Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold132
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: 2458301
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
File 6 of 15
Found at i:996316 original size:2 final size:2
Alignment explanation
Indices: 996309--996354 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
996299 GCATATGCCT
* *
996309 TC TC TC TC TC TC TC TC TC TC TC TC TC TC AC TC TC TC TC TC TT
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
996351 TC TC
1 TC TC
996355 CTATCCATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.02, C:0.48, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:997153 original size:20 final size:20
Alignment explanation
Indices: 997091--997155 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
997081 TTGTTTGGTG
*
997091 TTTTTATTTTTATATTTTGCT
1 TTTTTA-TTTTATTTTTTGCT
**
997112 ATTTTT-TCTTTATTTTCAGCT
1 -TTTTTAT-TTTATTTTTTGCT
997133 TTTTTATTTTATTTTTTGCT
1 TTTTTATTTTATTTTTTGCT
997153 TTT
1 TTT
997156 CATTTTTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
20 20 0.56
21 11 0.31
22 5 0.14
ACGTcount: A:0.12, C:0.08, G:0.05, T:0.75
Consensus pattern (20 bp):
TTTTTATTTTATTTTTTGCT
Found at i:997155 original size:19 final size:19
Alignment explanation
Indices: 997091--997161 Score: 61
Period size: 21 Copynumber: 3.5 Consensus size: 19
997081 TTGTTTGGTG
*
997091 TTTTTATTTTTATATTTTGC
1 TTTTTA-TTTTATTTTTTGC
* **
997111 TATTTTTTCTTTATTTTCAGC
1 T-TTTTAT-TTTATTTTTTGC
997132 TTTTTTATTTTATTTTTTGC
1 -TTTTTATTTTATTTTTTGC
*
997152 TTTTCATTTT
1 TTTTTATTTT
997162 TATTGAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
19 9 0.22
20 12 0.30
21 18 0.45
22 1 0.03
ACGTcount: A:0.13, C:0.08, G:0.04, T:0.75
Consensus pattern (19 bp):
TTTTTATTTTATTTTTTGC
Found at i:997162 original size:20 final size:19
Alignment explanation
Indices: 997092--997165 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 19
997082 TGTTTGGTGT
*
997092 TTTTATTTTTATATTTTGC
1 TTTTATTTTTATTTTTTGC
* **
997111 TATTTTTTCTTTATTTTCAGC
1 T-TTTATT-TTTATTTTTTGC
*
997132 TTTTTTATTTTATTTTTTGC
1 TTTTAT-TTTTATTTTTTGC
997152 TTTTCATTTTTATT
1 TTTT-ATTTTTATT
997166 GAAAAAAGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.02
20 31 0.70
21 12 0.27
ACGTcount: A:0.14, C:0.08, G:0.04, T:0.74
Consensus pattern (19 bp):
TTTTATTTTTATTTTTTGC
Found at i:998383 original size:2 final size:2
Alignment explanation
Indices: 998376--998411 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
998366 ATGTTTTCAA
998376 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
998412 GTATGTACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1001917 original size:34 final size:33
Alignment explanation
Indices: 1001864--1002083 Score: 248
Period size: 34 Copynumber: 6.5 Consensus size: 33
1001854 TGGTAAAAAC
* *
1001864 CACCATTTAATCAATAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
1001897 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
1001931 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
1001965 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
1001999 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
1002033 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
1002067 CA-CATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1002084 TCTCTCACTT
Statistics
Matches: 160, Mismatches: 18, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
