Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020877.1 Corchorus olitorius cultivar O-4 contig20910, 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: 129307
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1124 original size:331 final size:330
Alignment explanation
Indices: 1--1959 Score: 2787
Period size: 332 Copynumber: 5.8 Consensus size: 330
* *
1 GTTTTACCAATTTTTTCCTAAATTAATTTCTGATTAAATTGAAACAAGATTTAGATGCTCGCAAA
1 GTTTT-CCAATTTTTTCCTAAATTAATTTCTGATTAAATCGAAACAAGATTTAGATGCTCGTAAA
* *
66 AACAAATCCTGAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATATTAACGACTCA
65 AACAAATCCTCAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATATTAACGACTCT
* * * * *
131 CGGTGCCAAAAATCATACAAAATTGTGTCGATGCCCGGAATGCATTTTTAGTCAAAAACCGTGAT
130 CGGTGCCAAAAATCATGCAAAACTGTGTCGGTGCCCGGAACGCATTTTTAGCCAAAAACCGTGAT
* * *
196 AGTTAGTACACGATTTCGGCTAAAATTTTGCAAATATTGACCCGAAATATTTTTCCACAATTTTT
195 GGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTT
* * *
261 GGCCAAAATACTCATAAAAATATATAATTCAAATCCAAAAGGTTTGAAGGGCTTTTGACGTTTCT
260 GGCCAAAATACTCAAAAAAAAATATAATTCAAATCCAAAAAGTTTGAAGGGCTTTTGACGTTTCT
326 AATATC
325 AATATC
*
332 GTTTTCCAAATTTTTCCTAAATTAATTTCTGATTAAATCGAAACAAGATTTAGATGCTCGTAAAA
1 GTTTTCCAATTTTTTCCTAAATTAATTTCTGATTAAATCGAAACAAGATTTAGATGCTCGTAAAA
*
397 ACAAATCCTCAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATATTAACGACTCTT
66 ACAAATCCTCAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATATTAACGACTCTC
*
462 GGTGCCAAAATTCATGCAAAACTGTGTCGGTGCCCGGAACGCATTTTTAGCCAAAAACCGTGATG
131 GGTGCCAAAAATCATGCAAAACTGTGTCGGTGCCCGGAACGCATTTTTAGCCAAAAACCGTGATG
*
527 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCGATTTTTG
196 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTTG
* * *
592 GCCAAAATACTCAAAAAAATTATATAATTCAAATCCAAAACGTTTGAAGGGCTTTTGACATTTCT
261 GCCAAAATACTCAAAAAAA-AATATAATTCAAATCCAAAAAGTTTGAAGGGCTTTTGACGTTTCT
657 AATATC
325 AATATC
* *
663 ATTTTTCCAATTTTTTCCTAAATTAATTTCTGATTAAATCGAAACAAGATTTACATGCTCGTAAA
1 -GTTTTCCAATTTTTTCCTAAATTAATTTCTGATTAAATCGAAACAAGATTTAGATGCTCGTAAA
728 AACAAATCCTCAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATATTAACGACTCT
65 AACAAATCCTCAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATATTAACGACTCT
* * * *
793 CGGTGCCAAAAATCATGCAAAACAGTGTCGGTGCCTGAAACGCATTTTTAGGCAAAAACCGTGAT
130 CGGTGCCAAAAATCATGCAAAACTGTGTCGGTGCCCGGAACGCATTTTTAGCCAAAAACCGTGAT
* *
858 GGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTAACCCGAAATATTTTTCCTCGATTTTT
195 GGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTT
* *
923 TGCCAAAATACTCAAAAAAAAAAATAATTCAAATCCAAAAAGTTTGAAGGGCTTTTGACGTTTCT
260 GGCCAAAATACTCAAAAAAAAATATAATTCAAATCCAAAAAGTTTGAAGGGCTTTTGACGTTTCT
988 AATATC
325 AATATC
* *
994 GTTTTCCAGATTTTTTCCTAAATTACTTTCTGATTAAATAGAAACAAGATTTAGATGCTCGTAAA
1 GTTTTCCA-ATTTTTTCCTAAATTAATTTCTGATTAAATCGAAACAAGATTTAGATGCTCGTAAA
*
1059 AACAAATCCTCAAATCCAAT-TAGG-TAGAGATTTGATTAGATGAATATAGATATATTAACGACT
65 AACAAATCCTCAAATCCAATGT-GGCT-GAGATTTGGTTAGATGAATATAGATATATTAACGACT
* * *
1122 CTCGGTGCCAAAAATAATGCAAAACTGTGTCGGTGCCCGGAACGCATTTATAGCCAAAAACTGTG
128 CTCGGTGCCAAAAATCATGCAAAACTGTGTCGGTGCCCGGAACGCATTTTTAGCCAAAAACCGTG
* * *
1187 ATGGTTAGTACACAATTTCGGTTAAAATTTTGCAAAAATTGACTCGAAATATTTTTCCTCAATTT
193 ATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTT
* * *
1252 TTGGCCAAGATACTCAAAAAAAATATATAATTCAAATCCAAAATGTTTGAAAGGCTTTTGACGTT
258 TTGGCCAAAATACTCAAAAAAAA-ATATAATTCAAATCCAAAAAGTTTGAAGGGCTTTTGACGTT
1317 TCTAATATC
322 TCTAATATC
* *
1326 GTTTTTCAAATTTTTTCTTAAATTAATTTCTGATTAAATCGAAACAAGATTTAGATGCTCGTAAA
1 G-TTTTCCAATTTTTTCCTAAATTAATTTCTGATTAAATCGAAACAAGATTTAGATGCTCGTAAA
1391 AACAAATCCTCAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATATTAACGACTCT
65 AACAAATCCTCAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATATTAACGACTCT
* ** * * **
1456 CGATGCCAAAAAGAATGCAAAACTGTGTTGTTGCCCGGAACGCATTTTTAGCCAAAAATTGTGAT
130 CGGTGCCAAAAATCATGCAAAACTGTGTCGGTGCCCGGAACGCATTTTTAGCCAAAAACCGTGAT
1521 GGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTT
195 GGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTT
*
1586 GGCCAAAATACTCATATATATATATATATATATATATGTATATAAATCAACACCAAAAAGTTTGA
260 GGCCAAAATACTCA-A-A-A-A-A-A-A-ATATA-A--T-T-CAAAT-----CCAAAAAGTTTGA
* *
1651 AGGGCTTTTAACGTTTTTAATATC
307 AGGGCTTTTGACGTTTCTAATATC
* * * *
1675 GTTATTCCAATGTTTTTTTCCT-AATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTTGT
1 GTT-TTCCAA---TTTTTTCCTAAATTAATTTCTGATTAAATCGAAACAAGATTTAGATGCTCGT
* * * * *
1739 AAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTTGATGAATATAGATAT-TTAATGGA
62 AAAAACAAATCCTCAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATATTAA-CGA
* * * * * * * * * *
1803 GTCTCGGCGCCAAAAAACAAGAAAAACTGAG-CCGTGGCCCCAGAACGCGTTTTTAGCCAAAATC
126 CTCTCGGTGCCAAAAATCATGCAAAACTGTGTCGGT-G-CCCGGAACGCATTTTTAGCCAAAAAC
* * * * * *
1867 GGTGAT-GTAACAGTACACGATTTCGACTACAATTTTCCAAAAATTGATCCGAAATATTTTTCCT
189 CGTGATGGT--TAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCT
* ** * *
1931 CAGTTTTTGATCAAAATATTCATAAAAAA
252 CAATTTTTGGCCAAAATACTCAAAAAAAA
1960 TACATAAATT
Statistics
Matches: 1480, Mismatches: 113, Indels: 55
0.90 0.07 0.03
Matches are distributed among these distances:
330 266 0.18
331 351 0.24
332 563 0.38
333 9 0.01
334 1 0.00
335 1 0.00
336 1 0.00
337 1 0.00
338 1 0.00
339 7 0.00
340 1 0.00
342 1 0.00
343 1 0.00
344 4 0.00
346 1 0.00
347 1 0.00
348 3 0.00
349 40 0.03
350 6 0.00
351 119 0.08
352 35 0.02
353 67 0.05
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (330 bp):
GTTTTCCAATTTTTTCCTAAATTAATTTCTGATTAAATCGAAACAAGATTTAGATGCTCGTAAAA
ACAAATCCTCAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATATTAACGACTCTC
GGTGCCAAAAATCATGCAAAACTGTGTCGGTGCCCGGAACGCATTTTTAGCCAAAAACCGTGATG
GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTTG
GCCAAAATACTCAAAAAAAAATATAATTCAAATCCAAAAAGTTTGAAGGGCTTTTGACGTTTCTA
ATATC
Found at i:1302 original size:663 final size:663
Alignment explanation
Indices: 2--1966 Score: 2825
Period size: 663 Copynumber: 2.9 Consensus size: 663
1 G
* * *
2 TTTTACCAATTTTTTCCTAAATTAATTTCTGATTAAATTGAAACAAGATTTAGATGCTCGCAAAA
1 TTTTTCCAATTTTTTCCTAAATTAATTTCTGATTAAATCGAAACAAGATTTAGATGCTCGTAAAA
* *
67 ACAAATCCTGAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATATTAACGACTCAC
66 ACAAATCCTCAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATATTAACGACTCTC
* * * * *
132 GGTGCCAAAAATCATACAAAATTGTGTCGATGCCCGGAATGCATTTTTAGTCAAAAACCGTGATA
131 GGTGCCAAAAATCATGCAAAACTGTGTCGATGCCCGGAACGCATTTTTAGCCAAAAACCGTGATG
* *
197 GTTAGTACACGATTTCGGCTAAAATTTTGCAAATATTGACCCGAAATATTTTTCCACAATTTTTG
196 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTTG
* * * *
262 GCCAAAATACTCATAAAAATATATAATTCAAATCCAAAAGGTTTGAAGGGCTTTTGACGTTTCTA
261 GCCAAAATACTCAAAAAAAAAAATAATTCAAATCCAAAAAGTTTGAAGGGCTTTTGACGTTTCTA
*
327 ATATCGTTTTCCA-AATTTTTCCTAAATTAATTTCTGATTAAATCGAAACAAGATTTAGATGCTC
326 ATATCGTTTTCCAGATTTTTTCCTAAATTAATTTCTGATTAAATCGAAACAAGATTTAGATGCTC
*
391 GTAAAAACAAATCCTCAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATATTAACG
391 GTAAAAACAAATCCTCAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATATTAACG
* * *
456 ACTCTTGGTGCCAAAATTCATGCAAAACTGTGTCGGTGCCCGGAACGCATTTTTAGCCAAAAACC
456 ACTCTCGGTGCCAAAAATAATGCAAAACTGTGTCGGTGCCCGGAACGCATTTTTAGCCAAAAACC
* *
521 GTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCGA
521 GTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAATATTTTTCCTCAA
* *
586 TTTTTGGCCAAAATACTCAAAAAAATTATATAATTCAAATCCAAAACGTTTGAAGGGCTTTTGAC
586 TTTTTGGCCAAAATACTCAAAAAAAATATATAATTCAAATCCAAAACGTTTGAAAGGCTTTTGAC
651 ATTTCTAATATCA
651 ATTTCTAATATCA
*
664 TTTTTCCAATTTTTTCCTAAATTAATTTCTGATTAAATCGAAACAAGATTTACATGCTCGTAAAA
1 TTTTTCCAATTTTTTCCTAAATTAATTTCTGATTAAATCGAAACAAGATTTAGATGCTCGTAAAA
729 ACAAATCCTCAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATATTAACGACTCTC
66 ACAAATCCTCAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATATTAACGACTCTC
* * * * *
794 GGTGCCAAAAATCATGCAAAACAGTGTCGGTGCCTGAAACGCATTTTTAGGCAAAAACCGTGATG
131 GGTGCCAAAAATCATGCAAAACTGTGTCGATGCCCGGAACGCATTTTTAGCCAAAAACCGTGATG
* * *
859 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTAACCCGAAATATTTTTCCTCGATTTTTT
196 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTTG
924 GCCAAAATACTCAAAAAAAAAAATAATTCAAATCCAAAAAGTTTGAAGGGCTTTTGACGTTTCTA
261 GCCAAAATACTCAAAAAAAAAAATAATTCAAATCCAAAAAGTTTGAAGGGCTTTTGACGTTTCTA
* *
989 ATATCGTTTTCCAGATTTTTTCCTAAATTACTTTCTGATTAAATAGAAACAAGATTTAGATGCTC
326 ATATCGTTTTCCAGATTTTTTCCTAAATTAATTTCTGATTAAATCGAAACAAGATTTAGATGCTC
1054 GTAAAAACAAATCCTCAAATCCAAT-TAGG-TAGAGATTTGATTAGATGAATATAGATATATTAA
391 GTAAAAACAAATCCTCAAATCCAATGT-GGCT-GAGATTTGATTAGATGAATATAGATATATTAA
*
1117 CGACTCTCGGTGCCAAAAATAATGCAAAACTGTGTCGGTGCCCGGAACGCATTTATAGCCAAAAA
454 CGACTCTCGGTGCCAAAAATAATGCAAAACTGTGTCGGTGCCCGGAACGCATTTTTAGCCAAAAA
* * *
1182 CTGTGATGGTTAGTACACAATTTCGGTTAAAATTTTGCAAAAATTGACTCGAAATATTTTTCCTC
519 CCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAATATTTTTCCTC
* *
1247 AATTTTTGGCCAAGATACTCAAAAAAAATATATAATTCAAATCCAAAATGTTTGAAAGGCTTTTG
584 AATTTTTGGCCAAAATACTCAAAAAAAATATATAATTCAAATCCAAAACGTTTGAAAGGCTTTTG
* *
1312 ACGTTTCTAATATCG
649 ACATTTCTAATATCA
* *
1327 TTTTTCAAATTTTTTCTTAAATTAATTTCTGATTAAATCGAAACAAGATTTAGATGCTCGTAAAA
1 TTTTTCCAATTTTTTCCTAAATTAATTTCTGATTAAATCGAAACAAGATTTAGATGCTCGTAAAA
1392 ACAAATCCTCAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATATTAACGACTCTC
66 ACAAATCCTCAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATATTAACGACTCTC
* ** * * **
1457 GATGCCAAAAAGAATGCAAAACTGTGTTGTTGCCCGGAACGCATTTTTAGCCAAAAATTGTGATG
131 GGTGCCAAAAATCATGCAAAACTGTGTCGATGCCCGGAACGCATTTTTAGCCAAAAACCGTGATG
1522 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTTG
196 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTTG
1587 GCCAAAATACTCATATATATATATATATATATATATGTATAT-AAATCAACACCAAAAAGTTTGA
261 GCCAAAATACTCA-A-A-A-A-A-A-A-A-A-ATA---AT-TCAAAT-----CCAAAAAGTTTGA
* * * *
