Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007451.1 Corchorus capsularis cultivar CVL-1 contig07472, 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: 25904
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:1367 original size:27 final size:25
Alignment explanation
Indices: 1337--1394 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 25
1327 ACAATTAATC
1337 TGCTTTAGATTTAGATTTAATTTGTTT
1 TGCTTTAGATTTAG-TTTAA-TTGTTT
**
1364 TGCTTTATTTTTAGTTTAATTGTTT
1 TGCTTTAGATTTAGTTTAATTGTTT
1389 T-CTTTA
1 TGCTTTA
1395 TAATTAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 5 0.17
25 7 0.24
26 5 0.17
27 12 0.41
ACGTcount: A:0.19, C:0.05, G:0.12, T:0.64
Consensus pattern (25 bp):
TGCTTTAGATTTAGTTTAATTGTTT
Found at i:2936 original size:336 final size:331
Alignment explanation
Indices: 1565--4171 Score: 3335
Period size: 331 Copynumber: 7.9 Consensus size: 331
1555 GACACGATCA
* * * * * *
1565 GTTAGTACACAATTTTGACC-AAAGTTTGTAAAAACTGACCCGAAAAGATTTTCCTCAATTTTTG
1 GTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGACCCGAAAAAATTTTCCTCAATTTTTG
* * * *
1629 GCCAAAGTACGCATAAAAAATATATCATTCAACGCCAAAAATATTAAAGGATTTTTCACCCATTT
66 GCCAAAGTACGCATAAAATATATATAATTCAACGCCAAAAATATTGAAGGATTTTTCACGCATTT
* * *
1694 AATGTCGTTTTTCTTTTTCTTTTT-CAAATTAATTTTTCATTAAATCGAACCAAGATTCAAATGC
131 AATATCG-TTTTCTTTTT-TTTTTCCAAATTAATTTCTCATTAAATCGAACCAAGATTCAAATAC
* *
1758 TCGTAAAAA-AAATCCTTAAATCCAATGTGCCTGCGATTTGGTTAGATGAATATAGATATTCCAA
194 TCGTAAAAACAAATCCTTAAATCCAATGTGGCTGCGATTTTGTTAGATGAATATAGATATTCCAA
*** * *
1822 GAAGTCTTGGAG-CAAAAAATCATTCAAAACTGATTTGGGGCCCTGGAACGCGTTTTTAGTCAAA
259 GAAGTCTTGGAGTC-AAAAATCATTCAAAACTGAGCCGAGGCCCCGGAACGCGTTTTTAGT-AAA
* *
1886 AATCATGATG
322 AACCGTGATG
* * * *
1896 ATTAGTACATGATTTCGGCCAAAA-TTTGCAAAAATTGACCCGAAAAAATTTTCCACAATTTTTG
1 GTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGACCCGAAAAAATTTTCCTCAATTTTTG
* * * * *
1960 ACCAATGTACGCGTAAATTATATATAATTCAACGCCAAAATTATTGAAGGATTTTTCACGCATTT
66 GCCAAAGTACGCATAAAATATATATAATTCAACGCCAAAAATATTGAAGGATTTTTCACGCATTT
*
2025 -ATGATCG------TTTTTTTTTCCAAATTAATTTCTCATTAAATCGAACCAAGATTAAAATACT
131 AAT-ATCGTTTTCTTTTTTTTTTCCAAATTAATTTCTCATTAAATCGAACCAAGATTCAAATACT
** *
2083 CGTAAAAACAAATCCTTAAATGTAATGTGACTGCGATTTTGTTAGATGAATATAGATATTCCAAG
195 CGTAAAAACAAATCCTTAAATCCAATGTGGCTGCGATTTTGTTAGATGAATATAGATATTCCAAG
* *
2148 AAGTCTTGGAG-CAAAAAATCATTCAAAACTGAGCC-AGGGCCCGGAACGCGTTTTTAGCCAAAA
260 AAGTCTTGGAGTC-AAAAATCATTCAAAACTGAGCCGAGGCCCCGGAACGCGTTTTTAG-TAAAA
2211 ACCGTGATG
323 ACCGTGATG
* * *
2220 GTTAGTACACGATTTCGGCTAAAATTTTGTAAAAACTGACCC-AGAAATATTTTCCTCAATTTTT
1 GTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGACCCGA-AAAAATTTTCCTCAATTTTT
* * * *
2284 GGCCAAAGTACGCATAAAAAATGTATCATTCAACGCCAAAAATATTGAAGGATCTTTCACGCATT
65 GGCCAAAGTACGCATAAAATATATATAATTCAACGCCAAAAATATTGAAGGATTTTTCACGCATT
* * * * * **
2349 TAATATCATTTTTCTGTTTTTATT-CAAATTTATTTCTCATTAAATCGAACCGAGATTCAAATGT
130 TAATATC-GTTTTCTTTTTTTTTTCCAAATTAATTTCTCATTAAATCGAACCAAGATTCAAATAC
* * * * *
2413 TCGTAAAAAAAAATTCTTCAATCCAATGTGGCTGCGATTTTGTTGGATCAATATAGATATTCCAA
194 TCGTAAAAACAAATCCTTAAATCCAATGTGGCTGCGATTTTGTTAGATGAATATAGATATTCCAA
* * * * * * * * * *
2478 GAAGTTTTAGTGTAAAAAATCATTCAAAACTGAACCGGGGCCCCAGAACGCGTTTTAAGCCAATA
259 GAAGTCTTGGAGTCAAAAATCATTCAAAACTGAGCCGAGGCCCCGGAACGCGTTTTTAG-TAAAA
**
2543 ACTATGATG
323 ACCGTGATG
* * * * *
2552 GTTAGTATATGATTTCGGCTAAAATTTTGCAAAAACTAACCCAAAAAAATTTTCCTCAATTTTTG
1 GTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGACCCGAAAAAATTTTCCTCAATTTTTG
* *
2617 GCCAAAGTACCCATAAAATATATATAATTCAACGCCCAAAATATTGAAGGATTTTTCACGCATTT
66 GCCAAAGTACGCATAAAATATATATAATTCAACGCCAAAAATATTGAAGGATTTTTCACGCATTT
* *
2682 AATATCGTTTTTATTTTTAATTTTTTCCAAATTAATTTCTCATTAAATCGAACCACGATTCAAAT
131 AATATCG-TTTT-CTTTT--TTTTTTCCAAATTAATTTCTCATTAAATCGAACCAAGATTCAAAT
* * * *
