Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018281.1 Corchorus olitorius cultivar O-4 contig18314, 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: 13373
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:112 original size:13 final size:12
Alignment explanation
Indices: 76--122 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
66 TCAATCTTTA
*
76 TATATATTGATAA
1 TATATATT-ATAT
*
89 TA-ATGTTATAT
1 TATATATTATAT
100 TATATTATTATAT
1 TATA-TATTATAT
113 TATATATTAT
1 TATATATTAT
123 CAATAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:274 original size:17 final size:18
Alignment explanation
Indices: 251--326 Score: 95
Period size: 17 Copynumber: 4.4 Consensus size: 18
241 ATCAAAATCA
251 AACCCGAGCCCGAACCCG
1 AACCCGAGCCCGAACCCG
269 -ACCCGAGCCCGAACCC-
1 AACCCGAGCCCGAACCCG
**
285 TTCCCGAGCCCGAACCCG
1 AACCCGAGCCCGAACCCG
* *
303 AACCCTA-CCCGAGCCCG
1 AACCCGAGCCCGAACCCG
320 AACCCGA
1 AACCCGA
327 AAATACCCGA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
17 46 0.92
18 4 0.08
ACGTcount: A:0.25, C:0.51, G:0.20, T:0.04
Consensus pattern (18 bp):
AACCCGAGCCCGAACCCG
Found at i:296 original size:23 final size:23
Alignment explanation
Indices: 280--327 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
270 CCCGAGCCCG
*
280 AACCCTTCCCGAGCCCGAACCCG
1 AACCCTACCCGAGCCCGAACCCG
303 AACCCTACCCGAGCCCGAACCCG
1 AACCCTACCCGAGCCCGAACCCG
326 AA
1 AA
328 AATACCCGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.50, G:0.17, T:0.06
Consensus pattern (23 bp):
AACCCTACCCGAGCCCGAACCCG
Found at i:337 original size:16 final size:16
Alignment explanation
Indices: 316--407 Score: 91
Period size: 16 Copynumber: 5.8 Consensus size: 16
306 CCTACCCGAG
316 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
332 CCCGAACCCG-ACATAA
1 CCCGAACCCGAAAAT-A
* *
348 CCTGAGCCCGAAAATA
1 CCCGAACCCGAAAATA
*
364 CCCGAACCCGACTTAAT-
1 CCCGAACCCGA--AAATA
*
381 -CCGAGCCCGAAAATA
1 CCCGAACCCGAAAATA
396 CCCGAACCCGAA
1 CCCGAACCCGAA
408 CCCGCCCGAG
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
14 3 0.05
15 3 0.05
16 48 0.80
17 3 0.05
18 3 0.05
ACGTcount: A:0.37, C:0.39, G:0.15, T:0.09
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:342 original size:6 final size:6
Alignment explanation
Indices: 251--327 Score: 70
Period size: 6 Copynumber: 13.3 Consensus size: 6
241 ATCAAAATCA
* * ** *
251 AACCCG AGCCCG AACCCG -ACCCG AGCCCG AACCC- TTCCCG AGCCCG
1 AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG
* *
297 AACCCG AACCC- TACCCG AGCCCG AACCCG AA
1 AACCCG AACCCG AACCCG AACCCG AACCCG AA
328 AATACCCGAA
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
5 12 0.22
6 43 0.78
ACGTcount: A:0.26, C:0.51, G:0.19, T:0.04
Consensus pattern (6 bp):
AACCCG
Found at i:363 original size:32 final size:32
Alignment explanation
