Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013419.1 Corchorus capsularis cultivar CVL-1 contig13440, whole genome shotgun sequence
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: 172309
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:623 original size:2 final size:2
Alignment explanation
Indices: 616--650 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
606 ATGTAGGATA
616 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
651 GAACTTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:682 original size:21 final size:21
Alignment explanation
Indices: 656--697 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
646 TATATGAACT
656 TTTAATTATTATCAGGCCAAG
1 TTTAATTATTATCAGGCCAAG
* *
677 TTTAATTGTTATTAGGCCAAG
1 TTTAATTATTATCAGGCCAAG
698 ATATTAGTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (21 bp):
TTTAATTATTATCAGGCCAAG
Found at i:907 original size:22 final size:22
Alignment explanation
Indices: 881--934 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
871 GTTTGGTAAT
*
881 ATTTTATATTTTATGTAGGATG
1 ATTTTATATTTTATATAGGATG
* **
903 ATTTTATTTTTTATATAGTTTG
1 ATTTTATATTTTATATAGGATG
925 ATTTTTATAT
1 A-TTTTATAT
935 ATAATCATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (22 bp):
ATTTTATATTTTATATAGGATG
Found at i:15230 original size:180 final size:180
Alignment explanation
Indices: 14928--15288 Score: 677
Period size: 180 Copynumber: 2.0 Consensus size: 180
14918 TGGATATAGT
14928 GCTACCAAGTGTGACCCACCAAGTGCTCCCATGAAAATTGCAAATAATTCAGGGAGACAGTTGAA
1 GCTACCAAGTGTGACCCACCAAGTGCTCCCATGAAAATTGCAAATAATTCAGGGAGACAGTTGAA
* *
14993 TATGACTGAGTTGGGTTTCTGCAGATTAATAGATAAAGGTAAAGGTGCAGGATCAGGATGTGTTC
66 TATGACTGAGTTGGGTTTCTGCAGATTAATAGACAAAGGTAAAGGTGCAGGATCAGGATGTATTC
15058 CTGGTAGCCTTTGCACTGCAACAGATTCGGCACTTGGAATTCAAAAGCAG
131 CTGGTAGCCTTTGCACTGCAACAGATTCGGCACTTGGAATTCAAAAGCAG
15108 GCTACCAAGTGTGACCCACCAAGTGCTCCCATGAAAATTGCAAATAATTCAGGGAGACAGTTGAA
1 GCTACCAAGTGTGACCCACCAAGTGCTCCCATGAAAATTGCAAATAATTCAGGGAGACAGTTGAA
* *
15173 TATGCCTGAGTTGGGTTTCTGTAGATTAATAGACAAAGGTAAAGGTGCAGGATCAGGATGTATTC
66 TATGACTGAGTTGGGTTTCTGCAGATTAATAGACAAAGGTAAAGGTGCAGGATCAGGATGTATTC
*
15238 CTGGTGGCCTTTGCACTGCAACAGATTCGGCACTTGGAATTCAAAAGCAG
131 CTGGTAGCCTTTGCACTGCAACAGATTCGGCACTTGGAATTCAAAAGCAG
15288 G
1 G
15289 TTGAAAATTC
Statistics
Matches: 176, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
180 176 1.00
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25
Consensus pattern (180 bp):
GCTACCAAGTGTGACCCACCAAGTGCTCCCATGAAAATTGCAAATAATTCAGGGAGACAGTTGAA
TATGACTGAGTTGGGTTTCTGCAGATTAATAGACAAAGGTAAAGGTGCAGGATCAGGATGTATTC
CTGGTAGCCTTTGCACTGCAACAGATTCGGCACTTGGAATTCAAAAGCAG
Found at i:25471 original size:77 final size:82
Alignment explanation
Indices: 25365--25531 Score: 245
Period size: 85 Copynumber: 2.0 Consensus size: 82
25355 ATTATTATTA
25365 TTTTGGTACGTTGAAAAATTTTCTTGAATTAGTACT-T-A-ATTACTA-TATGTTTAACTTAATC
1 TTTTGGTACGTTGAAAAATTTTCTTGAATTAGTACTATAATATTACTACTATGTTTAACTTAATC
25426 TTTTGTTTCTCAAAGTT
66 TTTTGTTTCTCAAAGTT
* *
25443 TTTTGGTTCGTTG-AAAATTTTCTTGAATTAGTATTAAATAAATTATTACTACTATGTTTAACTT
1 TTTTGGTACGTTGAAAAATTTTCTTGAATTAGTACT--AT-AA-TATTACTACTATGTTTAACTT
25507 AATCTTTTGTTTCTCAAAGTT
62 AATCTTTTGTTTCTCAAAGTT
25528 TTTT
1 TTTT
25532 TTTTTGGGTG
Statistics
Matches: 79, Mismatches: 2, Indels: 9
0.88 0.02 0.10
Matches are distributed among these distances:
77 21 0.27
78 12 0.15
80 1 0.01
82 1 0.01
84 7 0.09
85 37 0.47
ACGTcount: A:0.28, C:0.10, G:0.11, T:0.51
Consensus pattern (82 bp):
TTTTGGTACGTTGAAAAATTTTCTTGAATTAGTACTATAATATTACTACTATGTTTAACTTAATC
TTTTGTTTCTCAAAGTT
Found at i:27406 original size:66 final size:66
Alignment explanation
Indices: 27300--27433 Score: 250
Period size: 66 Copynumber: 2.0 Consensus size: 66
27290 TATGCATTTG
* *
27300 AATACAAAGGGAAAATTAGATAAATAACATTGAATTCTATTCCATTAAACTTCTATACTGAAATG
1 AATACAAAGGAAAAATTAAATAAATAACATTGAATTCTATTCCATTAAACTTCTATACTGAAATG
27365 T
66 T
27366 AATACAAAGGAAAAATTAAATAAATAACATTGAATTCTATTCCATTAAACTTCTATACTGAAATG
1 AATACAAAGGAAAAATTAAATAAATAACATTGAATTCTATTCCATTAAACTTCTATACTGAAATG
27431 T
66 T
27432 AA
1 AA
27434 CAATCCAACA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (66 bp):
AATACAAAGGAAAAATTAAATAAATAACATTGAATTCTATTCCATTAAACTTCTATACTGAAATG
T
Found at i:33481 original size:3 final size:3
Alignment explanation
Indices: 33473--33516 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
33463 CCAAAGCAAG
33473 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
33517 TATTGCTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:42974 original size:18 final size:18
Alignment explanation
Indices: 42953--42996 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
42943 GTTTCCGGTA
42953 GTTGTTGGGTTTGTTGGT
1 GTTGTTGGGTTTGTTGGT
* *
42971 GTTGGTT-CGTTTGTTGTT
1 GTT-GTTGGGTTTGTTGGT
42989 GTTGTTGG
1 GTTGTTGG
42997 TCGGTAAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
17 3 0.14
18 15 0.71
19 3 0.14
ACGTcount: A:0.00, C:0.02, G:0.41, T:0.57
Consensus pattern (18 bp):
GTTGTTGGGTTTGTTGGT
Found at i:44108 original size:33 final size:35
Alignment explanation
Indices: 44066--44153 Score: 108
Period size: 33 Copynumber: 2.5 Consensus size: 35
44056 TAACTACACT
**
44066 AAACAGTAGTATGCAATTTAATG-TCAAA-AAAAA
1 AAACAGTAGTATGCAATTTAATGAAAAAATAAAAA
**
44099 AAACAGTAGTATGCAATTTTGTGAAAAAATAAAAA
1 AAACAGTAGTATGCAATTTAATGAAAAAATAAAAA
*
44134 ACAACAATAGTATGCAATTT
1 A-AACAGTAGTATGCAATTT
44154 TAGAGTCATA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
33 21 0.45
34 3 0.06
35 6 0.13
36 17 0.36
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.26
Consensus pattern (35 bp):
AAACAGTAGTATGCAATTTAATGAAAAAATAAAAA
Found at i:44583 original size:2 final size:2
Alignment explanation
Indices: 44578--44612 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
44568 TAATCGCGCG
44578 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 T
44613 TAAATCAGTA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49191 original size:32 final size:32
Alignment explanation
Indices: 49130--49192 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
49120 AGTATTAATT
* ** *
49130 GTCGGATAACATAATTTTTTTTTTTGGAAATA
1 GTCGGATAACATAATCTTAATTTTAGGAAATA
*
49162 GTCGGATAACATAGTCTTAATTTTAGGAAAT
1 GTCGGATAACATAATCTTAATTTTAGGAAAT
49193 TTATTTTTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.41
Consensus pattern (32 bp):
GTCGGATAACATAATCTTAATTTTAGGAAATA
Found at i:49592 original size:24 final size:22
Alignment explanation
Indices: 49532--49671 Score: 81
Period size: 22 Copynumber: 6.3 Consensus size: 22
49522 TTGTGATAAT
*
49532 TAACC-ACCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
49553 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* * **
