Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002312.1 Hibiscus syriacus cultivar Beakdansim tig00004711_pilon, 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: 75583
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:660 original size:32 final size:32
Alignment explanation
Indices: 591--662 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
581 CTAAGGTGAT
* * * *
591 CCTTGGGTAGGCTGTGAGGCCCCGAGAAACTT
1 CCTTGGGTAGGCTCTCAGGCCCCAAGAAACTC
* **
623 TCTTGGGTAGGCTCTCAGGCCCCAAGGCACTC
1 CCTTGGGTAGGCTCTCAGGCCCCAAGAAACTC
655 CCTTGGGT
1 CCTTGGGT
663 TAATCATGGA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.15, C:0.29, G:0.32, T:0.24
Consensus pattern (32 bp):
CCTTGGGTAGGCTCTCAGGCCCCAAGAAACTC
Found at i:1882 original size:20 final size:18
Alignment explanation
Indices: 1833--1883 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
1823 TAAGGTGAAC
* *
1833 ATAAATAAAATT-TTAAG
1 ATAAATATAATTAATAAG
*
1850 ATAAATATTATTAATAAG
1 ATAAATATAATTAATAAG
1868 ATATATATATAATTAA
1 ATA-A-ATATAATTAA
1884 AAATTAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 10 0.37
18 7 0.26
19 1 0.04
20 9 0.33
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (18 bp):
ATAAATATAATTAATAAG
Found at i:16413 original size:33 final size:34
Alignment explanation
Indices: 16365--16490 Score: 175
Period size: 33 Copynumber: 3.6 Consensus size: 34
16355 TTTTCACCCT
16365 AAACCCGAACCCGACCCGAATATCACACTTAAAA
1 AAACCCGAACCCGACCCGAATATCACACTTAAAA
16399 AAACCCG-ACCCGACCCGAATATCACACTTAAAAA
1 AAACCCGAACCCGACCCGAATATCACACTT-AAAA
*
16433 AACCGACCCGAACCCGACCCGAATATCAAACTTAAAA
1 AA---ACCCGAACCCGACCCGAATATCACACTTAAAA
*
16470 AAACCAG-ACCCGACCCCGAAT
1 AAACCCGAACCCGA-CCCGAAT
16491 TTTTTTTAAA
Statistics
Matches: 84, Mismatches: 2, Indels: 12
0.86 0.02 0.12
Matches are distributed among these distances:
33 28 0.33
34 24 0.29
37 11 0.13
38 21 0.25
ACGTcount: A:0.43, C:0.37, G:0.10, T:0.10
Consensus pattern (34 bp):
AAACCCGAACCCGACCCGAATATCACACTTAAAA
Found at i:16448 original size:38 final size:38
Alignment explanation
Indices: 16367--16488 Score: 182
Period size: 38 Copynumber: 3.3 Consensus size: 38
16357 TTCACCCTAA
16367 ACCCGAACCCGACCCGAATATCACACTT-AAAAAA---
1 ACCCGAACCCGACCCGAATATCACACTTAAAAAAACCG
16401 ACCCG-ACCCGACCCGAATATCACACTTAAAAAAACCG
1 ACCCGAACCCGACCCGAATATCACACTTAAAAAAACCG
*
16438 ACCCGAACCCGACCCGAATATCAAACTTAAAAAAACCAG
1 ACCCGAACCCGACCCGAATATCACACTTAAAAAAACC-G
*
16477 ACCCGACCCCGA
1 ACCCGAACCCGA
16489 ATTTTTTTTA
Statistics
Matches: 80, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
33 22 0.28
34 11 0.14
37 5 0.06
38 30 0.38
39 12 0.15
ACGTcount: A:0.42, C:0.38, G:0.11, T:0.10
Consensus pattern (38 bp):
ACCCGAACCCGACCCGAATATCACACTTAAAAAAACCG
Found at i:24351 original size:127 final size:127
Alignment explanation
Indices: 24120--24392 Score: 492
Period size: 127 Copynumber: 2.1 Consensus size: 127
24110 AGGACCTATA
24120 TAATCTGGTTTCTAATGTACAAAAGACCCTTCAATAGGTCTATCGATCCTCTAGGAAGTGCCATA
1 TAATCTGGTTTCTAATGTACAAAAGACCCTTCAATAGGTCTATCGATCCTCTAGGAAGTGCCATA
* *
24185 AATATGTGGACATCCAAATTCGTATTGTTTTTAGAAGAGGCCGCGTACCAAGTTGTTCGATT
66 AATATGTGGACATCCAAATTCGTATTGTTTTTAGAAGAGGCCGCCTACCAAGTTGTTCAATT
*
24247 TAATATGGTTTCTAATGTACAAAAGACCCTTCAATAGGTCTATCGATCCTCTAGGAAGTGCCATA
1 TAATCTGGTTTCTAATGTACAAAAGACCCTTCAATAGGTCTATCGATCCTCTAGGAAGTGCCATA
* *
24312 AATATGTGGACATCCAAATTCTTATTGTTTTTAGAAGAGGCTGCCTACCAAGTTGTTCAATT
66 AATATGTGGACATCCAAATTCGTATTGTTTTTAGAAGAGGCCGCCTACCAAGTTGTTCAATT
*
24374 TAATCTGGCTTCTAATGTA
1 TAATCTGGTTTCTAATGTA
24393 AGATAAAAAT
Statistics
Matches: 139, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
127 139 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (127 bp):
TAATCTGGTTTCTAATGTACAAAAGACCCTTCAATAGGTCTATCGATCCTCTAGGAAGTGCCATA
AATATGTGGACATCCAAATTCGTATTGTTTTTAGAAGAGGCCGCCTACCAAGTTGTTCAATT
Found at i:28691 original size:143 final size:143
Alignment explanation
Indices: 28444--28729 Score: 572
Period size: 143 Copynumber: 2.0 Consensus size: 143
28434 TTAATATAAA
28444 AAGCTTAATATTTCAAGATTCAAGATTACATTATGATATCACTTCAAATTGATGGGTTTGTCGAA
1 AAGCTTAATATTTCAAGATTCAAGATTACATTATGATATCACTTCAAATTGATGGGTTTGTCGAA
28509 CCAAGTAACTTCAATCGCTTAAAGACATCATTTAACCCTTCATATTAGTCGCTTAACACTATTTC
66 CCAAGTAACTTCAATCGCTTAAAGACATCATTTAACCCTTCATATTAGTCGCTTAACACTATTTC
28574 TTATTAAACTCTT
131 TTATTAAACTCTT
28587 AAGCTTAATATTTCAAGATTCAAGATTACATTATGATATCACTTCAAATTGATGGGTTTGTCGAA
1 AAGCTTAATATTTCAAGATTCAAGATTACATTATGATATCACTTCAAATTGATGGGTTTGTCGAA
28652 CCAAGTAACTTCAATCGCTTAAAGACATCATTTAACCCTTCATATTAGTCGCTTAACACTATTTC
66 CCAAGTAACTTCAATCGCTTAAAGACATCATTTAACCCTTCATATTAGTCGCTTAACACTATTTC
28717 TTATTAAACTCTT
131 TTATTAAACTCTT
28730 TTTTTTCCAT
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
143 143 1.00
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (143 bp):
AAGCTTAATATTTCAAGATTCAAGATTACATTATGATATCACTTCAAATTGATGGGTTTGTCGAA
CCAAGTAACTTCAATCGCTTAAAGACATCATTTAACCCTTCATATTAGTCGCTTAACACTATTTC
TTATTAAACTCTT
Found at i:29412 original size:17 final size:17
Alignment explanation
Indices: 29381--29422 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
29371 ATGTATAATT
*
29381 TATATTTTA-TTTTT-A
1 TATATTATACTTTTTAA
29396 TATAGTTATACTTTTTAA
1 TATA-TTATACTTTTTAA
29414 TATATTATA
1 TATATTATA
29423 ATTAAAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 4 0.17
16 4 0.17
17 10 0.43
18 5 0.22
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (17 bp):
TATATTATACTTTTTAA
Found at i:29719 original size:31 final size:31
Alignment explanation
Indices: 29684--29778 Score: 81
Period size: 31 Copynumber: 3.1 Consensus size: 31
29674 TGCATCACAT
29684 GTCCTTAAAGTATGAACATTATTTTAAATTA
1 GTCCTTAAAGTATGAACATTATTTTAAATTA
* * * * *
29715 GTCCTTAAATTTTTAA-A-TATTCTAATTTCA
1 GTCCTTAAAGTATGAACATTATTTTAAATT-A
* *
29745 -TCCCTAAGGTATG-ACTATTATTTTAAATTA
1 GTCCTTAAAGTATGAAC-ATTATTTTAAATTA
29775 GTCC
1 GTCC
29779 CCAAATTTTT
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
28 1 0.02
29 17 0.36
30 4 0.09
31 25 0.53
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (31 bp):
GTCCTTAAAGTATGAACATTATTTTAAATTA
Found at i:29768 original size:60 final size:59
Alignment explanation
Indices: 29690--29873 Score: 190
Period size: 60 Copynumber: 3.0 Consensus size: 59
29680 ACATGTCCTT
* * *
29690 AAAGTATGAACATTATTTTAAATTAGTCCTTAAATTTTTAAATATTCTAATTTCATCCCT
1 AAAGTATG-ACATTATTTTAAATTAGTCCTAAAATTTTTAAACATTCTAATTTCATCCCA
* ** *
29750 AAGGTATGACTATTATTTTAAATTAGTCCCCAAATTTTTTAACACTT-TAATTTCATCCCA
1 AAAGTATGAC-ATTATTTTAAATTAGTCCTAAAATTTTTAAACA-TTCTAATTTCATCCCA
** * * * *
29810 AAACAATGACATTCATTCTAAATTGGTCCCTAAAATTATTTGAACATTCTAATTTCATTCCA
1 AAAGTATGACATT-ATTTTAAATTAGT-CCTAAAATT-TTTAAACATTCTAATTTCATCCCA
29872 AA
1 AA
29874 CTAAATGTAT
Statistics
Matches: 103, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
59 5 0.05
60 66 0.64
61 11 0.11
62 21 0.20
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.41
Consensus pattern (59 bp):
AAAGTATGACATTATTTTAAATTAGTCCTAAAATTTTTAAACATTCTAATTTCATCCCA
Found at i:30194 original size:22 final size:24
Alignment explanation
Indices: 30163--30209 Score: 80
Period size: 22 Copynumber: 2.0 Consensus size: 24
30153 ATATTAAATC
30163 TAAAATTAATTATACATAAT-TAT
1 TAAAATTAATTATACATAATGTAT
30186 TAAAA-TAATTATACATAATGTAT
1 TAAAATTAATTATACATAATGTAT
30209 T
1 T
30210 TTTTACTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (24 bp):
TAAAATTAATTATACATAATGTAT
Found at i:31142 original size:115 final size:117
Alignment explanation
Indices: 31006--31247 Score: 301
Period size: 115 Copynumber: 2.1 Consensus size: 117
30996 AAAATATATA
** * *
31006 GACGATAACATAACCGGTTAATTATTGGAAACATTATCAAGCACAATAACATATT-GGTAGCG-T
1 GACGATAACATAACCAATTAATTACTAGAAACATTATCAAGCACAATAACATATTAGGTAGCGCT
*
31069 T-TATAACGTAATAAGTAGCGTCTTGTTAAAGCTAATGGAGCTTTGAAAATCC
66 TATATAACGTAATAAGTAGC-ACTTGTTAAAGCTAATGGAGCTTTGAAAATCC
* * * *
