Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015200.1 Corchorus olitorius cultivar O-4 contig15233, 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: 90562
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1324 original size:332 final size:324
Alignment explanation
Indices: 296--1515 Score: 1074
Period size: 332 Copynumber: 3.7 Consensus size: 324
286 ATAAACAATA
* * * * ** * * * *
296 GCTGGGATTTGGTTAGATTAATATAGACATTTTTAGGATTCTCGGCGCCAAAAATCATTC-AAAT
1 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGAGCCAAAAATCATGCAAAAT
*** * * * * *
360 CTGAAATGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTTATGATTATTACATGATTTCGGCTA
66 -TGAGCCGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTCGGCTA
** * * *
425 AAATTTTGCAAAAAATTGACCCGAAAGATATTTCCTCAATTTTTATCCATAATATTCATAAAAAT
130 AAATTTTG--AAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCCAAAATACTAATAAAAAT
*
490 ATAAAATTCAACGCCAAAAAGATTGAAGGACTTTTGACGCTTTTAATATCGTTTTTCATATTTTT
193 ATAAAATTCAACACCAAAAAGATTGAAGGACTTTTGACG-TTTTAATATCGTTTTTCATATTTTT
***
555 T-TAAATTAATTTCTAATTAAATCGAAACTTGATTCAGATGCTTGTTTAAAACAAAAAAAAATCT
257 TCTAAATTAATTTCTAATTAAATCGAAACAAAATTCA-ATGCTTG--TAAAAC------AAATCT
619 TAAATGCAATGTG
313 TAAAT-CAATGTG
* * * *
632 GCTAAGATTTAATTAGATGAATATAGTTATTTCAAGGAGT-TTCGGTGCCAAAAATCATGCAAAA
1 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTT-GGAGCCAAAAATCATGCAAAA
* *
696 TTGAGCTGGTGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGACGG----T------TTT-GGCT
65 TTGAGCCGG-GCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTCGGCT
* * * * * **
750 AAAATTTTGCAAAATATAACCCGAAAAAATTTTTCTTCAATTTTTGGATAAAATAATCCTAATAT
129 AAAATTTTGAAAAAT-TGACCCG-AAAGATATTTCCTCAATTTTTGGCCAAAAT-A--CT-A-AT
* *
815 ATATATATATATATATAATT-AACGGA-CAAAACGATTGGAGGTACTTTCT-ACGTTTTAATATC
187 A-A-A-A-ATATA-A-AATTCAAC--ACCAAAAAGATTGAAGG-ACTTT-TGACGTTTTAATATC
* ** * *
877 GTTTTTCATA-ATTTTCTTTATTAATTTCTAATTAAATCGAAACAAGATTTGAATGCTTGTAAAA
242 GTTTTTCATATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAA-AATTCAATGCTTGT-AAA
* *
941 ACAAATTTTTAAATCCACTGTG
305 ACAAA-TCTTAAAT-CAATGTG
* * * * *
963 GCTGTGATTTGATTAGATGAGTATAGATATATCAAGGAGTCTTGGCGCCAAAAATCATGCAAAAC
1 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGAGCCAAAAATCATGCAAAAT
* * * * *
1028 TGAGCCCGGGCCACAAAACGCTTTTTTATCCAAAAACTGTGATGGTTATTACACGATTTCGGCTA
66 TGAG-CCGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTCGGCTA
* *
1093 AAAATTTGTAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCCAAAATACTCATAAAAAAT
130 AAATTTTG-AAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCCAAAATACTAAT-AAAAAT
* * * * *
1158 ATATAACTCAACACCAAAAAGATCGAAGGGCTTTTGACGTTTCTAATATCGTTTTTCCTATTTTT
193 ATAAAATTCAACACCAAAAAGATTGAAGGACTTTTGACGTTT-TAATATCGTTTTTCATATTTTT
* * *
1223 TCCAAATTAATTTCTAATTAAATCGAAACAAAATACATATGCTCGTAAAGACAAATCCTTAAATC
257 TCTAAATTAATTTCTAATTAAATCGAAACAAAATTCA-ATGCTTGTAAA-ACAAAT-CTTAAATC
1288 TAATGTG
319 -AATGTG
* * * * *
1295 GGTGAGATTTGATTAGATGAATATAGATATTTCAAGTAGTCTTGGAGCTAGAAATCATGCGAAAT
1 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGAGCCAAAAATCATGCAAAAT
* * * * *
1360 TGAGCCGAGTCCCCGGAACGTGTTTTTAGTCAAAAACCGTGATGGTTTGTTAGCACACGATTTCG
66 TGAGCCG-GGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGG-TTATT---ACACGATTTCG
** * * *
1425 GCTAAAATTTTGCAAAAATTGACATGAAAGAT-TTCTTCTCAATGTTTGGCTAAAATACTAATAA
126 GCTAAAATTTTG-AAAAATTGACCCGAAAGATATT-TCCTCAATTTTTGGCCAAAATACTAATAA
*
1489 AAATATAAAATTCAACGCCAAAAAGAT
189 AAATATAAAATTCAACACCAAAAAGAT
1516 GATGTAGAGT
Statistics
Matches: 712, Mismatches: 118, Indels: 109
0.76 0.13 0.12
Matches are distributed among these distances:
324 5 0.01
325 6 0.01
326 35 0.05
327 4 0.01
329 2 0.00
330 14 0.02
331 146 0.21
332 150 0.21
333 11 0.02
334 2 0.00
335 37 0.05
336 129 0.18
337 105 0.15
338 13 0.02
339 1 0.00
340 1 0.00
341 28 0.04
342 18 0.03
343 5 0.01
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (324 bp):
GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGAGCCAAAAATCATGCAAAAT
TGAGCCGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTCGGCTAA
AATTTTGAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCCAAAATACTAATAAAAATATA
AAATTCAACACCAAAAAGATTGAAGGACTTTTGACGTTTTAATATCGTTTTTCATATTTTTTCTA