32 15 0.09
33 7 0.04
34 132 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:1001980 original size:68 final size:67
Alignment explanation
Indices: 1001866--1002079 Score: 279
Period size: 68 Copynumber: 3.2 Consensus size: 67
1001856 GTAAAAACCA
* * *
1001866 CCATTTAATCAATAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAATAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
1001931 CAC
65 CAC
* * *
1001934 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAATAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
1001999 CTC
65 CAC
* * * * *
1002002 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAATAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
1002067 CA-
65 CAC
1002069 -CATTTAATCAA
1 CCATTTAATCAA
1002080 CAATTCTCTC
Statistics
Matches: 128, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
66 10 0.08
67 2 0.02
68 115 0.90
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (67 bp):
CCATTTAATCAATAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:1002008 original size:102 final size:100
Alignment explanation
Indices: 1001867--1002083 Score: 335
Period size: 102 Copynumber: 2.1 Consensus size: 100
1001857 TAAAAACCAC
* * *
1001867 CATTTAATCAATAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAATC
1 CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAAATC
* * *
1001932 ACCCATTTAATCAATAATGGTAAGCTACCAAATTTCT
66 ACCCATTTAATCAACAATGGTAAACTACCAAA--TCA
* * *
1001969 CATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAATC
1 CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAAATC
1002034 ACCCATTTAATCAACAATGGTAAACTACCAAATCA
66 ACCCATTTAATCAACAATGGTAAACTACCAAATCA
1002069 CATTTAATCAACAAT
1 CATTTAATCAACAAT
1002084 TCTCTCACTT
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
100 17 0.16
102 89 0.84
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (100 bp):
CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAAATC
ACCCATTTAATCAACAATGGTAAACTACCAAATCA
Found at i:1006538 original size:34 final size:33
Alignment explanation
Indices: 1006490--1006709 Score: 246
Period size: 34 Copynumber: 6.5 Consensus size: 33
1006480 TGGTAAAAAC
*
1006490 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
1006523 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* * *
1006557 CACCCATTTAATCAATAATGTTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** * *
1006591 TTCTCATTTAATCAACAATGGTAAGCTACAAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
1006625 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
1006659 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
1006693 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
1006710 GTTTAATATG
Statistics
Matches: 157, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
33 22 0.14
34 129 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:1006606 original size:68 final size:67
Alignment explanation
Indices: 1006492--1006709 Score: 276
Period size: 68 Copynumber: 3.2 Consensus size: 67
1006482 GTAAAAACCA
* * *
1006492 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
1006557 CAC
65 CAC
* ** * * *
1006560 CCATTTAATCAATAATGTTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACAAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
1006625 CTC
65 CAC
* * * *
1006628 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
1006693 CA-
65 CAC
1006695 CCATTTAATCAACAA
1 CCATTTAATCAACAA