1651 AGGGCTTTTAACGTTTTTAATATCGTTATTCCAATGTTTTTTTCCT-AATTAATTTCTAATTAAA
307 AGGGCTTTTGACGTTTCTAATATCGTT-TTCC-A-GATTTTTTCCTAAATTAATTTCTGATTAAA
* * * * * *
1715 TCGAAACAAGATTCAAATGCTTGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTT
369 TCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTCAAATCCAATGTGGCTGAGATTTGATTA
* * * * * * *
1780 GATGAATATAGATAT-TTAATGGAGTCTCGGCGCCAAAAA-ACAAGAAAAACTGAG-CCGTGGCC
434 GATGAATATAGATATATTAA-CGACTCTCGGTGCCAAAAATA-ATGCAAAACTGTGTCGGT-G-C
* * * * * * * *
1842 CCAGAACGCGTTTTTAGCCAAAATCGGTGAT-GTAACAGTACACGATTTCGACTACAATTTTCCA
495 CCGGAACGCATTTTTAGCCAAAAACCGTGATGGT--TAGTACACGATTTCGGCTAAAATTTTGCA
* ** * * *
1906 AAAATTGA-TCCGAAATATTTTTCCTCAGTTTTTGATCAAAATATTCATAAAAAATACATAA
558 AAAATTGACT-CGAAATATTTTTCCTCAATTTTTGGCCAAAATACTCAAAAAAAATATATAA
1967 ATTAACGAAA
Statistics
Matches: 1172, Mismatches: 97, Indels: 45
0.89 0.07 0.03
Matches are distributed among these distances:
662 316 0.27
663 557 0.48
664 1 0.00
665 1 0.00
666 1 0.00
667 1 0.00
668 1 0.00
669 1 0.00
670 1 0.00
671 1 0.00
672 1 0.00
673 3 0.00
676 6 0.01
677 1 0.00
681 38 0.03
682 12 0.01
683 115 0.10
684 40 0.03
685 75 0.06
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (663 bp):
TTTTTCCAATTTTTTCCTAAATTAATTTCTGATTAAATCGAAACAAGATTTAGATGCTCGTAAAA
ACAAATCCTCAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATATTAACGACTCTC
GGTGCCAAAAATCATGCAAAACTGTGTCGATGCCCGGAACGCATTTTTAGCCAAAAACCGTGATG
GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTTG
GCCAAAATACTCAAAAAAAAAAATAATTCAAATCCAAAAAGTTTGAAGGGCTTTTGACGTTTCTA
ATATCGTTTTCCAGATTTTTTCCTAAATTAATTTCTGATTAAATCGAAACAAGATTTAGATGCTC
GTAAAAACAAATCCTCAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATATTAACG
ACTCTCGGTGCCAAAAATAATGCAAAACTGTGTCGGTGCCCGGAACGCATTTTTAGCCAAAAACC
GTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAATATTTTTCCTCAA
TTTTTGGCCAAAATACTCAAAAAAAATATATAATTCAAATCCAAAACGTTTGAAAGGCTTTTGAC
ATTTCTAATATCA
Found at i:1606 original size:2 final size:2
Alignment explanation
Indices: 1599--1629 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1589 CAAAATACTC
*
1599 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1630 AATCAACACC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3932 original size:40 final size:40
Alignment explanation
Indices: 3866--4055 Score: 238
Period size: 40 Copynumber: 4.8 Consensus size: 40
3856 TATTAAACGG
* * *
3866 CTCTCCGCAGTGATGCTCCCCACACACAACGCAGACACAA
1 CTCTCGGCAGTGATGCTCCCCACACACAACGCAGACGCGA
* * *
3906 GTCTCGGCAGTGATGCTCCCCGCACACATCGCAGACGCGA
1 CTCTCGGCAGTGATGCTCCCCACACACAACGCAGACGCGA
* *
3946 CTCTCGGAAGTGATGCTCCCCGCACACAACGCAGACGCGA
1 CTCTCGGCAGTGATGCTCCCCACACACAACGCAGACGCGA
** * * * *
3986 CTCTCAACAGTGATGCT-CACACACACATCGCAAACGTGA
1 CTCTCGGCAGTGATGCTCCCCACACACAACGCAGACGCGA
*
4025 CTCTCGGAAGTGATGCTCCCCACACACAACG
1 CTCTCGGCAGTGATGCTCCCCACACACAACG
4056 GAAGATTATT
Statistics
Matches: 127, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 31 0.24
40 96 0.76
ACGTcount: A:0.27, C:0.38, G:0.21, T:0.15
Consensus pattern (40 bp):
CTCTCGGCAGTGATGCTCCCCACACACAACGCAGACGCGA
Found at i:4051 original size:79 final size:80
Alignment explanation
Indices: 3874--4055 Score: 267
Period size: 79 Copynumber: 2.3 Consensus size: 80
3864 GGCTCTCCGC
* ** * *
3874 AGTGATGCTCCCCACACACAACGCAGACACAAGTCTCGGCAGTGATGCTCCCCGCACACATCGCA