AATTAATTTCTAATTAAATCGAAACAAAATTCAATGCTTGTAAAACAAATCTTAAATCAATGTG
Found at i:1808 original size:31 final size:31
Alignment explanation
Indices: 1770--1873 Score: 117
Period size: 31 Copynumber: 3.4 Consensus size: 31
1760 AAAGGCTAAG
1770 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
** * **
1801 TGCTCAAATAAGGGTTTAATC-TTT--TAATT
1 TGCTCAAATAAGGGCCTAA-CGTTTGCCAAAA
1830 TGAC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 TG-CTCAAATAAGGGCCTAACGTTTGCCAAAA
1861 TGCTCAAATAAGG
1 TGCTCAAATAAGG
1874 ATCCGATCTT
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 1 0.02
29 20 0.35
30 2 0.04
31 33 0.58
32 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
Found at i:1846 original size:60 final size:59
Alignment explanation
Indices: 1774--1966 Score: 262
Period size: 60 Copynumber: 3.2 Consensus size: 59
1764 GCTAAGTGCT
*
1774 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTTTAATCTTTTAATTTGAC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTTTGATCTTTTAATTTG-C
* **
1834 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGATCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTTTGATCTTTTAATTT-GC
* * * * *
1894 TAAATAAGAGCCTAACGTTAT-CGAAAATGCTCAAATAAGAGCTTGATCTTTTAATTTTGC
1 CAAATAAGGGCCTAACGTT-TGCCAAAATGCTCAAATAAGGGTTTGATCTTTTAA-TTTGC
1954 CAAATAAGGGCCT
1 CAAATAAGGGCCT
1967 GGCGTCGAAA
Statistics
Matches: 116, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
60 111 0.96
61 5 0.04
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (59 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTTTGATCTTTTAATTTGC
Found at i:2046 original size:31 final size:31
Alignment explanation
Indices: 2008--2108 Score: 82
Period size: 31 Copynumber: 3.3 Consensus size: 31
1998 TGACGCCAGT
*
2008 CCCTTATTTGAGCATTTTCGATAAGGTTAGG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGG
** * ** * *
2039 CCCTTATTTG-GCCAAATT--AAAATATCAGA
1 CCCTTATTTGAG-CATTTTCGATAACGTTAGG
*
2068 CTCTTATTTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGG
*
2099 CTCTTATTTG
1 CCCTTATTTG
2109 GCCAAATTAA
Statistics
Matches: 51, Mismatches: 15, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
29 19 0.37
30 2 0.04
31 30 0.59
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.40
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTCGATAACGTTAGG
Found at i:2083 original size:60 final size:60
Alignment explanation
Indices: 2008--2168 Score: 225
Period size: 60 Copynumber: 2.7 Consensus size: 60
1998 TGACGCCAGT
* *
2008 CCCTTATTTGAGCATTTTCGATAAGGTTAGGCCCTTATTTGGCCAAATTAAAATATCAGA
1 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
* * **
2068 CTCTTATTTGAGCATTTTCGATAACGTTAGGCTCTTATTTGGCCAAATTAAAAGATTGGA
1 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
* * *
2128 CCCTTATTTGAGTATTTTGGCA-AACGTTAGGTCCTTATTTG
1 CCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG
2169 AGCAATTAAC
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 88 0.99
61 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.39
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGA
Found at i:2323 original size:15 final size:16
Alignment explanation
Indices: 2304--2340 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
2294 TATAAATAAT
2304 AATATTATAAT-TAAA
1 AATATTATAATCTAAA
*
2319 TATATTATAATCTAAA
1 AATATTATAATCTAAA
2335 AATATT
1 AATATT
2341 TATTAGAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATTATAATCTAAA
Found at i:3536 original size:33 final size:32
Alignment explanation
Indices: 3487--3548 Score: 106
Period size: 33 Copynumber: 1.9 Consensus size: 32
3477 TACTATATAT
3487 TATATATATATATATATATAATTTTTGTATTC
1 TATATATATATATATATATAATTTTTGTATTC
*
3519 TATATATTATATTTATATATAATTTTTGTA
1 TATATA-TATATATATATATAATTTTTGTA
3549 CCTTACCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 6 0.21
33 22 0.79
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (32 bp):
TATATATATATATATATATAATTTTTGTATTC
Found at i:3536 original size:37 final size:40
Alignment explanation
Indices: 3459--3539 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
3449 TTACTAAAAG
3459 TATACTATAATTTTTGCATACTATATATTATATATATATA
1 TATACTATAATTTTTGCATACTATATATTATATATATATA
* * *
