC
66 AGAGAAGTAGACCAAATC
39677656 CGTCTTCCTG
Statistics
Matches: 182, Mismatches: 22, Indels: 9
0.85 0.10 0.04
Matches are distributed among these distances:
124 42 0.23
125 136 0.75
126 4 0.02
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (124 bp):
TCTTCTTTATGAGATACAGAGAAGCGAATTAAAACAGTGATGCGGTCATCTTCCTGATGAGATAC
AGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGTCAGTAAAACTTCAAACCCCCA
Found at i:39677702 original size:210 final size:209
Alignment explanation
Indices: 39677456--39678069 Score: 922
Period size: 210 Copynumber: 2.9 Consensus size: 209
39677446 CATCTTCTTT
* * * *
39677456 ATGAGATACAGAGAAGCGAATTAAAACAGGTGATGCGGTCATCTTCCTGATGAGATACAGAGAAG
1 ATGAGATACAAAGAAGCGGATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGATATAGAGAAG
* *
39677521 TAGACCAAATCGATGAAGCGAAGCTCAATGCGAGTGAAACTTCAAACCCTCATTTTCCTGATGAG
66 TAGACCAAATCGATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCC-CATATTCCTGATGAG
* * *
39677586 ATACTGAGAAGTGAGTCAAAGCAATAAAGCGATCGTTTTCCTGATGAGATACAGAGAAGTGGACC
130 ATACTGAGAAGTGAGTCAAAGCAATAAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGACC
39677651 AAATCCGTCTTCCTG
195 AAATCCGTCTTCCTG
*
39677666 ATGAGATACAAAGAAGCGGATTAAAACAAGTGATGCGGTCATCTTTCTGATGAGATATAGAGAAG
1 ATGAGATACAAAGAAGCGGATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGATATAGAGAAG
* * * *
39677731 TAAACCAAATCGATGAAGCGAAGCACAATGTGAGTGAAACTTCGAACCCCCATCTTCCTGATGAG
66 TAGACCAAATCGATGAAGCGAAGCTCAATGTGAGTGAAACTTC-AAACCCCATATTCCTGATGAG
* *
39677796 ATACTGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCTTGATGAGATACAGAGAAGTGGACC
130 ATACTGAGAAGTGAGTCAAAGCAATAAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGACC
* *
39677861 AAATCTGTCTTCTTG
195 AAATCCGTCTTCCTG
* * *
39677876 ATGAGATACAAAGAAGTGGATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGGTATAAAGAAG
1 ATGAGATACAAAGAAGCGGATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGATATAGAGAAG
* * * * * *
39677941 TAGACCAATTCAACGAAGTGAAGCTCAATGTGAGTAAAAGTTCAAACCCCATATTCCTGATGAGA
66 TAGACCAAATCGATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCATATTCCTGATGAGA
* * * * *
39678006 TACAGAAAAGTGAGTCAAAGTAATAAAGCGGTCATCTTCCTAATGAGATACAGAGAAGTAGACC
131 TACTGAGAAGTGAGTCAAAGCAATAAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGACC
39678070 GAGAGATGAA
Statistics
Matches: 365, Mismatches: 38, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
209 77 0.21
210 283 0.78
211 5 0.01
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (209 bp):
ATGAGATACAAAGAAGCGGATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGATATAGAGAAG
TAGACCAAATCGATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCATATTCCTGATGAGA
TACTGAGAAGTGAGTCAAAGCAATAAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCA
AATCCGTCTTCCTG
Found at i:39677773 original size:335 final size:332
Alignment explanation
Indices: 39677115--39677865 Score: 1031
Period size: 335 Copynumber: 2.2 Consensus size: 332
39677105 ACCAAATCCG
* * * *
39677115 TCTTCCTGATGAGATACAGAAAAGTGTATTAAAACAATGAAGCGGTCATCTTCCTAATAAGATAC
1 TCTTCCTGATGAGATACAGAGAAGTGAATTAAAACAATGAAGCGGTCATCTTCCTGATGAGATAC
*
39677180 AGAGAAGTAGACCAAATTCATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCTCATCTTTCT
66 AGAGAAGTAGACCAAA-TCATGAAGCGAAGCTCAATACGAATGAAACTTCAAACCTCATCTTTCT
* * *