31121 GACGATAACATAACCAATTAATTACTATAAATATTATCAAGCATAATAACATTTTAGGTAGCGCT
1 GACGATAACATAACCAATTAATTACTAGAAACATTATCAAGCACAATAACATATTAGGTAGCGCT
* * * * * * * *
31186 TATATAACGTAATAGGTAGCACTTTTTTAAGCTGATGGGGTTTTGGAAATTC
66 TATATAACGTAATAAGTAGCACTTGTTAAAGCTAATGGAGCTTTGAAAATCC
31238 GACGATAACA
1 GACGATAACA
31248 AAATAGGTTA
Statistics
Matches: 107, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
115 47 0.44
116 7 0.07
117 36 0.34
118 17 0.16
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (117 bp):
GACGATAACATAACCAATTAATTACTAGAAACATTATCAAGCACAATAACATATTAGGTAGCGCT
TATATAACGTAATAAGTAGCACTTGTTAAAGCTAATGGAGCTTTGAAAATCC
Found at i:31259 original size:117 final size:115
Alignment explanation
Indices: 31006--31261 Score: 282
Period size: 117 Copynumber: 2.2 Consensus size: 115
30996 AAAATATATA
* * * *
31006 GACGATAACATAACCGGTTAATTATTGGAAACATTATCAAGCACAATAACATATTGGTAGCGTTT
1 GACGATAACAAAACAGGTTAATTACTAGAAACATTATCAAGCACAATAACATATTGGTAGCGTTT
*
31071 ATAACGTAATAAGTAGCGTCTTGTTAAAGCTAATGGAGCTTTGAAAATCC
66 ATAACGTAATAAGTAGCGACTTGTTAAAGCTAATGGAGCTTTGAAAATCC
* * * * * *
31121 GACGATAACATAACCA-ATTAATTACTATAAATATTATCAAGCATAATAACATTTTAGGTAGCGC
1 GACGATAACA-AAACAGGTTAATTACTAGAAACATTATCAAGCACAATAACATATT-GGTAGCG-
* * * * * * * *
31185 TTATATAACGTAATAGGTAGC-ACTTTTTTAAGCTGATGGGGTTTTGGAAATTC
63 TT-TATAACGTAATAAGTAGCGACTTGTTAAAGCTAATGGAGCTTTGAAAATCC
*
31238 GACGATAACAAAATAGGTTAATTA
1 GACGATAACAAAACAGGTTAATTA
31262 TTGGATTTGT
Statistics
Matches: 114, Mismatches: 22, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
115 42 0.37
116 12 0.11
117 43 0.38
118 17 0.15
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.31
Consensus pattern (115 bp):
GACGATAACAAAACAGGTTAATTACTAGAAACATTATCAAGCACAATAACATATTGGTAGCGTTT
ATAACGTAATAAGTAGCGACTTGTTAAAGCTAATGGAGCTTTGAAAATCC
Found at i:33470 original size:10 final size:10
Alignment explanation
Indices: 33452--33521 Score: 74
Period size: 10 Copynumber: 7.1 Consensus size: 10
33442 AAATAAATGG
*
33452 ATAAGAAATA
1 ATAATAAATA
33462 ATAATAAATA
1 ATAATAAATA
*
33472 ATAGT-AATAA
1 ATAATAAAT-A
33482 ATAAT-AATAA
1 ATAATAAAT-A
33492 ATAA-AAATA
1 ATAATAAATA
*
33501 AAAATAAATA
1 ATAATAAATA
33511 ATAATAAATA
1 ATAATAAATA
33521 A
1 A
33522 ATCATTATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
9 7 0.13
10 45 0.87
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (10 bp):
ATAATAAATA
Found at i:33481 original size:16 final size:17
Alignment explanation
Indices: 33452--33521 Score: 83
Period size: 16 Copynumber: 4.2 Consensus size: 17
33442 AAATAAATGG
*
33452 ATAAGAAATAATAATAA
1 ATAATAAATAATAATAA
*
33469 ATAAT-AGTAATAA-ATA
1 ATAATAAATAATAATA-A
*
33485 ATAATAAATAAAAATAA
1 ATAATAAATAATAATAA
33502 A-AATAAATAATAATAA
1 ATAATAAATAATAATAA
33518 ATAA
1 ATAA
33522 ATCATTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
15 1 0.02
16 28 0.64
17 14 0.32
18 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
ATAATAAATAATAATAA
Found at i:33487 original size:26 final size:27
Alignment explanation
Indices: 33458--33523 Score: 100
Period size: 26 Copynumber: 2.5 Consensus size: 27
33448 ATGGATAAGA
**
33458 AATAAT-AATAAATAATAGTAATAAAT
1 AATAATAAATAAATAATAAAAATAAAT
33484 AATAATAAATAAA-AATAAAAATAAAT
1 AATAATAAATAAATAATAAAAATAAAT
33510 AATAATAAATAAAT
1 AATAATAAATAAAT
33524 CATTATTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 30 0.83
27 6 0.17
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (27 bp):
AATAATAAATAAATAATAAAAATAAAT
Found at i:33629 original size:33 final size:32
Alignment explanation
Indices: 33592--33686 Score: 104
Period size: 32 Copynumber: 2.9 Consensus size: 32
33582 CTACATATTA
*
33592 TATATAAATTTCCAAAAATGATTTTTAAAAGAC
1 TATAT-AATTTCCAAAAATGATTTTTAAAAAAC
*
33625 TATATAATTTTCAAAAAT-ACTTTTTAAAAAAC
1 TATATAATTTCCAAAAATGA-TTTTTAAAAAAC
* * *
33657 TATATGATTTTCAAAAAATG-TTTTCAAAAA
1 TATAT-AATTTCCAAAAATGATTTTTAAAAA
33687 TTAAATATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
31 1 0.02
32 37 0.70
33 15 0.28
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.39
Consensus pattern (32 bp):
TATATAATTTCCAAAAATGATTTTTAAAAAAC
Found at i:33640 original size:32 final size:32
Alignment explanation
Indices: 33592--33673 Score: 112
Period size: 32 Copynumber: 2.5 Consensus size: 32
33582 CTACATATTA
* *
33592 TATATAAATTTCCAAAAATGA-TTTTTAAAAGAC
1 TATAT-AATTTTCAAAAAT-ACTTTTTAAAAAAC
33625 TATATAATTTTCAAAAATACTTTTTAAAAAAC
1 TATATAATTTTCAAAAATACTTTTTAAAAAAC
*
33657 TATATGATTTTCAAAAA
1 TATATAATTTTCAAAAA
33674 ATGTTTTCAA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
31 1 0.02
32 39 0.87
33 5 0.11
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.39
Consensus pattern (32 bp):
TATATAATTTTCAAAAATACTTTTTAAAAAAC
Found at i:33824 original size:37 final size:38
Alignment explanation
Indices: 33657--33926 Score: 270
Period size: 39 Copynumber: 7.2 Consensus size: 38
33647 TTTAAAAAAC
* * * * *
33657 TATATGATTTTCAAAAAATGTTTTCAAAAATTAAATAT
1 TATATAATTTTCCAAAAATGTTTTTAAAAACTATATAT
33695 TATATAAGTTTT-CAAAAATGTTTTTTTTAAAAACTATATAT
1 TATATAA-TTTTCCAAAAATG---TTTTTAAAAACTATATAT
* *
33736 TATATAAATTTCAAAAAATGTTTTTTAAAAACTATATAT
1 TATATAATTTTCCAAAAATG-TTTTTAAAAACTATATAT
*
33775 TATATAAGTTTTCCAAAAATGATTTTAAAAACTATATAT
1 TATATAA-TTTTCCAAAAATGTTTTTAAAAACTATATAT
* *
33814 TATAT-ATTTTCCTAAAAT-ATTTTAAAAACTATATAT
1 TATATAATTTTCCAAAAATGTTTTTAAAAACTATATAT
* * * *
33850 TATACAGTTTT-C--AAGTG-TTTTAAAAACCATATAT
1 TATATAATTTTCCAAAAATGTTTTTAAAAACTATATAT
* *
33884 TATATACATTTT--TAAAATGTTTTTAGAAACTATATAT
1 TATATA-ATTTTCCAAAAATGTTTTTAAAAACTATATAT
33921 TATATA
1 TATATA
33927 CGTATTTTCA
Statistics
Matches: 200, Mismatches: 20, Indels: 25
0.82 0.08 0.10
Matches are distributed among these distances:
34 24 0.12
35 4 0.02
36 27 0.14
37 36 0.18
38 14 0.07
39 52 0.26
40 14 0.07
41 29 0.14
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (38 bp):
TATATAATTTTCCAAAAATGTTTTTAAAAACTATATAT
Found at i:34910 original size:21 final size:20
Alignment explanation
Indices: 34865--34904 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
34855 CCCTTTATCG
*
34865 ATATAAAAAAGTATCGATAC
1 ATATAAAAAAGTAGCGATAC
*
34885 ATATACAAAAGTAGCGATAC
1 ATATAAAAAAGTAGCGATAC
34905 TTTATATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.23
Consensus pattern (20 bp):
ATATAAAAAAGTAGCGATAC
Found at i:42567 original size:22 final size:23
Alignment explanation
Indices: 42540--42601 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
42530 TTTAGTGCAG
**
42540 AGGGAATCGATACCCCCTTGA-A
1 AGGGAATCGATACCCCCTCCACA
* * *
42562 GGGGAACCGATTCCCCC-CCACA
1 AGGGAATCGATACCCCCTCCACA
42584 AGGGAATCGATACCCCCT
1 AGGGAATCGATACCCCCT
42602 GAGGGTTCTG
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
21 1 0.03
22 29 0.97
ACGTcount: A:0.27, C:0.35, G:0.23, T:0.15
Consensus pattern (23 bp):
AGGGAATCGATACCCCCTCCACA
Found at i:44588 original size:15 final size:16
Alignment explanation
Indices: 44561--44593 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
44551 ATTTGAATAT
*
44561 TTTGGATTGTTTGTAC
1 TTTGGATTGTTTGAAC
44577 TTTGGA-TGTTTGAAC
1 TTTGGATTGTTTGAAC
44592 TT
1 TT
44594 ATATTTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.15, C:0.06, G:0.24, T:0.55
Consensus pattern (16 bp):
TTTGGATTGTTTGAAC
Found at i:44758 original size:2 final size:2
Alignment explanation
Indices: 44751--44781 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
44741 GTAGCTTAAG
44751 AT 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 AT A
44782 ATCAATTGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45217 original size:47 final size:47
Alignment explanation
Indices: 45148--45241 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
45138 GTTTTAATCT
*
45148 TAAAATAATTTCAAAATAATTTTACAAAGTATTTCTAACCATTTCAA
1 TAAAATAATTTCAAAATAATTTTACAAAGTATTTCGAACCATTTCAA
*
45195 TAAAATAATTTCGAAATAATTTTACAAAGTATTTCGAACCATTTCAA