3499 TATA-TATAATTTTTGTATTCTATATATTATATTTATATA
1 TATACTATAATTTTTGCATACTATATATTATATATATATA
3538 TA
1 TA
3540 ATTTTTGTAC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 34 0.89
40 4 0.11
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.54
Consensus pattern (40 bp):
TATACTATAATTTTTGCATACTATATATTATATATATATA
Found at i:13538 original size:41 final size:41
Alignment explanation
Indices: 13486--13600 Score: 212
Period size: 41 Copynumber: 2.8 Consensus size: 41
13476 GTAGTTGTAG
*
13486 TAATTTGGGTGATTAAATCACTAATATTTTTTACCTAGTAA
1 TAATATGGGTGATTAAATCACTAATATTTTTTACCTAGTAA
*
13527 TAATATGGGTGATTAAATCACTAATATTTTTTACCTAGTAT
1 TAATATGGGTGATTAAATCACTAATATTTTTTACCTAGTAA
13568 TAATATGGGTGATTAAATCACTAATATTTTTTA
1 TAATATGGGTGATTAAATCACTAATATTTTTTA
13601 GGGTAATTAT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (41 bp):
TAATATGGGTGATTAAATCACTAATATTTTTTACCTAGTAA
Found at i:16499 original size:16 final size:17
Alignment explanation
Indices: 16478--16513 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
16468 TATATCAATT
*
16478 ATTTATATTTTTAT-TA
1 ATTTATATATTTATATA
16494 ATTTATATATTTATATA
1 ATTTATATATTTATATA
16511 ATT
1 ATT
16514 ATGAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTATATATTTATATA
Found at i:16515 original size:24 final size:24
Alignment explanation
Indices: 16477--16525 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
16467 ATATATCAAT
** * *
16477 TATTTATATTTTTATTAATTTATA
1 TATTTATATAATTATGAATTAATA
16501 TATTTATATAATTATGAATTAATA
1 TATTTATATAATTATGAATTAATA
16525 T
1 T
16526 GCTTCCTTCG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TATTTATATAATTATGAATTAATA
Found at i:19786 original size:2 final size:2
Alignment explanation
Indices: 19779--19807 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19769 AGTTAGAAGA
19779 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19808 GTTGTGCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32989 original size:94 final size:94
Alignment explanation
Indices: 32882--33072 Score: 364
Period size: 94 Copynumber: 2.0 Consensus size: 94
32872 TATACTTTAT
32882 TTTTGGCCCAACTGGTAATTATCCTACTCTACTACTTATAGAAAATTAGTAGTAGCACATAGACA
1 TTTTGGCCCAACTGGTAATTATCCTACTCTACTACTTATAGAAAATTAGTAGTAGCACATAGACA
32947 CATCCGAACTTACACTTTCATACTAATAA
66 CATCCGAACTTACACTTTCATACTAATAA
* *
32976 TTTTGGCCCAACTGGTAATTATTCTACTCTACTACTTATATAAAATTAGTAGTAGCACATAGACA
1 TTTTGGCCCAACTGGTAATTATCCTACTCTACTACTTATAGAAAATTAGTAGTAGCACATAGACA
33041 CATCCGAACTTACACTTTCATACTAATAA
66 CATCCGAACTTACACTTTCATACTAATAA
33070 TTT
1 TTT
33073 ACTAGCCATT
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.34
Consensus pattern (94 bp):
TTTTGGCCCAACTGGTAATTATCCTACTCTACTACTTATAGAAAATTAGTAGTAGCACATAGACA
CATCCGAACTTACACTTTCATACTAATAA
Found at i:35504 original size:27 final size:28
Alignment explanation
Indices: 35472--35527 Score: 96
Period size: 27 Copynumber: 2.0 Consensus size: 28
35462 TTTTGCCTGT
*
35472 AAAAATTAAACCAACA-TGATTTTTTAG
1 AAAAATTAAACCAAAATTGATTTTTTAG
35499 AAAAATTAAACCAAAATTGATTTTTTAG
1 AAAAATTAAACCAAAATTGATTTTTTAG
35527 A
1 A
35528 TCTGTCTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 15 0.56
28 12 0.44
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (28 bp):
AAAAATTAAACCAAAATTGATTTTTTAG
Found at i:41253 original size:21 final size:21
Alignment explanation
Indices: 41227--41269 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
41217 TGGTGAGGTC
*
41227 ACCAAGTTATTAGAAAACATG
1 ACCAAGTTATTAAAAAACATG
41248 ACCAAGTTATTAAAAAACATG
1 ACCAAGTTATTAAAAAACATG
41269 A
1 A
41270 TTGCTTCTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (21 bp):
ACCAAGTTATTAAAAAACATG
Found at i:42424 original size:34 final size:34
Alignment explanation
Indices: 42385--42476 Score: 184
Period size: 34 Copynumber: 2.7 Consensus size: 34
42375 GCGAAATGGA
42385 ACTTGTGCATATTAAACATTCTCAAGAACTTCAT
1 ACTTGTGCATATTAAACATTCTCAAGAACTTCAT
42419 ACTTGTGCATATTAAACATTCTCAAGAACTTCAT
1 ACTTGTGCATATTAAACATTCTCAAGAACTTCAT
42453 ACTTGTGCATATTAAACATTCTCA
1 ACTTGTGCATATTAAACATTCTCA
42477 GTTGCAAAGG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.36
Consensus pattern (34 bp):
ACTTGTGCATATTAAACATTCTCAAGAACTTCAT
Found at i:51268 original size:24 final size:27