1 AGTGATGCTCCCCACACACAACGCAGACACAACTCTCAACAGTGATGCTCCACACACACATCGCA
*
3939 GACGCGACTCTCGGA
66 AACGCGACTCTCGGA
* * *
3954 AGTGATGCTCCCCGCACACAACGCAGACGCGACTCTCAACAGTGATGCT-CACACACACATCGCA
1 AGTGATGCTCCCCACACACAACGCAGACACAACTCTCAACAGTGATGCTCCACACACACATCGCA
*
4018 AACGTGACTCTCGGA
66 AACGCGACTCTCGGA
4033 AGTGATGCTCCCCACACACAACG
1 AGTGATGCTCCCCACACACAACG
4056 GAAGATTATT
Statistics
Matches: 91, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
79 48 0.53
80 43 0.47
ACGTcount: A:0.28, C:0.37, G:0.21, T:0.14
Consensus pattern (80 bp):
AGTGATGCTCCCCACACACAACGCAGACACAACTCTCAACAGTGATGCTCCACACACACATCGCA
AACGCGACTCTCGGA
Found at i:4341 original size:15 final size:15
Alignment explanation
Indices: 4321--4370 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
4311 TCAAGTTAAA
4321 AAGTTATAATATTTT
1 AAGTTATAATATTTT
*
4336 AAGTTATAATTTATTATA
1 AAGTTATAA--TATT-TT
*
4354 AAGTTATTATATTTT
1 AAGTTATAATATTTT
4369 AA
1 AA
4371 CTTCGAACTC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 12 0.41
16 4 0.14
17 4 0.14
18 9 0.31
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (15 bp):
AAGTTATAATATTTT
Found at i:11299 original size:12 final size:12
Alignment explanation
Indices: 11282--11307 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11272 ATTCAATAAT
11282 AGCCTAAAATCA
1 AGCCTAAAATCA
11294 AGCCTAAAATCA
1 AGCCTAAAATCA
11306 AG
1 AG
11308 GGATTTACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.23, G:0.12, T:0.15
Consensus pattern (12 bp):
AGCCTAAAATCA
Found at i:11394 original size:40 final size:40
Alignment explanation
Indices: 11346--11462 Score: 216
Period size: 40 Copynumber: 2.9 Consensus size: 40
11336 TAACTAGGGA
11346 CTAAACCTGGATTTAATTTCTTATCTTAATTATTAGGGGG
1 CTAAACCTGGATTTAATTTCTTATCTTAATTATTAGGGGG
11386 CTAAACCTGGATTTAATTTCTTATCTTAATTATTAGGGGG
1 CTAAACCTGGATTTAATTTCTTATCTTAATTATTAGGGGG
* *
11426 CTAAACCTGGATTTAATTTATTTTCTTAATTATTAGG
1 CTAAACCTGGATTTAATTTCTTATCTTAATTATTAGG
11463 AGGGACAAAT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 75 1.00
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.44
Consensus pattern (40 bp):
CTAAACCTGGATTTAATTTCTTATCTTAATTATTAGGGGG
Found at i:13559 original size:29 final size:29
Alignment explanation
Indices: 13517--13572 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
13507 TACAAGTTTA
*
13517 CAACACCACAATTACAAGTTTTCAACAAT
1 CAACACCACAATTACAAGCTTTCAACAAT
*
13546 CAACGCCACAATTACAAGCTTTCAACA
1 CAACACCACAATTACAAGCTTTCAACA
13573 CCGTACAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.43, C:0.30, G:0.05, T:0.21
Consensus pattern (29 bp):
CAACACCACAATTACAAGCTTTCAACAAT
Found at i:17549 original size:2 final size:2
Alignment explanation
Indices: 17542--17573 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17532 TAGAGTTTGG
17542 TA TA 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 TA TA
17574 ATTTGCGACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20593 original size:24 final size:24
Alignment explanation
Indices: 20561--20607 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
20551 TTTGAGGTAC
20561 TTTAAAAGAGTCTGAAATGTTTGT
1 TTTAAAAGAGTCTGAAATGTTTGT
20585 TTTAAAAGAGTCTGAAATGTTTG
1 TTTAAAAGAGTCTGAAATGTTTG
20608 CTTCTGATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.40
