Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2103
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: 74528
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:3422 original size:21 final size:20
Alignment explanation
Indices: 3398--3475 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 20
3388 ATGTCCAAAA
3398 TGTATCGATACATGTTTCTGT
1 TGTATCGATACATGTTTCT-T
* *
3419 TGTATCGATACATCTGGAAATTCTA
1 TGTATCGATACA--T-G--TTTCTT
*
3444 TGTATCGATACATTTTTCTT
1 TGTATCGATACATGTTTCTT
3464 TGTATCGATACA
1 TGTATCGATACA
3476 ATGTATCGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
20 16 0.34
21 12 0.26
23 2 0.04
24 1 0.02
25 12 0.26
26 4 0.09
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
TGTATCGATACATGTTTCTT
Found at i:3482 original size:13 final size:13
Alignment explanation
Indices: 3464--3501 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
3454 CATTTTTCTT
3464 TGTATCGATACAA
1 TGTATCGATACAA
*
3477 TGTATCGATACAC
1 TGTATCGATACAA
3490 TGTATCGATACA
1 TGTATCGATACA
3502 GGTTTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5949 original size:20 final size:20
Alignment explanation
Indices: 5926--5998 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
5916 ACAATTCAAA
5926 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
5946 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
5967 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
5987 GTATCGATACAT
1 GTATCGATACAT
5999 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:5970 original size:21 final size:21
Alignment explanation
Indices: 5944--6019 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
5934 ACATGTTGCA
5944 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
5965 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
5985 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
6006 ATGTATCGATACAT
1 ATGTATCGATACAT
6020 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:5977 original size:41 final size:41
Alignment explanation
Indices: 5926--6019 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
5916 ACAATTCAAA
*
5926 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
5967 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
6008 GTATCGATACAT
1 GTATCGATACAT
6020 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:6076 original size:13 final size:13
Alignment explanation
Indices: 6058--6083 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6048 TACAGCAAGT
6058 ATGTATCGATACA
1 ATGTATCGATACA
6071 ATGTATCGATACA
1 ATGTATCGATACA
6084 CAAAAAATTG
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:8602 original size:22 final size:21
Alignment explanation
Indices: 8567--8616 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
8557 TTTGTTGATG
*
8567 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
8587 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
8608 AATTTGAAG
1 ATTTTGAAG
8617 AAGATTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:8613 original size:21 final size:22
Alignment explanation
Indices: 8574--8616 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
8564 ATGATTTTGA
* *
8574 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
8596 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
8617 AAGATTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:12536 original size:52 final size:51
Alignment explanation
Indices: 12458--12606 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
12448 CGAAATATGA
12458 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* * *
12510 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATTTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
12562 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
12607 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:12613 original size:13 final size:13
Alignment explanation
Indices: 12595--12619 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12585 CAAAGATCAG
12595 TGTATCGATACAA
1 TGTATCGATACAA
12608 TGTATCGATACA
1 TGTATCGATACA
12620 TTTAAGTGAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:12697 original size:33 final size:33
Alignment explanation
Indices: 12660--12726 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
12650 AGTAGCTTAA
12660 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
12693 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
12726 A
1 A
12727 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:12700 original size:13 final size:13
Alignment explanation
Indices: 12682--12706 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12672 CAAAAAAATA
12682 TGTATCGATACAT
1 TGTATCGATACAT
12695 TGTATCGATACA
1 TGTATCGATACA
12707 ACACTTTATG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:17200 original size:13 final size:13
Alignment explanation