2747 ACTCGTAAAAACAAATTCTTAAATCCAATATGGCTGTGATTTGGTTAGATGAATATAGATATTCC
192 ACTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGCGATTTTGTTAGATGAATATAGATATTCC
* * *
2812 AAGAAGTCTTGGAGTCAAAAATCATTCTAAATTGAGCTGAGGCCCCGGAACGCGTTTTTAGTAAA
257 AAGAAGTCTTGGAGTCAAAAATCATTCAAAACTGAGCCGAGGCCCCGGAACGCGTTTTTAGTAAA
* *
2877 ACCCGTTATG
322 AACCGTGATG
* * * *
2887 CTTAGTACACAATTTCGGCCAAAATTTTGCAAAAGCTGACCCGAAAAAAAATTTCCTCAATTTTT
1 GTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGACCCG-AAAAAATTTTCCTCAA--TTT
* *
2952 TTTGCCAAAGTACGTATAAAATATATATAATTCAACGCCAAAAATATTGAAGGATTTTTCACGCA
63 TTGGCCAAAGTACGCATAAAATATATATAATTCAACGCCAAAAATATTGAAGGATTTTTCACGCA
* *
3017 TTTAATATCGTTTTCTTTTTTTTTT-AAAATTAATTTCTCATTAAATCGAACCACGATTCAAATA
128 TTTAATATCGTTTTCTTTTTTTTTTCCAAATTAATTTCTCATTAAATCGAACCAAGATTCAAATA
* * *
3081 CTCGTAAAAACAAATCCTTAAATCCAATATGGCTGTGATTTTGTTAGATGAATATAAATATTCCA
193 CTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGCGATTTTGTTAGATGAATATAGATATTCCA
* * * * **
3146 AGAAATCTTGGAGGCAAAAATTATTCAAAACTGAGCCGAGGTCCCGGAATACGTTTTTAGTAAAA
258 AGAAGTCTTGGAGTCAAAAATCATTCAAAACTGAGCCGAGGCCCCGGAACGCGTTTTTAGT-AAA
*
3211 AACTGTGATG
322 AACCGTGATG
* * ** *
3221 GTTAGTACACGATTTCGGCTAAAATTTTGTAAATGCTGACCCGAAAAAATTTTCCTCAATTTTTT
1 GTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGACCCGAAAAAATTTTCCTCAATTTTTG
* *
3286 GCCAAAGTACGCATAAAATATATATAATTTAACGCCAAAAATATTGAAGGATATTTCACGCATTT
66 GCCAAAGTACGCATAAAATATATATAATTCAACGCCAAAAATATTGAAGGATTTTTCACGCATTT
* *
3351 AAGATCGATTTTCTTTTTTTTTTTTTCAAAATTAATTT-TCCATTAAATCGAACCAAGATTCAAA
131 AATATCG-TTTTC---TTTTTTTTTTCCAAATTAATTTCT-CATTAAATCGAACCAAGATTCAAA
*
3415 TACTCGTAAAAACAAATCCTTAAATTCAATGTGGCTGCGATTTTGTTAGATGAATATAGATATTC
191 TACTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGCGATTTTGTTAGATGAATATAGATATTC
* * * *
3480 CAGGAAGTCTTGGAGCCAAAAAATTCATTCAAAACTGAGCCGGGGCCTCGGAACGCGTTTTTAGC
256 CAAGAAGTCTTGGAGTC-AAAAA-TCATTCAAAACTGAGCCGAGGCCCCGGAACGCGTTTTTAG-
*
3545 AAAAAAAACCGTGATG
318 --TAAAAACCGTGATG
* * * * * *
3561 GTTAGTACACGATTTTGACCAAAATTTTGCAAAAGCAGACCCG-AAAATTTTTTCTCAATTTTTG
1 GTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGACCCGAAAAAATTTTCCTCAATTTTTG
*
3625 GCCAAAGTACGCATAAAATATATATAATTCAACGCTAAAAATATTGAAGGATTTTTCACGCATTT
66 GCCAAAGTACGCATAAAATATATATAATTCAACGCCAAAAATATTGAAGGATTTTTCACGCATTT
* * * * *
3690 AATATCAATTTTCCTTTTTTTTTCCCAAATTAATTTTTTATTAAATCGAACCGAGATTCAAATAC
131 AATATC-GTTTT-CTTTTTTTTTTCCAAATTAATTTCTCATTAAATCGAACCAAGATTCAAATAC
* * *
3755 TCGTTAAAAAAAAATCCTTAAATCCAATGTGGCTGCAATTTGGTTAGATGAATATAGATATTCCA
194 TCG-TAAAAACAAATCCTTAAATCCAATGTGGCTGCGATTTTGTTAGATGAATATAGATATTCCA
* * ** * *
3820 AGAAGTCTTTGAGTAAAAAATCATTCAAAACTGATTCG-GGACCCCGGAACGCGTTTTTAATCAT
258 AGAAGTCTTGGAGTCAAAAATCATTCAAAACTGAGCCGAGG-CCCCGGAACGCGTTTTTAGT-AA
3884 AAACCGTGATG
321 AAACCGTGATG
* * *
3895 GTTAGTATACGATTTCGGCCAAAA-ATTGCAAAAACTGACCCGAAAAAAATTTTCCTCAATATTT
1 GTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGACCCG-AAAAAATTTTCCTCAATTTTT
* *
3959 GGCCAAAGTACGCATAAAATATGTATAATTCAACGCCAAAAATACTGAAGGATTTTTCACGCATT
65 GGCCAAAGTACGCATAAAATATATATAATTCAACGCCAAAAATATTGAAGGATTTTTCACGCATT
* *
4024 TAAGATCG-------TTTTTTTTCCAAATTAATTTCTCATTAAATCGAACCAATATTCAAATACT
130 TAATATCGTTTTCTTTTTTTTTTCCAAATTAATTTCTCATTAAATCGAACCAAGATTCAAATACT
* * * *
4082 CGTAAAAACAAATCCTTAAATGCAATGTGGGTGTGATTTTGTTAGATGAATATAGATATTCCAAT
195 CGTAAAAACAAATCCTTAAATCCAATGTGGCTGCGATTTTGTTAGATGAATATAGATATTCCAAG
* *
4147 AAGTCTTGGAGTCAATAATTATTCA
260 AAGTCTTGGAGTCAAAAATCATTCA
4172 TTTAATATCG
Statistics
Matches: 1989, Mismatches: 241, Indels: 98
0.85 0.10 0.04
Matches are distributed among these distances:
323 5 0.00
324 102 0.05
325 254 0.13
326 49 0.02
330 2 0.00
331 306 0.15
332 172 0.09
333 186 0.09
334 87 0.04
335 146 0.07
336 302 0.15
337 62 0.03
338 177 0.09
339 89 0.04
340 50 0.03
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (331 bp):
GTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGACCCGAAAAAATTTTCCTCAATTTTTG
GCCAAAGTACGCATAAAATATATATAATTCAACGCCAAAAATATTGAAGGATTTTTCACGCATTT
AATATCGTTTTCTTTTTTTTTTCCAAATTAATTTCTCATTAAATCGAACCAAGATTCAAATACTC
GTAAAAACAAATCCTTAAATCCAATGTGGCTGCGATTTTGTTAGATGAATATAGATATTCCAAGA
AGTCTTGGAGTCAAAAATCATTCAAAACTGAGCCGAGGCCCCGGAACGCGTTTTTAGTAAAAACC
GTGATG
Found at i:3303 original size:669 final size:656
Alignment explanation
Indices: 1565--4161 Score: 3411
Period size: 669 Copynumber: 3.9 Consensus size: 656
1555 GACACGATCA
* * * *
1565 GTTAGTACACAATTTTGACC-AAAGTTTGTAAAAACTGACCCGAAAAGATTTTCCTCAATTTTTG
1 GTTAGTACACAATTTCGACCAAAATTTTGCAAAAACTGACCCGAAAAAATTTTCCTCAATTTTTG
* * *
1629 GCCAAAGTACGCATAAAAAATATATCATTCAACGCCAAAAATATTAAAGGATTTTTCACCCATTT
66 GCCAAAGTACGCATAAAAAATATATAATTCAACGCCAAAAATATTGAAGGATTTTTCACGCATTT
* * * *
1694 AATGTC-GTTTTTCTTTTTCTTTTTCAAATTAATTTTTCATTAAATCGAACCAAGATTCAAATGC
131 AATATCAG-TTTTCTTTTT-TTTTTCAAATTAATTTCTCATTAAATCGAACCGAGATTCAAATAC
*
1758 TCGT-AAAAAAAATCCTTAAATCCAATGTGCCTGCGATTTGGTTAGATGAATATAGATATTCCAA
194 TCGTAAAAAAAAATCCTTAAATCCAATGTGGCTGCGATTTGGTTAGATGAATATAGATATTCCAA
* ** *
1822 GAAGTCTTGGAGCAAAAAATCATTCAAAACTGATTTGGGGCCCTGGAACGCGTTTTTAGTCAAAA
259 GAAGTCTTGGAGGAAAAAATCATTCAAAACTGA-TCCGGGCCCCGGAACGCGTTTTTAGTCAAAA
* * * *
1887 A-TCATGATGATTAGTACATGATTTCGGCCAAAATTTGCAAAAATTGACCCGAAAAAATTTTCCA
323 ACT-ATGATGGTTAGTACACGATTTCGGCCAAAATTTGCAAAAACTGACCCGAAAAAATTTTCCT
* * * * *
1951 CAATTTTTGACCAATGTACGCGTAAATTATATATAATTCAACGCCAAAATTATTGAAGGATTTTT
387 CAATTTTTGGCCAAAGTACGCATAAAATATATATAATTCAACGCCAAAAATATTGAAGGATTTTT
* *
2016 CACGCATTTATGATCGTTTTTTTTTCCAAATTAATTTCTCATTAAATCGAACCAAGATTAAAATA
452 CACGCATTTAAGATCGTTTTTTTTTCCAAATTAATTTCTCATTAAATCGAACCAAGATTCAAATA
* *
2081 CTCGTAAAAACAAATCCTTAAATGTAATGTGACTGCGATTTTGTTAGATGAATATAGATATTCCA
517 CTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGCGATTTTGTTAGATGAATATAGATATTCCA
* * **
2146 AGAAGTCTTGGAG-CAAAAAATCATTCAAAACTGAGCCAGGGCCCGGAACGCGTTTTTAGCCAAA
582 AGAAGTCTTGGAGTCAAAAAATCATTCAAAACTGAGCGAGGCCCCGGAACGCGTTTTTAGAAAAA
2210 AACCGTGATG
647 AACCGTGATG
* * * * *
2220 GTTAGTACACGATTTCGGCTAAAATTTTGTAAAAACTGACCC-AGAAATATTTTCCTCAATTTTT
1 GTTAGTACACAATTTCGACCAAAATTTTGCAAAAACTGACCCGA-AAAAATTTTCCTCAATTTTT
* * *
2284 GGCCAAAGTACGCATAAAAAATGTATCATTCAACGCCAAAAATATTGAAGGATCTTTCACGCATT
65 GGCCAAAGTACGCATAAAAAATATATAATTCAACGCCAAAAATATTGAAGGATTTTTCACGCATT
* * * * **
2349 TAATATCATTTTTCTGTTTTTATTCAAATTTATTTCTCATTAAATCGAACCGAGATTCAAATGTT
130 TAATATCAGTTTTCTTTTTTTTTTCAAATTAATTTCTCATTAAATCGAACCGAGATTCAAATACT
* * * * *
2414 CGTAAAAAAAAATTCTTCAATCCAATGTGGCTGCGATTTTGTTGGATCAATATAGATATTCCAAG
195 CGTAAAAAAAAATCCTTAAATCCAATGTGGCTGCGATTTGGTTAGATGAATATAGATATTCCAAG
* * * * * * * * *
2479 AAGTTTTAGTGTAAAAAATCATTCAAAACTGAACCGGGGCCCCAGAACGCGTTTTAAGCCAATAA
260 AAGTCTTGGAGGAAAAAATCATTCAAAACTGATCC-GGGCCCCGGAACGCGTTTTTAGTCAAAAA
* * * * *
2544 CTATGATGGTTAGTATATGATTTCGGCTAAAATTTTGCAAAAACTAACCCAAAAAAATTTTCCTC
324 CTATGATGGTTAGTACACGATTTCGGCCAAAA-TTTGCAAAAACTGACCCGAAAAAATTTTCCTC
* *
2609 AATTTTTGGCCAAAGTACCCATAAAATATATATAATTCAACGCCCAAAATATTGAAGGATTTTTC
388 AATTTTTGGCCAAAGTACGCATAAAATATATATAATTCAACGCCAAAAATATTGAAGGATTTTTC
* *
2674 ACGCATTTAATATCGTTTTTATTTTTAATTTTTTCCAAATTAATTTCTCATTAAATCGAACCACG
453 ACGCATTTAAGATCG--------TTT--TTTTTTCCAAATTAATTTCTCATTAAATCGAACCAAG
* * * * *
2739 ATTCAAATACTCGTAAAAACAAATTCTTAAATCCAATATGGCTGTGATTTGGTTAGATGAATATA
508 ATTCAAATACTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGCGATTTTGTTAGATGAATATA
* *
2804 GATATTCCAAGAAGTCTTGGAGTC-AAAAATCATTCTAAATTGAGCTGAGGCCCCGGAACGCGTT
573 GATATTCCAAGAAGTCTTGGAGTCAAAAAATCATTCAAAACTGAGC-GAGGCCCCGGAACGCGTT
* * *
2868 TTTAG-TAAAACCCGTTATG
637 TTTAGAAAAAAACCGTGATG
* * * *
2887 CTTAGTACACAATTTCGGCCAAAATTTTGCAAAAGCTGACCCGAAAAAAAATTTCCTCAATTTTT