Indices: 317--406 Score: 146
Period size: 32 Copynumber: 2.8 Consensus size: 32
307 CTACCCGAGC
*
317 CCGAACCCGAAAATACCCGAACCCGACATAA-
1 CCGAGCCCGAAAATACCCGAACCCGACATAAT
*
348 CCTGAGCCCGAAAATACCCGAACCCGACTTAAT
1 CC-GAGCCCGAAAATACCCGAACCCGACATAAT
381 CCGAGCCCGAAAATACCCGAACCCGA
1 CCGAGCCCGAAAATACCCGAACCCGA
407 ACCCGCCCGA
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
31 2 0.04
32 51 0.93
33 2 0.04
ACGTcount: A:0.37, C:0.39, G:0.16, T:0.09
Consensus pattern (32 bp):
CCGAGCCCGAAAATACCCGAACCCGACATAAT
Found at i:417 original size:32 final size:31
Alignment explanation
Indices: 298--421 Score: 122
Period size: 32 Copynumber: 3.8 Consensus size: 31
288 CCGAGCCCGA
* *
298 ACCCGAACCCTACCCGAGCCCGAACCCGAAAAT
1 ACCCGAACCCGACCC-A-CCCGAGCCCGAAAAT
** *
331 ACCCGAACCCGACATAACCTGAGCCCGAAAAT
1 ACCCGAACCCGAC-CCACCCGAGCCCGAAAAT
** *
363 ACCCGAACCCGACTTAATCCGAGCCCGAAAAT
1 ACCCGAACCCGAC-CCACCCGAGCCCGAAAAT
*
395 ACCCGAACCCGAACCCGCCCGAGCCCG
1 ACCCGAACCCG-ACCCACCCGAGCCCG
422 CCCAATTGCC
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
32 62 0.81
33 15 0.19
ACGTcount: A:0.32, C:0.44, G:0.17, T:0.07
Consensus pattern (31 bp):
ACCCGAACCCGACCCACCCGAGCCCGAAAAT
Found at i:1361 original size:658 final size:658
Alignment explanation
Indices: 437--1984 Score: 1773
Period size: 658 Copynumber: 2.3 Consensus size: 658
427 TTGCCAGCTC
** * **
437 TACACGATTTCGGCTAAAATTTTGCAAAAAATGACAAAAAAAAAATTTCCTCAATTTTTTACTAA
1 TACACGATTTCGGCTAAAATTTTGCAAAAAATGAC-ACGAAAAATTTTCCTCAATTTTGGA-TAA
* *
502 AATACTCATGAAATATATATAATTTAACACCAAAAAAATTGGAGGACTTTTCACGCTTTTAATAT
64 AATACTCATAAAATATATATAATTTAACGCCAAAAAAATTGGA-GACTTTTCACGCTTTTAATAT
** *
567 CGTTTTTCATATTTTTTGAATTAATTTCTAATTAAATTGAAACAAGATTCAGATGCTTGTAAAAA
128 CGTTTTTCATATTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAA
* * * * ** * * * *
632 AATTATTAAATGCAGTGTGGTTGAGATTTGATTAGATGAATATGGATATCGCAAGGAGTCTTAGT
193 AAATCTTAAATCCAATGTTCTTGAGATTTGATTAAATGAATATAGATATCGCAAGGAGTCTGAGC
*
697 GCCAAAAATCATGCAAAACTGA-CTTG-GGACCCTAGAA-AGCGTTTTTAGCCAAAAAC-CG-TG
258 GCCAAAAATCATGCAAAACTGAGC-CGAGGACCC-AGAACA-CGTTTTTAGCCAAAAACGCGATG
* **
757 GTGATTATTACACAATTTCAGCTAAAAATTTGCAAAAATTGAAAGGAAAGATATTTCCTCAACTT
320 GTG-TTATTACACAATTTCAGCTAAAAATTTGCAAAAATCGAAACAAAAGATATTTCCTCAACTT
* ** *
822 TTAGCCATAATACTCATAAATTATATATAATTAAATGCCAAAAAAAATTGAAGGGCTTTTCACGA
384 TTAGCCAAAATACTCATAAAAAATATATAATTAAATGCC-AAAAAAATTGAAGGGCTTGTCACGA
* * ** * *
887 TTTTAATATCGTTTTTCATATTTTTTCTGAATTAA-TTCTTAATTAAATCAAAACCATATTCAGA
448 TTCTAATATAGTTTTTCATA-TTTTTCCAAATTAATTTC-TAATTAAATCAAAACAAGATTCAGA
* * * *
951 TGCTCGT-AAAACAAATCCTTAAATGCAATGTGGCT-ATGATTTTATTAGATGAATATAGATATT
511 TGCTCGTAAAAACAAATCCTTAAATCCAATGTGACTGA-GATTTGATCAGATGAATATAGATATT
* * * *
1014 TTAAGTAGTGTCGGCGCCAAAAATCATG-AAAACTGAGGCGGGGCCCCGA-AACACATTTTTAGT