Indices: 17182--17207 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17172 CAATTTTTTG
17182 TGTATCGATACAT
1 TGTATCGATACAT
17195 TGTATCGATACAT
1 TGTATCGATACAT
17208 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:17272 original size:21 final size:21
Alignment explanation
Indices: 17246--17321 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
17236 CTGCCAAGAA
*
17246 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
17267 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
17287 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
17308 ATGTATCGATACAT
1 ATGTATCGATACAT
17322 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:17292 original size:20 final size:20
Alignment explanation
Indices: 17267--17339 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
17257 CATCTTTTTT
17267 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
17287 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
17308 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
17328 ATGTATCGATAC
1 ATGTATCGATAC
17340 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:17303 original size:41 final size:41
Alignment explanation
Indices: 17246--17339 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
17236 CTGCCAAGAA
*
17246 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
17287 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
17328 ATGTATCGATAC
1 ATGTATCGATAC
17340 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:19783 original size:13 final size:13
Alignment explanation
Indices: 19765--19802 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
19755 ATAAACACCC
19765 TGTATCGATACAG
1 TGTATCGATACAG
*
19778 TGTATCGATACAT
1 TGTATCGATACAG
19791 TGTATCGATACA
1 TGTATCGATACA
19803 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:19816 original size:20 final size:20
Alignment explanation
Indices: 19791--19867 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
19781 ATCGATACAT
19791 TGTATCGATACAAAGAAAAA
1 TGTATCGATACAAAGAAAAA
* *
19811 TGTATCGATACATAGAATTTCCAGA
1 TGTATCGATACAAAGAA-----AAA
* *
19836 TGTATCGATACACAGAAACA
1 TGTATCGATACAAAGAAAAA
19856 TGTATCGATACA
1 TGTATCGATACA
19868 TTTTGGACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
20 30 0.62
25 18 0.38
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.26
Consensus pattern (20 bp):
TGTATCGATACAAAGAAAAA
Found at i:23690 original size:21 final size:21
Alignment explanation
Indices: 23661--23705 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
23651 AAGTTTTCAT
*
23661 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
23681 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
23703 TTT
1 TTT
23706 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:25936 original size:13 final size:13
Alignment explanation
Indices: 25918--25943 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25908 CAATTTTTTG
25918 TGTATCGATACAT
1 TGTATCGATACAT
25931 TGTATCGATACAT
1 TGTATCGATACAT
25944 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:26008 original size:21 final size:21
Alignment explanation
Indices: 25982--26057 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
25972 CTGCCAAGAA
*
25982 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
26003 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
26023 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
26044 ATGTATCGATACAT
1 ATGTATCGATACAT
26058 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:26028 original size:20 final size:20
Alignment explanation
Indices: 26003--26075 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
25993 CATCTTTTTT
26003 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
26023 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
26044 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
26064 ATGTATCGATAC
1 ATGTATCGATAC
26076 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:26039 original size:41 final size:41
Alignment explanation
Indices: 25982--26075 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
25972 CTGCCAAGAA
*
25982 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
26023 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
26064 ATGTATCGATAC
1 ATGTATCGATAC
26076 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:29055 original size:48 final size:48
Alignment explanation
Indices: 28984--29079 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
28974 TATTCCTAGA
* * * *
28984 TAACCACCGACAATGAAGAGATATATCATGATCGAACCTTCTTTGCAT
1 TAACCACCAACAATGAAGAGATATATCACGATCAAACCTCCTTTGCAT
* *
29032 TAACCCCCAACAATGAAGAGATATATCCCGATCAAACCTCCTTTGCAT
1 TAACCACCAACAATGAAGAGATATATCACGATCAAACCTCCTTTGCAT
29080 GCCTTGTTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (48 bp):
TAACCACCAACAATGAAGAGATATATCACGATCAAACCTCCTTTGCAT