1 TAAAATAATTTCAAAATAATTTTACAAAGTATTTCGAACCATTTCAA
45242 AACCAAACAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (47 bp):
TAAAATAATTTCAAAATAATTTTACAAAGTATTTCGAACCATTTCAA
Found at i:45230 original size:23 final size:23
Alignment explanation
Indices: 45155--45232 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 23
45145 TCTTAAAATA
*
45155 ATTTCAAAATAATTTTACAAAGT
1 ATTTCGAAATAATTTTACAAAGT
* ** * * *
45178 ATTTC-TAACCATTTCAATAAAAT
1 ATTTCGAAATAATTT-TACAAAGT
45201 AATTTCGAAATAATTTTACAAAGT
1 -ATTTCGAAATAATTTTACAAAGT
45225 ATTTCGAA
1 ATTTCGAA
45233 CCATTTCAAA
Statistics
Matches: 40, Mismatches: 12, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
22 6 0.15
23 18 0.45
24 10 0.25
25 6 0.15
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (23 bp):
ATTTCGAAATAATTTTACAAAGT
Found at i:46633 original size:24 final size:24
Alignment explanation
Indices: 46614--46669 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
46604 CGAAATTTAT
46614 ATTGAAATTCAAACTCAAATTGAA
1 ATTGAAATTCAAACTCAAATTGAA
* * *
46638 ATTTAAATTCAAACTCCAATTAAA
1 ATTGAAATTCAAACTCAAATTGAA
*
46662 AATGAAAT
1 ATTGAAAT
46670 GAACATGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.30
Consensus pattern (24 bp):
ATTGAAATTCAAACTCAAATTGAA
Found at i:46637 original size:18 final size:18
Alignment explanation
Indices: 46614--46650 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
46604 CGAAATTTAT
46614 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
46632 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
46650 A
1 A
46651 CTCCAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:49373 original size:7 final size:7
Alignment explanation
Indices: 49321--49369 Score: 89
Period size: 7 Copynumber: 7.0 Consensus size: 7
49311 AAGAAAGGTT
49321 GAATGAG
1 GAATGAG
49328 GAATGAG
1 GAATGAG
49335 GAATGAG
1 GAATGAG
49342 GAATGAG
1 GAATGAG
49349 GAATGAG
1 GAATGAG
49356 GAATGAG
1 GAATGAG
*
49363 AAATGAG
1 GAATGAG
49370 AAATTAAGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.45, C:0.00, G:0.41, T:0.14
Consensus pattern (7 bp):
GAATGAG
Found at i:49380 original size:21 final size:21
Alignment explanation
Indices: 49322--49380 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
49312 AGAAAGGTTG
* * *
49322 AATGAGGAATGAGGAATGAGG
1 AATGAGAAATGAAGAATGAGA
* *
49343 AATGAGGAATGAGGAATGAGA
1 AATGAGAAATGAAGAATGAGA
*
49364 AATGAGAAATTAAGAAT
1 AATGAGAAATGAAGAAT
49381 CGACGGAGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.49, C:0.00, G:0.34, T:0.17
Consensus pattern (21 bp):
AATGAGAAATGAAGAATGAGA
Found at i:50498 original size:23 final size:23
Alignment explanation
Indices: 50472--50523 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
50462 ACAAACAAGC
50472 TATGAACCAAAATGTTTGGTTTA
1 TATGAACCAAAATGTTTGGTTTA
50495 TATGAACCAAAATGTTTGGTTTA
1 TATGAACCAAAATGTTTGGTTTA
50518 TATGAA
1 TATGAA
50524 AACAGGAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (23 bp):
TATGAACCAAAATGTTTGGTTTA
Found at i:50780 original size:34 final size:34
Alignment explanation
Indices: 50737--50850 Score: 121
Period size: 34 Copynumber: 3.5 Consensus size: 34
50727 GTCCTACTAG
50737 GATTCAAACTCCTAAAAATATGATAGAATTTTAT
1 GATTCAAACTCCTAAAAATATGATAGAATTTTAT
* *
50771 GATTCAAACTCATAAAGATATGATAGAA-TTT-T
1 GATTCAAACTCCTAAAAATATGATAGAATTTTAT
* * * *
50803 G-CT-AGGA-TTCAAAAAATATGATAGAATTTTAT
1 GATTCA-AACTCCTAAAAATATGATAGAATTTTAT
*
50835 GATTTAAACTCCTAAA
1 GATTCAAACTCCTAAA
50851 GATAGGATCC
Statistics
Matches: 62, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
30 16 0.26
31 5 0.08
32 4 0.06
33 5 0.08
34 32 0.52
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (34 bp):
GATTCAAACTCCTAAAAATATGATAGAATTTTAT
Found at i:51201 original size:24 final size:24
Alignment explanation
Indices: 51136--51204 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 24
51126 TTTCATGTAA
* *
51136 TATTTTTTTACATTTTATGTATTT
1 TATTTTTTTACATTATATATATTT
*
51160 TA--TTTTTACTTTAGTATATATTT
1 TATTTTTTTACATTA-TATATATTT
*
51183 TATTTTTTTAGATTATATATAT
1 TATTTTTTTACATTATATATAT
51205 AATATATTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
22 9 0.24
23 10 0.27
24 9 0.24
25 9 0.24
ACGTcount: A:0.26, C:0.03, G:0.04, T:0.67
Consensus pattern (24 bp):
TATTTTTTTACATTATATATATTT
Found at i:51271 original size:40 final size:40
Alignment explanation
Indices: 51180--51314 Score: 138
Period size: 41 Copynumber: 3.4 Consensus size: 40
51170 TTAGTATATA
51180 TTTTA-TTTTT-TTAGATTATATATATA-ATATATTA-TTTT
1 TTTTATTTTTTATTA-ATTATATATATATATAT-TTACTTTT
* *
51218 TATTATCAGTTTTATTAATTATATATATATATATTTACTTTT
1 TTTTAT--TTTTTATTAATTATATATATATATATTTACTTTT
*
51260 TTTTATTTTTTATT--TTATATATATATTATTTTTACTTTT
1 TTTTATTTTTTATTAATTATATATATA-TATATTTACTTTT
51299 TTATTATTATTTTATT
1 TT-TTATT-TTTTATT
51315 TATTTGTTTT
Statistics
Matches: 83, Mismatches: 5, Indels: 15
0.81 0.05 0.15
Matches are distributed among these distances:
38 15 0.18
39 14 0.17
40 12 0.14
41 26 0.31
42 16 0.19
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.67
Consensus pattern (40 bp):
TTTTATTTTTTATTAATTATATATATATATATTTACTTTT
Found at i:51281 original size:30 final size:30
Alignment explanation
Indices: 51245--51375 Score: 98
Period size: 29 Copynumber: 4.4 Consensus size: 30
51235 ATTATATATA
51245 TATATATTTACTTTTTTTTATTTTTTATTT
1 TATATATTTACTTTTTTTTATTTTTTATTT
* *
51275 TATATATATA-TTATTTTTACTTTTTTATTAT
1 TATATATTTACTTTTTTTTA-TTTTTTATT-T
* * *
51306 TATTTTATTTA-TTTGTTTTATTTCTATATTT
1 TA-TATATTTACTTTTTTTTATTT-TTTATTT
*
51337 T-T-T-TCTT-CTTTTTCTTTATTTTTTATAT
1 TATATAT-TTACTTTTT-TTTATTTTTTATTT
51365 T-TAT-TTTACTT
1 TATATATTTACTT
51376 ACTATTTTAT
Statistics
Matches: 82, Mismatches: 10, Indels: 19
0.74 0.09 0.17
Matches are distributed among these distances:
27 1 0.01
28 16 0.20
29 21 0.26
30 18 0.22
31 8 0.10
32 18 0.22
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (30 bp):
TATATATTTACTTTTTTTTATTTTTTATTT
Found at i:51289 original size:23 final size:23
Alignment explanation
Indices: 51262--51340 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 23
51252 TTACTTTTTT
51262 TTATTTTTTATTTTATATATATA
1 TTATTTTTTATTTTATATATATA
* *
51285 TTA-TTTTTACTTTTTTATTATTATT
1 TTATTTTTTA-TTTTATA-TA-TATA
* * *
51310 TTATTTATTTGTTTTATTTCTATA
1 TTATTT-TTTATTTTATATATATA
51334 TT-TTTTT
1 TTATTTTT
51341 CTTCTTTTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
22 8 0.18
23 12 0.27
24 7 0.16
25 7 0.16
26 7 0.16
27 3 0.07
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.75
Consensus pattern (23 bp):
TTATTTTTTATTTTATATATATA
Found at i:51317 original size:40 final size:41
Alignment explanation
Indices: 51195--51317 Score: 143
Period size: 39 Copynumber: 3.1 Consensus size: 41
51185 TTTTTTTAGA
*
51195 TTATATATATA-ATATA-TTA--TTTTTATTATCAGTTTTAT
1 TTATATATATATATATATTTACTTTTTTATTATTA-TTTTAT
*
51233 TAATTATATATATATATATTTACTTTTTT-TTATT-TTTTAT
1 TTA-TATATATATATATATTTACTTTTTTATTATTATTTTAT
*
51273 TT-TATATATATATTATTTTTACTTTTTTATTATTATTTTAT
1 TTATATATATATA-TATATTTACTTTTTTATTATTATTTTAT
51314 TTAT
1 TTAT
51318 TTGTTTTATT
Statistics
Matches: 72, Mismatches: 4, Indels: 14
0.80 0.04 0.16
Matches are distributed among these distances:
38 12 0.17
39 22 0.31
40 17 0.24
41 11 0.15
42 5 0.07
43 5 0.07
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (41 bp):
TTATATATATATATATATTTACTTTTTTATTATTATTTTAT
Found at i:51335 original size:21 final size:20
Alignment explanation
Indices: 51295--51370 Score: 59
Period size: 21 Copynumber: 3.8 Consensus size: 20
51285 TTATTTTTAC
51295 TTTTTTATTATTATTT-TAT-
1 TTTTTTATT-TTATTTCTATA
* *
51314 TTATTTGTTTTATTTCTATA
1 TTTTTTATTTTATTTCTATA
* *
51334 TTTTTT-TCTTCTTTTTCTTTA
1 TTTTTTAT-TT-TATTTCTATA
51355 TTTTTTATATTTATTT
1 TTTTTTAT-TTTATTT
51371 TACTTACTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
20 7 0.16
21 18 0.40
22 3 0.07
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.78