575 TCAAATAGTCTCGGAGCCAAAAATCATGCAAAACTGAGGC-GGG-CCCGACAACACATTTTTAG-
*
1077 C-ATA-ACC-G-TGTTAGTTAG
637 CAAAACACCGGATGTTAGTTAG
** *
1095 TACACGATTTTAGCTAAAATTTTGCAAAAAATGACCCGAAAAATTTTTCCTCAATTTTGGATAAA
1 TACACGATTTCGGCTAAAATTTTGCAAAAAATGACACGAAAAA-TTTTCCTCAATTTTGGATAAA
* **
1160 ATACTCATAAAATATATATAATTTAATGCCAAAATTATTGGAGAACTTTTCACGCTTTTAATATC
65 ATACTCATAAAATATATATAATTTAACGCCAAAAAAATTGGAG-ACTTTTCACGCTTTTAATATC
* * * * * *
1225 ATTTTTCATATTATTCAGAGTTCATTTCTTATTATATCGAAACAAGAATCAGATGCTTGTAAAAA
129 GTTTTTCATATT-TTCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAA
*
1290 AAATCTTAAATCCAATGTTCTTGAGATTTGATTAAATGAATATAGATATCTCAAGGAGTCCTGA-
193 AAATCTTAAATCCAATGTTCTTGAGATTTGATTAAATGAATATAGATATCGCAAGGAGT-CTGAG
* * * * *
1354 CGCCAAAAATCATGGAAAACTGAGCCGAGGTCGCAGAACACTTTTTTAGCCAAAAACTGTGATGG
257 CGCCAAAAATCATGCAAAACTGAGCCGAGGACCCAGAACACGTTTTTAGCCAAAAAC-GCGATGG
* * * ** * *
1419 TGTTATTACACGATTTCAGCTAAAATTTTGTAAAAATCGACCCAAAAGATATTTTCTCAATTTTT
321 TGTTATTACACAATTTCAGCTAAAAATTTGCAAAAATCGAAACAAAAGATATTTCCTCAACTTTT
* * * * * ** *
1484 GGCTAAAATACTCATAAAAAATATATAATTCAATGTCAAAAAGATTTTAGGGCTTGTGACGATTC
386 AGCCAAAATACTCATAAAAAATATATAATTAAATGCCAAAAAAATTGAAGGGCTTGTCACGATTC
* * *
1549 TAATATAGTTTTTCCTATTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATTCTC
451 TAATATAGTTTTTCATATTTTTCCAAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTC
1614 GTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGATCAGATGAATATAGATATTTCAAAT
516 GTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGATCAGATGAATATAGATATTTCAAAT
* * * * *** *
1679 AGTCTCGGAGCCAAAAATCATGCAAAATTGAGTCGGGTCCTACAGGGCGTTTTTAGCGAAAACAC
581 AGTCTCGGAGCCAAAAATCATGCAAAACTGAGGCGGGCCCGACAACACATTTTTAGC-AAAACAC
*
1744 CGTGATTGTTTGTTAG
645 CG-GA-TGTTAGTTAG
* * * * * *
1760 TATACAATTTCGGCTAAAATTTTGCAAAAATTGACACGAAAGATTCTCCTCAATTTTTGGCTAAA
1 TACACGATTTCGGCTAAAATTTTGCAAAAAATGACACGAAAAATTTTCCTCAA-TTTTGGATAAA
* * * *
1825 ATATTCATAAAA-ATATATAATTTAACGTCAAAAAGATTGGATGGCTTTTCTACGCTTTTAATAT
65 ATACTCATAAAATATATATAATTTAACGCCAAAAAAATTGGA-GACTTTTC-ACGCTTTTAATAT
* * * *
1889 CGTATTTCTTATTTTTTCTA-AATTAATTTCTAATTAAATCGAAACAAGATTCAGGTGCTCGTAA
128 CGT-TTT-TCATATTTTC-AGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAA
1953 AAACAAATTCTTAAATCCAATGTTGC-TGAGAT
190 AAA-AAA-TCTTAAATCCAATGTT-CTTGAGAT
1985 AATTGGTTAG
Statistics
Matches: 746, Mismatches: 113, Indels: 52
0.82 0.12 0.06
Matches are distributed among these distances:
656 1 0.00
657 78 0.10
658 227 0.30
659 135 0.18
660 96 0.13
661 8 0.01
663 1 0.00
664 40 0.05
665 82 0.11
666 46 0.06
667 9 0.01
668 22 0.03
669 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (658 bp):
TACACGATTTCGGCTAAAATTTTGCAAAAAATGACACGAAAAATTTTCCTCAATTTTGGATAAAA
TACTCATAAAATATATATAATTTAACGCCAAAAAAATTGGAGACTTTTCACGCTTTTAATATCGT
TTTTCATATTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAAAAA
TCTTAAATCCAATGTTCTTGAGATTTGATTAAATGAATATAGATATCGCAAGGAGTCTGAGCGCC
AAAAATCATGCAAAACTGAGCCGAGGACCCAGAACACGTTTTTAGCCAAAAACGCGATGGTGTTA
TTACACAATTTCAGCTAAAAATTTGCAAAAATCGAAACAAAAGATATTTCCTCAACTTTTAGCCA
AAATACTCATAAAAAATATATAATTAAATGCCAAAAAAATTGAAGGGCTTGTCACGATTCTAATA
TAGTTTTTCATATTTTTCCAAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAA
AACAAATCCTTAAATCCAATGTGACTGAGATTTGATCAGATGAATATAGATATTTCAAATAGTCT
CGGAGCCAAAAATCATGCAAAACTGAGGCGGGCCCGACAACACATTTTTAGCAAAACACCGGATG
TTAGTTAG
Found at i:1599 original size:331 final size:327
Alignment explanation
Indices: 437--1998 Score: 1499
Period size: 331 Copynumber: 4.7 Consensus size: 327
427 TTGCCAGCTC
* * * * **
437 TACACGATTTCGGCTAAAATTTTGCAAAAAATGACAAAAAAAAAATTTCCTCAATTTTTTACTAA
1 TACACGATTTCAGCTAAAATTTTG-AAAAAATGACACAAAAGATATTTCCTCAATTTTTGGCTAA
* ** *
502 AATACTCATGAAATATATATAATTTAACACCAAAAAAATTGGAGGACTTTTCACGCTTTTAATAT
65 AATACTCATAAAATATATATAATTTAATGCCAAAAAAATTGGAGGGCTTTTCACGCTTTTAATAT
* * *
567 CGTTTTTCATATTTTT-TGAATTAATTTCTAATTAAATTGAAACAAGATTCAGATGCTTGTAAAA
130 CGTTTTTCATATTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
* * * * * * * *
631 AAATTATTAAATGCAGTGTGGTTGAGATTTGATTAGATGAATATGGATATCGCAAGGAGTCTTAG
195 AAAATCTTAAATCCAATGT-GCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTGA-
* * *
696 TGCCAAAAATCATGCAAAACTGA-CTTGGGACCCTAGAA-AGCGTTTTTAGCCAAAAACC--GTG
258 CGCCAAAAATCATGCAAAACTGAGC-CGGGTCCCTAGAACA-CGTTTTTAGCCAAAAACCGTGTG
*
757 GTGATTAT
321 GTG-TTAG
* * * * ** * * * *
765 TACACAATTTCAGCTAAAAATTTGCAAAAATTGAAAGGAAAGATATTTCCTCAACTTTTAGCCAT
1 TACACGATTTCAGCTAAAATTTTG-AAAAAATGACACAAAAGATATTTCCTCAATTTTTGGCTAA
* * * *
830 AATACTCATAAATTATATATAATTAAATGCCAAAAAAAATTGAAGGGCTTTTCACGATTTTAATA
65 AATACTCATAAAATATATATAATTTAATGCC-AAAAAAATTGGAGGGCTTTTCACGCTTTTAATA
* * * *
895 TCGTTTTTCATATTTTTTCTGAATTAA-TTCTTAATTAAATCAAAACCATATTCAGATGCTCGTA
129 TCGTTTTTCATA-TTTTTCTAAATTAATTTC-TAATTAAATCGAAACAAGATTCAGATGCTCGTA
* * * * * *
959 AAACAAATCCTTAAATGCAATGTGGCT-ATGATTTTATTAGATGAATATAGATATTTTAAGTAGT
192 AAAAAAAT-CTTAAATCCAATGT-GCTGA-GATTTGATTAGATGAATATAGATATCTCAAGGAGT
* * * * * * * *
1023 GTCGGCGCCAAAAATCATG-AAAACTGAGGCGGGGCCC-CGAAACACATTTTTAGTC-ATAACCG
254 CT-GACGCCAAAAATCATGCAAAACTGAGCCGGGTCCCTAG-AACACGTTTTTAGCCAAAAACCG
1085 TGT--TAGTTAG
317 TGTGGT-GTTAG
* * * *
1095 TACACGATTTTAGCTAAAATTTTGCAAAAAATGACCCGAAAA-ATTTTTCCTCAA-TTTTGGATA
1 TACACGATTTCAGCTAAAATTTTG-AAAAAATGACAC-AAAAGATATTTCCTCAATTTTTGGCTA
** **
1158 AAATACTCATAAAATATATATAATTTAATGCCAAAATTATTGGAGAACTTTTCACGCTTTTAATA
64 AAATACTCATAAAATATATATAATTTAATGCCAAAAAAATTGGAGGGCTTTTCACGCTTTTAATA
* * * * * * * *
1223 TCATTTTTCATATTATTC-AGAGTTCATTTCTTATTATATCGAAACAAGAATCAGATGCTTGTAA
129 TCGTTTTTCATATTTTTCTA-AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
* *