Consensus pattern (24 bp):
TTTAAAAGAGTCTGAAATGTTTGT
Found at i:23941 original size:19 final size:20
Alignment explanation
Indices: 23917--23974 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
23907 CTGTTTAACA
23917 ACTGTACAGATGAGATTA-C
1 ACTGTACAGATGAGATTAGC
* * *
23936 ACTGTACATATTAGATTAGGT
1 ACTGTACAGATGAGATTA-GC
23957 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
23975 TTAGAGCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (20 bp):
ACTGTACAGATGAGATTAGC
Found at i:34146 original size:23 final size:23
Alignment explanation
Indices: 34115--34158 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
34105 GTATCCGTAC
* *
34115 AAAGGAAAAGAAAGGAAAATGAA
1 AAAGAAAAAGAAAAGAAAATGAA
34138 AAAGAAAAAGAAAAGAAAATG
1 AAAGAAAAAGAAAAGAAAATG
34159 TTGTGAGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.05
Consensus pattern (23 bp):
AAAGAAAAAGAAAAGAAAATGAA
Found at i:43488 original size:13 final size:13
Alignment explanation
Indices: 43466--43497 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
43456 TTTTGCCACA
*
43466 TGGCCGGGTGATG
1 TGGCCAGGTGATG
43479 TGGCCAGGTGATG
1 TGGCCAGGTGATG
43492 TGGCCA
1 TGGCCA
43498 AAGTTAACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.12, C:0.19, G:0.47, T:0.22
Consensus pattern (13 bp):
TGGCCAGGTGATG
Found at i:44487 original size:12 final size:12
Alignment explanation
Indices: 44472--44513 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
44462 AAATCATCGC
44472 TATCATAATTGA
1 TATCATAATTGA
* * *
44484 TATCATCATCGC
1 TATCATAATTGA
44496 TATCATAATTGA
1 TATCATAATTGA
44508 TATCAT
1 TATCAT
44514 CATCGTCATC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.40
Consensus pattern (12 bp):
TATCATAATTGA
Found at i:44496 original size:24 final size:24
Alignment explanation
Indices: 44464--44518 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
44454 CATCGTTAAA
44464 ATCATCGCTATCATAATTGATATC
1 ATCATCGCTATCATAATTGATATC
44488 ATCATCGCTATCATAATTGATATC
1 ATCATCGCTATCATAATTGATATC
44512 ATCATCG
1 ATCATCG
44519 TCATCGTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (24 bp):
ATCATCGCTATCATAATTGATATC
Found at i:44567 original size:24 final size:24
Alignment explanation
Indices: 44540--44598 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
44530 ATTAACGTTA
44540 TCATCATCGTTAACCCGCCGGTGT
1 TCATCATCGTTAACCCGCCGGTGT
44564 TCATCATCGTTAACCCGCCGGTGT
1 TCATCATCGTTAACCCGCCGGTGT
44588 TCATCATCGTT
1 TCATCATCGTT
44599 GTAATGTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.17, C:0.32, G:0.19, T:0.32
Consensus pattern (24 bp):
TCATCATCGTTAACCCGCCGGTGT
Found at i:53904 original size:15 final size:15
Alignment explanation
Indices: 53884--53914 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
53874 TTTGATACGT
53884 CGGATAACAGAGTCA
1 CGGATAACAGAGTCA
53899 CGGATAACAGAGTCA
1 CGGATAACAGAGTCA
53914 C
1 C
53915 AGACAATTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.13
Consensus pattern (15 bp):
CGGATAACAGAGTCA
Found at i:56583 original size:24 final size:23
Alignment explanation
Indices: 56524--56587 Score: 110
Period size: 23 Copynumber: 2.7 Consensus size: 23
56514 ATTGGAATAA
56524 AAAAAAATTGATATGATATGAAT
1 AAAAAAATTGATATGATATGAAT
*
56547 AAAAAAATTGATATGGTATGAAT
1 AAAAAAATTGATATGATATGAAT
56570 AAAAGAAATTGATATGAT
1 AAAA-AAATTGATATGAT