39677245 GATGGGATACAGAGAAGTGGGTCAAAGCAATAAAGCAGTCATCTTCCTAATAAGATACAAAGGAG
130 GATGAGATACAGAGAAGTGAGTCAAAGCAATAAAGCAGTCATCTTCCTAATAAGATACAAAGAAG
** *
39677310 TGGACCAAATCCGTCTTTTTGATGAGATACAGAGAAGCAGATTAAAACAAGTGATGCGGTCATCT
195 TGGACCAAATCCGTCTTCCTGATGAGATACAAAGAAGCAGATTAAAACAAGTGATGCGGTCATCT
* * *
39677375 TCTTGATAAGATACAGAAAAGTAGACCAAATCAATTAAGCGAAGCTCAATGTCAGTAAAACTTCA
260 TCTTGATAAGATACAGAAAAGTAAACCAAATCAATGAAGCGAAGCACAATGTCAGTAAAACTTCA
39677440 AACCCCCA
325 AACCCCCA
* * * * *
39677448 TCTTCTTTATGAGATACAGAGAAGCGAATTAAAACAGGTGATGCGGTCATCTTCCTGATGAGATA
1 TCTTCCTGATGAGATACAGAGAAGTGAATTAAAACA-ATGAAGCGGTCATCTTCCTGATGAGATA
* *
39677513 CAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGCGAGTGAAACTTCAAACCCTCAT-TTT
65 CAGAGAAGTAGACCAAATC-ATGAAGCGAAGCTCAATACGAATGAAACTTCAAA-CCTCATCTTT
* * * * * *
39677577 CCTGATGAGATACTGAGAAGTGAGTCAAAGCAATAAAGC-GATCGTTTTCCTGATGAGATACAGA
128 -CTGATGAGATACAGAGAAGTGAGTCAAAGCAATAAAGCAG-TCATCTTCCTAATAAGATACAAA
*
39677641 GAAGTGGACCAAATCCGTCTTCCTGATGAGATACAAAGAAGCGGATTAAAACAAGTGATGCGGTC
191 GAAGTGGACCAAATCCGTCTTCCTGATGAGATACAAAGAAGCAGATTAAAACAAGTGATGCGGTC
* * * * * *
39677706 ATCTT-TCTGATGAGATATAGAGAAGTAAACCAAATCGATGAAGCGAAGCACAATGTGAGTGAAA
256 ATCTTCT-TGATAAGATACAGAAAAGTAAACCAAATCAATGAAGCGAAGCACAATGTCAGTAAAA
*
39677770 CTTCGAACCCCCA
320 CTTCAAACCCCCA
* ** * * * *
39677783 TCTTCCTGATGAGATACTGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCTTGATGAGATAC
1 TCTTCCTGATGAGATACAGAGAAGTGAATTAAAACAATGAAGCGGTCATCTTCCTGATGAGATAC
*
39677848 AGAGAAGTGGACCAAATC
66 AGAGAAGTAGACCAAATC
39677866 TGTCTTCTTG
Statistics
Matches: 364, Mismatches: 48, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
333 33 0.09
334 119 0.33
335 212 0.58
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (332 bp):
TCTTCCTGATGAGATACAGAGAAGTGAATTAAAACAATGAAGCGGTCATCTTCCTGATGAGATAC
AGAGAAGTAGACCAAATCATGAAGCGAAGCTCAATACGAATGAAACTTCAAACCTCATCTTTCTG
ATGAGATACAGAGAAGTGAGTCAAAGCAATAAAGCAGTCATCTTCCTAATAAGATACAAAGAAGT
GGACCAAATCCGTCTTCCTGATGAGATACAAAGAAGCAGATTAAAACAAGTGATGCGGTCATCTT
CTTGATAAGATACAGAAAAGTAAACCAAATCAATGAAGCGAAGCACAATGTCAGTAAAACTTCAA
ACCCCCA
Found at i:39677940 original size:86 final size:85
Alignment explanation
Indices: 39677783--39677948 Score: 206
Period size: 86 Copynumber: 1.9 Consensus size: 85
39677773 CGAACCCCCA
** * * *
39677783 TCTTCCTGATGAGATACTGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCTTGATGAGATAC
1 TCTTCCTGATGAGATACAAAGAAGTGGATCAAAACAATAAAGCGGTCATCTTCCTGATGAGATAC
* *
39677848 AGAGAAGTGGACCAAATCTG
66 AAAGAAGTAGACCAAATCTG
* * * * *
39677868 TCTTCTTGATGAGATACAAAGAAGTGGATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGGTA
1 TCTTCCTGATGAGATACAAAGAAGTGGATCAAAACAA-TAAAGCGGTCATCTTCCTGATGAGATA
*
39677933 TAAAGAAGTAGACCAA
65 CAAAGAAGTAGACCAA
39677949 TTCAACGAAG
Statistics
Matches: 67, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
85 31 0.46
86 36 0.54
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (85 bp):
TCTTCCTGATGAGATACAAAGAAGTGGATCAAAACAATAAAGCGGTCATCTTCCTGATGAGATAC
AAAGAAGTAGACCAAATCTG
Found at i:39678260 original size:14 final size:14
Alignment explanation
Indices: 39678243--39678274 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
39678233 AAGATGTAGA
39678243 GAAGCAGATGCAGT
1 GAAGCAGATGCAGT
39678257 GAAGCAGATGCAGT
1 GAAGCAGATGCAGT
39678271 GAAG