49575 TAACTTGATCCTATGAAATTTTGG
1 TAAC--CAACCTATGAAATTTTAA
* **
49599 TAA-CTACACTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* *
49621 TAACC-ACACTATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* * *
49643 TAACC-TCCTCATGGAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
49665 TAACCAA
1 TAACCAA
49672 AGTAAAATAT
Statistics
Matches: 96, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
21 8 0.08
22 71 0.74
23 1 0.01
24 16 0.17
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:49613 original size:22 final size:22
Alignment explanation
Indices: 49585--49647 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
49575 TAACTTGATC
*
49585 CTATGAAATTTTGGTAACTACA
1 CTATGAAATTTTGGTAACCACA
49607 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
* *
49629 CTATGGAATTTTGATAACC
1 CTATGAAATTTTGGTAACC
49648 TCCTCATGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:49656 original size:22 final size:22
Alignment explanation
Indices: 49585--49670 Score: 84
Period size: 22 Copynumber: 3.9 Consensus size: 22
49575 TAACTTGATC
* * *
49585 CTATGAAATTTTGGTAACTACA
1 CTATGGAATTTTGATAACCACA
* *
49607 CTATGAAATTTTGGTAACCACA
1 CTATGGAATTTTGATAACCACA
*
49629 CTATGGAATTTTGATAACCTC-
1 CTATGGAATTTTGATAACCACA
* *
49650 CTCATGGAATTATAATAACCA
1 CT-ATGGAATTTTGATAACCA
49671 AAGTAAAATA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
21 2 0.04
22 54 0.96
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (22 bp):
CTATGGAATTTTGATAACCACA
Found at i:49788 original size:31 final size:32
Alignment explanation
Indices: 49752--49818 Score: 111
Period size: 30 Copynumber: 2.2 Consensus size: 32
49742 TCTAGTAATG
49752 ACAATTTAGAAATATGTTTTAAAAA-AAGGGT
1 ACAATTTAGAAATATGTTTTAAAAATAAGGGT
*
49783 ACAA-TTGGAAATATGTTTTAAAAATAAGGGT
1 ACAATTTAGAAATATGTTTTAAAAATAAGGGT
49814 ACAAT
1 ACAAT
49819 CGGAAAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 19 0.58
31 14 0.42
ACGTcount: A:0.48, C:0.04, G:0.16, T:0.31
Consensus pattern (32 bp):
ACAATTTAGAAATATGTTTTAAAAATAAGGGT
Found at i:49795 original size:30 final size:31
Alignment explanation
Indices: 49760--49824 Score: 114
Period size: 30 Copynumber: 2.1 Consensus size: 31
49750 TGACAATTTA
*
49760 GAAATATGTTTTAAAAA-AAGGGTACAATTG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
49790 GAAATATGTTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
49821 GAAA
1 GAAA
49825 ATATAAAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 17 0.52
31 16 0.48
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.28
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATCG
Found at i:49860 original size:2 final size:2
Alignment explanation
Indices: 49853--49902 Score: 82
Period size: 2 Copynumber: 24.5 Consensus size: 2
49843 TTCATACTTT
*
49853 TA TA TA TA GTA TA TA CA 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 TA TA TA TA TA TA TA
49896 TA TA TA T
1 TA TA TA T
49903 GAGCATTGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 43 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:51439 original size:20 final size:19
Alignment explanation
Indices: 51393--51439 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 19
51383 TGTCTCTGTT
51393 TTTTTCTCCACGCATGCTTC
1 TTTTT-TCCACGCATGCTTC
51413 TTATTTTCCACGTCA-GCTCTC
1 TT-TTTTCCACG-CATGCT-TC
51434 TTTTTT
1 TTTTTT
51440 ATTTTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.11, C:0.30, G:0.09, T:0.51