56588 GGTACAAGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
23 26 0.68
24 12 0.32
ACGTcount: A:0.55, C:0.00, G:0.16, T:0.30
Consensus pattern (23 bp):
AAAAAAATTGATATGATATGAAT
Found at i:56987 original size:60 final size:60
Alignment explanation
Indices: 56900--57062 Score: 211
Period size: 60 Copynumber: 2.7 Consensus size: 60
56890 ACTAATTGTT
** ** * *
56900 CAAATAAGGATCTAATGTTTATT-AAAATATTCAAATAAGGGTTCGATCTTTTAAATTGAC
1 CAAATAAGGGCCTAATG-TTATTGAAAATGCTCAAATAAGGGTCCGATATTTTAAATTGAC
* *
56960 CAAATAAGGGCCTAATGTTATTGAAAATGCTCAAATAAGGGCCCGATATTTTAATTTGAC
1 CAAATAAGGGCCTAATGTTATTGAAAATGCTCAAATAAGGGTCCGATATTTTAAATTGAC
* * *
57020 CAAATAAGGGCCTAACGTCATCGAAAATGCTCAAATAAGGGTC
1 CAAATAAGGGCCTAATGTTATTGAAAATGCTCAAATAAGGGTC
57063 TGGCGTCAGT
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
59 5 0.06
60 85 0.94
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (60 bp):
CAAATAAGGGCCTAATGTTATTGAAAATGCTCAAATAAGGGTCCGATATTTTAAATTGAC
Found at i:56998 original size:31 final size:31
Alignment explanation
Indices: 56960--57060 Score: 100
Period size: 31 Copynumber: 3.3 Consensus size: 31
56950 TTAAATTGAC
56960 CAAATAAGGGCCTAATGTTATTGAAAATGCT
1 CAAATAAGGGCCTAATGTTATTGAAAATGCT
** * **
56991 CAAATAAGGGCCCGATATT-TT-AATTTGAC-
1 CAAATAAGGGCCTAATGTTATTGAAAATG-CT
* * *
57020 CAAATAAGGGCCTAACGTCATCGAAAATGCT
1 CAAATAAGGGCCTAATGTTATTGAAAATGCT
57051 CAAATAAGGG
1 CAAATAAGGG
57061 TCTGGCGTCA
Statistics
Matches: 53, Mismatches: 13, Indels: 8
0.72 0.18 0.11
Matches are distributed among these distances:
29 18 0.34
30 5 0.09
31 30 0.57
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.25
Consensus pattern (31 bp):
CAAATAAGGGCCTAATGTTATTGAAAATGCT
Found at i:57031 original size:29 final size:29
Alignment explanation
Indices: 56931--57031 Score: 96
Period size: 29 Copynumber: 3.4 Consensus size: 29
56921 TTAAAATATT
** *
56931 CAAATAAGGGTTCGATCTTTTAAATTGAC
1 CAAATAAGGGCCCGATATTTTAAATTGAC
** * *
56960 CAAATAAGGGCCTAATGTTATTGAAAATG-C
1 CAAATAAGGGCCCGATATT-TT-AAATTGAC
*
56990 TCAAATAAGGGCCCGATATTTTAATTTGAC
1 -CAAATAAGGGCCCGATATTTTAAATTGAC
57020 CAAATAAGGGCC
1 CAAATAAGGGCC
57032 TAACGTCATC
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
29 30 0.53
30 6 0.11
31 21 0.37
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.29
Consensus pattern (29 bp):
CAAATAAGGGCCCGATATTTTAAATTGAC
Found at i:75936 original size:2 final size:2
Alignment explanation
Indices: 75929--75956 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
75919 TTCTGAGAAG
75929 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
75957 ACATTGGGGT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:76419 original size:37 final size:37
Alignment explanation
Indices: 76378--76448 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
76368 TGGTAAGTAA
76378 TTTTTTTTTTGGCTT-AGAGATAAGCAAAATCTTTTT
1 TTTTTTTTTTGGCTTAAGAGATAAGCAAAATCTTTTT
* * *
76414 TTTTTTTTTTGGGTTAAGAGGTAAGTAAAATCTTT
1 TTTTTTTTTTGGCTTAAGAGATAAGCAAAATCTTT
76449 GATTCTCTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
36 14 0.45
37 17 0.55
ACGTcount: A:0.25, C:0.06, G:0.17, T:0.52
Consensus pattern (37 bp):
TTTTTTTTTTGGCTTAAGAGATAAGCAAAATCTTTTT
Found at i:79257 original size:37 final size:37
Alignment explanation