1 GAAG
39678275 TTGAACGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.38, T:0.12
Consensus pattern (14 bp):
GAAGCAGATGCAGT
Found at i:39681256 original size:19 final size:18
Alignment explanation
Indices: 39681234--39681276 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
39681224 AAATTACAAA
*
39681234 AAAAATCAAAATAATTTTT
1 AAAAATCAAAAT-ATTTAT
* *
39681253 AAAATTTAAAATATTTAT
1 AAAAATCAAAATATTTAT
39681271 AAAAAT
1 AAAAAT
39681277 TTCAAAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAAATCAAAATATTTAT
Found at i:39683758 original size:16 final size:15
Alignment explanation
Indices: 39683731--39683769 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
39683721 TCCTGTCAAT
39683731 AATCATTTTTATAAC
1 AATCATTTTTATAAC
*
39683746 AATCATCTTTTATAAT
1 AATCAT-TTTTATAAC
39683762 AA-CATTTT
1 AATCATTTT
39683770 ATTATAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 3 0.14
15 9 0.41
16 10 0.45
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (15 bp):
AATCATTTTTATAAC
Found at i:39685857 original size:22 final size:23
Alignment explanation
Indices: 39685829--39685874 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
39685819 ATTGTTTAGA
39685829 TAATATA-AAAGAAAAT-TAAAAT
1 TAATATATAAA-AAAATATAAAAT
39685851 TAATATATTAAAAAAATATAAAAT
1 TAATATA-TAAAAAAATATAAAAT
39685875 ACAAAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 7 0.33
23 5 0.24
24 9 0.43
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (23 bp):
TAATATATAAAAAAATATAAAAT
Found at i:39685883 original size:25 final size:24
Alignment explanation
Indices: 39685830--39685884 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
39685820 TTGTTTAGAT
* *
39685830 AATATAAAAGAAAATTAAAATTAA
1 AATATTAAAGAAAATTAAAATCAA
*
39685854 TATATTAAA-AAAATATAAAATACAA
1 AATATTAAAGAAAAT-TAAAAT-CAA
39685879 AATATT
1 AATATT
39685885 TTTATTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 5 0.20
24 13 0.52
25 7 0.28
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (24 bp):
AATATTAAAGAAAATTAAAATCAA
Found at i:39686241 original size:29 final size:29
Alignment explanation
Indices: 39686159--39686243 Score: 89
Period size: 31 Copynumber: 2.8 Consensus size: 29
39686149 GATTAAATCA
* *
39686159 AAATTAAAACTTCAAGTATACATTTGAACC
1 AAATTAAAA-TTCATGTATACAATTGAACC
* * * *
39686189 ACAATTAGAATTTCGTGTGTACAATTGCACC
1 A-AATTA-AAATTCATGTATACAATTGAACC
39686220 AAATTAAAATTCATGTATACAATT
1 AAATTAAAATTCATGTATACAATT
39686244 ACACATTAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
29 15 0.34
30 6 0.14
31 21 0.48
32 2 0.05
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.33
Consensus pattern (29 bp):
AAATTAAAATTCATGTATACAATTGAACC
Found at i:39687727 original size:16 final size:16
Alignment explanation
Indices: 39687677--39687727 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
39687667 AATGAATTAA
* *
39687677 AAATATTTTTATTAATT
1 AAATATATTT-TTAAGT
* *
39687694 AAATTTAGTTTT-AGT
1 AAATATATTTTTAAGT
39687709 AAATATATTTTTAAGT
1 AAATATATTTTTAAGT
39687725 AAA
1 AAA
39687728 AATAATTTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
15 12 0.44
16 8 0.30
17 7 0.26
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (16 bp):
AAATATATTTTTAAGT
Found at i:39690109 original size:62 final size:62
Alignment explanation
Indices: 39690042--39690158 Score: 164