1006710 GTTTAATATG
Statistics
Matches: 127, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
67 16 0.13
68 110 0.87
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.25
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:1006669 original size:102 final size:101
Alignment explanation
Indices: 1006490--1006709 Score: 332
Period size: 102 Copynumber: 2.2 Consensus size: 101
1006480 TGGTAAAAAC
* * *
1006490 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACAAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* * *
1006555 ATCACCCATTTAATCAATAATGTTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * *
1006591 TTCTCATTTAATCAACAATGGTAAGCTACAAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACAAAATCTACCATTTAGTCAACAATGGCAAACCACCA
1006656 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1006693 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
1006710 GTTTAATATG
Statistics
Matches: 105, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
101 15 0.14
102 90 0.86
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACAAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:1008991 original size:9 final size:9
Alignment explanation
Indices: 1008977--1009001 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1008967 TTTATGTCAA
1008977 ATAAAAAAT
1 ATAAAAAAT
1008986 ATAAAAAAT
1 ATAAAAAAT
1008995 ATAAAAA
1 ATAAAAA
1009002 TTCTTGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:1012541 original size:27 final size:27
Alignment explanation
Indices: 1012502--1012557 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
1012492 ATTTAATTTA
*
1012502 TTTAAATTAAAAATTAATTTAATAAAT
1 TTTAAATTAAAAATTAATTGAATAAAT
* *
1012529 TTTAATATT-AAAATTGATTGAATTAAT
1 TTTAA-ATTAAAAATTAATTGAATAAAT
1012556 TT
1 TT
1012558 ATTTTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 22 0.88
28 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (27 bp):
TTTAAATTAAAAATTAATTGAATAAAT
Found at i:1012715 original size:23 final size:23
Alignment explanation
Indices: 1012689--1012741 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1012679 TTTTTTTTGT
* * *
1012689 TTTAATTAAACTTTTAGTTTAAG
1 TTTAAATAAACTTTTAATTTAAA
* *
1012712 TTTAAATGAGCTTTTAATTTAAA
1 TTTAAATAAACTTTTAATTTAAA
1012735 TTTAAAT
1 TTTAAAT
1012742 GGATTTAAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.51
Consensus pattern (23 bp):
TTTAAATAAACTTTTAATTTAAA
Found at i:1012742 original size:23 final size:22
Alignment explanation
Indices: 1012699--1012760 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
1012689 TTTAATTAAA
* *
1012699 CTTTTAGTTTAAGTTTAAATGAG
1 CTTTTAATTTAAATTTAAATG-G
1012722 CTTTTAATTTAAATTTAAATGG
1 CTTTTAATTTAAATTTAAATGG
*
1012744 -ATTTAAGTTTAAATTTA
1 CTTTTAA-TTTAAATTTA
1012761 TATTTTATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 5 0.14
22 11 0.31
23 19 0.54
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.50
Consensus pattern (22 bp):
CTTTTAATTTAAATTTAAATGG
Found at i:1013398 original size:25 final size:26
Alignment explanation
Indices: 1013348--1013399 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1013338 TTTATATAAT
* *
1013348 TTTTATTTTTTTACTTTATCGTATTG
1 TTTTATTTTTTTACTTGATCGAATTG
*
1013374 TTTTATTTTTTTA-TTGGTCGAATTG
1 TTTTATTTTTTTACTTGATCGAATTG
1013399 T
1 T
1013400 ATTGCTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.15, C:0.06, G:0.12, T:0.67