1287 AAAAAATCTTAAATCCAATGTTCTTGAGATTTGATTAAATGAATATAGATATCTCAAGGAGTCCT
193 AAAAAATCTTAAATCCAATGTGC-TGAGATTTGATTAGATGAATATAGATATCTCAAGGAGT-CT
* * * *
1352 GACGCCAAAAATCATGGAAAACTGAGCCGAGGTCGC-AGAACACTTTTTTAGCCAAAAACTGTGA
256 GACGCCAAAAATCATGCAAAACTGAGCCG-GGTCCCTAGAACACGTTTTTAGCCAAAAACCGTG-
*
1416 TGGTGTTAT
319 TGGTGTTAG
* * *
1425 TACACGATTTCAGCTAAAATTTTGTAAAAATCGACCCAAAAGATATTTTCTCAATTTTTGGCTAA
1 TACACGATTTCAGCTAAAATTTTGAAAAAAT-GACACAAAAGATATTTCCTCAATTTTTGGCTAA
* * * * ** * * * *
1490 AATACTCATAAAAAATATATAATTCAATGTCAAAAAGATTTTAGGGCTTGTGACGATTCTAATAT
65 AATACTCATAAAATATATATAATTTAATGCCAAAAAAATTGGAGGGCTTTTCACGCTTTTAATAT
* * * *
1555 AGTTTTTCCTATTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATTCTCGTAAAA
130 CGTTTTTCATATTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
* * **
1620 ACAAATCCTTAAATCCAATGTGACTGAGATTTGATCAGATGAATATAGATATTTCAAATAGTCTC
195 A-AAAT-CTTAAATCCAATGTG-CTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCT-
* * * *** *
1685 GGA-GCCAAAAATCATGCAAAATTGAGTCGGGT-CCTACAGGGCGTTTTTAGCGAAAACACCGTG
256 -GACGCCAAAAATCATGCAAAACTGAGCCGGGTCCCTAGAACACGTTTTTAGCCAAAA-ACCGTG
*
1748 ATTGTTTGTTAG
319 --TG-GTGTTAG
* * * * * *
1760 TATACAATTTCGGCTAAAATTTTGCAAAAATTGACACGAAAGAT-TCTCCTCAATTTTTGGCTAA
1 TACACGATTTCAGCTAAAATTTTG-AAAAAATGACACAAAAGATATTTCCTCAATTTTTGGCTAA
* * * * *
1824 AATATTCATAAAA-ATATATAATTTAACGTCAAAAAGATTGGATGGCTTTTCTACGCTTTTAATA
65 AATACTCATAAAATATATATAATTTAATGCCAAAAAAATTGGAGGGCTTTTC-ACGCTTTTAATA
* * *
1888 TCGTATTTCTTATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGGTGCTCGTAA
129 TCGTTTTTCATA-TTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
*
1953 AAACAAATTCTTAAATCCAATGTTGCTGAGATAATTGGTTAGATGA
193 AAA-AAA-TCTTAAATCCAATG-TGCTGAGAT--TTGATTAGATGA
1999 TTTAAAGTAT
Statistics
Matches: 1011, Mismatches: 178, Indels: 81
0.80 0.14 0.06
Matches are distributed among these distances:
325 1 0.00
326 59 0.06
327 68 0.07
328 130 0.13
329 88 0.09
330 101 0.10
331 188 0.19
332 86 0.09
333 106 0.10
334 54 0.05
335 112 0.11
336 8 0.01
337 10 0.01
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (327 bp):
TACACGATTTCAGCTAAAATTTTGAAAAAATGACACAAAAGATATTTCCTCAATTTTTGGCTAAA
ATACTCATAAAATATATATAATTTAATGCCAAAAAAATTGGAGGGCTTTTCACGCTTTTAATATC
GTTTTTCATATTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
AAATCTTAAATCCAATGTGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTGACGC
CAAAAATCATGCAAAACTGAGCCGGGTCCCTAGAACACGTTTTTAGCCAAAAACCGTGTGGTGTT
AG
Found at i:2367 original size:15 final size:16
Alignment explanation
Indices: 2349--2378 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2339 ATAAATAATA
2349 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
2364 ATATTATAATCTAAA
1 ATATTATAATCTAAA
2379 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:2638 original size:5 final size:5