Period size: 62 Copynumber: 1.9 Consensus size: 62
39690032 TTAAGAGAGC
* * *
39690042 TTAATTAAAATTTTCTGAAAACTTT-AAGAGAGAAATAAAAATTTCCAAAAATTTTGGAGAAT
1 TTAATTAAAATTTGCT-AAAAATTTCAAGAGAGAAATAAAAATATCCAAAAATTTTGGAGAAT
* * *
39690104 TTAATTAAAATTTGCTAAAAATTTCAAGGGAGAAATCAAAATATCCCAAAATTTT
1 TTAATTAAAATTTGCTAAAAATTTCAAGAGAGAAATAAAAATATCCAAAAATTTT
39690159 TGGGAGGGGG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
61 7 0.15
62 41 0.85
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.33
Consensus pattern (62 bp):
TTAATTAAAATTTGCTAAAAATTTCAAGAGAGAAATAAAAATATCCAAAAATTTTGGAGAAT
Found at i:39690805 original size:8 final size:8
Alignment explanation
Indices: 39690784--39690860 Score: 66
Period size: 9 Copynumber: 9.1 Consensus size: 8
39690774 TTAAAATCGA
*
39690784 TATAAACT
1 TATAAAAT
*
39690792 TTTAAAAT
1 TATAAAAT
39690800 TATAAAACT
1 TATAAAA-T
39690809 TATAAATAT
1 TATAAA-AT
*
39690818 TACAAAA-
1 TATAAAAT
*
39690825 TATAAAAA
1 TATAAAAT
39690833 TATAATAAAT
1 TAT-A-AAAT
39690843 TATAAAAT
1 TATAAAAT
39690851 TAATAAAAT
1 T-ATAAAAT
39690860 T
1 T
39690861 TATTCAAAAC
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
7 6 0.11
8 21 0.37
9 23 0.40
10 7 0.12
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (8 bp):
TATAAAAT
Found at i:39690809 original size:17 final size:18
Alignment explanation
Indices: 39690787--39690824 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
39690777 AAATCGATAT
* *
39690787 AAACTTTTAAA-ATTATA
1 AAACTTATAAATATTACA
39690804 AAACTTATAAATATTACA
1 AAACTTATAAATATTACA
39690822 AAA
1 AAA
39690825 TATAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (18 bp):
AAACTTATAAATATTACA
Found at i:39691543 original size:11 final size:11
Alignment explanation
Indices: 39691527--39691563 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
39691517 AGTTTTTATG
39691527 ATTTTATATAA
1 ATTTTATATAA
39691538 ATTTTA-ATAA
1 ATTTTATATAA
*
39691548 TTTTTATA-AA
1 ATTTTATATAA
39691558 ATTTTA
1 ATTTTA
39691564 ATATCTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTTATATAA
Found at i:39691550 original size:20 final size:20
Alignment explanation
Indices: 39691528--39691566 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
39691518 GTTTTTATGA
39691528 TTTTATATAAATTTTAATAAT
1 TTTTATA-AAATTTTAATAAT
39691549 TTTTATAAAATTTTAATA
1 TTTTATAAAATTTTAATA
39691567 TCTATTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTATAAAATTTTAATAAT
Found at i:39694299 original size:24 final size:25
Alignment explanation
Indices: 39694272--39694330 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
39694262 TAAAATTAAA
*
39694272 AAAAAATAAACT-TACTAAATAATT
1 AAAAAATAAACTCAACTAAATAATT
39694296 AAAAAATAAACTCAACTAAATAATT
1 AAAAAATAAACTCAACTAAATAATT
*
39694321 AAACAATAAA
1 AAAAAATAAA
39694331 ACTAAAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 12 0.38
25 20 0.62
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (25 bp):
AAAAAATAAACTCAACTAAATAATT
Found at i:39698643 original size:19 final size:20
Alignment explanation
Indices: 39698605--39698644 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
39698595 ATTATAAACG
*
39698605 TATATAATTCTTTATACATT
1 TATATAATTATTTATACATT
*
39698625 TATATATTTATTT-TACATT
1 TATATAATTATTTATACATT
39698644 T
1 T