Consensus pattern (26 bp):
TTTTATTTTTTTACTTGATCGAATTG
Found at i:1017638 original size:103 final size:104
Alignment explanation
Indices: 1017460--1017675 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 104
1017450 TTTACTGTAA
1017460 GAAA-TTGCCAAATTTTGTAAAAAATCAATCAAGGCTTCAATGTTTTTTTCAAGATTTTGTTAAA
1 GAAATTTGCCAAATTTTGTAAAAAATCAATCAAGGCTTCAATGTTTTTTTCAAGATTTTGTTAAA
1017524 ATACTATGCTTC-ATTAAGTTTATTCACTTGTTACAAGT
66 ATACTATGCTTCTATTAAGTTTATTCACTTGTTACAAGT
1017562 GAAATTTGCCAAATTTTGTAAAAAATCAATCAAGGCTTCAATGTTTTTTTCAAGATTTTGTTAAA
1 GAAATTTGCCAAATTTTGTAAAAAATCAATCAAGGCTTCAATGTTTTTTTCAAGATTTTGTTAAA
1017627 ATACTATGCTTCATTATTAAGTTTATTCACTTGTTACAAGT
66 ATACTATGCTTC--TATTAAGTTTATTCACTTGTTACAAGT
1017668 GAAATTTG
1 GAAATTTG
1017676 ATGATTCTTG
Statistics
Matches: 110, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
102 4 0.04
103 72 0.65
106 34 0.31
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (104 bp):
GAAATTTGCCAAATTTTGTAAAAAATCAATCAAGGCTTCAATGTTTTTTTCAAGATTTTGTTAAA
ATACTATGCTTCTATTAAGTTTATTCACTTGTTACAAGT
Found at i:1018019 original size:27 final size:27
Alignment explanation
Indices: 1017981--1018051 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
1017971 AATATGCCAT
*
1017981 CATTTTTGACAAATAAAAAAAAACTAC
1 CATTTTTGACAAACAAAAAAAAACTAC
* **
1018008 CATTTTTGACAAACACAAAGTAACTAC
1 CATTTTTGACAAACAAAAAAAAACTAC
1018035 CATTTTTGACAAACAAA
1 CATTTTTGACAAACAAA
1018052 TGGTGGCTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.49, C:0.18, G:0.06, T:0.27
Consensus pattern (27 bp):
CATTTTTGACAAACAAAAAAAAACTAC
Found at i:1021564 original size:38 final size:38
Alignment explanation
Indices: 1021513--1021591 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
1021503 TTGTTTGTCT
* *
1021513 TTCTTCCTTAGTTCATAACTATACAAAGCTGCACATCC
1 TTCTTCCTCAGTTCATAACTATACAAAGCTGCACATAC
1021551 TTCTTCCTCAGTTCATAACTATACAAAGCTGCACATAC
1 TTCTTCCTCAGTTCATAACTATACAAAGCTGCACATAC
1021589 TTC
1 TTC
1021592 ACTAAGGGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (38 bp):
TTCTTCCTCAGTTCATAACTATACAAAGCTGCACATAC
Found at i:1022534 original size:27 final size:26
Alignment explanation
Indices: 1022502--1022613 Score: 111
Period size: 27 Copynumber: 4.3 Consensus size: 26
1022492 TCCATTTTGT
* *
1022502 AATAAAAATTAATTATAAATTTTGATA
1 AATAAAAA-TAATTATTATTTTTGATA
* * *
1022529 AAT-AAAAT-ATCATCATTTTTGACA
1 AATAAAAATAATTATTATTTTTGATA
* *
1022553 AATAAAAAAAATTATTATTTTTTATA
1 AATAAAAATAATTATTATTTTTGATA
* *
1022579 AATATAAAATAATTATTATTTTTAACA
1 AATA-AAAATAATTATTATTTTTGATA
1022606 AATAAAAA
1 AATAAAAA
1022614 ATAACTTTTA
Statistics
Matches: 70, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
24 15 0.21
25 5 0.07
26 24 0.34
27 26 0.37
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (26 bp):
AATAAAAATAATTATTATTTTTGATA
Found at i:1022561 original size:26 final size:26
Alignment explanation
Indices: 1022532--1022616 Score: 98
Period size: 26 Copynumber: 3.2 Consensus size: 26
1022522 TTTGATAAAT
* * *
1022532 AAAATATCATCATTTTTGACAAATAA
1 AAAATATTATTATTTTTAACAAATAA
* * * *
1022558 AAAAAATTATTATTTTTTATAAATAT
1 AAAATATTATTATTTTTAACAAATAA
1022584 AAAATAATTATTATTTTTAACAAATAA
1 AAAAT-ATTATTATTTTTAACAAATAA
1022611 AAAATA
1 AAAATA
1022617 ACTTTTATTG
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
26 25 0.52
27 23 0.48
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (26 bp):
AAAATATTATTATTTTTAACAAATAA