Consensus pattern (19 bp):
TTTTTTCCACGCATGCTTC
Found at i:51903 original size:14 final size:14
Alignment explanation
Indices: 51879--51912 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
51869 AATATACGTA
*
51879 TATATGTATATGTG
1 TATATATATATGTG
51893 TATATATATATGTG
1 TATATATATATGTG
*
51907 TGTATA
1 TATATA
51913 CGATATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (14 bp):
TATATATATATGTG
Found at i:51908 original size:16 final size:16
Alignment explanation
Indices: 51876--51922 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
51866 TGTAATATAC
*
51876 GTATATATGTATATGT
1 GTATATATATATATGT
*
51892 GTATATATATATGTGT
1 GTATATATATATATGT
*
51908 GTATACGATATATAT
1 GTATA-TATATATAT
51923 AGAGAGAGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 19 0.73
17 7 0.27
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (16 bp):
GTATATATATATATGT
Found at i:51928 original size:2 final size:2
Alignment explanation
Indices: 51923--51964 Score: 52
Period size: 2 Copynumber: 21.5 Consensus size: 2
51913 CGATATATAT
*
51923 AG AG AG AG AG ATC AG AG AG -G AG -G AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG A-G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
51964 A
1 A
51965 TGGAGAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 32 0.91
3 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.48, T:0.02
Consensus pattern (2 bp):
AG
Found at i:53089 original size:27 final size:27
Alignment explanation
Indices: 53058--53111 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
53048 TAGCGTTGAA
53058 GGCATGGTATTTCCATGATGTTGCGAC
1 GGCATGGTATTTCCATGATGTTGCGAC
53085 GGCATGGTATTTCCATGATGTTGCGAC
1 GGCATGGTATTTCCATGATGTTGCGAC
53112 CTTGAAGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.33
Consensus pattern (27 bp):
GGCATGGTATTTCCATGATGTTGCGAC
Found at i:59514 original size:84 final size:84
Alignment explanation
Indices: 59297--59598 Score: 518
Period size: 84 Copynumber: 3.6 Consensus size: 84
59287 GGGGTATCTG
* * * *
59297 ATAATTACGTCGCAT-CTGACTAATTCGGAGTCGAGATATTTGTTTTCAAACATAAGAGATTGGA
1 ATAATTACATTGCATCCT-ACTAATTCAGAGTCGAGACATTTGTTTTCAAACATAAGAGATTGGA
*
59361 ATAACCGTGGAATGGATCCG
65 ATAACCGTGGAATGGATCCC
*
59381 AT-ATTACATTGTATCCTACTAATTCAGAGTCGAGACATTTGTTTTCAAACATAAGAGATTGGAA
1 ATAATTACATTGCATCCTACTAATTCAGAGTCGAGACATTTGTTTTCAAACATAAGAGATTGGAA
59445 TAACCGTGGAATGGATCCC
66 TAACCGTGGAATGGATCCC
*
59464 ATAATTACATTACATCCTACTAATTCAGAGTCGAGACATTTGTTTTCAAACATAAGAGATTGGAA
1 ATAATTACATTGCATCCTACTAATTCAGAGTCGAGACATTTGTTTTCAAACATAAGAGATTGGAA
59529 TAACCGTGGAATGGATCCC
66 TAACCGTGGAATGGATCCC
59548 ATAATTACATTGCATCCTACTAATTCAGAGTCGAGACATTTGTTTTCAAAC
1 ATAATTACATTGCATCCTACTAATTCAGAGTCGAGACATTTGTTTTCAAAC
59599 CTGGAATAAC
Statistics
Matches: 207, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
83 74 0.36
84 133 0.64
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (84 bp):
ATAATTACATTGCATCCTACTAATTCAGAGTCGAGACATTTGTTTTCAAACATAAGAGATTGGAA
TAACCGTGGAATGGATCCC
Found at i:62374 original size:28 final size:28
Alignment explanation
Indices: 62333--62388 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
62323 CTGTATTTTG
*
62333 AGGAGAGGTTGTTTGAATGAGCACGCAA
1 AGGAGAGGTGGTTTGAATGAGCACGCAA
*
62361 AGGAGAGGTGGTTTGGATGAGCACGCAA
1 AGGAGAGGTGGTTTGAATGAGCACGCAA
62389 CACCGCTGCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.39, T:0.20