Found at i:31152 original size:56 final size:57
Alignment explanation
Indices: 30958--31156 Score: 168
Period size: 56 Copynumber: 3.4 Consensus size: 57
30948 CCTTTAGAAG
* *
30958 GAAAATACCTTAACTTCAATATCGAGGCTCGACCTGTTTAAAAGAAATTCAATTT-AAAA
1 GAAAATACCTTAACTTCAATA-CCAAGCTCGACCTGTTTAAAA-AAATT-AATTTAAAAA
* ** * * * * * * *
31017 GAAAATATCTCGACTACAATTCTAAGGCTCAACCCATTTTTAAAAATAAGTTCAAATTAAGAA
1 GAAAATACCTTAACTTCAATACCAA-GCTCGA-CC-TGTTTAAAAA-AA-TT-AATTTAAAAA
* *
31080 GAAAATACCTTGACTTCAATACCAAGCTTGACCTGTTTAAAAAAATT-ATTTAAAAA
1 GAAAATACCTTAACTTCAATACCAAGCTCGACCTGTTTAAAAAAATTAATTTAAAAA
*
31136 GAAAATATCTTAACTTCAATA
1 GAAAATACCTTAACTTCAATA
31157 TTGGGGCTCA
Statistics
Matches: 111, Mismatches: 23, Indels: 15
0.74 0.15 0.10
Matches are distributed among these distances:
56 26 0.23
58 4 0.04
59 23 0.21
60 12 0.11
61 12 0.11
62 11 0.10
63 23 0.21
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.30
Consensus pattern (57 bp):
GAAAATACCTTAACTTCAATACCAAGCTCGACCTGTTTAAAAAAATTAATTTAAAAA
Found at i:31166 original size:119 final size:122
Alignment explanation
Indices: 30953--31190 Score: 299
Period size: 119 Copynumber: 2.0 Consensus size: 122
30943 CTTGACCTTT
* *
30953 AGAAGGAAAATACCTTAACTTCAATATCGAGGCTCGACCTGTTTAAAAGAAATTCAATTTAAAAG
1 AGAAGGAAAATACCTTAACTTCAATATCCAAGCTCGACCTGTTTAAAAGAAATT-AATTTAAAAG
*
31018 AAAATATCTCGACTACAATTCTAAGGCTCAACCCATTTTTAAA-AATAAGTTCAAATTA
65 AAAATATCTCAACTACAATTCTAAGGCTCAACCCA-TTTTAAATAATAAGTTCAAATTA
* *
31076 AGAA-GAAAATACCTTGACTTCAATA-CCAAGCTTGACCTGTTTAAAA-AAATT-ATTTAAAAAG
1 AGAAGGAAAATACCTTAACTTCAATATCCAAGCTCGACCTGTTTAAAAGAAATTAATTT-AAAAG
* * ** * *
31137 AAAATATCTTAACTTCAATAT-TGGGGCTCAATCCATTTTAAATAATGAGTTCAA
65 AAAATATCTCAACTACAAT-TCTAAGGCTCAACCCATTTTAAATAATAAGTTCAA
31191 CCTAAAAAAG
Statistics
Matches: 101, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
118 11 0.11
119 42 0.42
120 6 0.06
121 18 0.18
122 20 0.20
123 4 0.04
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (122 bp):
AGAAGGAAAATACCTTAACTTCAATATCCAAGCTCGACCTGTTTAAAAGAAATTAATTTAAAAGA
AAATATCTCAACTACAATTCTAAGGCTCAACCCATTTTAAATAATAAGTTCAAATTA
Found at i:33174 original size:20 final size:20
Alignment explanation
Indices: 33136--33174 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
33126 CAATAAACAA
* *
33136 GCATTCATGTGGAATATATT
1 GCATTCATGTAGAAAATATT
33156 GCATTCATGTAGAAAATAT
1 GCATTCATGTAGAAAATAT
33175 CAAGACAAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (20 bp):
GCATTCATGTAGAAAATATT
Found at i:34931 original size:33 final size:33
Alignment explanation
Indices: 34867--34932 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
34857 AATAGTACCT
*
34867 ATATATTGATACAAAGAACTCAGTATCGATACA
1 ATATATTGATACAAAGAACTCAGCATCGATACA
* *
34900 ATATATTGATACTAAGAACGT-AGCATTGATACA
1 ATATATTGATACAAAGAAC-TCAGCATCGATACA
34933 TTTGGATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.29
Consensus pattern (33 bp):
ATATATTGATACAAAGAACTCAGCATCGATACA
Found at i:37840 original size:13 final size:13
Alignment explanation
Indices: 37822--37846 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37812 CATAAAGTGT
37822 TGTATCGATACAA
1 TGTATCGATACAA
37835 TGTATCGATACA
1 TGTATCGATACA
37847 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:37844 original size:33 final size:33
Alignment explanation
Indices: 37802--37868 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
37792 TTCAATGATT
37802 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
37835 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
37868 T
1 T
37869 TCAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:37999 original size:52 final size:52
Alignment explanation
Indices: 37943--38071 Score: 204
Period size: 52 Copynumber: 2.5 Consensus size: 52
37933 CACTGATCTT
* *
37943 TGTATCGATACATGCAGGCAAATTTGCCCAGATTTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* **
37995 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATATACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
38047 TTTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
38072 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:44926 original size:80 final size:80
Alignment explanation
Indices: 44790--44937 Score: 185
Period size: 80 Copynumber: 1.9 Consensus size: 80
44780 TAAAAAAAAT
* ** **
44790 CGGGGTTAGAGTATCCCCGATTGTGAAAAAATCGATGCTTTTGAAATAAGGCCGGGGTT-GAAGT
1 CGGGGTTAGAGTATCCCCGATTATGAAAAAATCGATGCTTTAAAAATAAAACCGGGGTTAG-AGT
44854 ATCCCCGTGAAAATAA
65 ATCCCCGTGAAAATAA
* *
44870 CGGGGTTAGAGTATCCCCGATTATG-AAAAATCGGTG-TTCTAAAAAATAAAATCGGGGTTAGAG
1 CGGGGTTAGAGTATCCCCGATTATGAAAAAATCGATGCTT-T-AAAAATAAAACCGGGGTTAGAG
44933 TATCC
64 TATCC
44938 TCGATTGTGA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
78 2 0.03
79 11 0.19
80 44 0.76