39698645 TTATCTATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (20 bp):
TATATAATTATTTATACATT
Found at i:39715615 original size:22 final size:21
Alignment explanation
Indices: 39715584--39715635 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
39715574 TAATTTTAAT
*
39715584 TTTTTTAATA-AATTTTATGA
1 TTTTTTAAAATAATTTTATGA
* *
39715604 TTTTTTAAAATAACTTAATTGA
1 TTTTTTAAAATAATTTTA-TGA
39715626 TTTTTTAAAA
1 TTTTTTAAAA
39715636 ATAGTTGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 9 0.33
21 5 0.19
22 13 0.48
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTTTAAAATAATTTTATGA
Found at i:39716124 original size:44 final size:43
Alignment explanation
Indices: 39716076--39716168 Score: 107
Period size: 44 Copynumber: 2.1 Consensus size: 43
39716066 TTTTGGTTAC
* * *
39716076 TGTTTTCATGTTGTTTTTGTTGTTATTTTTGTTGCTATT-TTTAT
1 TGTTTTAATGTTG-TTTTGCTGTTATTTTGGTTGCTATTATTT-T
* *
39716120 TGTTTTTAATGTTGTTTTGCTGTTGTTTTGGTTGTTATTATTTT
1 TG-TTTTAATGTTGTTTTGCTGTTATTTTGGTTGCTATTATTTT
39716164 TGTTT
1 TGTTT
39716169 GGATGTTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
43 3 0.07
44 26 0.62
45 13 0.31
ACGTcount: A:0.09, C:0.03, G:0.18, T:0.70
Consensus pattern (43 bp):
TGTTTTAATGTTGTTTTGCTGTTATTTTGGTTGCTATTATTTT
Found at i:39716169 original size:20 final size:19
Alignment explanation
Indices: 39716146--39716183 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
39716136 TTGCTGTTGT
*
39716146 TTTGGTTGTTATTATTTTTG
1 TTTGGATGTTATT-TTTTTG
39716166 TTTGGATGTTATTTTTTT
1 TTTGGATGTTATTTTTTT
39716184 ATGTGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.11, C:0.00, G:0.18, T:0.71
Consensus pattern (19 bp):
TTTGGATGTTATTTTTTTG
Found at i:39718297 original size:22 final size:22
Alignment explanation
Indices: 39718272--39718320 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
39718262 TGTTTTCCAT
*
39718272 ATTTTACTATTATTTTGTTATC
1 ATTTTACTATTATGTTGTTATC
* *
39718294 ATTTCACTATTATGTTGTTATT
1 ATTTTACTATTATGTTGTTATC
39718316 ATTTT
1 ATTTT
39718321 GTTGTTAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.08, G:0.06, T:0.63
Consensus pattern (22 bp):
ATTTTACTATTATGTTGTTATC
Found at i:39733820 original size:10 final size:10
Alignment explanation
Indices: 39733805--39733846 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
39733795 AATGGAAAAA
39733805 AAAAAAAGT-T
1 AAAAAAA-TAT
39733815 AAAAAAATAT
1 AAAAAAATAT
39733825 AAAAAAATAT
1 AAAAAAATAT
39733835 AAAAAAAT-T
1 AAAAAAATAT
39733844 AAA
1 AAA
39733847 TTACTCAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 5 0.16
10 26 0.84
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (10 bp):
AAAAAAATAT
Found at i:39736445 original size:15 final size:15
Alignment explanation
Indices: 39736401--39736475 Score: 64
Period size: 15 Copynumber: 5.0 Consensus size: 15
39736391 TGTGACCTGC
39736401 CTTCATGTAAATGCA
1 CTTCATGTAAATGCA
* * *
39736416 GC-TCGTGTGATTGCA
1 -CTTCATGTAAATGCA
39736431 CTTCATGTAAATGCAA
1 CTTCATGTAAATGC-A
* * *
39736447 CTT-GTGTGATTGCA
1 CTTCATGTAAATGCA
39736461 CTTCATGTAAATGCA
1 CTTCATGTAAATGCA
39736476 GCTCGTGCGA
Statistics
Matches: 44, Mismatches: 12, Indels: 7
0.70 0.19 0.11
Matches are distributed among these distances:
14 5 0.11
15 34 0.77
16 5 0.11
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Consensus pattern (15 bp):
CTTCATGTAAATGCA
Done.