1 GTTAGTACACAATTTCGACCAAAATTTTGCAAAAACTGACCCG-AAAAAATTTTCCTCAA--TTT
* * *
2952 TTTGCCAAAGTACGTATAAAATATATATAATTCAACGCCAAAAATATTGAAGGATTTTTCACGCA
63 TTGGCCAAAGTACGCATAAAAAATATATAATTCAACGCCAAAAATATTGAAGGATTTTTCACGCA
*
3017 TTTAATATC-GTTTTCTTTTTTTTTTAAAATTAATTTCTCATTAAATCGAACC-ACGATTCAAAT
128 TTTAATATCAGTTTTCTTTTTTTTTTCAAATTAATTTCTCATTAAATCGAACCGA-GATTCAAAT
* * * * *
3080 ACTCGTAAAAACAAATCCTTAAATCCAATATGGCTGTGATTTTGTTAGATGAATATAAATATTCC
192 ACTCGTAAAAAAAAATCCTTAAATCCAATGTGGCTGCGATTTGGTTAGATGAATATAGATATTCC
* * * * * ** *
3145 AAGAAATCTTGGAGGCAAAAATTATTCAAAACTGAGCCGAGGTCCCGGAATACGTTTTTAGTAAA
257 AAGAAGTCTTGGAGGAAAAAATCATTCAAAACTGATCCG-GGCCCCGGAACGCGTTTTTAGTCAA
* * * **
3210 AAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAATGCTGACCCGAAAAAATTTTC
321 AAACTATGATGGTTAGTACACGATTTCGGCCAAAA-TTTGCAAAAACTGACCCGAAAAAATTTTC
* * *
3275 CTCAATTTTTTGCCAAAGTACGCATAAAATATATATAATTTAACGCCAAAAATATTGAAGGATAT
385 CTCAATTTTTGGCCAAAGTACGCATAAAATATATATAATTCAACGCCAAAAATATTGAAGGATTT
*
3340 TTCACGCATTTAAGATCGATTTTCTTTTTTTTTTTTTCAAAATTAATTT-TCCATTAAATCGAAC
450 TTCACGCATTTAAGATCG----------TTTTTTTTTCCAAATTAATTTCT-CATTAAATCGAAC
*
3404 CAAGATTCAAATACTCGTAAAAACAAATCCTTAAATTCAATGTGGCTGCGATTTTGTTAGATGAA
504 CAAGATTCAAATACTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGCGATTTTGTTAGATGAA
* * * *
3469 TATAGATATTCCAGGAAGTCTTGGAGCCAAAAAATTCATTCAAAACTGAGCCGGGGCCTCGGAAC
569 TATAGATATTCCAAGAAGTCTTGGAGTCAAAAAA-TCATTCAAAACTGAG-CGAGGCCCCGGAAC
3534 GCGTTTTTAGCAAAAAAAACCGTGATG
632 GCGTTTTTAG--AAAAAAACCGTGATG
* * * * * *
3561 GTTAGTACACGATTTTGACCAAAATTTTGCAAAAGCAGACCCG-AAAATTTTTTCTCAATTTTTG
1 GTTAGTACACAATTTCGACCAAAATTTTGCAAAAACTGACCCGAAAAAATTTTCCTCAATTTTTG
* *
3625 GCCAAAGTACGCATAAAATATATATAATTCAACGCTAAAAATATTGAAGGATTTTTCACGCATTT
66 GCCAAAGTACGCATAAAAAATATATAATTCAACGCCAAAAATATTGAAGGATTTTTCACGCATTT
* * * *
3690 AATATCAATTTTCCTTTTTTTTTCCCAAATTAATTTTTTATTAAATCGAACCGAGATTCAAATAC
131 AATATCAGTTTT-CTTTTTTTTT-TCAAATTAATTTCTCATTAAATCGAACCGAGATTCAAATAC
*
3755 TCGTTAAAAAAAAATCCTTAAATCCAATGTGGCTGCAATTTGGTTAGATGAATATAGATATTCCA
194 TCG-TAAAAAAAAATCCTTAAATCCAATGTGGCTGCGATTTGGTTAGATGAATATAGATATTCCA
* * * * *
3820 AGAAGTCTTTGAGTAAAAAATCATTCAAAACTGATTCGGGACCCCGGAACGCGTTTTTAATCATA
258 AGAAGTCTTGGAGGAAAAAATCATTCAAAACTGATCCGGG-CCCCGGAACGCGTTTTTAGTCAAA
** * *
3885 AACCGTGATGGTTAGTATACGATTTCGGCCAAAAATTGCAAAAACTGACCCGAAAAAAATTTTCC
322 AACTATGATGGTTAGTACACGATTTCGGCCAAAATTTGCAAAAACTGACCCG-AAAAAATTTTCC
* * *
3950 TCAATATTTGGCCAAAGTACGCATAAAATATGTATAATTCAACGCCAAAAATACTGAAGGATTTT
386 TCAATTTTTGGCCAAAGTACGCATAAAATATATATAATTCAACGCCAAAAATATTGAAGGATTTT
*
4015 TCACGCATTTAAGATCG-TTTTTTTTCCAAATTAATTTCTCATTAAATCGAACCAATATTCAAAT
451 TCACGCATTTAAGATCGTTTTTTTTTCCAAATTAATTTCTCATTAAATCGAACCAAGATTCAAAT
* *
4079 ACTCGTAAAAACAAATCCTTAAATGCAATGTGGGTGTGATTTTGTTAGATGAATATAGATATTCC
516 ACTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGCGATTTTGTTAGATGAATATAGATATTCC
*
4144 AATAAGTCTTGGAGTCAA
581 AAGAAGTCTTGGAGTCAA
4162 TAATTATTCA
Statistics
Matches: 1700, Mismatches: 200, Indels: 76
0.86 0.10 0.04
Matches are distributed among these distances:
655 61 0.04
656 249 0.15
657 100 0.06
663 120 0.07
664 1 0.00
665 3 0.00
667 182 0.11
668 38 0.02
669 399 0.23
670 150 0.09
671 47 0.03
672 23 0.01
673 54 0.03
674 273 0.16
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (656 bp):
GTTAGTACACAATTTCGACCAAAATTTTGCAAAAACTGACCCGAAAAAATTTTCCTCAATTTTTG
GCCAAAGTACGCATAAAAAATATATAATTCAACGCCAAAAATATTGAAGGATTTTTCACGCATTT
AATATCAGTTTTCTTTTTTTTTTCAAATTAATTTCTCATTAAATCGAACCGAGATTCAAATACTC
GTAAAAAAAAATCCTTAAATCCAATGTGGCTGCGATTTGGTTAGATGAATATAGATATTCCAAGA
AGTCTTGGAGGAAAAAATCATTCAAAACTGATCCGGGCCCCGGAACGCGTTTTTAGTCAAAAACT
ATGATGGTTAGTACACGATTTCGGCCAAAATTTGCAAAAACTGACCCGAAAAAATTTTCCTCAAT
TTTTGGCCAAAGTACGCATAAAATATATATAATTCAACGCCAAAAATATTGAAGGATTTTTCACG
CATTTAAGATCGTTTTTTTTTCCAAATTAATTTCTCATTAAATCGAACCAAGATTCAAATACTCG