81 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (80 bp):
CGGGGTTAGAGTATCCCCGATTATGAAAAAATCGATGCTTTAAAAATAAAACCGGGGTTAGAGTA
TCCCCGTGAAAATAA
Found at i:44988 original size:133 final size:131
Alignment explanation
Indices: 44752--45083 Score: 452
Period size: 133 Copynumber: 2.5 Consensus size: 131
44742 CAGCGCTGGA
* *
44752 TATCCCCGATTATGGAAAATCGATGTTCTAAAA-AAAATCGGGGTTAGAGTATCCCCGATTGTG-
1 TATCCCCGATTATGAAAAATCGGTGTTCTAAAATAAAATCGGGGTTAGAGTATCCCCGATTGTGA
* ** *
44815 AAAAAATCGATGCTTTTGAAATAAGGCCGGGGTTGAAGTATCCCCGTGAAAATAACGGGGTTAGA
66 AAAAAATCGATGCTTTAGAAATAAGGCCAAGGTTGAAGTATCCCCGTGAAAATAACGAGGTTAGA
44880 G
131 G
*
44881 TATCCCCGATTATGAAAAATCGGTGTTCTAAAAAATAAAATCGGGGTTAGAGTATCCTCGATTGT
1 TATCCCCGATTATGAAAAATCGGTGTTCT--AAAATAAAATCGGGGTTAGAGTATCCCCGATTGT
* * *
44946 GAAAAAAATCGATGCTTTAGAAATAAGGCCAAGGTTGGAGTATCTCCGTGAAAATAACGAGGTTG
64 GAAAAAAATCGATGCTTTAGAAATAAGGCCAAGGTTGAAGTATCCCCGTGAAAATAACGAGGTTA
45011 GAG
129 GAG
* * * * * * * * *
45014 TATCCCTGATTGTGAGAAATTGGTGTTATGGAACTAAAATCGGAGTTGGAGTATCCCCGATTGTG
1 TATCCCCGATTATGAAAAATCGGTGTTCT-AAAATAAAATCGGGGTTAGAGTATCCCCGATTGTG
45079 AAAAA
65 AAAAA
45084 TTAATATTTT
Statistics
Matches: 178, Mismatches: 21, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
129 27 0.15
131 4 0.02
132 64 0.36
133 83 0.47
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (131 bp):
TATCCCCGATTATGAAAAATCGGTGTTCTAAAATAAAATCGGGGTTAGAGTATCCCCGATTGTGA
AAAAAATCGATGCTTTAGAAATAAGGCCAAGGTTGAAGTATCCCCGTGAAAATAACGAGGTTAGA
G
Found at i:45076 original size:51 final size:51
Alignment explanation
Indices: 45007--45122 Score: 142
Period size: 51 Copynumber: 2.3 Consensus size: 51
44997 AAATAACGAG
* * ** * * *
45007 GTTGGAGTATCCCTGATTGTGAGAAATTGGTGTTATGGAACTAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTAATATTATAGAAATAAAATCGGA
* *
45058 GTTGGAGTATCCCCGATTGTGAAAAATTAATATTTTAGAAATAAAATCGGG
1 GTTGGAGTATCCCCGATTGTGAAAAATTAATATTATAGAAATAAAATCGGA
*
45109 GTTGGAATATCCCC
1 GTTGGAGTATCCCC
45123 TCGAAAATAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTAATATTATAGAAATAAAATCGGA
Found at i:45282 original size:109 final size:107
Alignment explanation
Indices: 45059--45339 Score: 332
Period size: 109 Copynumber: 2.6 Consensus size: 107
45049 AAAATCGGAG
* *
45059 TTGGAGTATCCCCGATTGTGAAAAATTAATATTTTAGAAATAAAATCGGGGTTGGAATATCCCCT
1 TTGGAGTATCCCCAATTGTGAAAAATCAATATTTTAGAAATAAAATCGGGGTTGGAATATCCCCT
* *
45124 CGAAAATAACGGGATGGGAGTATCCCCGATGACATAACGGGG
66 CGAAAATAACGGGATGGGAGTATCCCCGATGAAATAACGGGA
* * * * * *
45166 TTAGAGTATCCCCCAATTATGAAAGAATCAATATTTTGGATAT-AAAGCTGGGGTTGGACTATCC
1 TTGGAGTAT-CCCCAATTGTGAAA-AATCAATATTTTAGAAATAAAATC-GGGGTTGGAATATCC
* *
45230 CCTCGAAAATAACGAGG-TTGGAGTATCCCCGATGAAATGACGGGA
63 CCTCGAAAATAACG-GGATGGGAGTATCCCCGATGAAATAACGGGA
*** * * * *
45275 TTGGAGTATCCCCAATTGTGAAAAAATTGGTATTTTGGAAATAAAATCAGAGTTGGAGTATCCCC
1 TTGGAGTATCCCCAATTGTG-AAAAATCAATATTTTAGAAATAAAATCGGGGTTGGAATATCCCC
45340 GATTAAGAAA
Statistics
Matches: 146, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
107 8 0.05
108 54 0.37
109 82 0.56
110 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (107 bp):
TTGGAGTATCCCCAATTGTGAAAAATCAATATTTTAGAAATAAAATCGGGGTTGGAATATCCCCT
CGAAAATAACGGGATGGGAGTATCCCCGATGAAATAACGGGA
Found at i:57262 original size:1 final size:1
Alignment explanation
Indices: 57256--57316 Score: 59
Period size: 1 Copynumber: 61.0 Consensus size: 1
57246 ATTCTCTTCT
* * * * * * *
57256 AAAAAAAACAAAAACAAAAAAAAAACAAAAAAAAACAAAAAAAAACAAAACAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
57317 GAGAGAAAAG
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.89, C:0.10, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:57316 original size:11 final size:10
Alignment explanation
Indices: 57256--57305 Score: 75
Period size: 10 Copynumber: 5.0 Consensus size: 10
57246 ATTCTCTTCT
*
57256 AAAAA-AAAC
1 AAAAACAAAA
57265 AAAAACAAAAA
1 AAAAAC-AAAA
57276 AAAAACAAAA
1 AAAAACAAAA
57286 AAAAACAAAA
1 AAAAACAAAA
57296 AAAAACAAAA
1 AAAAACAAAA
57306 CAAAGAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
9 5 0.13
10 24 0.63
11 9 0.24
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:58466 original size:55 final size:55
Alignment explanation
Indices: 58391--58642 Score: 238
Period size: 55 Copynumber: 4.4 Consensus size: 55
58381 TTCACCCTTT
* * *
58391 AGTCCTCAAAGAGAACGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTCTTC
* * * * *
58446 AGTCCTCAAAAAGCAGGACGCTTTTTAAAGCCCACACGAGTTGGTGGCACCCTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTCTTC
* * * * *
58501 AGTCCTCAAAGACCAGGACGACTTTTTCTTTTAAAGCCCACATAAGCTAGTGGCAC-CTTC
1 AGTCCTCAAAGAGCAGGACG-C-----CTTTCAAAGCCCACACAAGTTGGTGGCACTCTTC
* *
58561 AGTCCTCAAAGAACAGGACACCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTT-
1 AGTCCTCAAAGAGCAGGACGCCTT-T-C----AAAGCCCACACAAGTTGGTGGCAC-TCTTC