Consensus pattern (20 bp):
TTTTTTATTTTATTTCTATA
Found at i:51477 original size:15 final size:15
Alignment explanation
Indices: 51459--51488 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
51449 TATTTATTTC
*
51459 TTACCTTTTTATCTA
1 TTACATTTTTATCTA
51474 TTACATTTTTATCTA
1 TTACATTTTTATCTA
51489 ACATGGTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACATTTTTATCTA
Found at i:55694 original size:183 final size:183
Alignment explanation
Indices: 55386--55735 Score: 646
Period size: 183 Copynumber: 1.9 Consensus size: 183
55376 ATTAAATACG
55386 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** *
55451 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
55516 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
55569 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
55634 ATAGATTACATTCAAACCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
* *
55699 TTGTCAGGCCAAAGACTTTGTGATGAGATGAATCCTT
131 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTT
55736 TAGTTAAACC
Statistics
Matches: 161, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 161 1.00
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
Found at i:57090 original size:37 final size:37
Alignment explanation
Indices: 57022--57109 Score: 106
Period size: 37 Copynumber: 2.4 Consensus size: 37
57012 CATTGAAAAC
** * * *
57022 ATTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACA
57058 ATTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACA
1 ATTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACA
* *
57095 GTTTCTCTTGAAACA
1 ATTTCCCTTGAAACA
57110 TAAACATTGA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
36 13 0.30
37 31 0.70
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.40
Consensus pattern (37 bp):
ATTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACA
Found at i:57168 original size:34 final size:36
Alignment explanation
Indices: 57124--57209 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 36
57114 CATTGAAAGC
* * *
57124 ATTTCCCTTGAAA-TAAA-TTGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACA
*
57158 GTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACA
1 ATTTCCCTTGAAACAAAA-TTTGTCTCCCTTGAGACA
*
57195 ATTTCTCTTGAAACA
1 ATTTCCCTTGAAACA
57210 TAAACATTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
34 12 0.28
35 3 0.07
37 28 0.65
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACA
Found at i:57200 original size:100 final size:102
Alignment explanation
Indices: 56934--57338 Score: 645
Period size: 102 Copynumber: 4.0 Consensus size: 102
56924 TTAAAACAAG
* * * *
56934 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAGTTTTGTCTCACTTGAGACAGTTTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA-AAA-TTTTGTCTCCCTTGAGACAGTTTCT
*
56999 CTTTAAACATAAACATTGAAAACATTTCCCTTGAAATGA
64 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
* *
57038 ATTTTGTCTCTCTTGAGATAATTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
*
57103 TGAAACATAAACATTGAAAGCATTTCCCTTGAAAT-A
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
* *
57139 A-ATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
57203 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
* *
57240 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAATTTTGTCTCCTTTGAGACAGTTTCTAT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
*
57304 TGAAACATAAACTTTGAAAACAGTTTCCCTTGAAA
66 TGAAACATAAACATTGAAAACA-TTTCCCTTGAAA
57339 CAAAATCTTT
Statistics
Matches: 280, Mismatches: 18, Indels: 8
0.92 0.06 0.03
Matches are distributed among these distances:
100 93 0.33
101 52 0.19
102 101 0.36
103 3 0.01
104 31 0.11
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.37
Consensus pattern (102 bp):
ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
Found at i:57272 original size:36 final size:36
Alignment explanation
Indices: 57225--57310 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
57215 ATTGAAAACA
** *
57225 TTTCCCTTGAAATGAATTTTGTCT-CTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCT-TTGAGACAG
57261 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
**
57297 TTTCTATTGAAACA
1 TTTCCCTTGAAACA
57311 TAAACTTTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
36 42 0.95
37 2 0.05
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
Found at i:57328 original size:30 final size:30
Alignment explanation
Indices: 57293--57351 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
57283 CTCCTTTGAG
*
57293 ACAGTTTCTATTGAAACATAAA-CTTTGAAA
1 ACAGTTTCCATTGAAACA-AAATCTTTGAAA
*
57323 ACAGTTTCCCTTGAAACAAAATCTTTGAA
1 ACAGTTTCCATTGAAACAAAATCTTTGAA
57352 TATGTTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (30 bp):
ACAGTTTCCATTGAAACAAAATCTTTGAAA
Found at i:57333 original size:202 final size:204
Alignment explanation
Indices: 56940--57338 Score: 669
Period size: 202 Copynumber: 2.0 Consensus size: 204
56930 CAAGATTTTA
* *
56940 TCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAGTTTTGTCTCACTTGAGACAGTTTCTCTTTAA
1 TCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAGTTTTGTCTCACTTGAGACAATTTCTCTTGAA
57005 ACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAATTTCCCTTGAA
66 ACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAATTTCCCTTGAA
* *
57070 ACAAAATTTTATCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAGCATTTCCCTTGA
131 ACAAAATTTTATCTCCCTTGAGACAGTTTCTATTGAAACATAAACATTGAAAACATTTCCCTTGA
57135 AATAAATTG
196 AATAAATTG
* * *
57144 TCTCTCTTGAGATAGTTTCCCTTGAAACA-AAA-TTTTGTCTCCCTTGAGACAATTTCTCTTGAA
1 TCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAGTTTTGTCTCACTTGAGACAATTTCTCTTGAA
*
57207 ACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAA
66 ACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAATTTCCCTTGAA
* * *
57272 AC-AAATTTTGTCTCCTTTGAGACAGTTTCTATTGAAACATAAACTTTGAAAACAGTTTCCCTTG
131 ACAAAATTTTATCTCCCTTGAGACAGTTTCTATTGAAACATAAACATTGAAAACA-TTTCCCTTG
57336 AAA
195 AAA
57339 CAAAATCTTT
Statistics
Matches: 183, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
201 47 0.26
202 106 0.58
203 3 0.02
204 27 0.15
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.37
Consensus pattern (204 bp):
TCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAGTTTTGTCTCACTTGAGACAATTTCTCTTGAA
ACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAATTTCCCTTGAA
ACAAAATTTTATCTCCCTTGAGACAGTTTCTATTGAAACATAAACATTGAAAACATTTCCCTTGA
AATAAATTG
Found at i:57426 original size:36 final size:36
Alignment explanation
Indices: 57365--57477 Score: 156
Period size: 36 Copynumber: 3.1 Consensus size: 36
57355 GTTTTACATT
*
57365 AAACAAATTTCGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * *
57401 AAACAAATTTTGTCTATCTTAAGACATGTTT-TCTTA
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCTCTTG
* *
57437 AAACAAAATTTGTCTCCCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
57473 AAACA
1 AAACA
57478 TCAATCCTTG
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
35 4 0.06
36 58 0.88
37 4 0.06
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:57559 original size:36 final size:35
Alignment explanation
Indices: 57518--57632 Score: 152
Period size: 33 Copynumber: 3.4 Consensus size: 35
57508 CCTTGATACA
*
57518 GTTTCTCTTGAAACACAAAAAGAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAA-AAACCTTTGAAAAT
57554 GTTTCTCTTGAAACAC--AAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAAAT
*
57587 GTTTCTCTTGAAACAC----AAAACCTTTGAGAAT
1 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAAAT
*
57618 GTTTCCCTTGAAACA
1 GTTTCTCTTGAAACA
57633 AATTTTGTCT
Statistics
Matches: 76, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
31 28 0.37
33 29 0.38
34 3 0.04
36 16 0.21
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.31
Consensus pattern (35 bp):
GTTTCTCTTGAAACACAAAAAAAACCTTTGAAAAT
Found at i:57582 original size:33 final size:32
Alignment explanation
Indices: 57518--57632 Score: 153