Found at i:1022580 original size:50 final size:53
Alignment explanation
Indices: 1022502--1022614 Score: 133
Period size: 53 Copynumber: 2.2 Consensus size: 53
1022492 TCCATTTTGT
* *
1022502 AATAAAAATTAATTATAAATTTTGAT-AA-ATAAAAT-ATCATCATTTTTGACA
1 AATAAAAA-AAATTATAAATTTTGATAAATATAAAATAATCATCATTTTTAACA
* * * * *
1022553 AATAAAAAAAATTATTATTTTTTATAAATATAAAATAATTATTATTTTTAACA
1 AATAAAAAAAATTATAAATTTTGATAAATATAAAATAATCATCATTTTTAACA
1022606 AATAAAAAA
1 AATAAAAAA
1022615 TAACTTTTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
50 13 0.25
51 10 0.19
52 7 0.13
53 22 0.42
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (53 bp):
AATAAAAAAAATTATAAATTTTGATAAATATAAAATAATCATCATTTTTAACA
Found at i:1022614 original size:27 final size:27
Alignment explanation
Indices: 1022543--1022630 Score: 108
Period size: 27 Copynumber: 3.3 Consensus size: 27
1022533 AAATATCATC
*
1022543 ATTTTTGACAAATAAAAAA-AATTATT
1 ATTTTTAACAAATAAAAAATAATTATT
* * *
1022569 ATTTTTTATAAATATAAAATAATTATT
1 ATTTTTAACAAATAAAAAATAATTATT
1022596 ATTTTTAACAAATAAAAAATAACTT-TT
1 ATTTTTAACAAATAAAAAATAA-TTATT
1022623 ATTGTTTA
1 ATT-TTTA
1022631 GACATCCACC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
26 16 0.30
27 31 0.58
28 6 0.11
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45
Consensus pattern (27 bp):
ATTTTTAACAAATAAAAAATAATTATT
Found at i:1024260 original size:22 final size:22
Alignment explanation
Indices: 1024235--1024277 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1024225 AAATATTATA
*
1024235 TTTA-AATTAATATTTATATAAT
1 TTTATAATTAA-ATTTAAATAAT
1024257 TTTATAATTAAATTTAAATAA
1 TTTATAATTAAATTTAAATAA
1024278 AATAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTATAATTAAATTTAAATAAT
Found at i:1026023 original size:3 final size:3
Alignment explanation
Indices: 1026015--1026042 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1026005 TCTCAAGGAG
1026015 AAC AAC AAC AAC AAC AAC AAC AAC AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC A
1026043 GCATCAAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:1028055 original size:109 final size:109
Alignment explanation
Indices: 1027864--1028080 Score: 344
Period size: 109 Copynumber: 2.0 Consensus size: 109
1027854 AGGGGAAAAA
** * * *
1027864 AGAATTGTAACTTGGGTTTTCTTTAGTTGTTGTTGTATGATCTAGGTGGTATGATAATGAATCAA
1 AGAATTGTAACTTAAGTTTCCTTTAGTTGTTGTTGTATAATCTAGGTGGTATAATAATGAATCAA
* *
1027929 GGAGAAAAACTTTGAGAATATTGCTTTAATATTTCCTAATTTGC
66 GAAGAAAAACTTTGAGAATATTGCTTGAATATTTCCTAATTTGC
1027973 AGAATTGTAACTTAAGTTTCCTTTAGTTGTTGTTGTATAATCTAGGTGGTATAATAATGAATCAA
1 AGAATTGTAACTTAAGTTTCCTTTAGTTGTTGTTGTATAATCTAGGTGGTATAATAATGAATCAA
* * *
1028038 GAAGACAAACTTTGAGAATGTTGCTTGAATTTTTCCTAATTTG
66 GAAGAAAAACTTTGAGAATATTGCTTGAATATTTCCTAATTTG
1028081 AAGTGTTTCT
Statistics
Matches: 98, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
109 98 1.00
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (109 bp):
AGAATTGTAACTTAAGTTTCCTTTAGTTGTTGTTGTATAATCTAGGTGGTATAATAATGAATCAA
GAAGAAAAACTTTGAGAATATTGCTTGAATATTTCCTAATTTGC
Found at i:1029140 original size:31 final size:31
Alignment explanation
Indices: 1029074--1029144 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
1029064 TAAATTGTTG
* * * **
1029074 AGAAGTGTCTTTGTTTCAGCTCAAGTTGTTG
1 AGAAGTGTCTTTGTTTCAACACAAGCTGTCA
1029105 AGAAGTGTCTTTGTTTCAACACAAGCTGTCA
1 AGAAGTGTCTTTGTTTCAACACAAGCTGTCA