58622 AGTCCTCAAAGAGCAGGACGC
1 AGTCCTCAAAGAGCAGGACGC
58643 TCTCTCATTT
Statistics
Matches: 160, Mismatches: 23, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
54 3 0.02
55 66 0.41
56 1 0.01
59 1 0.01
60 43 0.27
61 43 0.27
62 3 0.02
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTCTTC
Found at i:58578 original size:60 final size:59
Alignment explanation
Indices: 58412--58641 Score: 251
Period size: 60 Copynumber: 3.9 Consensus size: 59
58402 AGAACGACGC
* *
58412 CTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAA-AAGCAGGACG-C---T
1 CTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAGAA-CAGGACGACTTTT
* *
58468 -TTTTAAAGCCCACACGAGTTGGTGGCACCCTTCAGTCCTCAAAGACCAGGACGACTTTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTCAGTCCTCAAAGAACAGGACGAC-TTTT
* * * *
58528 CTTTTAAAGCCCACATAAGCTAGTGGCACCTTCAGTCCTCAAAGAACAGGAC-ACCTTCTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAACAGGACGA-CTT-TT
*
58588 CTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCTTAGTCCTCAAAGAGCAGGACG
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTC--AGTCCTCAAAGAACAGGACG
58642 CTCTCTCATT
Statistics
Matches: 147, Mismatches: 14, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
55 45 0.31
56 3 0.02
59 7 0.05
60 51 0.35
61 41 0.28
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (59 bp):
CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAACAGGACGACTTTT
Found at i:58779 original size:215 final size:214
Alignment explanation
Indices: 58447--58851 Score: 546
Period size: 215 Copynumber: 1.9 Consensus size: 214
58437 GCACTTTTCA
* * *
58447 GTCCTCAAAAAGCAGGACGCTTTTTAAAGCCCACACGAGTTGGTGGCACCCTTCAGTCCTCAAAG
1 GTCCTCAAAAAGCAGGACGCCTTTTAAAGCCCACACAAGCTGGTGGCACCCTTCAGTCCTCAAAG
* * *
58512 ACCAGGACGACTTTTTCTTTTAAAGCCCACATAAGCTAGTGGCACCTTCAGTCCTCAAAGAACAG
66 ACCAGGACGACTTCTCCTTTTAAAGCCCACACAAGCTAGTGGCACCTTCAGTCCTCAAAGAACAG
58577 GACACCTTCTCCTTTT-AAAGCCCACACAAGTTGGTGGCACTTCTT-AGTCCTCAAAGAGCAGGA
131 G--ACCTTCTCCTTTTCAAAGCCCACACAAGTTGGTGGCACTT-TTCAGTCCTCAAAGAGCAGGA
58640 CGCTCTCTCATTTCGCCTTTTT
193 CGCTCTCTCATTTCGCCTTTTT
* * * **
58662 GTCCTCAAAGAGTAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCA-CCTTCAGTTTTCAAAG
1 GTCCTCAAAAAGCAGGACGCCTTTTAAAGCCCACACAAGCTGGTGGCACCCTTCAGTCCTCAAAG
** * * * * * *
58726 AGTAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCA
66 ACCAGGACGACTTCTCCTTTTAAAGCCCACACAAGCTAGTGGCAC-CTTCAGTCCTCAAAGAACA
* * *
58791 GGATCTTTTCTTTTTGCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCA
130 GGACCTTCTCCTTTT-CAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCA
58852 AGATGCTTTC
Statistics
Matches: 164, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
213 10 0.06
214 52 0.32
215 102 0.62
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.27
Consensus pattern (214 bp):
GTCCTCAAAAAGCAGGACGCCTTTTAAAGCCCACACAAGCTGGTGGCACCCTTCAGTCCTCAAAG
ACCAGGACGACTTCTCCTTTTAAAGCCCACACAAGCTAGTGGCACCTTCAGTCCTCAAAGAACAG
GACCTTCTCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGC
TCTCTCATTTCGCCTTTTT
Found at i:58812 original size:61 final size:61
Alignment explanation
Indices: 58683--58976 Score: 375
Period size: 61 Copynumber: 4.9 Consensus size: 61
58673 GTAGGATGCC
* * ** * * *
58683 TTTT-AAAGCCCACACAAGCTGGTGGCAC-CTTCAGTTTTCAAAGAGTAGGATGCCTTCTCC
1 TTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATG-CTTTTCT
58743 TTTT-AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGAT-CTTTTCT
1 TTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTTCT
*
58802 TTTTGCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAAGATGC-TTTCT
1 TTTT-CAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTTCT
* * * * * *
58863 TTTTGCAAAGCCCATACGAGTTGGTGGCACCTTCCAGTCCTCAAAGGGTAGGATGCCTTTTC-
1 TTTT-CAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATG-CTTTTCT
*
58925 TTTTCAAAGCCCACACGAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA
1 TTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA
58977 CACACTTCCT
Statistics
Matches: 208, Mismatches: 20, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
59 9 0.04
60 27 0.13
61 162 0.78
62 6 0.03
63 4 0.02
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (61 bp):
TTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTTCT
Found at i:59639 original size:102 final size:102
Alignment explanation
Indices: 59463--59649 Score: 243
Period size: 102 Copynumber: 1.8 Consensus size: 102
59453 GTTAAATTTC
* * *
59463 TCAATTTTTCTTAATCGGAGATACTCCAACTCCGATTTTATTTCTAAAGCATCGATCTACCACAA
1 TCAATTTTTCTTAATCGGAGATACTCCAACTCCGATTTTATTTCTAAAACACCAATCTACCACAA
59528 CCAGGGATACTCCAATCCCGGTTTCATCTCCACAACA
66 CCAGGGATACTCCAATCCCGGTTTCATCTCCACAACA
* * * * *
59565 TCAATTTTTCTTAATCGGGGATACTTCAACTCTGATTTTATTT-TCAAAATACCAAT-TTCTCAC