Period size: 31 Copynumber: 3.5 Consensus size: 32
57508 CCTTGATACA
57518 GTTTCTCTTGAAACACAAAAAGAAACCTTTGAAATT
1 GTTTCTCTTGAAACAC--AAA-AAACCTTTGAAA-T
57554 GTTTCTCTTGAAACACAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAACCTTTG-AAAT
57587 GTTTCTCTTGAAACAC--AAAACCTTTGAGAAT
1 GTTTCTCTTGAAACACAAAAAACCTTTGA-AAT
*
57618 GTTTCCCTTGAAACA
1 GTTTCTCTTGAAACA
57633 AATTTTGTCT
Statistics
Matches: 76, Mismatches: 1, Indels: 9
0.88 0.01 0.10
Matches are distributed among these distances:
30 1 0.01
31 27 0.36
33 26 0.34
34 6 0.08
36 16 0.21
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.31
Consensus pattern (32 bp):
GTTTCTCTTGAAACACAAAAAACCTTTGAAAT
Found at i:57679 original size:67 final size:66
Alignment explanation
Indices: 57587--57779 Score: 233
Period size: 67 Copynumber: 2.8 Consensus size: 66
57577 CTTTGAAAAT
*
57587 GTTTCTCTTGAAACACAAAACCTTTGAGAATGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
1 GTTTCTCTTGAAACACAAAATCTTTGAG-ATGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
57652 CA
65 CA
* * * *
57654 GTTTCTCTTGAAACACAAAATCTTTGAGTTTATTTCCTTTAAAACAAAATTTTGTCTCCCTTGAG
1 GTTTCTCTTGAAACACAAAATCTTTGAG-ATGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAG
* *
57719 GCC
64 ACA
* * * *
57722 GTTTCTCATGAAACAACATATATCTTTAAGATCGTTTCCCTTGAAACGAATTTTGTCT
1 GTTTCTCTTGAAAC-ACA-AAATCTTTGAGAT-GTTTCCCTTGAAACAAATTTTGTCT
57780 TTTTTAAGAC
Statistics
Matches: 106, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
67 39 0.37
68 33 0.31
69 14 0.13
70 20 0.19
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (66 bp):
GTTTCTCTTGAAACACAAAATCTTTGAGATGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGAC
A
Found at i:58697 original size:98 final size:101
Alignment explanation
Indices: 58377--58789 Score: 377
Period size: 105 Copynumber: 4.0 Consensus size: 101
58367 TCGTGCCACT
* *
58377 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTTCCAAT
1 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTCCAGT
** * * * ** * * *
58442 -TTCAAAGCTGATTTTCCACGACGGAGGATATCATGCTACC
65 GAGCCAATCTCAACTT-CACAACGAAGGATAT--TG-GACC
* *
58482 TATGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAATTTCCCAGT
1 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT-CCAG-
* * * *
58546 TTCAGGGCCAATTTCAACTTCACAGCGGAGGATATTGGACC
64 -T--GAGCCAATCTCAACTTCACAACGAAGGATATTGGACC
* * * * **
58587 CAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTT-C-G-G
1 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCAGTG
*
58649 AGCCAATCTCAACTTCACAACGAAGGATATTGGACT
66 AGCCAATCTCAACTTCACAACGAAGGATATTGGACC
* * *
58685 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTTAACAAACAATTTTCCGGT
1 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTCCAG-
* * *
58750 TCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGGAC
64 T---GAGCCAATCTCAACTTCACAACGAAGGATATTGGAC
58790 TTGGAACAAT
Statistics
Matches: 255, Mismatches: 38, Indels: 29
0.79 0.12 0.09
Matches are distributed among these distances:
98 80 0.31
99 3 0.01
100 1 0.00
101 1 0.00
103 4 0.02
104 9 0.04
105 93 0.36
106 44 0.17
108 13 0.05
109 7 0.03
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (101 bp):
CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCAGTG
AGCCAATCTCAACTTCACAACGAAGGATATTGGACC
Found at i:59376 original size:34 final size:34
Alignment explanation
Indices: 59333--59401 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
59323 TTCGTCCTAC
59333 TAGGATTCAAACTCCTAAAAATAAGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAAGATAGAATTT
* *
59367 TAGGATTCAAACTCCTAAAGATATGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAAGATAGAATTT
59401 T
1 T
59402 GCTAGGATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAAGATAGAATTT
Found at i:59756 original size:23 final size:22
Alignment explanation
Indices: 59725--59790 Score: 57
Period size: 22 Copynumber: 2.9 Consensus size: 22
59715 CTTTTCTTTT
59725 TTTTCATGTAATATTTTTTTTAC
1 TTTT-ATGTAATATTTTTTTTAC
*
59748 ATTTTATGT-ATTTTCTTTTTTAC
1 -TTTTATGTAATATT-TTTTTTAC
59771 -TTTA-GTATATATTTTATTTT
1 TTTTATGTA-ATATTTT-TTTT
59791 TTTAGATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
20 2 0.06
21 6 0.17
22 12 0.33
23 12 0.33
24 4 0.11
ACGTcount: A:0.21, C:0.06, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTTATGTAATATTTTTTTTAC
Found at i:59783 original size:24 final size:23
Alignment explanation
Indices: 59740--59806 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 23
59730 ATGTAATATT
* *
59740 TTTTTTACATTTTATGTATTTTC
1 TTTTTTACATTTTATATATTTTA
59763 TTTTTTAC-TTTAGTATATATTTTA
1 TTTTTTACATTT--TATATATTTTA
* *
59787 TTTTTTTAGATTATATATAT
1 -TTTTTTACATTTTATATAT
59807 AAATATTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
22 3 0.08
23 8 0.22
24 16 0.44
25 7 0.19
26 2 0.06
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (23 bp):
TTTTTTACATTTTATATATTTTA
Found at i:59867 original size:6 final size:6
Alignment explanation
Indices: 59858--59972 Score: 60
Period size: 6 Copynumber: 18.7 Consensus size: 6
59848 ATATTTACTT
* *
59858 TTTTTA TTTTTA TTTTATA TATATATA TTTTTA CTTTTTA TTATTA --TTTA
1 TTTTTA TTTTTA TTTT-TA T-T-TTTA TTTTTA -TTTTTA TTTTTA TTTTTA
* * * *
59908 TTATTTA -TTTTA TTTCTA TATTTT- TTCTTC TTTTTC TTCTTT- TTTTTA
1 TT-TTTA TTTTTA TTTTTA T-TTTTA TTTTTA TTTTTA TT-TTTA TTTTTA
*
59956 TTTTTTA TATTTA TTTT
1 -TTTTTA TTTTTA TTTT
59973 ACTTACTATT
Statistics
Matches: 86, Mismatches: 10, Indels: 26
0.70 0.08 0.21
Matches are distributed among these distances:
4 3 0.03
5 10 0.12
6 42 0.49
7 26 0.30
8 4 0.05
9 1 0.01
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTTA
Found at i:59877 original size:28 final size:27
Alignment explanation
Indices: 59845--59972 Score: 91
Period size: 28 Copynumber: 4.5 Consensus size: 27
59835 TAATTATATA
59845 TATATATTTACTTTTTTTATTTTTATTT
1 TATATATTTA-TTTTTTTATTTTTATTT
* *
59873 TATATATATATATTTTTACTTTTTATTAT
1 TATATATTTATTTTTTTA-TTTTTATT-T
*
59902 TATTTA-TTATTTATTTTATTTCTATATTT
1 TATATATTTATTT-TTTTATTT-T-TATTT
* * *
59931 T-T-TCTTCTTTTTCTTCTTTTTTTTATTT
1 TATATATT-TATTT-TT-TTATTTTTATTT
*
59959 TTTATATTTATTTT
1 TATATATTTATTTT
59973 ACTTACTATT
Statistics
Matches: 79, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
27 8 0.10
28 33 0.42
29 26 0.33
30 12 0.15
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.74
Consensus pattern (27 bp):
TATATATTTATTTTTTTATTTTTATTT
Found at i:59881 original size:34 final size:36
Alignment explanation
Indices: 59782--59912 Score: 135
Period size: 36 Copynumber: 3.5 Consensus size: 36
59772 TTAGTATATA
* * *
59782 TTTTATT-TTTTTA-GATTATATATATAAATATTATT
1 TTTTATTATTTTTATTATTATATATATATAT-TTACT
59817 TTTTATTATCAGTTTTATTAATTATATATATATATTTACT
1 TTTTATTAT---TTTTATT-ATTATATATATATATTTACT
59857 TTTT-TTATTTTTATT-TTATATATATATATTTTTACT
1 TTTTATTATTTTTATTATTATATATATATA--TTTACT
59893 TTTTATTATTATTTATTATT
1 TTTTATTATT-TTTATTATT
59913 TATTTTATTT
Statistics
Matches: 82, Mismatches: 3, Indels: 18
0.80 0.03 0.17
Matches are distributed among these distances:
34 13 0.16
35 7 0.09
36 18 0.22
37 5 0.06
38 6 0.07
39 11 0.13
40 8 0.10
41 14 0.17
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (36 bp):
TTTTATTATTTTTATTATTATATATATATATTTACT
Found at i:59918 original size:45 final size:43
Alignment explanation
Indices: 59860--59986 Score: 129
Period size: 43 Copynumber: 3.0 Consensus size: 43
59850 ATTTACTTTT
59860 TTTATTTTTATTTTATATATATATATTTTTACTT-TTTATTATTA
1 TTTATTTTTATTTTAT-TATATATATTTTTACTTCTTT-TTATTA
* * * *
59904 TTTATTATTTATTTTATT-TCTATATTTTTTCTTCTTTTTCTTC
1 TTTATT-TTTATTTTATTATATATATTTTTACTTCTTTTTATTA
*
59947 TTT-TTTTTATTTT-TTATATTTA-TTTTACTTACTATTTTAT
1 TTTATTTTTATTTTATTATATATATTTTTACTT-CT-TTTTAT
59987 CTTTGTTTTC
Statistics
Matches: 70, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
40 9 0.13
41 14 0.20
42 7 0.10
43 20 0.29
44 10 0.14
45 10 0.14