Alignment explanation
Indices: 51240--51293 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
51230 CATGAAAGAG
*
51240 ATTATTATTACTAATTAATCAGAGGTT
1 ATTATAATTACTAATTAATCAGAGGTT
*
51267 ATTACTAATTACTAATTAATTAGAGGT
1 ATTA-TAATTACTAATTAATCAGAGGT
51294 CTATGTCGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (27 bp):
ATTATAATTACTAATTAATCAGAGGTT
Found at i:51744 original size:50 final size:50
Alignment explanation
Indices: 51675--51782 Score: 182
Period size: 50 Copynumber: 2.2 Consensus size: 50
51665 GCAATAATGA
* * *
51675 ATAT-ATTTTTACTAATGAAGGTATTTAAAAGTTTGAAACTGCTAAATAT
1 ATATCATTATTACTAATGAAGGTATTCAAAAGTTTAAAACTGCTAAATAT
51724 ATATCATTATTACTAATGAAGGTATTCAAAAGTTTAAAACTGCTAAATAT
1 ATATCATTATTACTAATGAAGGTATTCAAAAGTTTAAAACTGCTAAATAT
51774 ATATCATTA
1 ATATCATTA
51783 ACTTTGCCAT
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
49 4 0.07
50 51 0.93
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (50 bp):
ATATCATTATTACTAATGAAGGTATTCAAAAGTTTAAAACTGCTAAATAT
Found at i:52365 original size:5 final size:5
Alignment explanation
Indices: 52355--52417 Score: 67
Period size: 5 Copynumber: 12.8 Consensus size: 5
52345 GTGGGGAGAA
* * *
52355 TTTTG TTTTG TTTAG TTTAG TTTTA TTTTG TTTTG TTTTG TTTT- TTGTT-
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TT-TTG
*
52404 TTTTT TTTTG TTTT
1 TTTTG TTTTG TTTT
52418 TGGTTTTTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
4 4 0.08
5 47 0.92
ACGTcount: A:0.05, C:0.00, G:0.14, T:0.81
Consensus pattern (5 bp):
TTTTG
Found at i:52402 original size:7 final size:7
Alignment explanation
Indices: 52390--52426 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
52380 TTTTGTTTTG
52390 TTTTGTT
1 TTTTGTT
52397 TTTTG-T
1 TTTTGTT
52403 TTTT-TT
1 TTTTGTT
52409 TTTTGTT
1 TTTTGTT
*
52416 TTTGGTT
1 TTTTGTT
52423 TTTT
1 TTTT
52427 AATCTTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
6 10 0.38
7 16 0.62
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (7 bp):
TTTTGTT
Found at i:52408 original size:25 final size:24
Alignment explanation
Indices: 52354--52426 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 24
52344 AGTGGGGAGA
* *
52354 ATTTTGTTTTGTTTAGTTTAGTTTT
1 ATTTTGTTTTGTTTTGTTT-TTTTT
52379 ATTTTGTTTTGTTTTGTTTTTTGTT
1 ATTTTGTTTTGTTTTGTTTTTT-TT
* *
52404 -TTTTTTTTTGTTTTTGGTTTTTT
1 ATTTTGTTTTG-TTTTGTTTTTTT
52427 AATCTTTTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 12 0.29
25 30 0.71
ACGTcount: A:0.05, C:0.00, G:0.15, T:0.79
Consensus pattern (24 bp):
ATTTTGTTTTGTTTTGTTTTTTTT
Found at i:52412 original size:19 final size:19
Alignment explanation
Indices: 52385--52426 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
52375 TTTTATTTTG
*
52385 TTTTGTTTTGTTTTTTGTT
1 TTTTGTTTTGTTTTTGGTT
*
52404 TTTTTTTTTGTTTTTGGTT
1 TTTTGTTTTGTTTTTGGTT
52423 TTTT
1 TTTT
52427 AATCTTTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (19 bp):
TTTTGTTTTGTTTTTGGTT
Found at i:52418 original size:12 final size:12
Alignment explanation
Indices: 52380--52418 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
52370 TTTAGTTTTA
*
52380 TTTTGTTTTGTT
1 TTTTTTTTTGTT
*
52392 TTGTTTTTTGTT
1 TTTTTTTTTGTT
52404 TTTTTTTTTGTT
1 TTTTTTTTTGTT
52416 TTT
1 TTT
52419 GGTTTTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (12 bp):
TTTTTTTTTGTT
Found at i:68186 original size:26 final size:27
Alignment explanation
Indices: 68157--68213 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
68147 TTTTAATAAG
**
68157 TATTCTTTTTAG-TCATTTAACTTTTT
1 TATTCTTTTTAGATCATCCAACTTTTT
* *
68183 TATTTTTTTTAGATGATCCAACTTTTT
1 TATTCTTTTTAGATCATCCAACTTTTT
68210 TATT
1 TATT
68214 AATTTTGGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.21, C:0.11, G:0.05, T:0.63
Consensus pattern (27 bp):
TATTCTTTTTAGATCATCCAACTTTTT
Found at i:68345 original size:15 final size:16
Alignment explanation
Indices: 68320--68349 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
68310 AATAATTATT
68320 TTTAGATTATAATATA
1 TTTAGATTATAATATA
68336 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
68350 TATTATTTAT
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:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:70065 original size:660 final size:654