TAAAAACAAATCCTTAAATGCAATGTGGCTGCGATTTTGTTAGATGAATATAGATATTCCAAGAA
GTCTTGGAGTCAAAAAATCATTCAAAACTGAGCGAGGCCCCGGAACGCGTTTTTAGAAAAAAACC
GTGATG
Found at i:7044 original size:330 final size:329
Alignment explanation
Indices: 6326--8768 Score: 1737
Period size: 332 Copynumber: 7.4 Consensus size: 329
6316 GATTGGAAAA
* * *
6326 CTTTTCACG-ATTTAATATCG-TTTT-ATATATTTTTTCTAAATTAATTTCTAATTAAATCGAAA
1 CTTTTCACGCTTTTAATATCGTTTTTCCTAT-TTTTTTC-GAATTAATTTCTAATTAAATCGAAA
** * ** * * *
6388 CAAGATTCAGATG--CAAAAAAACAAATCCTTGCATCAAATGTGGCTGAGATTTAATTAGATGAA
64 CAAGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGATTAGATTAA
* * * * * * *
6451 TAAACATATTTCAAGGAGTCTTGGCGCCAATAATCATGCAAAACAGA-ATCGTGG-CCCTGTAAC
129 TATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCT-G-GGCCCCAG-AAC
* * * **
6514 GTGTTTTTAGCCAAAAATCGTAATGGTTAGTACACGATTTCGGCTAAAATTTTGTTAAAATTGAC
191 GCGTTTTTAGCAAAAAATCGTGATGGTTAGTACACGATTTCGGCT-AAATTTTGCAAAAATTGAC
* * * *
6579 CCGAAAGATATTTCCA-CAATTTTTTAACTAAAATACTCATGAAAAATATATACTTCGATA-TC-
255 CCG-AA-ATATTTCCATCAA-TTTTTAGCTAAAATACTCATAAAAAATATATAATTC-A-ACGCT
6641 AAAAAGATTGAAGGG
315 AAAAAGATTGAAGGG
* *
6656 CTTTTAACGCTTTTAATATTGTTTTTCCTATTTTTTTCCGAATTAATTTCTAATTAAATCGAAAC
1 CTTTTCACGCTTTTAATATCGTTTTTCCTATTTTTTT-CGAATTAATTTCTAATTAAATCGAAAC
* * *
6721 AAGATTCAGATGCTCGTAAAAACAAATCTTTAAATCTAATGTGGCTGAGATTTGGTTAGATTTAT
65 AAGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGATTAGATTAAT
* * *
6786 ATAAATATTTCAAGGAGTCTTGACACCAAAAATCATGCAAAACTGAGCTGGGCCCCATAACGCGT
130 ATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCTGGGCCCCAGAACGCGT
** * ** *
6851 TTTTAGCTGAAAATCGTGATGGTTAGTACACGATTTGGGCTAAATTTTAAAAAAATTGACCCGGA
195 TTTTAGCAAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAATTTTGCAAAAATTGACCCGAA
** * * *
6916 ATATTTTTATCAATTTTCAGCTAGAATACTCATAAAAAATATATAATTCAACGCTAAAAAGACTG
260 ATATTTCCATCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGCTAAAAAGATTG
*
6981 AAGAG
325 AAGGG
** * * * * *
6986 CGATTGACGCTTCTAATATCATTTTTCCTATTTGTTTTCAAATTAATTTCTAATTAAATTGAAAC
1 CTTTTCACGCTTTTAATATCGTTTTTCCTATTT-TTTTCGAATTAATTTCTAATTAAATCGAAAC
* * * *
7051 ATGATTCAAATGCTCGTAAAAACAAAT-TCTTAAATCCAATGTGGCT-AGGATTTGGTTAGATGA
65 AAGATTCAGATGCTCGTAAAAACAAATCT-TTAAATCCAATGTGGCTGA-GATTTGATTAGATTA
* * * * * * *
7114 ATATAGATATTTCAAGGAATGTTGCCACTAAAAATCATGCAAAACTGACCTGGGACCTCAGAACG
128 ATATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCTGGG-CCCCAGAACG
* * * * *
7179 CGTTTTTAGTCAAAAAACCGTGAT-GATA-TACACAATTTCGGGTAAAATTTTGCAAAAATTGAT
192 CGTTTTTAG-CAAAAAATCGTGATGGTTAGTACACGATTTCGGCT-AAATTTTGCAAAAATTGAC
* * * * * * * *
7242 CCGAAATATTTTCC-TCAATTTTTAACCACAATACTCATAGAATATATATAATTAAAAGTTAAAA
255 CCGAAATA-TTTCCATCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGCTAAAA
*
7306 AGATTGGAGGG
319 AGATTGAAGGG
* ** * * * * * *
7317 CTGTTCACATTTTTAATATCGTTTTT--AATTTTTTTTGCACTAATTTGTAATTAAATCAAAACA
1 CTTTTCACGCTTTTAATATCGTTTTTCCTATTTTTTTCGAATTAATTTCTAATTAAATCGAAACA
* * * * * * * *
7380 AGATTCAGATGCACGTAAAAGTTAGCAAATCCTTAAATTCAATGTGCCTAAAATTTTATTAGATG
66 AGATTCAGATGCTCGTAAAA---A-CAAATCTTTAAATCCAATGTGGCTGAGATTTGATTAGATT
* * * * *
7445 AATATAGATATTTCAAGGAGT-GTCAGCGCCAAAAATCATGCAAAACTAAGCCGGGGTCCC-GAA
127 AATATAGATATTTCAAGGAGTCTTGA-CGCCAAAAATCATGCAAAACTGAG-CTGGGCCCCAG-A
* * * *
7508 ACGCGCTATTAGCCAAAAATCGTGATGGTTAGTATACGATTT----T--A----G------TT-A
189 ACGCGTTTTTAGCAAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAATTTTGCAAAAATTGA
* * * * *
7556 ----AAATTTTTCCGTCAATTTTTGGC-ATAAATACTCATAAAATATATATAAATT-AACGCTTA
254 CCCGAAATATTTCCATCAATTTTTAGCTA-AAATACTCATAAAAAATATAT-AATTCAACGCTAA
* * *
7615 AAGGATTGGAGGA
317 AAAGATTGAAGGG
* * * *
7628 CTTTTCACGCCTTTAATATCGTTTTTCATATTTTTCT-GAATTAATTTTTCAATTAAATCGAAAC
1 CTTTTCACGCTTTTAATATCGTTTTTCCTATTTTTTTCGAATTAATTTCT-AATTAAATCGAAAC
* * *
7692 AAGATTTAGATGCTCGTAAAAA-AAGAT-TCTTAAATCCAATGTAGCTCAGATTTGATTAGATTA