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.73
Consensus pattern (43 bp):
TTTATTTTTATTTTATTATATATATTTTTACTTCTTTTTATTA
Found at i:59930 original size:17 final size:17
Alignment explanation
Indices: 59860--59922 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
59850 ATTTACTTTT
*
59860 TTTATTTTTATTT-TATA
1 TTTATTATTATTTAT-TA
*
59877 TATATATATT-TTTACTT-
1 TTTAT-TATTATTTA-TTA
59894 TTTATTATTATTTATTA
1 TTTATTATTATTTATTA
59911 TTTATT-TTATTT
1 TTTATTATTATTT
59923 CTATATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
16 12 0.32
17 21 0.55
18 4 0.11
19 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATTATTATTTATTA
Found at i:59959 original size:9 final size:9
Alignment explanation
Indices: 59885--59973 Score: 54
Period size: 9 Copynumber: 9.7 Consensus size: 9
59875 TATATATATA
59885 TTTTTACTTT
1 TTTTTA-TTT
*
59895 TTATTATTAT
1 TTTTTATT-T
*
59905 TTATTATTT
1 TTTTTATTT
*
59914 ATTTTA-TT
1 TTTTTATTT
* *
59922 TCTATATTT
1 TTTTTATTT
*
59931 TTTCTTCTTT
1 TTT-TTATTT
* *
59941 TTCTTCTTT
1 TTTTTATTT
59950 TTTTTATTT
1 TTTTTATTT
*
59959 TTTATATTT
1 TTTTTATTT
*
59968 ATTTTA
1 TTTTTA
59974 CTTACTATTT
Statistics
Matches: 61, Mismatches: 15, Indels: 7
0.73 0.18 0.08
Matches are distributed among these distances:
8 5 0.08
9 36 0.59
10 20 0.33
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTATTT
Found at i:59962 original size:43 final size:44
Alignment explanation
Indices: 59860--59976 Score: 115
Period size: 44 Copynumber: 2.8 Consensus size: 44
59850 ATTTACTTTT
*
59860 TTTATTTTTATTTTATATATATATATTTTTACTTTTTATTATTA
1 TTTATTTTTATTTTTTATATATATATTTTTACTTTTTATTATTA
* * *
59904 TTTATTATTTATTTTATT-TCTATAT-TTTTT-CTTCTTT-TTCTTC
1 TTTATT-TTTATTTT-TTATATATATATTTTTACTT-TTTATTATTA
59947 TTT-TTTTTATTTTTTATAT-T-TA-TTTTACTT
1 TTTATTTTTATTTTTTATATATATATTTTTACTT
59977 ACTATTTTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
39 5 0.08
40 6 0.10
41 10 0.16
42 2 0.03
43 10 0.16
44 14 0.23
45 14 0.23
46 1 0.02
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (44 bp):
TTTATTTTTATTTTTTATATATATATTTTTACTTTTTATTATTA
Found at i:59998 original size:50 final size:52
Alignment explanation
Indices: 59886--60013 Score: 118
Period size: 55 Copynumber: 2.4 Consensus size: 52
59876 ATATATATAT
* * * *
59886 TTTTACTTTTTATTATTATTTATTATTTATTTTATTTCTATATTTTTTCTTCTTT
1 TTTT-CTTTTTATTATTTTTTA-TATTTATTTTATTAC-ATATTTTATCTTCTTG
*
59941 TTCTTCTTTTTTTTATTTTTTATATTTATTTTACTTAC-TATTTTATC-T-TTG
1 TT-TTCTTTTTATTATTTTTTATATTTATTTTA-TTACATATTTTATCTTCTTG
* * *
59992 TTTTCTTTATCTTATCTTTTAT
1 TTTTCTTTTTATTATTTTTTAT
60014 TTAATTTGTT
Statistics
Matches: 63, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
50 17 0.27
51 4 0.06
52 1 0.02
53 8 0.13
54 11 0.17
55 20 0.32
56 2 0.03
ACGTcount: A:0.16, C:0.09, G:0.01, T:0.73
Consensus pattern (52 bp):
TTTTCTTTTTATTATTTTTTATATTTATTTTATTACATATTTTATCTTCTTG
Found at i:60024 original size:30 final size:31
Alignment explanation
Indices: 59988--60050 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
59978 CTATTTTATC
*
59988 TTTG-TTT-TCTTTATCTTATCTTTTATTTAA
1 TTTGTTTTCTCTTTATCTTAT-TTTAATTTAA
*
60018 TTTGTTTTCTCTTTATTTTATTTTAATTTAA
1 TTTGTTTTCTCTTTATCTTATTTTAATTTAA
60049 TT
1 TT
60051 AATTAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 4 0.14
31 14 0.48
32 11 0.38
ACGTcount: A:0.17, C:0.08, G:0.03, T:0.71
Consensus pattern (31 bp):
TTTGTTTTCTCTTTATCTTATTTTAATTTAA
Found at i:60083 original size:15 final size:15
Alignment explanation
Indices: 60065--60094 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
60055 AATTTATTTC
60065 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
60080 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
60095 ACATGATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:63098 original size:17 final size:16
Alignment explanation
Indices: 63057--63100 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
63047 TGATTCAACG
63057 TAATATTAAATATAATT
1 TAATATTAAA-ATAATT
*
63074 T-ATTTTAAAATAATT
1 TAATATTAAAATAATT
63089 TAATAATTAAAA
1 TAAT-ATTAAAA
63101 GTTTAGTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 7 0.30
16 9 0.39
17 7 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATATTAAAATAATT
Found at i:63808 original size:64 final size:64
Alignment explanation
Indices: 63728--63868 Score: 149
Period size: 64 Copynumber: 2.2 Consensus size: 64
63718 TCGGATCCTG
* * * * *
63728 TCAGGTCGGGTAAAATCGGATACATGTTA-AGTCAGGTAAATTTGACACCAGATCCAGTTCGGTT
1 TCAGGTCAGGTCAAATCAG-TACAGGTTATAGTCAGGTAAATTTGACACCAGATCCAGATCGGTT
* * ** **
63792 TCAGGTCAGGTCAAATCAGTTCGGGTTATTTTCAGGTTGATTTGACACCAGATCCAGATCGGTT
1 TCAGGTCAGGTCAAATCAGTACAGGTTATAGTCAGGTAAATTTGACACCAGATCCAGATCGGTT
* *
63856 TCAGCTTAGGTCA
1 TCAGGTCAGGTCA
63869 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
63 6 0.10
64 57 0.90
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (64 bp):
TCAGGTCAGGTCAAATCAGTACAGGTTATAGTCAGGTAAATTTGACACCAGATCCAGATCGGTT
Found at i:64563 original size:17 final size:16
Alignment explanation
Indices: 64532--64579 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
64522 AAATTGAAAA
*
64532 AATATAATATATATAT
1 AATATAATTTATATAT
64548 AATATAAGTTTATATAT
1 AATATAA-TTTATATAT
*
64565 AAAATATATTTATAT
1 AATATA-ATTTATAT
64580 TAGAAACTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 7 0.25
17 20 0.71
18 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
AATATAATTTATATAT
Found at i:64620 original size:13 final size:13
Alignment explanation
Indices: 64605--64652 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
64595 TATTATAAGT
*
64605 TATATATATAAAT
1 TATATATATAAAC
* *
64618 TATGCTTATATGAAC
1 TAT--ATATATAAAC
64633 TATATATATAAAC
1 TATATATATAAAC
64646 TATATAT
1 TATATAT
64653 GTAAGAGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
13 18 0.64
15 10 0.36
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:64844 original size:20 final size:20
Alignment explanation
Indices: 64778--64951 Score: 165
Period size: 20 Copynumber: 8.7 Consensus size: 20
64768 ACCCAGTTTC
*
64778 CAAATTCGCAACGCGAATTTGT
1 CAAATTCGCAACGCG-A-TAGT
*
64800 -AAA-TCGCAACAC-ATAAGT
1 CAAATTCGCAACGCGAT-AGT
* * *
64818 AAAATTCGTAATGCGATAGT
1 CAAATTCGCAACGCGATAGT
* * * *
64838 CAAATTCTCAACACAAAAGT
1 CAAATTCGCAACGCGATAGT
* * *
64858 CAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGCGATAGT
64878 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
64898 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
* *
64918 CAAATTCGCAACGTGAAAGT
1 CAAATTCGCAACGCGATAGT
*
64938 CAAAGTCGCAACGC
1 CAAATTCGCAACGC
64952 TAAATACAAT
Statistics
Matches: 128, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
17 1 0.01
18 3 0.02
19 3 0.02
20 116 0.91
21 5 0.04
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACGCGATAGT
Found at i:64937 original size:60 final size:60
Alignment explanation
Indices: 64803--64951 Score: 190
Period size: 60 Copynumber: 2.5 Consensus size: 60
64793 AATTTGTAAA
* * * * *
64803 TCGCAACACATAAGTAAAATTCGTAATGCGATAGTCAAATTCTCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAAT
* * *
64863 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAAT
*** *
64923 TCGCAACGTGAAAGTCAAAGTCGCAACGC
1 TCGCAACACAAAAGTCAAATTCGCAACGC
64952 TAAATACAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 77 1.00
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.19
Consensus pattern (60 bp):
TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAAT
Found at i:65090 original size:22 final size:22
Alignment explanation
Indices: 65065--65115 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
65055 CTACGGCGAC
*
65065 ATCCGTCCCGATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
65087 ATCCGTCCCCATCTTCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
65109 ATCCGTC
1 ATCCGTC
65116 TGTCTCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.41, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:65647 original size:15 final size:13