1 TCAATTTTTCTTAATCGGAGATACTCCAACTCCGATTTTATTTCT-AAAACACCAATCTAC-CAC
***
59628 AATTGGGGATACTCCAATCCCG
64 AACCAGGGATACTCCAATCCCG
59650 TCATTTCATC
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
101 3 0.04
102 69 0.96
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (102 bp):
TCAATTTTTCTTAATCGGAGATACTCCAACTCCGATTTTATTTCTAAAACACCAATCTACCACAA
CCAGGGATACTCCAATCCCGGTTTCATCTCCACAACA
Found at i:59664 original size:28 final size:28
Alignment explanation
Indices: 59632--59705 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
59622 TCTCACAATT
* *
59632 GGGGATACTCCAATCCCGTCATTTCAT-C
1 GGGGATACTCCAACCCCGTCATTT-ATGA
* *
59660 GGGGATACTCCAACCCCGTTATTTTTGA
1 GGGGATACTCCAACCCCGTCATTTATGA
59688 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
59706 GCTTTATATC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 1 0.02
28 40 0.98
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.26
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTCATTTATGA
Found at i:60911 original size:49 final size:52
Alignment explanation
Indices: 60858--60969 Score: 133
Period size: 52 Copynumber: 2.2 Consensus size: 52
60848 AACAGGGCTG
* * *
60858 GAGTATCCCCGATTATG-GAAAATCGGTG-TTCTA-AAA-AAAATCGGGGTTA
1 GAGTATCCCCGATTATGAAAAAATCGATGCTT-TAGAAATAAAACCGGGGTTA
* * *
60907 GAGTATCCCCGATTGTGAAAAAATCGATGCTTTAGAAATAAAGCCGGGGTTG
1 GAGTATCCCCGATTATGAAAAAATCGATGCTTTAGAAATAAAACCGGGGTTA
60959 GAGTATCCCCG
1 GAGTATCCCCG
60970 TGAAAATAAC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
49 16 0.30
50 11 0.21
51 5 0.09
52 21 0.40
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (52 bp):
GAGTATCCCCGATTATGAAAAAATCGATGCTTTAGAAATAAAACCGGGGTTA
Found at i:61035 original size:80 final size:79
Alignment explanation
Indices: 60899--61047 Score: 185
Period size: 80 Copynumber: 1.9 Consensus size: 79
60889 TAAAAAAAAT
* * **
60899 CGGGGTTAGAGTATCCCCGATTGTGAAAAAATCGATGCTTTAGAAATAAAGCCGGGGTTGGAGTA
1 CGGGGTTAGAGTATCCCCGATTGTG-AAAAATCGATGCTTTAAAAATAAAACCGGGGTTAAAGTA
60964 TCCCCGTGAAAATAA
65 TCCCCGTGAAAATAA
* * *
60979 CGGGGTTAGAGTATCCCCGATTATTG-AAAATCGGTG-TTCTAAAAAATAAAATCGGGGTTAAAG
1 CGGGGTTAGAGTATCCCCGATT-GTGAAAAATCGATGCTT-T-AAAAATAAAACCGGGGTTAAAG
61042 TATCCC
63 TATCCC
61048 TGATTGTGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
78 2 0.03
79 10 0.17
80 45 0.76
81 2 0.03
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (79 bp):
CGGGGTTAGAGTATCCCCGATTGTGAAAAATCGATGCTTTAAAAATAAAACCGGGGTTAAAGTAT
CCCCGTGAAAATAA
Found at i:61085 original size:132 final size:129
Alignment explanation
Indices: 60858--61261 Score: 492
Period size: 132 Copynumber: 3.1 Consensus size: 129
60848 AACAGGGCTG
*
60858 GAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAAAAATCGGGGTTAGAGTATCCCCGATTGT
1 GAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAAAAATCGGGGTTAAAGTATCCCCGATTGT
60923 GAAAAAATCGATGCTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCGTGAAAATAACGGGGTTA
66 GAAAAAATCGATGCTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCGTGAAAATAACGGGGTTA
* *
60987 GAGTATCCCCGATTATTGAAAATCGGTGTTCTAAAAAATAAAATCGGGGTTAAAGTATCCCTGAT
1 GAGTATCCCCGATTATGGAAAATCGGTGTTCT--AAAA-AAAATCGGGGTTAAAGTATCCCCGAT
*
61052 TGTGAAAAAATCGATGCTTTAGAAATAAGGCCGGGGTTGGAGTATCCCCGTGAAAATAACGGGGT
63 TGTGAAAAAATCGATGCTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCGTGAAAATAACGGGGT
*
61117 TG
128 TA
* * * * * ** * * **
61119 GAGTATCCCCGATTGTGAAAAATTGGTATTTTTGAACTAAAATCAGAGTTGGAGTATCCCCGATT
1 GAGTATCCCCGATTATGGAAAATCGGT-GTTCT-AAAAAAAATCGGGGTTAAAGTATCCCCGATT
** * **
61184 GTGAAAATTTGGTAT--TTTAGAAATAAAATCGGGGTTGGAGTATCCCC-TCGGAAAA-AACGGG
64 GTGAAAAAATCG-ATGCTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCGT--GAAAATAACGGG
* **
61245 ATGG
126 GTTA
61249 GAGTATCCCCGAT
1 GAGTATCCCCGAT
61262 GACATAACGG
Statistics
Matches: 241, Mismatches: 27, Indels: 13
0.86 0.10 0.05
Matches are distributed among these distances:
129 32 0.13
130 50 0.21
131 40 0.17
132 116 0.48
133 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.27
Consensus pattern (129 bp):
GAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAAAAATCGGGGTTAAAGTATCCCCGATTGT
GAAAAAATCGATGCTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCGTGAAAATAACGGGGTTA
Found at i:61182 original size:51 final size:51
Alignment explanation
Indices: 61115--61230 Score: 187
Period size: 51 Copynumber: 2.3 Consensus size: 51
61105 AAATAACGGG
* *
61115 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGAACTAAAATCAGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTAGAAATAAAATCAGA
* * *
61166 GTTGGAGTATCCCCGATTGTGAAAATTTGGTATTTTAGAAATAAAATCGGG
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTAGAAATAAAATCAGA
61217 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
61231 TCGGAAAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTAGAAATAAAATCAGA
Found at i:61362 original size:28 final size:28
Alignment explanation
Indices: 61322--61395 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 28
61312 GATATAAAGC
61322 CGGGGTTGGAGTATCCCCTCGA-AAATAA
1 CGGGGTTGGAGTATCCCC-CGAGAAATAA
*
61350 CGGGGTTGGAGTAT-CCCCGATGAAATGA
1 CGGGGTTGGAGTATCCCCCGA-GAAATAA
*
61378 CGGGATTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
61396 AATTGTGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
26 3 0.07
27 3 0.07
28 32 0.78
29 3 0.07
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCCGAGAAATAA
Found at i:61504 original size:102 final size:102
Alignment explanation
Indices: 61378--61564 Score: 261
Period size: 102 Copynumber: 1.8 Consensus size: 102
61368 GATGAAATGA
* * *
61378 CGGGATTGGAGTATCCCCAATTGT-GAAAATTTGGTA-TTTTGAAAATAAAATCAGAGTTGGAGT
1 CGGGATTGGAGTATCCCCAATTGTGGAAAA-TCGATACTTTAG-AAATAAAATCAGAGTTGGAGT
* *
61441 ATCCCCGATTAAGAAAAATTGATGTTGTGGAGATGAAAC
64 ATACCCAATTAAGAAAAATTGATGTTGTGGAGATGAAAC
* * * *
61480 CGGGATTGGAGTATCCCCAATTGTGGTAGATCGATGCTTTAGAAATAAAATCGGAGTTGGAGTAT
1 CGGGATTGGAGTATCCCCAATTGTGGAAAATCGATACTTTAGAAATAAAATCAGAGTTGGAGTAT
61545 ACCCAATTAAGAAAAATTGA
66 ACCCAATTAAGAAAAATTGA
61565 GAAATTTAAC
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
102 67 0.91
103 7 0.09
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (102 bp):
CGGGATTGGAGTATCCCCAATTGTGGAAAATCGATACTTTAGAAATAAAATCAGAGTTGGAGTAT
ACCCAATTAAGAAAAATTGATGTTGTGGAGATGAAAC
Found at i:63854 original size:20 final size:20
Alignment explanation
Indices: 63829--63935 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
63819 AAAATGCCTG
*
63829 AATGTATCGATACATTGTA-A
1 AATGTATCGATACAATG-AGA
*
63849 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAGA
63869 AATGTATCGATAC-------
1 AATGTATCGATACAATGAGA
* **
63882 AATGCATCGATACAATGATC
1 AATGTATCGATACAATGAGA
63902 AATGTATCGATACAATGCA-A
1 AATGTATCGATACAATG-AGA
63922 AATGTATCGATACA
1 AATGTATCGATACA
63936 TCTGGGTAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
13 12 0.16
19 1 0.01
20 59 0.81
21 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (20 bp):
AATGTATCGATACAATGAGA
Found at i:63896 original size:33 final size:33
Alignment explanation
Indices: 63849--63920 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
63839 TACATTGTAA
*
63849 AATGTATCGATACAATGAGCAATGTATCGATAC
1 AATGCATCGATACAATGAGCAATGTATCGATAC
*
63882 AATGCATCGATACAATGATCAATGTATCGATAC
1 AATGCATCGATACAATGAGCAATGTATCGATAC
63915 AATGCA
1 AATGCA
63921 AAATGTATCG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (33 bp):
AATGCATCGATACAATGAGCAATGTATCGATAC
Found at i:63917 original size:13 final size:13
Alignment explanation
Indices: 63868--63898 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
63858 ATACAATGAG
*
63868 CAATGTATCGATA
1 CAATGCATCGATA
63881 CAATGCATCGATA
1 CAATGCATCGATA
63894 CAATG
1 CAATG
63899 ATCAATGTAT
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:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (13 bp):
CAATGCATCGATA
Found at i:64007 original size:20 final size:20
Alignment explanation
Indices: 63829--64008 Score: 83
Period size: 20 Copynumber: 8.8 Consensus size: 20
63819 AAAATGCCTG
*
63829 AATGTATCGATACATTG-TAA
1 AATGTATCGATACATTGAT-C
* *
63849 AATGTATCGATACAATGAGC
1 AATGTATCGATACATTGATC
63869 AATGTATCG----A-T-A-C
1 AATGTATCGATACATTGATC
* *
63882 AATGCATCGATACAATGATC
1 AATGTATCGATACATTGATC
* *
63902 AATGTATCGATACAATGCA-A
1 AATGTATCGATACATTG-ATC
63922 AATGTATCGATACATCTGGGTAAACTTCC
1 AATGTATCGATACAT-T--G---A--T-C
**
63951 TAGATGTATCGATACAAAGATC
1 -A-ATGTATCGATACATTGATC
63973 AATGTATCGATACATTGAAT-
1 AATGTATCGATACATTG-ATC
63993 AATGTATCGATACATT
1 AATGTATCGATACATT
64009 TCCTTGGTAG
Statistics
Matches: 126, Mismatches: 13, Indels: 42
0.70 0.07 0.23
Matches are distributed among these distances:
13 9 0.07
14 1 0.01
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 1 0.01
20 86 0.68
21 5 0.04
22 1 0.01
23 2 0.02
25 2 0.02
28 1 0.01
30 1 0.01
31 13 0.10
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACATTGATC
Found at i:67924 original size:32 final size:32
Alignment explanation
Indices: 67883--68367 Score: 534
Period size: 32 Copynumber: 15.1 Consensus size: 32
67873 TAGTGCTAAG
*
67883 GGTTGCCACCGACTTGTGTGGGCTTT-GAAGAA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAA-AA
* *
67915 GGTTGCCACCGACTTGTGTGGGCTTTAGAAAG
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAAAA
67947 GGTTGCCACCAACTTGTGTGGGCTTTA-AAGAA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAA-AA
* * * * *
67979 GGTTGCCACCGACTTATGTAGACTTTAGAAAG
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAAAA
* *
68011 GGTCGCCACCAACTTGTGTGGGCTTTAAAAAA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAAAA
* * *