Indices: 79207--79282 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
79197 AACTGATGAA
79207 AAGCAGAGACTGTAATATTCATGCAGTGCCAATTGCT
1 AAGCAGAGACTGTAATATTCATGCAGTGCCAATTGCT
79244 AAGCAGAGACTGTAATATTCATGCAGTGCCAATTGCT
1 AAGCAGAGACTGTAATATTCATGCAGTGCCAATTGCT
79281 AA
1 AA
79283 ATTCCAATCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (37 bp):
AAGCAGAGACTGTAATATTCATGCAGTGCCAATTGCT
Found at i:83430 original size:49 final size:49
Alignment explanation
Indices: 83358--83457 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
83348 CATTGCCTTG
83358 ATAAGAAGCTTCATCTTTGTTTTCTATTTCTATTCATAATTCAGCTTAC
1 ATAAGAAGCTTCATCTTTGTTTTCTATTTCTATTCATAATTCAGCTTAC
83407 ATAAGAAGCTTCATCTTTGTTTTCTATTTCTATTCATAATTCAGCTTAC
1 ATAAGAAGCTTCATCTTTGTTTTCTATTTCTATTCATAATTCAGCTTAC
83456 AT
1 AT
83458 TATAACTTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.47
Consensus pattern (49 bp):
ATAAGAAGCTTCATCTTTGTTTTCTATTTCTATTCATAATTCAGCTTAC
Found at i:91183 original size:25 final size:25
Alignment explanation
Indices: 91150--91200 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
91140 CTCCTTAGCT
91150 TTTTTCTCTTGAGTGAGTGATTTTC
1 TTTTTCTCTTGAGTGAGTGATTTTC
*
91175 TTTTTCTCTTTAGTGAGTGATTTTC
1 TTTTTCTCTTGAGTGAGTGATTTTC
91200 T
1 T
91201 CTTCAGTGAG
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:0.12, C:0.12, G:0.18, T:0.59
Consensus pattern (25 bp):
TTTTTCTCTTGAGTGAGTGATTTTC
Found at i:96242 original size:69 final size:69
Alignment explanation
Indices: 96128--96281 Score: 188
Period size: 69 Copynumber: 2.2 Consensus size: 69
96118 AATAGATGCT
* * * * *
96128 GGAAGAGC-TCCCCAATATAAGGTCTGACCCGGCTCGACTCTGGAGTAGT-AGGGGCCAATGTGG
1 GGAAGAGCTTCCCCAATACAAGGTCTGACCCGGCTCAACTCCGGAGTAGTCA-AGGCCAATGTAG
96191 TCACG
65 TCACG
* *
96196 GGAAGAGCTTCCCCAATACAAGTTTTG-CCCTGGCTCAACTCCGGAGTAGTCAAGGCCAATGTAG
1 GGAAGAGCTTCCCCAATACAAGGTCTGACCC-GGCTCAACTCCGGAGTAGTCAAGGCCAATGTAG
*
96260 TCACT
65 TCACG
*
96265 GGAAGAGCTTACCCAAT
1 GGAAGAGCTTCCCCAAT
96282 GTAAGGTCCG
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
68 11 0.15
69 62 0.84
70 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.27, T:0.21
Consensus pattern (69 bp):
GGAAGAGCTTCCCCAATACAAGGTCTGACCCGGCTCAACTCCGGAGTAGTCAAGGCCAATGTAGT
CACG
Found at i:126120 original size:2 final size:2
Alignment explanation
Indices: 126113--126140 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
126103 CTTTCATGAC
126113 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
126141 GGTAATTAAA
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):
AT
Found at i:126239 original size:16 final size:17
Alignment explanation
Indices: 126208--126242 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
126198 GATGAGTCTA
*
126208 AATTTATAATTTTTTTT
1 AATTTATAAGTTTTTTT
126225 AATTT-TAAGTTTTTTT
1 AATTTATAAGTTTTTTT
126241 AA
1 AA
126243 GTGAGAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
AATTTATAAGTTTTTTT
Found at i:126588 original size:13 final size:13
Alignment explanation
Indices: 126570--126596 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
126560 AAACAACTAA
126570 AAAGCACTTCTGG
1 AAAGCACTTCTGG
126583 AAAGCACTTCTGG
1 AAAGCACTTCTGG
126596 A
1 A
126597 TTTTCCGTTT
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:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (13 bp):
AAAGCACTTCTGG
Done.