Alignment explanation
Indices: 65615--65751 Score: 61
Period size: 13 Copynumber: 10.2 Consensus size: 13
65605 ATTTGAAAAA
65615 ATATAATATATAT
1 ATATAATATATAT
65628 ATATAATATAAGTTTAT
1 ATATAATAT-A---TAT
65645 ATATAA-ACTATAT
1 ATATAATA-TATAT
*
65658 ATATAAAATATAT
1 ATATAATATATAT
* * * *
65671 TTATATTAGAAACT
1 ATATAATATATA-T
65685 ATATAAT-TAT-T
1 ATATAATATATAT
*
65696 ATA-AGT-TATAT
1 ATATAATATATAT
* *
65707 ATATAAATTATGTTT
1 ATAT-AA-TATATAT
65722 ATATGAACTATATAT
1 ATAT-AA-TATATAT
65737 ATATAA-ACTATAT
1 ATATAATA-TATAT
65750 AT
1 AT
65752 GTAAGAGAAA
Statistics
Matches: 94, Mismatches: 17, Indels: 26
0.69 0.12 0.19
Matches are distributed among these distances:
10 5 0.05
11 8 0.09
12 1 0.01
13 39 0.41
14 11 0.12
15 18 0.19
16 2 0.02
17 10 0.11
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.45
Consensus pattern (13 bp):
ATATAATATATAT
Found at i:65649 original size:30 final size:30
Alignment explanation
Indices: 65615--65751 Score: 106
Period size: 30 Copynumber: 4.5 Consensus size: 30
65605 ATTTGAAAAA
65615 ATATAATA-TATATATATAATATAAGTTTAT
1 ATATAA-ACTATATATATAATATAAGTTTAT
*
65645 ATATAAACTATATATATAAAATATA-TTTAT
1 ATATAAACTATATATATAATATA-AGTTTAT
* *
65675 ATTAGAAACTATATA-ATTATTATAAGTTATAT
1 A-TATAAACTATATATA-TAATATAAGTT-TAT
* * *
65707 ATATAAA-T-TATGT-TTATATGAACTATATAT
1 ATATAAACTATATATATAATAT-AAGT-T-TAT
65737 ATATAAACTATATAT
1 ATATAAACTATATAT
65752 GTAAGAGAAA
Statistics
Matches: 86, Mismatches: 10, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
28 4 0.05
29 7 0.08
30 41 0.48
31 26 0.30
32 8 0.09
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.45
Consensus pattern (30 bp):
ATATAAACTATATATATAATATAAGTTTAT
Found at i:65950 original size:20 final size:20
Alignment explanation
Indices: 65925--65969 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
65915 TTCCATATTT
65925 GCAACGCGAATCTGTAAATC
1 GCAACGCGAATCTGTAAATC
*
65945 GCAACGCGAATTTGTAAATC
1 GCAACGCGAATCTGTAAATC
65965 GCAAC
1 GCAAC
65970 ACAAAAGTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
GCAACGCGAATCTGTAAATC
Found at i:66010 original size:20 final size:20
Alignment explanation
Indices: 65963--66015 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
65953 AATTTGTAAA
* *
65963 TCGCAACACAAAAGTCAAAT
1 TCGCAACGCGAAAGTCAAAT
65983 TCGCAACGCGAAAGTCAAAT
1 TCGCAACGCGAAAGTCAAAT
66003 TCGCAACGCGAAA
1 TCGCAACGCGAAA
66016 TATAATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.43, C:0.26, G:0.17, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAGTCAAAT
Found at i:66149 original size:22 final size:22
Alignment explanation
Indices: 66124--66171 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
66114 TCTACGCGAC
*
66124 ATCCGTCCCGATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
66146 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
66168 ATCC
1 ATCC
66172 TTCTATCTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.44, G:0.17, T:0.19
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:66595 original size:14 final size:14
Alignment explanation
Indices: 66576--66602 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
66566 TTTAGTATCG
66576 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
66590 CGTTGCGATTTTC
1 CGTTGCGATTTTC
66603 ATTTTCGCGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.22, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTCT
Found at i:66628 original size:20 final size:20
Alignment explanation
Indices: 66585--66628 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
66575 GCGTTGCGAT
* * * *
66585 TTTCTCGTTGCGATTTTCAT
1 TTTCGCGTTGCGAATTTAAG
66605 TTTCGCGTTGCGAATTTAAG
1 TTTCGCGTTGCGAATTTAAG
66625 TTTC
1 TTTC
66629 AGAAACTACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.18, G:0.18, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTAAG
Found at i:68393 original size:21 final size:21
Alignment explanation
Indices: 68369--68418 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
68359 TGGTGCATGG
68369 CGTGATGAGGTTCG-TTTTTTA
1 CGTGATGAGG-TCGATTTTTTA
* *
68390 CGTGGTGAGGTGGATTTTTTA
1 CGTGATGAGGTCGATTTTTTA
*
68411 CGCGATGA
1 CGTGATGA
68419 CAATGGTGCG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.16, C:0.10, G:0.34, T:0.40
Consensus pattern (21 bp):
CGTGATGAGGTCGATTTTTTA
Found at i:68816 original size:21 final size:21
Alignment explanation
Indices: 68792--68859 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
68782 CTCATTATCG
68792 AAGAGGCCCCTCCCGTCGTTC
1 AAGAGGCCCCTCCCGTCGTTC
* ** *
68813 AAGATGCCCCTGTCATCGTTC
1 AAGAGGCCCCTCCCGTCGTTC
** * *
68834 AAGAGATCCCGCCCGCCGTTC
1 AAGAGGCCCCTCCCGTCGTTC
68855 AAGAG
1 AAGAG
68860 CCCGATTCAC
Statistics
Matches: 35, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.21, C:0.37, G:0.24, T:0.19
Consensus pattern (21 bp):
AAGAGGCCCCTCCCGTCGTTC
Found at i:70318 original size:64 final size:64
Alignment explanation
Indices: 70185--70357 Score: 242
Period size: 65 Copynumber: 2.6 Consensus size: 64
70175 GGGGTACACT
70185 TTTTTTGCTTGTTTAATTGAATTT-TACATTGAAAGTTGATTTGTTTAATTGATGAGGAAATAAG
1 TTTTTTGCTTGTTTAATTG-ATTTGT--A---AAAGTTGATTTGTTTAATTGATGAGGAAATAAG
70249 AATTA
60 AATTA
* *
70254 TTTTTT-CTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTA
1 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA
*
70318 TTTTTTGTTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
70358 GTTTTAAATT
Statistics
Matches: 98, Mismatches: 3, Indels: 10
0.88 0.03 0.09
Matches are distributed among these distances:
63 17 0.17
64 25 0.26
65 32 0.33
66 1 0.01
67 4 0.04
68 13 0.13
69 6 0.06
ACGTcount: A:0.28, C:0.02, G:0.17, T:0.53
Consensus pattern (64 bp):
TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA
Found at i:70360 original size:34 final size:37
Alignment explanation
Indices: 70282--70361 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 37
70272 ATTTGTAAAA
70282 GTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTT
1 GTTG-TTTGTTTAATTTGATGTGTAAATAAG-ATTATTT
* *
70321 TTTGTTTGTTTAA-TTGATTTGT-AA-AAG-TTGATTT
1 GTTGTTTGTTTAATTTGATGTGTAAATAAGATT-ATTT
70355 GTTGTTT
1 GTTGTTT
70362 TAAATTCAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
33 2 0.05
34 10 0.27
35 3 0.08
36 2 0.05
37 8 0.22
38 9 0.24
39 3 0.08
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (37 bp):
GTTGTTTGTTTAATTTGATGTGTAAATAAGATTATTT
Found at i:70476 original size:20 final size:20
Alignment explanation
Indices: 70451--70510 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
70441 TTGTGATTTT
70451 GTCAAATTCGCAATGCGAAA
1 GTCAAATTCGCAATGCGAAA
* *
70471 GTCAAATTCGTAATGCAAAA
1 GTCAAATTCGCAATGCGAAA
*
70491 GTCAAATTCGCAACGCGAAA
1 GTCAAATTCGCAATGCGAAA
70511 TAAGCGTTGC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (20 bp):
GTCAAATTCGCAATGCGAAA
Found at i:70593 original size:14 final size:13
Alignment explanation
Indices: 70549--70594 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
70539 GCAAAAGTCA
70549 ATTTTGCGTTGCG
1 ATTTTGCGTTGCG
70562 ATTTT-CAGTTTGCG
1 ATTTTGC-G-TTGCG
70576 ATTTTGCGTTGCG
1 ATTTTGCGTTGCG
*
70589 AATTTG
1 ATTTTG
70595 ACTTTCGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
12 1 0.03
13 16 0.55
14 11 0.38
15 1 0.03
ACGTcount: A:0.13, C:0.13, G:0.26, T:0.48
Consensus pattern (13 bp):
ATTTTGCGTTGCG
Found at i:73975 original size:16 final size:16
Alignment explanation
Indices: 73954--73987 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
73944 AAATCATTGA
*
73954 AAAATTATATAGAAAC
1 AAAATTATATAAAAAC
*
73970 AAAATTATGTAAAAAC
1 AAAATTATATAAAAAC
73986 AA
1 AA
73988 TTTAGAGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (16 bp):
AAAATTATATAAAAAC
Found at i:74171 original size:19 final size:18
Alignment explanation
Indices: 74128--74174 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
74118 CAAAACATTT