Alignment explanation
Indices: 2630--2673 Score: 74
Period size: 5 Copynumber: 9.2 Consensus size: 5
2620 TATATAGTAG
2630 TAAGA TAAGA TAAGA TAAGA TAAGA T-AG- TAAGA TAAGA TAAGA T
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA T
2674 TACTAATTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 1 0.03
4 4 0.11
5 32 0.86
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (5 bp):
TAAGA
Found at i:11221 original size:333 final size:331
Alignment explanation
Indices: 10478--11988 Score: 1539
Period size: 333 Copynumber: 4.6 Consensus size: 331
10468 ATACTTTACA
* * * * * * *
10478 TCATCTAACCAAATCTCAGCAATATTGCATTTAAAAATTTGTTTTTACGAGTATTTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGT
* * * * *
10543 TTCGATTTAATAAGAAATTAATTTAGAAAAAACAAGAAATACGATATTAAAAGCGT-AGAAAGTC
66 TTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATTAAAAGCGTCA-AAAGCC
* *
10607 CTCCAATCTTTTTGGCGTTGAATTATATA-TTTTTAAGAGTGTTTTAGCCAAAAATTGAGGATAA
130 CTCCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGA-AA
* ** * * **
10671 -ATCTTTCATGTTAATTTTTTAAAATTTT-GCCGAAATTGTGTACTAACAAACCATATCATGGTT
194 TATTTTTCGGGTCAATTTTTTAAAATTTTAGCCAAAATCATG---TAA-AAACC--ATCATGG-T
** * * * *
10734 TTTTGTCTAAAAACGCG-TTCTGAGGACCCGGCTCAATTTTGCATGATTTTTGGCTCCGAGACTA
252 TTTTGGATAAAAACGCGTTTC-GGGGACCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTC
*
10798 CTTGAAATGTCTATAT
316 CTTGAAATATCTATAT
* * * * * * * *
10814 TCTTCTAATCAAATCACATCCACAATGGATTTAAGGATTTGTTTTTACGAGAATCTAAATATTGT
1 TCATCTAATCAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGT
* * *
10879 TTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACGATATTAGAAA-TGTCAAAAGCC
66 TTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATTA-AAAGCGTCAAAAGCC
* * *
10943 CTTCAATCTTTTTGGTGTT-AAGTTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAAGAAA
130 CTCCAATCTTTTTGGCGTTGAA-TTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAA
* * **
11007 TATCTTTT-GGGTCAATTTTTATAAAATTTTAGCCAAAATTATGTAATAACCATCAAAGTTTTTG
194 TAT-TTTTCGGGTCAATTTTT-TAAAATTTTAGCCAAAATCATGTAAAAACCATCATGGTTTTTG
** * * * **
11071 GATAAAATAAACGTTTTGGGGCCCCGGCTCAGTTTTGCATGACTTTTGGCGCAAAGACTCCTTGA
257 GATAAAA-ACGCGTTTCGGGGACCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGA
*
11136 GATATCTATAT
321 AATATCTATAT
* * * *
11147 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTATTTTTACAAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGT
* * * *
11212 TTTGATTTAATTAGAAATTAATTCA-AAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
66 TTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATTAAAAGCGTCAAAAGCCC
* * * * * * *
11276 TCCAATCTTTTTGCCTTTAAATTATATATATTTTATGAGTATTTTATCCAAAAACTGAGGAAAAA
131 TCCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATA
* * *
11341 TTTTTCGTGTCATTTTTTTTGCAAAATTTTAGCCAAAATCATGTAATAACCATCATGGTTTTTGG