Consensus pattern (28 bp):
AGGAGAGGTGGTTTGAATGAGCACGCAA
Found at i:91387 original size:25 final size:25
Alignment explanation
Indices: 91353--91403 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
91343 ACAAAATAAA
*
91353 AAGGTGCTTACCATAATTCAAGTGT
1 AAGGTACTTACCATAATTCAAGTGT
91378 AAGGTACTTACCATAATTCAAGTGT
1 AAGGTACTTACCATAATTCAAGTGT
91403 A
1 A
91404 CCACCAAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (25 bp):
AAGGTACTTACCATAATTCAAGTGT
Found at i:91794 original size:13 final size:13
Alignment explanation
Indices: 91776--91802 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
91766 GTTCCAAAAC
91776 GTTTCTATTTTCT
1 GTTTCTATTTTCT
91789 GTTTCTATTTTCT
1 GTTTCTATTTTCT
91802 G
1 G
91803 ATAGCTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.15, G:0.11, T:0.67
Consensus pattern (13 bp):
GTTTCTATTTTCT
Found at i:95265 original size:55 final size:55
Alignment explanation
Indices: 95188--95297 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
95178 TTACATGCCT
95188 TCATGCCCCATAAGAAACATATGAATGTACATATAAATTTCTTTTGAGCATGCTA
1 TCATGCCCCATAAGAAACATATGAATGTACATATAAATTTCTTTTGAGCATGCTA
95243 TCATGCCCCATAAGAAACATATGAATGTACATATAAATTTCTTTTGAGCATGCTA
1 TCATGCCCCATAAGAAACATATGAATGTACATATAAATTTCTTTTGAGCATGCTA
95298 AAAATATCAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (55 bp):
TCATGCCCCATAAGAAACATATGAATGTACATATAAATTTCTTTTGAGCATGCTA
Found at i:96792 original size:19 final size:19
Alignment explanation
Indices: 96768--96807 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
96758 CATATACAGG
96768 CATATTAATTCAGATTTTA
1 CATATTAATTCAGATTTTA
96787 CATATTAATTCAGATTTTA
1 CATATTAATTCAGATTTTA
96806 CA
1 CA
96808 AAAGAGGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (19 bp):
CATATTAATTCAGATTTTA
Found at i:97344 original size:37 final size:37
Alignment explanation
Indices: 97282--97353 Score: 119
Period size: 37 Copynumber: 1.9 Consensus size: 37
97272 ATAGATATAG
97282 ATATAGACTAGATTAAGTTTAGAGTTCCCACGTCCTAT
1 ATATAGACTAGATTAAGTTTAGAGTTCCCAC-TCCTAT
*
97320 ATATAGACTAG-TTTAGTTTAGAGTTCCCACTCCT
1 ATATAGACTAGATTAAGTTTAGAGTTCCCACTCCT
97354 TTACTGTCTC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
36 4 0.12
37 18 0.55
38 11 0.33
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.36
Consensus pattern (37 bp):
ATATAGACTAGATTAAGTTTAGAGTTCCCACTCCTAT
Found at i:137093 original size:40 final size:40
Alignment explanation
Indices: 137031--137111 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
137021 ACTTAACCCT
* *
137031 CCTAATAATTAAGGAAATAAATTAAATTCAGATTTAGCCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAGATTTAGCCC
* *
137071 CCTAATAATTAAGGTAAGAAATTAAATCCAGGTTTAGCCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAGATTTAGCCC
137111 C
1 C
137112 TAGTTATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (40 bp):
CCTAATAATTAAGGAAAGAAATTAAATCCAGATTTAGCCC
Found at i:138780 original size:19 final size:19
Alignment explanation
Indices: 138756--138793 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
138746 TAAGTGCATG
138756 CTCTCTTAAATATTACTCC
1 CTCTCTTAAATATTACTCC
*
138775 CTCTCTTACATATTACTCC
1 CTCTCTTAAATATTACTCC
138794 TTCTATTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.34, G:0.00, T:0.42
Consensus pattern (19 bp):
CTCTCTTAAATATTACTCC
Found at i:139904 original size:22 final size:22