65 AAGATTCAGATGCTCGTAAAAACAA-ATCT-TTAAATCCAATGTGGCTGAGATTTGATTAGATTA
* * * * * * * ** *
7755 ATATGGATATTTCAAAGAGTTTTGGCGTCAAAAATCATGCAAAACTTAG-TCGTGGTCCTGGAAT
128 ATATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCT-G-GGCCCCAGAAC
* * * * * *
7819 GCGTTTTTAACAAAAAATTGTGATGATTATTGCATGATTTCGGCTAGAATTTTGCAAAAATTGAC
191 GCGTTTTTAGCAAAAAATCGTGATGGTTAGTACACGATTTCGGCTA-AATTTTGCAAAAATTGAC
* * * * * * * * *
7884 TCGAAAGTTATTT-CTTCAAGTTTTAGCCACAATACTCATAAAAATTATATAATTTAATGCCAAA
255 CCGAAA--TATTTCCATCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGCTAAA
*
7948 AATATTGAAGGG
318 AAGATTGAAGGG
* * * * *
7960 CTTTTCATGCTTCTAGTATCGTTTTTCCTATTATTTTCTGAATTAATCTCTAATTAAATCGAAAC
1 CTTTTCACGCTTTTAATATCGTTTTTCCTATTTTTTTC-GAATTAATTTCTAATTAAATCGAAAC
* * *** * * * * *
8025 ATGATTCAGATGCTTGT-TTTACAAATCCTTAAATCCATTATGGATGAGATTTGGTTAGATTAAT
65 AAGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGATTAGATTAAT
* ** ** * * * * *
8089 ATAGATATTTTAAGGAGTCCCGGTGTCAAAAATCATGCAACACTGAACCGGGCCCCGGAACGCGT
130 ATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCTGGGCCCCAGAACGCGT
* * * * * * **
8154 TTTTAGAAAAAAAAAACCGTTACTTCGACTAATGTACACGATTTTCAGCTAATATTTTATAAAAA
195 TTTTAG---CAAAAAATCGTGA--T-G-GTTA-GTACACGA-TTTCGGCTAA-ATTTTGCAAAAA
** ** * *
8219 TTGACAAGAAATAGTTTTCC-TCAA-TTTCCGTCTAAAATACTCTTAAAAAGTATATAATTCAAC
250 TTGACCCGAAATA--TTTCCATCAATTTTTAG-CTAAAATACTCATAAAAAATATATAATTCAAC
* * * **
8282 TCCAAAAATATT-ACAGCA
312 GCTAAAAAGATTGA-AGGG
* * **
8300 CTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCT-GAATTAAAATCTAATTAAATCGAAACA
1 CTTTTCACGCTTTTAATATCGTTTTTCCTATTTTTTTCGAATTAATTTCTAATTAAATCGAAACA
* **
8364 AGATTCAGATGCTCGTAAAAA-AAATATTTAAATGTAATGT-GCTTGAGATTTGATTAGATTAAA
66 AGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGC-TGAGATTTGATTAGATT-AA
* * * * *
8427 TATATATATTTCAAGGAGCCTAGATGCCAAAAATCATGCAAAACTGATCTCGGGGCCCC-GAAAC
129 TATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCT--GGGCCCCAG-AAC
* * * * * *
8491 GC-ATTTTAGCAAAAAAAAACTGTGATGATTAGTATACAATTTCGCCTAAAATTTTGACAAAAAA
191 GCGTTTTTAGC--AAAAAATC-GTGATGGTTAGTACACGATTTCGGCT-AAATTTTG-C---AAA
** ** * * * * * * * * * *
8555 AAAAGACCAAAAAAATTTTTCCTTTAATTTTTGGCTTAAATACTTATGAGATATATATAATTTAA
248 AATTGACC--CGAAATATTTCCATCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAA
*
8620 CG-TCAAAAAGATTGGAGGG
311 CGCT-AAAAAGATTGAAGGG
* * * * * * *
8639 CGTTTCATGATTTTCATATCGTTTTTCATATTTTTCT-GAATTAATTTCTAATTAAATCGAAATA
1 CTTTTCACGCTTTTAATATCGTTTTTCCTATTTTTTTCGAATTAATTTCTAATTAAATCGAAACA
* * * ** *
8703 AGATTTAGATGCTCGTAAAAACAAAT-TCTTAAATGCATTGTATCTGAGATTTGATTAGATGAAT
66 AGATTCAGATGCTCGTAAAAACAAATCT-TTAAATCCAATGTGGCTGAGATTTGATTAGATTAAT
8767 AT
130 AT
8769 GCAAAACTTA
Statistics
Matches: 1669, Mismatches: 334, Indels: 211
0.75 0.15 0.10
Matches are distributed among these distances:
308 3 0.00
309 106 0.06
310 9 0.01
311 71 0.04
312 13 0.01
313 40 0.02
315 1 0.00
316 3 0.00
320 1 0.00
322 1 0.00
326 3 0.00
327 1 0.00
328 43 0.03
329 9 0.01
330 225 0.13
331 167 0.10
332 311 0.19
333 97 0.06
334 115 0.07
335 9 0.01
336 3 0.00
337 3 0.00
338 86 0.05
339 181 0.11
340 154 0.09
341 14 0.01
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (329 bp):
CTTTTCACGCTTTTAATATCGTTTTTCCTATTTTTTTCGAATTAATTTCTAATTAAATCGAAACA
AGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGATTAGATTAATA
TAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCTGGGCCCCAGAACGCGTT
TTTAGCAAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAATTTTGCAAAAATTGACCCGAAA
TATTTCCATCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGCTAAAAAGATTGA
AGGG
Found at i:10378 original size:333 final size:328
Alignment explanation
Indices: 8783--10550 Score: 1509
Period size: 331 Copynumber: 5.4 Consensus size: 328
8773 AACTTACTCG
* * * * *