68043 GGTTGCCACCGACTTATGTGGGCTTTAGAAAG
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAAAA
* *
68075 GGTCGCCACCAACTTATGTGGGCTTTAG-AAA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAAAA
* * *
68106 GAGTTGCCACCGATTTGTGTGGGCTTTAGAAAG
1 G-GTTGCCACCAACTTGTGTGGGCTTTAGAAAA
*
68139 GGTCGCCACCAACTTGTGTGGGCTTT-GAAGAA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAA-AA
* *
68171 GGTTGCCACCAACTTGTGTTGGCTTTAGAAAG
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAAAA
* *
68203 GGTTGCCACCAACTTATGTGGGCTTTAGAAAG
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAAAA
* * *
68235 GGTCGCCACCAACTTATGTGGGCTTTAGAAAG
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAAAA
* * * *
68267 GGTCGCCACCAAGTTTTGTGGG-TTTTGAAGAA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAA-AA
*
68299 GGTCT-CCACCGACTTGTGTGGGCTTT-GAAGAA
1 GGT-TGCCACCAACTTGTGTGGGCTTTAGAA-AA
* * * *
68331 GGTTGCCACCGACTTGTGTAGGTTTTTGAGAAA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGA-AAA
68364 GGTT
1 GGTT
68368 TCTTCATTGG
Statistics
Matches: 392, Mismatches: 48, Indels: 25
0.84 0.10 0.05
Matches are distributed among these distances:
31 15 0.04
32 354 0.90
33 22 0.06
34 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (32 bp):
GGTTGCCACCAACTTGTGTGGGCTTTAGAAAA
Found at i:68356 original size:64 final size:64
Alignment explanation
Indices: 67880--68349 Score: 626
Period size: 64 Copynumber: 7.3 Consensus size: 64
67870 TCTTAGTGCT
* *
67880 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGA
1 AAGGGTCGCCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGA
* * * * *
67944 AAGGGTTGCCACCAACTTGTGTGGGCTTTAAAGAAGGTTGCCACCGACTTATGTAGACTTTAGA
1 AAGGGTCGCCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGA
* * *
68008 AAGGGTCGCCACCAACTTGTGTGGGCTTTAAAAAAGGTTGCCACCGACTTATGTGGGCTTTAGA
1 AAGGGTCGCCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGA
* *
68072 AAGGGTCGCCACCAACTTATGTGGGCTTT--AGAAAGAGTTGCCACCGATTTGTGTGGGCTTTAG
1 AAGGGTCGCCACCAACTTGTGTGGGCTTTGAAG-AAG-GTTGCCACCGACTTGTGTGGGCTTTAG
68135 A
64 A
* *
68136 AAGGGTCGCCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCAACTTGTGTTGGCTTTAGA
1 AAGGGTCGCCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGA
* * * * * *
68200 AAGGGTTGCCACCAACTTATGTGGGCTTTAGAA-AGGGTCGCCACCAACTTATGTGGGCTTTAGA
1 AAGGGTCGCCACCAACTTGTGTGGGCTTT-GAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGA
* * *
68264 AAGGGTCGCCACCAAGTTTTGTGGGTTTTGAAGAAGGTCT-CCACCGACTTGTGTGGGCTTT-GA
1 AAGGGTCGCCACCAACTTGTGTGGGCTTTGAAGAAGGT-TGCCACCGACTTGTGTGGGCTTTAGA
* * *
68327 AGAAGGTTGCCACCGACTTGTGT
1 A-AGGGTCGCCACCAACTTGTGT
68350 AGGTTTTTGA
Statistics
Matches: 362, Mismatches: 36, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
62 1 0.00
63 9 0.02
64 344 0.95
65 6 0.02
66 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.28
Consensus pattern (64 bp):
AAGGGTCGCCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGA
Found at i:68833 original size:27 final size:27
Alignment explanation
Indices: 68789--68846 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
68779 CTTTGAAAAG
* * *
68789 AAAAAGATGTCACGGAGTTGTGGGCTT
1 AAAAAGATGCCACAGAGTTGTGGACTT
68816 AAAAAGATGCCACAGAGTTGTGGACTT
1 AAAAAGATGCCACAGAGTTGTGGACTT
68843 AAAA
1 AAAA
68847 GGGGAAGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.22
Consensus pattern (27 bp):
AAAAAGATGCCACAGAGTTGTGGACTT
Found at i:68872 original size:32 final size:31
Alignment explanation
Indices: 68817--69016 Score: 134
Period size: 32 Copynumber: 6.2 Consensus size: 31
68807 TGTGGGCTTA
* *
68817 AAAAGATGCCACAGAGTTGTGGACTTAAAAGG
1 AAAAGATGCCA-AGGGTTATGGACTTAAAAGG
**
68849 GGAAGATGCCATAGGGTTATGGACTTAAAAGG
1 AAAAGATGCCA-AGGGTTATGGACTTAAAAGG
* *
68881 AAAAGACGCCACGGAGTTATGGACTTAAAAGG
1 AAAAGATGCCAAGG-GTTATGGACTTAAAAGG
* * * *
68913 TAAAAAGGTGCCACAGAGTTGTGG-CTTTGGAAAA-A
1 --AAAAGATGCCA-AGGGTTATGGAC-TT--AAAAGG
* * *
68948 AAAAGGTGCCATGGAGTTGTGGACTTAAAAGG
1 AAAAGATGCCAAGG-GTTATGGACTTAAAAGG
** * *
68980 GGAAGATGCCATGGTGTTGTGGACTTAAAAGG
1 AAAAGATGCCAAGG-GTTATGGACTTAAAAGG
69012 AAAAG
1 AAAAG
69017 GATTCCACTA
Statistics
Matches: 134, Mismatches: 24, Indels: 20
0.75 0.13 0.11
Matches are distributed among these distances:
31 6 0.04
32 84 0.63
33 21 0.16
34 18 0.13
35 1 0.01
36 4 0.03
ACGTcount: A:0.37, C:0.11, G:0.32, T:0.20
Consensus pattern (31 bp):
AAAAGATGCCAAGGGTTATGGACTTAAAAGG
Found at i:69057 original size:30 final size:29
Alignment explanation
Indices: 69010--69068 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 29
69000 GGACTTAAAA
*
69010 GGAAAAGGATTCCACTAAGTCGTGGACTT
1 GGAAAAGGATGCCACTAAGTCGTGGACTT
69039 GGAAAAGAGATGCCACTAAGTCGTGGACTT
1 GGAAAAG-GATGCCACTAAGTCGTGGACTT
69069 TTGGAAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (29 bp):
GGAAAAGGATGCCACTAAGTCGTGGACTT
Done.