Alignment explanation
Indices: 139876--140048 Score: 115
Period size: 22 Copynumber: 7.8 Consensus size: 22
139866 TATCTCTATG
139876 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
139898 TGGTTATTATAATTCCAT----
1 TGGTTATCAAAATTTCATAAGA
139916 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
*
139938 TGGTTATTATCAAAATTTCAT-AGTG
1 TGG---TTATCAAAATTTCATAAG-A
*
139963 TGGTTACCAAAATTTCAT-AGA
1 TGGTTATCAAAATTTCATAAGA
* *
139984 GTGGTTACCAAAATTTCATAGGA
1 -TGGTTATCAAAATTTCATAAGA
* * * * *
140007 TCATGTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAAGA
**
140031 TGGTTATTGAAATTTCAT
1 TGGTTATCAAAATTTCAT
140049 TGGGTGGTTA
Statistics
Matches: 121, Mismatches: 18, Indels: 24
0.74 0.11 0.15
Matches are distributed among these distances:
18 15 0.12
22 67 0.55
23 2 0.02
24 19 0.16
25 18 0.15
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:140235 original size:22 final size:22
Alignment explanation
Indices: 140184--140239 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
140174 ACTTCATCGG
140184 GAGGTTATCAAAATTTTATATT
1 GAGGTTATCAAAATTTTATATT
* *
140206 GTGTTTATCAAAATTTTATA-T
1 GAGGTTATCAAAATTTTATATT
140227 GAAGGTTAT-AAAA
1 G-AGGTTATCAAAA
140240 GTCTCAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.43
Consensus pattern (22 bp):
GAGGTTATCAAAATTTTATATT
Found at i:140314 original size:22 final size:22
Alignment explanation
Indices: 140279--140494 Score: 124
Period size: 22 Copynumber: 9.8 Consensus size: 22
140269 TAATATAAGT
*
140279 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGAGTGA
* *
140300 TTATCGAAATTTCATAAAGATAAGA
1 TTATCAAAATTTCATAGAG-T--GA
**
140325 TTATCAAAATTT-ATATGA-AAA
1 TTATCAAAATTTCATA-GAGTGA
*
140346 TTATCAAAATTTCATAGTGTTG-
1 TTATCAAAATTTCATAGAG-TGA
*
140368 TTATCAAAATTACATA-ATGTGA
1 TTATCAAAATTTCATAGA-GTGA
* *
140390 TTATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGAGTGA
* * * *
140412 TCAACAAAATTTTATAAAGATG-
1 TTATCAAAATTTCATAGAG-TGA
* * *
140434 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGAGTGA
* * *
140456 TTATCAAATTTTCA-AAATCTGA
1 TTATCAAAATTTCATAGA-GTGA
140478 TTA-CAAAAATTTCATAG
1 TTATC-AAAATTTCATAG
140495 TGGTATTTCT
Statistics
Matches: 150, Mismatches: 29, Indels: 30
0.72 0.14 0.14
Matches are distributed among these distances:
21 26 0.17
22 103 0.69
23 4 0.03
24 3 0.02
25 14 0.09
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGAGTGA
Found at i:140378 original size:68 final size:64
Alignment explanation
Indices: 140262--140401 Score: 149
Period size: 68 Copynumber: 2.1 Consensus size: 64
140252 TAAGGAGTAC
** * *
140262 CAAAATTTAATATAAGTTTATCAAATCTCATAGAGTGATTATCGAAATTTCATAAAGATAAGATT
1 CAAAATTTAATATAAAATTATCAAATCTCATAGAGTGATTATCAAAATTACATAAAG-T--GATT
140327 AT
63 AT
* * *
140329 CAAAATTT-ATATGAAAATTATCAAAATTTCATAGTGTTG-TTATCAAAATTACATAATGTGATT
1 CAAAATTTAATAT-AAAATTATC-AAATCTCATAGAG-TGATTATCAAAATTACATAAAGTGATT
140392 AT
63 AT
140394 CAAAATTT
1 CAAAATTT
140402 CATAGAGGGG
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
65 14 0.22
66 4 0.06
67 16 0.25
68 27 0.43
69 2 0.03
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (64 bp):
CAAAATTTAATATAAAATTATCAAATCTCATAGAGTGATTATCAAAATTACATAAAGTGATTAT
Found at i:140399 original size:44 final size:44
Alignment explanation
Indices: 140184--140494 Score: 165
Period size: 44 Copynumber: 7.0 Consensus size: 44