Alignment explanation
Indices: 68940--72060 Score: 2437
Period size: 661 Copynumber: 4.7 Consensus size: 654
68930 ACCATCATAG
* * * * * *
68940 TTTTTAGCTAAAAACGCGTTACGGGGACCCGACTCAA-TTTTGCATGATTTTTGGC-TCAGAGAC
1 TTTTTGGCAAAAAACGCATTCCGGGGCCCCAACT-AAGTTTTGCATGATTTTTGGCATCA-AGAC
* * * * * *
69003 TACTTGAAATATCTATATTCATCAAATCAAATCT-TGAATACATTTAAGGATTTGTTT-TTACGA
64 TCCTTGAAATATCCATATTCATCTAATCAAATCTATGATTGCATTTAAGAATTTGTTTCTTACGA
* * *
69066 GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAATAATAGGAAAAATGATATTAGA
129 GCATCTGAATCTTGTTT-GATTTAATTAG-AA-TAATTCAGAAAAATATGAAAAATGATATTAAA
* * * * * * ** * *
69131 AGTGTAAAAAATCCAT-CAATATTTTTGGCATTGAATTATATTTTTTTTCCGAGTTTTTTAGCCA
191 AGCGTGAAAAGTCC-TCCAATCTTTTTGGCATTGAATTATATATATTTTATGAGTATTTTAGACA
* * * * * * *
69195 AAAATTGAGTAAATATCTTTC-GGCTTAATTTTTGTAAAATTTTAGTCGAAAATCGTGTAATAAT
255 AAAATTGAGTAAA-ATATTTCTTG-TCAATTTTTGCAAAATTTTAGCCG-AAATCGTGTACTAAC
* * ** * *
69259 CATCACGGTTTTTTGGCTAAAAACGCGTTCCAGGGTCCCGGGTCAGTTTTGTATGATTTTTGGCA
317 CATCACGG-TTTTGGGCTAAAAACGCGTTCCAGGGCCCCGTCTCAGTTTTGCATGATTTTTGGCG
* * * * * * *
69324 CCAAGA-TCCTTGAGATATCCATATTCATCTAATCAAATCTCAACCAGATTGCATTTAAGGATAT
381 CCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATTTCAGCCACATTGGATTTAAGGAT-T
** * * *
69388 GTTTTTACGAGCATTTGAATTTTCTTTCAATTTAATTAGAAATTAATTC-AGAAAAACGATATGA
445 -TTTAAACAAGCATCTGAATTTT-TTTCAATTTAATTAGAAATTAATTCAAGAAAAACGATATTA
* * * * * *
69452 AAAGCGTGAAAGATCCTCCAATCTTTTTGGCGTT-ACATTGTATATATTTCATGAGTATTTTAGC
508 AAAGCATGAAA-ACCCTCCAATCTTTTTGGCGTTGA-ATTATATATATTTTATGAGTATTGTGGC
* *
69516 CAAAAATTGAGGAAAAAAATTTCGGGTCATTTTTTTTTTTTTGCAAAATTTTAGCCGAAATCGTG
571 TAAAAATTGAGGAAAAAAATTTCGGGTCATTTTTTTTTTTTTGCAAAATTTTAGCCGAAACCGTG
69581 TACTAACCATCACAGTTTTT
636 TACTAACCATCAC-GTTTTT
* * * * * ** * **
69601 TTTTTTGCTAAAAATGCGTTTC-GGGCCCCGGCTCAGTTTTGCATGATTTTTGGCATTGAGACTC
1 TTTTTGGCAAAAAACGCATTCCGGGGCCCCAACTAAGTTTTGCATGATTTTTGGCATCAAGACTC
** * *
69665 CTTGAAATATTTATATTCATCTAATCAAATCTCAATCAGATTGCATTTAAGGATTT-TTCCTTAC
66 CTTGAAATATCCATATTCATCTAATCAAATCT--AT--GATTGCATTTAAGAATTTGTTTCTTAC
69729 GAGCATCTGAATCTTGTTTGATTTAATTAG-A-AATT-AGAAAAATATGAAAAATGATATTAAAA
127 GAGCATCTGAATCTTGTTTGATTTAATTAGAATAATTCAGAAAAATATGAAAAATGATATTAAAA
* * * * *
69791 GAGGGAATAGTCCTCCAATCTTTTTGGAATTGAATTATATATATTTTATGAGTATTTTAGACGAA
192 GCGTGAAAAGTCCTCCAATCTTTTTGGCATTGAATTATATATATTTTATGAGTATTTTAGACAAA
* *
69856 AATTGAGTAAAATATTTCTTGTCAATTTTTGCAAAATATTAGCTGAAATCGTGTACGTTAATCGA
257 AATTGAGTAAAATATTTCTTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC--TAA-C--
* * *
69921 AATCACAGTTTAT-GGCTAAAAACGCGTTCCAGGGCCCCGGT-TCAGTGTTGCATGATTTTTGGC
317 CATCACGGTTT-TGGGCTAAAAACGCGTTCCAGGGCCCC-GTCTCAGTTTTGCATGATTTTTGGC
* *
69984 GCCGAGACTCCTTGAAATATCTATACTCATCTAATCAAATTTCAGTCACATTGGATTTAAGG-TT
380 GCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATTTCAGCCACATTGGATTTAAGGATT
* * * * *
70048 TTCTAAACAAACATTTGAATCATGTTTTGATGTAATTAAAAATTATTTTTGAAAATAA-T-AAGA
445 TT-TAAACAAGCATCTGAAT--T-TTTT--T-CAATT--TAATTA-----GAAATTAATTCAAGA
* * * *
70111 AAAACAATATTAGAAGCATGAAAACCCTTCAATCTTTTTGGCATTGAATTATATA-ATTTTTATG
496 AAAACGATATTAAAAGCATGAAAACCCTCCAATCTTTTTGGCGTTGAATTATATATA-TTTTATG
* ** * *
70175 AGTATTGTGGCTAAAAATTGAGGAAATAGCTTTTGGGTCGATGTTTGCAAATTTTAGCTGAAATC
560 AGTATTGTGGCTAAAAATTGAGGAAAAAAATTTCGGGTC-AT-TTT-----TTTT---T----TT
* * ** * * * *
70240 GTGTAATTTTTTTTTGGCCGAACGAAACCGTGTAATAATCATCACG---GT
611 TTGCAA---AATTTTAG-C---CGAAACCGTGTACTAACCATCACGTTTTT
* * * * *
70288 TTTTTGGCAAAAAATGCATTCCGAGGCCCCAGCAAAGTTTTGCATGATTTTTGACATCAAGACTC
1 TTTTTGGCAAAAAACGCATTCCGGGGCCCCAACTAAGTTTTGCATGATTTTTGGCATCAAGACTC
* * * * *
70353 TTTGAGATATCCATATTCATCTAATCAAATCTTAGCTATATTGGATTTAAGAATTTGTTTCTT-T
66 CTTGAAATATCCATATTCATCTAATCAAATC-TA--T-GATTGCATTTAAGAATTTGTTTCTTAC
*
70417 GAGCATCTGAATCTTATTTTGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAATGATATTA
127 GAGCATCTGAATCTT-GTTTGATTTAATTAG-AA-TAATTCAGAAAAATATGAAAAATGATATTA
** *
70482 AAAGCGTGAAAAGTCCTCCAATCTTTTTGGTGTT-AAGTTATATATATATTATG-GTTATTTTAG
189 AAAGCGTGAAAAGTCCTCCAATCTTTTTGGCATTGAA-TTATATATATTTTATGAG-TATTTTAG
* * ** *
70545 CCAAAAATTGAGGAAAA-ATTT-TTCAACTAGTTTTTTGCAAAATTTTAGCCGAAATCGTGTACT