8783 GGGCCCTGAAACGCATTTTTAACCAAAAATCGTGATGATTATTATTACACGGTTTCAGCTAAAAT
1 GGGCCCCGAAACGCGTTTTTAGCCAAAACTCGTGATG---ATTATTACACGATTTCAGCTAAAAT
* * * * **
8848 TTTGCAAAAATTGTCCGGAAAGATATTTTCTCGTTC--TTTTTTGTTA-AATTA-TCAT-AAAAA
63 TTTGTAAAAATTGACCCGAAAGAT-TTTTC-C--TCAATTTTTAGCCATAA-TACTCATAAAAAA
* * * ** * * * *
8908 -ATATAATTCTAC-AC-CAATATTGAAGGATTTTTTACGCTTCTAATATCGGTTTTCCTACTTTT
123 TATATAATTCAACGACAAAAAATTGAAGGGCTTTTGACGCTTTTAATATCGTTTTTCATA-TTTT
* * * * * * * * *
8970 CCCAAATTAATTTCTAATTAAACCGAAACAATATTTAGATGCTCGTAAAAACAAGTCCTTAAATC
187 TCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCTTAAAAAAAAAT-CTTAAATG
* * * * * * * *
9035 CAATGTGACTTAGATTTGATTAGATGAATATAAATAGTTCAACGAGTCTTGGCGCCAAAAATCAT
251 CAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCCAAAAATCAT
* * **
9100 GTAATACT-AACCC
316 GCAAAACTGAA-AT
* * **** * *
9113 GGGCACCTGGAACGCGTTTTTAGTCCAAAA--AAAAATTG-TTATGTTGCACGATTTC-GACTAG
1 GGGC-CCCGAAACGCGTTTTTAG-CCAAAACTCGTGA-TGATTA--TTACACGATTTCAG-CTAA
* * * * * * * *
9174 TATTTTGCAAAAAATAACCCGAAATATTTTTCCTCAATTTTTAGTCACAATACTCAT-AAAATTA
60 AATTTTGTAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGCCATAATACTCATAAAAAATA
* * * * *
9238 TATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATACCGTTTTTCCTATTTTT-
125 TATAATTCAACGACAAAAA-ATTGAAGGGCTTTTGACGCTTTTAATATCGTTTTTCATATTTTTC
* * * *
9302 TAGGAATTAATTTCTAATTAAAACGAAACATGATTTAGATG--CTT-----ATAA----AAA--C
189 TA--AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCTTAAAAAAAAATCTTAAATGC
* * *
9354 AA--TGGCTGAGATTTGGTTAGATGATTATAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATT
252 AATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATG
9417 CAAAACTGAAAT
317 CAAAACTGAAAT
* *
9429 GAGCCGCGAAACGCGTTTTTAGCCAAAAC-CGTGATGATTATTACACGATTTCAGCTAAAATTTT
1 GGGCCCCGAAACGCGTTTTTAGCCAAAACTCGTGATGATTATTACACGATTTCAGCTAAAATTTT
*
9493 ATAAAAATTGACCCGAAAGATATTTT-CTCAATTTTTAGCCATAATACTCATAAAAAAATATATA
66 GTAAAAATTGACCCGAAAGAT-TTTTCCTCAATTTTTAGCCATAATACTCAT-AAAAAATATATA
* * *
9557 ATTCAATGCCAAAAATATTGAAGGGTTTTTGACGCTTTTAATATCGTTTTTCATATTTTTCTAAA
129 ATTCAACGACAAAAA-ATTGAAGGGCTTTTGACGCTTTTAATATCGTTTTTCATATTTTTCTAAA
*
9622 TTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTTAAAAAAAAATCTTAAATGCAATGT
193 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC-TTAAAAAAAAATCTTAAATGCAATGT
*
9687 GGCTAAGATTTGGTTAGATGATTATAGATATTTCAAGGAGTC-CGG-GCACAAAAAATCAAT-CA
257 GGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGTGC-C-AAAAATC-ATGCA
9749 AAACTGAAAT
319 AAACTGAAAT
* * * * * * *
9759 GGGTCCCGGAACGCGTTTTTATCTAAAAACT-GTGATGATTATTATACAATTTCAACTAAAATTT
1 GGGCCCCGAAACGCGTTTTTAGC-CAAAACTCGTGATGATTATTACACGATTTCAGCTAAAATTT
* * *
9823 TGTAAAAATTGATCCGAAAGATATTTCCTCAACTTTTAGCCATAATACTCATAAAAAATATATAA
65 TGTAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGCCATAATACTCATAAAAAATATATAA
* *
9888 TTCAACGTCAAAAAATTTTGAAGGGCTTTTGACGCTTTTAATATCGTTTTTCATGTTTTTCTAAA
130 TTCAACGACAAAAAA--TTGAAGGGCTTTTGACGCTTTTAATATCGTTTTTCATATTTTTCTAAA
*
9953 TTAATTTATAATTAAATCGAAACATA-ATTCAGATGCTCGTTTAAAAAAAAATCTTAAATGCAAT
193 TTAATTTCTAATTAAATCGAAACA-AGATTCAGATGCTC--TTAAAAAAAAATCTTAAATGCAAT
* ** * * * *
10017 GTGACTAAGATTTTTTTAGATTAATATAGTTATTTCAAGGAGTGTTGGTGCCAAAAATCATGCAA
255 GTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATGCAA
*
10082 AACT-AAGCT
320 AACTGAA-AT
* ** * **
10091 GGTGCCCCGAAACGCGTTTTTAGCCAAAACTCGTGATGGTTGGTGCACGATTTTGGCTAAAATTT
1 GG-GCCCCGAAACGCGTTTTTAGCCAAAACTCGTGATGATTATTACACGATTTCAGCTAAAATTT
* * ** * * *
10156 TGTAAAAAAGTAT-ACCCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTCCTAAAATATATA
65 TGT-AAAAA-T-TGACCCGAAAGATTTTTCCTCAATTTTTAGCCATAATACTCATAAAAAATATA
* * * * * *
10220 TAATTTAACAACAAAAAGATTGGAGGACTTTTCACGCTTATAATATCGTTTTTCATATTTTTCTA
127 TAATTCAACGACAAAAA-ATTGAAGGGCTTTTGACGCTTTTAATATCGTTTTTCATATTTTTCTA
* * * * * *
10285 TATTAATTTCTAATTAAATCGAAACAAGATTTAGACGCT-TTGAAAAATAAATTTTTAAATTCAA