140174 ACTTCATCGG
* * * *
140184 GAGGTTATCAAAATTTTATATTGTGTTTATCAAAATTTTATATGA
1 GAGGTTATCAAAATTTCATAATGTGATTATCAAAATTTCATA-GA
* * * * *
140229 -AGGTTATAAAAGTCTCAATTTCATAA-G-GAGTACCAAAATTTAATATA
1 GAGGTTAT-CAA-----AATTTCATAATGTGATTATCAAAATTTCATAGA
* * *
140276 -AGTTTATC-AAATCTCATAGA-GTGATTATCGAAATTTCATAAAGA
1 GAGGTTATCAAAATTTCATA-ATGTGATTATCAAAATTTCAT--AGA
* * ** *
140320 TAAGATTATCAAAATTT-AT-ATGAAAATTATCAAAATTTCATAGT
1 -GAGGTTATCAAAATTTCATAATG-TGATTATCAAAATTTCATAGA
** *
140364 GTTGTTATCAAAATTACATAATGTGATTATCAAAATTTCATAGA
1 GAGGTTATCAAAATTTCATAATGTGATTATCAAAATTTCATAGA
* * * * * *
140408 GGGGTCAACAAAATTTTATAAAGATG-TTATCAAAATTTCATAAA
1 GAGGTTATCAAAATTTCATAATG-TGATTATCAAAATTTCATAGA
* * *
140452 GAGGTTATCAAATTTTCAAAATCTGATTA-CAAAAATTTCATAG
1 GAGGTTATCAAAATTTCATAATGTGATTATC-AAAATTTCATAG
140495 TGGTATTTCT
Statistics
Matches: 199, Mismatches: 47, Indels: 41
0.69 0.16 0.14
Matches are distributed among these distances:
40 8 0.04
41 2 0.01
42 13 0.07
43 14 0.07
44 94 0.47
45 9 0.05
46 24 0.12
47 12 0.06
48 14 0.07
49 1 0.01
50 8 0.04
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (44 bp):
GAGGTTATCAAAATTTCATAATGTGATTATCAAAATTTCATAGA
Found at i:140608 original size:19 final size:19
Alignment explanation
Indices: 140586--140641 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
140576 TCAAAATTTT
140586 AGGGAGGAT-ACTAAAATTC
1 AGGGAGGATAAC-AAAATTC
140605 AGGGAGGATAACAAAATTC
1 AGGGAGGATAACAAAATTC
* * *
140624 AGTGAGTATATCAAAATT
1 AGGGAGGATAACAAAATT
140642 TCATATGAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 31 0.94
20 2 0.06
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (19 bp):
AGGGAGGATAACAAAATTC
Found at i:140660 original size:22 final size:22
Alignment explanation
Indices: 140632--140924 Score: 140
Period size: 22 Copynumber: 13.5 Consensus size: 22
140622 TCAGTGAGTA
*
140632 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATAGGAAGGT
* **
140654 TATCAAATTTTCATAGTTTA-GT
1 TATCAAAATTTCATAG-GAAGGT
* * *
140676 TTTCAAAATTTCATAAGATGGT
1 TATCAAAATTTCATAGGAAGGT
* * *
140698 TATCAAAAGTTCATA-GTATGT
1 TATCAAAATTTCATAGGAAGGT
* * *
140719 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATAGGAAGGT
* *
140742 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-AGGAAGGT
** * *
140764 TATCAAAAAATCATAGGGAGCT
1 TATCAAAATTTCATAGGAAGGT
*
140786 TATCAAAA-TT--T--GTA-GT
1 TATCAAAATTTCATAGGAAGGT
* * * *
140802 AATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATAGGAAGGT
* *
140824 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAGGAAGG-T
* * *
140847 TATTAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATAGGAAG-GT
*
140870 TATCAAAATTTCATAGCG-AGAT
1 TATCAAAATTTCATAG-GAAGGT
* * * *
140892 TATGACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATAG-GAAGGT
140914 TATCAAAATTT
1 TATCAAAATTT
140925 TAAAGTGTGA
Statistics
Matches: 203, Mismatches: 53, Indels: 30
0.71 0.19 0.10
Matches are distributed among these distances:
16 7 0.03
17 4 0.02
19 2 0.01
21 8 0.04
22 139 0.68
23 42 0.21
24 1 0.00
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATAGGAAGGT
Found at i:140854 original size:23 final size:23
Alignment explanation
Indices: 140823--140926 Score: 90
Period size: 23 Copynumber: 4.6 Consensus size: 23
140813 CATAAGAAAG
* *
140823 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGAAGAT
*