252 ACAAAAATTGAGTAAAATATTTCTT-GTC-A-ATTTTTGCAAAATTTTAGCCGAAATCGTGTACT
* * * * *
70608 AACCATCATGGTTTTGGGCTAAAAACGCGTTTC-GGGGCCCGTCTTAGTTTTCCATGATTTTTGG
314 AACCATCACGGTTTTGGGCTAAAAACGCGTTCCAGGGCCCCGTCTCAGTTTTGCATGATTTTTGG
* * * *
70672 TGCTGAGACTCCTTGAAATATCTATATTCATCTAATCAAATTTCAGTCACATTAGATTTAAGGAT
379 CGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATTTCAGCCACATTGGATTTAAGGAT
* * *
70737 TTGTAAAACAAGCATCTGAATCATGTTTT-GATTTAATTAGAAATTAATTCTGAAAATAATAAGA
444 TT-TTAAACAAGCATCTGAAT--TTTTTTCAATTTAATTAGAAATTAATTC----------AAGA
* * * *
70801 AAAACGACATTAGAAGCATGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATAT-TTTTTTATG
496 AAAACGATATTAAAAGCATGAAAA-CCCTCCAATCTTTTTGGCGTTGAATTATATATATTTTATG
* *
70865 AGTATTGTGGCTAAAAATTGAGGAAATAAATTTCGGGTCA-------ATTTTTGCAAAATTTTAG
560 AGTATTGTGGCTAAAAATTGAGGAAAAAAATTTCGGGTCATTTTTTTTTTTTTGCAAAATTTTAG
*
70923 CCGAAACCGTGTTA-TAATCATCACGTTTTT
625 CCGAAACCGTG-TACTAACCATCACGTTTTT
*
70953 TTTTTGGCAAAAAACGCATTCCGGGGCCCCAACTAAGTTTTGCATGATTTTTGGCACCAAGACTC
1 TTTTTGGCAAAAAACGCATTCCGGGGCCCCAACTAAGTTTTGCATGATTTTTGGCATCAAGACTC
* * * *
71018 TTTGAGATATCCATATTCATCTAATCAAAGCTAT-ATTGGATTTAAGAATTTGTTTC-TACGAGC
66 CTTGAAATATCCATATTCATCTAATCAAATCTATGATTGCATTTAAGAATTTGTTTCTTACGAGC
* *
71081 ATCTGAATCTAGTTTTGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAG
131 ATCTGAATCTTG-TTTGATTTAATTAG-AA-TAATTCAGAAAAATATGAAAAATGATATTAAAAG
* * * * * *
71146 CGTGAAAAGTTCTCCAATCCTTTTGGCGTTAAATTATATATATTTTAAGATTATTTTAGACAAAA
193 CGTGAAAAGTCCTCCAATCTTTTTGGCATTGAATTATATATATTTTATGAGTATTTTAGACAAAA
* * ** * *
71211 ATTGAGGAAAAAAATTTTCAAGTCATTTTTTGCAAAATTTTAACCGAAATCGTGTACTAACCATC
258 ATTGA-GTAAAATA-TTTCTTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATC
* * * *
71276 ACGGTTTTGGGTTAAAAACGCGTTCCGGGGCCCCGTCTTAGTTTTGCATGAATTTTGGCGCCGAG
321 ACGGTTTTGGGCTAAAAACGCGTTCCAGGGCCCCGTCTCAGTTTTGCATGATTTTTGGCGCCGAG
** * *
71341 ACTCCTTGAAATATCTATATTCATCTAATCAAATAACAGCCACATTGAATTTAAGGATTTGTTTT
386 ACTCCTTGAAATATCTATATTCATCTAATCAAATTTCAGCCACATTGGATTTAAGGA-TT-TTTA
* ** *
71406 TATGAGCATCTGAATTTTATTTCGATTTAATTAGAAATTAATTCTAAAAAATAGGAAAAACGATA
449 AACAAGCATCTGAATTTT-TTTCAATTTAATTAGAAATTAATTC------A-A-GAAAAACGATA
* * *
71471 TTAAAAGCGTGAAAAGGTCCTCCAATATTTTTGGCGTTGAATTATATATA--TTATGAGTATTGT
505 TTAAAAGCATGAAAA--CCCTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTGT
* *
71534 GGCTAAAAATTGAGGAAAAATATTTCGGGTCA-------ATTTTTGCAAAATTTTAGCC-AAA--
568 GGCTAAAAATTGAGGAAAAAAATTTCGGGTCATTTTTTTTTTTTTGCAAAATTTTAGCCGAAACC
* ** * *
71589 ATAAAGT-ACCATCACG---GT
633 GTGTACTAACCATCACGTTTTT
** * * * *** *** *** *
71607 TTTTTGGCTCAAAACACGTTTCGGGGTTGCGGGTAAGTTTTGCATGATTTTTGGTGGCAAAACTC
1 TTTTTGGCAAAAAACGCATTCCGGGGCCCCAACTAAGTTTTGCATGATTTTTGGCATCAAGACTC
* * * *
71672 CTCGAAATATCTATATTCATCTAACCAAATCT-TAGCCACATTGGATTTAA-AGATTTGTTT-TT
66 CTTGAAATATCCATATTCATCTAATCAAATCTAT-G----ATTGCATTTAAGA-ATTTGTTTCTT
* * * * * * * *
71734 ACGAGCATTTGAATCATGTTTCGATTTAATTAGGAATTATTTTGAAAAAAAAAAGGAAAAACGAT
125 ACGAGCATCTGAATCTTGTTT-GATTTAATTA-GAA-TA-ATT-CAGAAAAATATGAAAAATGAT
* * * ** *
71799 ATTAGAAGCATGAGAAA-CCCTTTAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTG
185 ATTAAAAGCGTGA-AAAGTCCTCCAATCTTTTTGGCATTGAATTATATATATTTTATGAGTATT-
** * *
71863 TT-G-CTAAAAATTGAG-AACAATATTTCGGGTAAATTTTTGCAAAATTTTAACCGAAAT--TG-
248 TTAGAC-AAAAATTGAGTAA-AATATTTCTTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
* * * * * *
71922 --TAACCACACACGGTTTTTTTTTTGGCTAAAAA-GCGTTTCGGGGCCCCAG-GTCAATTTTGCA
311 ACTAACCA-TCACGG-----TTTTGGGCTAAAAACGCGTTCCAGGGCCCC-GTCTCAGTTTTGCA
* * * *
71983 TGATTTTTGGCGCCAAGACTCCTTAAAATATATCTATATTCAAT-T-ACCAAATCTCAGCCACAT
369 TGATTTTTGGCGCCGAGACTCCTT-GAA-ATATCTATATTC-ATCTAATCAAATTTCAGCCACAT
*
72046 TGTATTTAAGGATTT
431 TGGATTTAAGGATTT
72061 GTTTTTACGA
Statistics
Matches: 2044, Mismatches: 278, Indels: 279
0.79 0.11 0.11
Matches are distributed among these distances:
653 1 0.00
654 83 0.04
655 5 0.00
657 21 0.01
658 33 0.02
659 226 0.11
660 279 0.14
661 317 0.16
662 205 0.10
663 46 0.02
664 17 0.01
665 134 0.07
666 5 0.00
667 5 0.00
669 6 0.00
670 64 0.03
671 26 0.01
672 10 0.00
673 1 0.00
677 4 0.00
678 7 0.00
679 1 0.00
680 1 0.00
683 5 0.00
684 5 0.00
685 3 0.00
687 26 0.01