74128 GTGTTGCGAAACTAAAAC
1 GTGTTGCGAAACTAAAAC
* * *
74146 CTGTTGCGAAATTAAATTC
1 GTGTTGCGAAACTAAA-AC
74165 GTGTTGCGAA
1 GTGTTGCGAA
74175 TTCAAAAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (18 bp):
GTGTTGCGAAACTAAAAC
Found at i:74208 original size:19 final size:19
Alignment explanation
Indices: 74148--74258 Score: 116
Period size: 19 Copynumber: 5.7 Consensus size: 19
74138 ACTAAAACCT
* *
74148 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTC-A
** *
74167 GTTGCGAATTCAAAAATCTA
1 GTTGCGAATTTGAAATTC-A
*
74187 GTTACGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
74206 GTTGTGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
74225 GTTGCGAATTTGAAATTCTGA
1 GTTGCGAATTTGAAATTC--A
74246 GTTGCGAATTTGA
1 GTTGCGAATTTGA
74259 CTTTTGTGTT
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
19 44 0.57
20 19 0.25
21 14 0.18
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.37
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:74275 original size:20 final size:20
Alignment explanation
Indices: 74250--74312 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
74240 TTCTGAGTTG
74250 CGAATTTGACTTTTGTGTTA
1 CGAATTTGACTTTTGTGTTA
* *** *
74270 CGAATTTGACTATCACGTTG
1 CGAATTTGACTTTTGTGTTA
*
74290 CGAATTTGACTTCTGTGTTA
1 CGAATTTGACTTTTGTGTTA
74310 CGA
1 CGA
74313 TTTACAAATT
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.41
Consensus pattern (20 bp):
CGAATTTGACTTTTGTGTTA
Found at i:74331 original size:40 final size:40
Alignment explanation
Indices: 74247--74380 Score: 107
Period size: 40 Copynumber: 3.4 Consensus size: 40
74237 AAATTCTGAG
* * * *
74247 TTGCGAATTTGACTTTTGTGTTACGAATTTGAC-TA-TCACG
1 TTGCGAATTTGACTTCTGTGTTACG-ATTT-ACAAATTCGCA
74287 TTGCGAATTTGACTTCTGTGTTACGATTTACAAATTCGCA
1 TTGCGAATTTGACTTCTGTGTTACGATTTACAAATTCGCA
** * *
74327 TTGCG-ATTT-ACAGATTC-GCATTGCGATTTACAGATTCGCA
1 TTGCGAATTTGAC---TTCTGTGTTACGATTTACAAATTCGCA
*
74367 TTACGAATTTGACT
1 TTGCGAATTTGACT
74381 ATCGCGTTGC
Statistics
Matches: 78, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
38 4 0.05
39 10 0.13
40 55 0.71
41 7 0.09
42 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.40
Consensus pattern (40 bp):
TTGCGAATTTGACTTCTGTGTTACGATTTACAAATTCGCA
Found at i:74335 original size:20 final size:20
Alignment explanation
Indices: 74310--74368 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
74300 TTCTGTGTTA
*
74310 CGATTTACAAATTCGCATTG
1 CGATTTACAGATTCGCATTG
74330 CGATTTACAGATTCGCATTG
1 CGATTTACAGATTCGCATTG
74350 CGATTTACAGATTCGCATT
1 CGATTTACAGATTCGCATT
74369 ACGAATTTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (20 bp):
CGATTTACAGATTCGCATTG
Found at i:74385 original size:20 final size:20
Alignment explanation
Indices: 74370--74497 Score: 120
Period size: 20 Copynumber: 6.4 Consensus size: 20
74360 ATTCGCATTA
74370 CGAATTTGACTATCGCGTTG
1 CGAATTTGACTATCGCGTTG
* * * *
74390 CGAATTTGACTTTTGTGTCG
1 CGAATTTGACTATCGCGTTG
74410 CGAATTTGACTATCGCGTTG
1 CGAATTTGACTATCGCGTTG
*
74430 CGAATTTGACTTAT-GTGTTG
1 CGAATTTGAC-TATCGCGTTG
*
74450 CG-ATTT-ACAAATTCGCGTTG
1 CGAATTTGAC-TA-TCGCGTTG
* *
74470 CGAAATTGGAGT-TCGCGTTG
1 CG-AATTTGACTATCGCGTTG
74490 CGAATTTG
1 CGAATTTG
74498 TTGGTCATTT
Statistics
Matches: 86, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
18 3 0.03
19 10 0.12
20 66 0.77
21 3 0.03
22 3 0.03
23 1 0.01
ACGTcount: A:0.20, C:0.16, G:0.26, T:0.38
Consensus pattern (20 bp):
CGAATTTGACTATCGCGTTG
Found at i:74391 original size:40 final size:40
Alignment explanation
Indices: 74290--74392 Score: 104
Period size: 40 Copynumber: 2.6 Consensus size: 40
74280 TATCACGTTG
* * *
74290 CGAATTTGACT-TCTGTGTTACGATTTACAAATTCGCATTG
1 CGAATTTGACTATC-GCGTTGCGATTTACAAATTCGCATTA
* * *
74330 CG-ATTT-ACAGATTCGCATTGCGATTTACAGATTCGCATTA
1 CGAATTTGAC-TA-TCGCGTTGCGATTTACAAATTCGCATTA
74370 CGAATTTGACTATCGCGTTGCGA
1 CGAATTTGACTATCGCGTTGCGA
74393 ATTTGACTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
38 2 0.04
39 4 0.08
40 35 0.70
41 7 0.14
42 2 0.04
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.36
Consensus pattern (40 bp):
CGAATTTGACTATCGCGTTGCGATTTACAAATTCGCATTA
Found at i:74414 original size:40 final size:40
Alignment explanation
Indices: 74370--74473 Score: 149
Period size: 40 Copynumber: 2.6 Consensus size: 40
74360 ATTCGCATTA
*
74370 CGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTCG
1 CGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTCG
*
74410 CGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTTG
1 CGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTCG
*
74450 CG-ATTT-ACAAATTCGCGTTGCGAA
1 CGAATTTGAC-TA-TCGCGTTGCGAA
74474 ATTGGAGTTC
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
38 2 0.03
39 5 0.08
40 52 0.88
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (40 bp):
CGAATTTGACTATCGCGTTGCGAATTTGACTTATGTGTCG
Found at i:74431 original size:100 final size:100
Alignment explanation
Indices: 74267--74497 Score: 249
Period size: 100 Copynumber: 2.3 Consensus size: 100
74257 GACTTTTGTG
* *
74267 TTACGAATTTGACTATCACGTTGCGAATTTGACTTCTGTGTTACGATTTACAAATTCGCATTGCG
1 TTACGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTCACGATTTACAAATTCGCATTGCG
*
74332 -ATTT-ACAGAT-TCGCATTGCGATTTACAGATTCGCA
66 AATTTGACAGATGT-G--TTGCGATTTACAAATTCGCA
* * * *
74367 TTACGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTCGCGAATTTGAC-TA-TCGCGTTG
1 TTACGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTCACG-ATTT-ACAAATTCGCATTG
** *
74430 CGAATTTGACTTATGTGTTGCGATTTACAAATTCGCG
64 CGAATTTGACAGATGTGTTGCGATTTACAAATTCGCA
* * *
74467 TTGCGAAATTGGAGT-TCGCGTTGCGAATTTG
1 TTACG-AATTTGACTATCGCGTTGCGAATTTG
74498 TTGGTCATTT
Statistics
Matches: 112, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
100 88 0.79
101 16 0.14
102 7 0.06
103 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (100 bp):
TTACGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTCACGATTTACAAATTCGCATTGCG
AATTTGACAGATGTGTTGCGATTTACAAATTCGCA
Found at i:74776 original size:20 final size:20
Alignment explanation
Indices: 74732--74807 Score: 93
Period size: 19 Copynumber: 3.9 Consensus size: 20
74722 TTTATTTGGG
* *
74732 AATTTAGAGGGAAATT-TAG
1 AATTTAGAGGGAAATTGAAA
74751 AATTTAGAGGGAAATTGAAA
1 AATTTAGAGGGAAATTGAAA
* *
74771 AATTTAGAAGG-AATAGAAA
1 AATTTAGAGGGAAATTGAAA
*
74790 AATTTGGAGGGAAATTGA
1 AATTTAGAGGGAAATTGA
74808 GAATTGAGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
19 32 0.67
20 16 0.33
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26
Consensus pattern (20 bp):
AATTTAGAGGGAAATTGAAA
Found at i:75009 original size:4 final size:4
Alignment explanation
Indices: 75000--75583 Score: 1096
Period size: 4 Copynumber: 148.2 Consensus size: 4
74990 TAATTTTCTA
75000 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
75048 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
75096 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
75144 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
75192 TATG TATG TATG TATG TATG TATG TAGG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
75240 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
75288 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
75336 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
75384 TATG TATG TATG TATG TA-- TATG TAT- TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
75429 TATG TAT- TATG TATG TATG TATG TATG TATG TATG TAT- TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
75475 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
75523 TATG TATG TATG TATG TAT- TATG --TG TATG TATG -ATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
75567 TATG TATG TATG TATG T
1 TATG TATG TATG TATG T
Statistics
Matches: 569, Mismatches: 2, Indels: 18
0.97 0.00 0.03
Matches are distributed among these distances:
2 4 0.01
3 15 0.03
4 550 0.97
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Done.