191 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCTT-AAAAA-AAAATCTTAAATGCAA
* * * * * * *
10349 TGTGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGCGTCAAAAATCATGTA
254 TGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATGCA
* **
10414 ATACTGAGTT
319 AAACTGAAAT
* * * * * *
10424 GGGGACAC-AGAACGC-TTCTTTATCCAAAAAC-AGTGATGATTATTACACGATTTTCGGTTAAA
1 -GGGCCCCGA-AACGCGTT-TTTAGCC-AAAACTCGTGATGATTATTACACGA-TTTCAGCTAAA
* ** * * *
10486 ATTTTGT-AAAATTGACCCGAAAGATATTTAATCAATTTTTGGCTAAAATACTCATAAAAAATAT
61 ATTTTGTAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGCCATAATACTCATAAAAAATAT
10550 A
126 A
10551 CAAATCAATA
Statistics
Matches: 1189, Mismatches: 179, Indels: 139
0.79 0.12 0.09
Matches are distributed among these distances:
313 58 0.05
314 48 0.04
315 82 0.07
316 62 0.05
317 4 0.00
318 3 0.00
320 3 0.00
322 3 0.00
325 3 0.00
326 3 0.00
327 14 0.01
328 21 0.02
329 50 0.04
330 117 0.10
331 236 0.20
332 170 0.14
333 149 0.13
334 105 0.09
335 56 0.05
336 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.35
Consensus pattern (328 bp):
GGGCCCCGAAACGCGTTTTTAGCCAAAACTCGTGATGATTATTACACGATTTCAGCTAAAATTTT
GTAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGCCATAATACTCATAAAAAATATATAAT
TCAACGACAAAAAATTGAAGGGCTTTTGACGCTTTTAATATCGTTTTTCATATTTTTCTAAATTA
ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCTTAAAAAAAAATCTTAAATGCAATGTGGCT
AAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATGCAAAACTGA
AAT
Found at i:13127 original size:29 final size:29
Alignment explanation
Indices: 13085--13147 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
13075 TGTTTGGATG
*
13085 TTTTGTCCCCTAAACTTCAATTTTAGACA
1 TTTTATCCCCTAAACTTCAATTTTAGACA
* * *
13114 TTTTATCCTCTAAATTTCAATTTTGGACA
1 TTTTATCCCCTAAACTTCAATTTTAGACA
13143 TTTTA
1 TTTTA
13148 ATGCCACGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.48
Consensus pattern (29 bp):
TTTTATCCCCTAAACTTCAATTTTAGACA
Found at i:13254 original size:29 final size:29
Alignment explanation
Indices: 13200--13274 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 29
13190 TAGGCTGAGG
* *
13200 GGCAAAACGTCGCAGAATTGATGTTCAGGA
1 GGCAAAACGTC-CAAAATTGAAGTTCAGGA
* *
13230 GGCAAAATGTCCAAAATTGAAGTTCAGGC
1 GGCAAAACGTCCAAAATTGAAGTTCAGGA
13259 GGACAAAACGTCCAAA
1 GG-CAAAACGTCCAAA
13275 CACTACAAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 17 0.44
30 22 0.56
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (29 bp):
GGCAAAACGTCCAAAATTGAAGTTCAGGA
Found at i:14450 original size:25 final size:25
Alignment explanation
Indices: 14421--14470 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
14411 AATAGGATAA
14421 AATTAAGTTCACTAAAAATGAAAAT
1 AATTAAGTTCACTAAAAATGAAAAT
14446 AATTAAGTTCACTAAAAATGAAAAT
1 AATTAAGTTCACTAAAAATGAAAAT
14471 TACCGTAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (25 bp):
AATTAAGTTCACTAAAAATGAAAAT
Found at i:15280 original size:5 final size:5
Alignment explanation
Indices: 15238--15297 Score: 61
Period size: 5 Copynumber: 11.6 Consensus size: 5
15228 CCATATCTTT
*
15238 AAAAG AAAGAG AATTAAG TAAA- AAAA- AAAAG AAGAAG AAAAG AAAAG
1 AAAAG AAA-AG AA--AAG AAAAG AAAAG AAAAG AA-AAG AAAAG AAAAG
15285 AAAAG AAAAG AAA
1 AAAAG AAAAG AAA
15298 GCAATTAAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
4 7 0.15
5 28 0.58
6 9 0.19
7 3 0.06
8 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (5 bp):
AAAAG
Found at i:22265 original size:21 final size:21
Alignment explanation
Indices: 22239--22280 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
22229 TATGTCGCTT
22239 TTGAAAGTTTTCTATTGATTA
1 TTGAAAGTTTTCTATTGATTA
*
22260 TTGAAAGTTTTCTGTTGATTA
1 TTGAAAGTTTTCTATTGATTA
22281 AATTACACAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.17, T:0.52
Consensus pattern (21 bp):
TTGAAAGTTTTCTATTGATTA
Done.