196 TTTTTCGGGTCA-ATTTTTT--AAAATTTTAGCCAAAATCATGTAAAAACCATCATGGTTTTTGG
* * * * *
11406 CTAAAAACGCATTTCGGGG-CACCAGCTCAGTTTTACATGATTTTTGGCGCCGACACTCCTTGAA
258 ATAAAAACGCGTTTCGGGGAC-CCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAA
11470 ATATCTATAT
322 ATATCTATAT
* *
11480 TCATCTAATAAAATCTTAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGT
* *
11545 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTCAAAAGCAC
66 TTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATTAAAAGCGTCAAAAGCCC
* * * * * *
11610 TTCAATCTTTTTGGCGTTGAATCATATATTTTTT-T-AATATTATGGCTAAAAATTG-GGAAATA
131 TCCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATA
* * * * *
11672 TTTTTCGGGTCAATTTTGGTAAAATTTTAGCCGAAATCGTGTAAAAATCATCATGGTTATT-GAC
196 TTTTTCGGGTCAATTTT-TTAAAATTTTAGCCAAAATCATGTAAAAACCATCATGGTTTTTGGA-
* * * *
11736 TAAAAACGCG-TTCCGGGACCCGGTTCAGTTTTGAATGATTTTTGGCGCTGAGACTCCTTGAAAT
259 TAAAAACGCGTTTCGGGGACCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAAT
11800 ATCTATAT
324 ATCTATAT
* * * * *
11808 TCATCTAATC-GATCCCAG-C-CATTG--TTTTATAA---GTTTCT--GA--ATC---A---T-T
1 TCATCTAATCAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGT
* * * * * * *
11854 TTC-ATTTTAATCAGAAATTAA-TTCGGAAAAATAGGAAAAACGGTATTAGAAGCGTGAAAAGCC
66 TTCGA-TTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATTAAAAGCGTCAAAAGCC
* * * *
11917 CTTCAAT-TTTTTGGCGTTGAATTATATATTTTTTTATGAGTATTGTGGCTAAAAATTGAGGAAA
130 CTCCAATCTTTTTGGCGTTGAATTATATA-TTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAA
11981 TATATTTT
194 TAT-TTTT
11989 GCTAAAAACG
Statistics
Matches: 996, Mismatches: 152, Indels: 78
0.81 0.12 0.06
Matches are distributed among these distances:
307 20 0.02
308 48 0.05
309 20 0.02
310 19 0.02
311 8 0.01
312 4 0.00
313 1 0.00
316 3 0.00
318 2 0.00
320 5 0.01
323 6 0.01
325 5 0.01
326 1 0.00
327 5 0.01
328 63 0.06
329 46 0.05
330 4 0.00
331 25 0.03
332 117 0.12
333 280 0.28
334 111 0.11
335 6 0.01
336 131 0.13
337 44 0.04
338 12 0.01
339 10 0.01
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (331 bp):
TCATCTAATCAAATCTCAGCCACATTGCATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGT
TTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAACGATATTAAAAGCGTCAAAAGCCC
TCCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATA
TTTTTCGGGTCAATTTTTTAAAATTTTAGCCAAAATCATGTAAAAACCATCATGGTTTTTGGATA
AAAACGCGTTTCGGGGACCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATAT
CTATAT
Found at i:12718 original size:2 final size:2
Alignment explanation
Indices: 12711--12746 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
12701 CCTTGAAATT
*
12711 TA TA TA TA TA TA TA -A TG TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12747 TCATCTAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Done.