688 96 0.05
689 109 0.05
690 114 0.06
691 51 0.02
692 3 0.00
693 15 0.01
694 91 0.04
695 29 0.01
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (654 bp):
TTTTTGGCAAAAAACGCATTCCGGGGCCCCAACTAAGTTTTGCATGATTTTTGGCATCAAGACTC
CTTGAAATATCCATATTCATCTAATCAAATCTATGATTGCATTTAAGAATTTGTTTCTTACGAGC
ATCTGAATCTTGTTTGATTTAATTAGAATAATTCAGAAAAATATGAAAAATGATATTAAAAGCGT
GAAAAGTCCTCCAATCTTTTTGGCATTGAATTATATATATTTTATGAGTATTTTAGACAAAAATT
GAGTAAAATATTTCTTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGT
TTTGGGCTAAAAACGCGTTCCAGGGCCCCGTCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCC
TTGAAATATCTATATTCATCTAATCAAATTTCAGCCACATTGGATTTAAGGATTTTTAAACAAGC
ATCTGAATTTTTTTCAATTTAATTAGAAATTAATTCAAGAAAAACGATATTAAAAGCATGAAAAC
CCTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTGGCTAAAAATTGAGGAAA
AAAATTTCGGGTCATTTTTTTTTTTTTGCAAAATTTTAGCCGAAACCGTGTACTAACCATCACGT
TTTT
Found at i:72126 original size:333 final size:327
Alignment explanation
Indices: 71133--72207 Score: 1070
Period size: 333 Copynumber: 3.2 Consensus size: 327
71123 AATATGAAAA
* ** * * * * * *
71133 ACGATATTAAAAGCGTGAAAAGTTCTCCAATCCTTTTGGCGTTAAATTATATATATTTTAAGATT
1 ACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGT
** *
71198 ATT-TTAGAC-AAAAATTGAGGAAAAAAATTTTCAAGTCATTTTTTGCAAAATTTTAACCGAAAT
66 ATTGTT-G-CTAAAAATTGAGGAAAAAAA-TTTCGGGTCAATTTTTGCAAAATTTTAACCGAAAT
* * * * * *
71261 CGTGTACTAACCATCACGG-TTTTGGGTTAAAAACGCGTTCCGGGGCCCCGTCTTAGTTTTGCAT
128 -ATG---TAACCAACACGGTTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGTC--AATTTTGCAT
* * * ** *
71325 GAATTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATAACAGCCACATTGAA
187 GATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGA
* * * *
71390 TTTAAGGATTTGTTTTTATGAGCATCTGAATTTTATTTCGATTTAATTAGAAATTAATTCT--AA
252 TTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATT-TGAAA
71453 AAAATAGGAAAA
316 AAAATAGGAAAA
* * * * *
71465 ACGATATTAAAAGCGTGAAAAGGTCCTCCAATATTTTTGGCGTTGAATTATATA--TATTATGAG
1 ACGATATTAGAAGCGTGAAAA-GCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAG
* * * *
71528 TATTGTGGCTAAAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATAA
65 TATTGTTGCTAAAAATTGAGGAAAAAAATTTCGGGTCAATTTTTGCAAAATTTTAACCGAAAT-A
* * * * * **
71593 AGT-ACCATCACGGTTTTTTGGCTCAAAACACGTTTCGGGGTTGCGGGT-AAGTTTTGCATGATT
129 TGTAACCAACACGGTTTTTTGGCTAAAAACGCGTTTCGGGG--CCCCGTCAA-TTTTGCATGATT
* * * * *
71656 TTTGGTGGCAAAACTCCTCGAAATATCTATATTCATCTAACCAAATCTTAGCCACATTGGATTTA
191 TTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTA
* * * * * *
71721 AAGATTTGTTTTTACGAGCATTTGAATCATGTTTCGATTTAATTAGGAATTATTTTGAAAAAAAA
256 AGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTTG-AAAAAAA
*
71786 AAGGAAAA
320 TAGGAAAA
* * *
71794 ACGATATTAGAAGCATGAGAAA-CCCTTTAATCTTTTTGGCATTGAATTATATATTTTTTATGAG
1 ACGATATTAGAAGCGTGA-AAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAG
* * *
71858 TATTGTTGCTAAAAATTGA-GAACAATATTTCGGGTAAATTTTTGCAAAATTTTAACCGAAAT-T
65 TATTGTTGCTAAAAATTGAGGAAAAAAATTTCGGGTCAATTTTTGCAAAATTTTAACCGAAATAT
71921 GTAACCACACACGGTTTTTTTTTTGGCTAAAAA-GCGTTTCGGGGCCCCAGGTCAATTTTGCATG
130 GTAACCA-ACACGG----TTTTTTGGCTAAAAACGCGTTTCGGGGCCCC--GTCAATTTTGCATG
*
71985 ATTTTTGGCGCCAAGACTCCTTAAAATATATCTATATTCAAT-T-ACCAAATCTCAGCCACATTG
188 ATTTTTGGCGCCAAGACTCCTT-GAA-ATATCTATATTC-ATCTAACCAAATCTCAGCCACATTG
* * *
72048 TATTTAAGGATTTGTTTTTACGAGTATCT-AATTCTTGTTTTGATTTAATCAGAAA-TAATTTGG
250 GATTTAAGGATTTGTTTTTACGAGCATCTGAA-TCTTGTTTTGATTTAATTAGAAATTAATTT-G
72111 AAATAAAATAGGAAAA
313 AAA-AAAATAGGAAAA
* * * * * * * *
72127 GCGATATTAGAAGCGTAAAAAGGCTTTCAATTTTTTTGGCATTGAATTATATATTCTTTACGAGT
1 ACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGT
*
72192 ATT-TTCGCTAGAAATT
66 ATTGTT-GCTAAAAATT
72208 ATTCATCTAA
Statistics
Matches: 621, Mismatches: 92, Indels: 59
0.80 0.12 0.08
Matches are distributed among these distances:
326 12 0.02
327 137 0.22
328 30 0.05
329 76 0.12
330 62 0.10
331 28 0.05
332 76 0.12
333 185 0.30
334 13 0.02
335 2 0.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (327 bp):
ACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGT
ATTGTTGCTAAAAATTGAGGAAAAAAATTTCGGGTCAATTTTTGCAAAATTTTAACCGAAATATG
TAACCAACACGGTTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGTCAATTTTGCATGATTTTTGG
CGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGAT
TTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTTGAAAAAAATAGGAA
AA
Found at i:72716 original size:522 final size:517
Alignment explanation
Indices: 71685--72718 Score: 1252
Period size: 522 Copynumber: 2.0 Consensus size: 517
71675 GAAATATCTA
** * * *
71685 TATTCATCTAACCAAATCTTAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCATTTGAATCA
1 TATTCATCTAACCAAATCGCAGCCACATTGGATTTAAAGATTGGTTTTTACGAGCATCTAAATCA
* * * *
71750 TGTTTCGATTTAATTAGGAATTATTTTGAAAAAAAAAAGGAAAAACGATATTAGAAGCATGAGAA
66 TGTTTCGATTAAATTAGGAATTAATTTGAAAAAAAAAAGGAAAAACGATATTAGAAGCATAAAAA
* *
71815 ACCCTTTAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTGTTGCTAAAAATTGAGAA
131 ACCCTTTAATCTTTTTGACATTGAATTATATATTTTTCATGAGTATTGTTGCTAAAAATTGAGAA
* * * *
71880 CAATATTTCGGGTAAATTTTTGCAAAATTTTAACCGAAATTGTAACCACACACGGTTTTTTTTTT
196 AAATATTTCAGGTAAATTTTTGCAAAATTTTAACCGAAATTCTAACCACACACGG----TTTTTC
*
71945 GGCTAAAAAGCGTTTCGGGGCCCCAGGTCAATTTTGCATGATTTTTGGCGCCAAGACTCCTTAAA
257 GGCTAAAAAGCGTTCCGGGGCCCCAGGTCAATTTTGCATGATTTTTGGCGCCAAGACTCCTTAAA
* * * * *
72010 ATATATCTATATTCAATTACCAAATCTCAGCCACATTGTATTTAAGGATTTGTTTTTACGAGTAT
322 ATATATCTATATTCAATTAACAAATCTCAACCACATTGGATTTAAGGATTTATTTTTACGAGCAT
* * * *
72075 CTAATTCTTGTTTTGATTTAATCAGAAATAATTTGGAAATAAAATAGGAAAAGCGATATTAGAAG
387 CTAATTCTTGTTTGGATTTAATCAGAAATAATTCGGAAATAAAATAGAAAAAGCAATATTAGAAG
* * *
72140 CGTAAAAAGGCTTTCAATTTTTTTGGCATTGAATTATATATTCTTTACGAGTATTTTCGCTAGAA
452 CGTAAAAAGCCCTTCAATTTTTTT-GCATTGAATTATATATTCTTTAAGAGTATTTTCGCTAGAA
72205 AT
516 AT
* * * *
72207 TATTCATCTAACCAAATCGCAGCCACATTGTATTTAAGGATTGGTTTTTACGAGTATCTAAATCT
1 TATTCATCTAACCAAATCGCAGCCACATTGGATTTAAAGATTGGTTTTTACGAGCATCTAAATCA
* * * * *
72272 TGTTTCGATTAAATCT-GTAATTAATTTGGAATAAAATAGGAAAAGCGATATTAGAAGCATAAAA
66 TGTTTCGATTAAAT-TAGGAATTAATTTGAAAAAAAAAAGGAAAAACGATATTAGAAGCATAAAA
** * *
72336 AAGGCTTTCAACTTTTTTTGACATTGAATTATATATTTTTCATGCGTATT-TTCGCTAAAAATTG
130 AACCCTTT-AA-TCTTTTTGACATTGAATTATATATTTTTCATGAGTATTGTT-GCTAAAAATTG
* * * *
72400 ATGAAAAATCTTTCAGGTCAATTTTTGCAAAATTTTAGCTGAAATCATATACTAACCAC-CACGG
192 A-GAAAAATATTTCAGGTAAATTTTTGCAAAATTTTAACCG-AA--AT-T-CTAACCACACACGG
* * *
72464 -TTTTCGGCTAATAACGCGTTCCGGGG-CCC-GGCTCAGTTTTGCATGATTTTTGGTGCCAAGAC
251 TTTTTCGGCTAA-AAAGCGTTCCGGGGCCCCAGG-TCAATTTTGCATGATTTTTGGCGCCAAGAC
* *
72526 TCCTTGAAATAT-T-TATATTC-ATCTAAACAAATCTCAACCGCATTGGATTTAAGGATTTATTT
314 TCCTTAAAATATATCTATATTCAAT-T-AACAAATCTCAACCACATTGGATTTAAGGATTTATTT
*
72588 TTACGAGCATCTGAA-TCTTGTTTGGATTTAATTAGAAATTAATTCGG-AA-AAAATATGAAAAA
377 TTACGAGCATCT-AATTCTTGTTTGGATTTAATCAGAAA-TAATTCGGAAATAAAATA-GAAAAA
* * *
72650 G-AATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTT-TATGTCGAATTATATGTT-TTTAAGA
439 GCAATATTAGAAGCGTAAAAAGCCCTTCAAT-TTTTTTGCAT-T-GAATTATATATTCTTTAAGA
72712 GTATTTT
501 GTATTTT
72719 TGGCAAAAAT
Statistics
Matches: 438, Mismatches: 54, Indels: 40
0.82 0.10 0.08
Matches are distributed among these distances:
521 4 0.01
522 168 0.38
523 97 0.22
524 107 0.24
525 45 0.10
526 2 0.00
528 2 0.00
529 6 0.01
530 7 0.02
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (517 bp):
TATTCATCTAACCAAATCGCAGCCACATTGGATTTAAAGATTGGTTTTTACGAGCATCTAAATCA
TGTTTCGATTAAATTAGGAATTAATTTGAAAAAAAAAAGGAAAAACGATATTAGAAGCATAAAAA
ACCCTTTAATCTTTTTGACATTGAATTATATATTTTTCATGAGTATTGTTGCTAAAAATTGAGAA
AAATATTTCAGGTAAATTTTTGCAAAATTTTAACCGAAATTCTAACCACACACGGTTTTTCGGCT
AAAAAGCGTTCCGGGGCCCCAGGTCAATTTTGCATGATTTTTGGCGCCAAGACTCCTTAAAATAT
ATCTATATTCAATTAACAAATCTCAACCACATTGGATTTAAGGATTTATTTTTACGAGCATCTAA
TTCTTGTTTGGATTTAATCAGAAATAATTCGGAAATAAAATAGAAAAAGCAATATTAGAAGCGTA
AAAAGCCCTTCAATTTTTTTGCATTGAATTATATATTCTTTAAGAGTATTTTCGCTAGAAAT
Found at i:90426 original size:33 final size:33
Alignment explanation
Indices: 90384--90458 Score: 141
Period size: 33 Copynumber: 2.3 Consensus size: 33
90374 GTTTATTTAT
*
90384 GTATGATCTTATTTGTAGTGCCATTGCATATTC
1 GTATGATCTTATTTGTAGCGCCATTGCATATTC
90417 GTATGATCTTATTTGTAGCGCCATTGCATATTC
1 GTATGATCTTATTTGTAGCGCCATTGCATATTC
90450 GTATGATCT
1 GTATGATCT
90459 AGCTAATATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (33 bp):
GTATGATCTTATTTGTAGCGCCATTGCATATTC
Done.