140846 TTATTAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGAT
*
140869 TTATCAAAATTTCATAGCG-AGA-
1 TTATCAAAATTTTATAG-GAAGAT
* * * *
140891 TTATGACAATTTCATAGTG-TGA-
1 TTATCAAAATTTTATAG-GAAGAT
140913 TTATCAAAATTTTA
1 TTATCAAAATTTTA
140927 AAGTGTGATT
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
22 29 0.43
23 38 0.56
24 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAT
Found at i:141005 original size:22 final size:22
Alignment explanation
Indices: 140977--141040 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 22
140967 TTTATAAAGT
*
140977 GGTTATCAATATATCATATGGA
1 GGTTATCAAAATATCATATGGA
* * **
140999 GGTTATCAACATCTCATAGTGTT
1 GGTTATCAAAATATCATA-TGGA
*
141022 GGTTATCAAAATTTCATAT
1 GGTTATCAAAATATCATAT
141041 TGAGACCTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 17 0.49
23 18 0.51
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (22 bp):
GGTTATCAAAATATCATATGGA
Found at i:141029 original size:23 final size:22
Alignment explanation
Indices: 140975--141040 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
140965 TTTTTATAAA
*
140975 GTGGTTATCAATATATCATATG
1 GTGGTTATCAAAATATCATATG
* * *
140997 GAGGTTATCAACATCTCATAGTG
1 GTGGTTATCAAAATATCATA-TG
* *
141020 TTGGTTATCAAAATTTCATAT
1 GTGGTTATCAAAATATCATAT
141041 TGAGACCTTC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 18 0.50
23 18 0.50
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (22 bp):
GTGGTTATCAAAATATCATATG
Found at i:141182 original size:21 final size:20
Alignment explanation
Indices: 141136--141182 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
141126 GTATCGTTAT
*
141136 TAAAATTTCATAGGAGATTA
1 TAAAATTTCATAGGAGATCA
141156 TCAAAATTTCATAATGG-GATCA
1 T-AAAATTTCAT-A-GGAGATCA
141178 TAAAA
1 TAAAA
141183 GATAGTCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 14 0.61
22 6 0.26
23 2 0.09
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.32
Consensus pattern (20 bp):
TAAAATTTCATAGGAGATCA
Found at i:159658 original size:6 final size:6
Alignment explanation
Indices: 159647--159671 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
159637 GATTTTTTGT
159647 CTGAGA CTGAGA CTGAGA CTGAGA C
1 CTGAGA CTGAGA CTGAGA CTGAGA C
159672 AGACTTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.20, G:0.32, T:0.16
Consensus pattern (6 bp):
CTGAGA
Found at i:163863 original size:3 final size:3
Alignment explanation
Indices: 163840--163904 Score: 103
Period size: 3 Copynumber: 21.0 Consensus size: 3
163830 CCAACTTGGG
*
163840 TAT TAAT TAT AAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
163887 TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
163905 ATATATATAT
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
3 52 0.90
4 6 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:165208 original size:28 final size:31
Alignment explanation
Indices: 165142--165221 Score: 103
Period size: 33 Copynumber: 2.6 Consensus size: 31
165132 GACTAAAGTC
165142 CTTTTTGTCCCCTAAACTTTAATTTAAAATTGA
1 CTTTTTGTCCCCTAAACTTTAATTTAAAA-T-A
*
165175 CTTTTTGTCCCCTAAACTTTAATTT-AGA-A
1 CTTTTTGTCCCCTAAACTTTAATTTAAAATA
*
165204 CTTTTT-CCCCCTAAACTT
1 CTTTTTGTCCCCTAAACTT
165222 GCAATATGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
28 11 0.24
29 7 0.16
32 2 0.04
33 25 0.56
ACGTcount: A:0.26, C:0.24, G:0.05, T:0.45
Consensus pattern (31 bp):
CTTTTTGTCCCCTAAACTTTAATTTAAAATA
Done.