1029136 AGAAGTGTC
1 AGAAGTGTC
1029145 CCTGAATTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.35
Consensus pattern (31 bp):
AGAAGTGTCTTTGTTTCAACACAAGCTGTCA
Found at i:1032295 original size:14 final size:15
Alignment explanation
Indices: 1032256--1032295 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
1032246 ATATTTTTTA
1032256 TATAT-TTAAATAAT
1 TATATCTTAAATAAT
*
1032270 TATATCTT-AATACT
1 TATATCTTAAATAAT
1032284 TAT-TCTTAAATA
1 TATATCTTAAATA
1032296 TATGTTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 4 0.17
14 17 0.74
15 2 0.09
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (15 bp):
TATATCTTAAATAAT
Found at i:1037535 original size:29 final size:30
Alignment explanation
Indices: 1037481--1037549 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
1037471 TATAATAAAG
1037481 ATTATATTATTAAATTAAATATATATTTTT
1 ATTATATTATTAAATTAAATATATATTTTT
* * *
1037511 ATTA-ATTATT-AATTATATTTAATATTTAT
1 ATTATATTATTAAATTAAATAT-ATATTTTT
*
1037540 CTTATATTAT
1 ATTATATTAT
1037550 ATTTAAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 8 0.24
29 16 0.48
30 9 0.27
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (30 bp):
ATTATATTATTAAATTAAATATATATTTTT
Found at i:1038198 original size:17 final size:17
Alignment explanation
Indices: 1038158--1038199 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
1038148 AATTTATGAA
1038158 TTTATTTAGATAAATTT
1 TTTATTTAGATAAATTT
1038175 TTATATTTA-ATATAATTT
1 TT-TATTTAGATA-AATTT
1038193 TTTATTT
1 TTTATTT
1038200 TTAATTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTATTTAGATAAATTT
Found at i:1038208 original size:18 final size:19
Alignment explanation
Indices: 1038167--1038208 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1038157 ATTTATTTAG
*
1038167 ATAAATTTTTATATTTAAT
1 ATAATTTTTTATATTTAAT
*
1038186 ATAATTTTTTATTTTTAAT
1 ATAATTTTTTATATTTAAT
1038205 -TAAT
1 ATAAT
1038209 ATTAAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATAATTTTTTATATTTAAT
Found at i:1038221 original size:23 final size:21
Alignment explanation
Indices: 1038196--1038268 Score: 69
Period size: 23 Copynumber: 3.4 Consensus size: 21
1038186 ATAATTTTTT
*
1038196 ATTTTTAATTAATATTAAAATAT
1 ATTTTTAATT-ATATT-AAATAA
* *
1038219 ATTTTTAAATATATT--TTAA
1 ATTTTTAATTATATTAAATAA
1038238 ATTTTTAATTTATATTTAAATAA
1 ATTTTTAA-TTATA-TTAAATAA
1038261 ATTTTTAA
1 ATTTTTAA
1038269 AATAAATAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 10 0.24
20 4 0.10
21 2 0.05
22 5 0.12
23 20 0.49
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTTTAATTATATTAAATAA
Found at i:1038231 original size:43 final size:43
Alignment explanation
Indices: 1038183--1038273 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 43
1038173 TTTTATATTT
** *
1038183 AATATAATTTTTTATTTTTAATTAATATTAAAATATATTTTTA
1 AATATAATTTTAAATTTTTAATTAATATTAAAATAAATTTTTA
* *
1038226 AATAT-ATTTTAAATTTTTAATTTATATTTAAATAAATTTTTA
1 AATATAATTTTAAATTTTTAATTAATATTAAAATAAATTTTTA
1038268 AA-ATAA
1 AATATAA
1038274 ATAAATTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
41 2 0.05
42 35 0.83
43 5 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (43 bp):
AATATAATTTTAAATTTTTAATTAATATTAAAATAAATTTTTA
Found at i:1038251 original size:20 final size:18
Alignment explanation
Indices: 1038219--1038258 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
1038209 ATTAAAATAT
1038219 ATTTTTAAATATATTTTAA
1 ATTTTTAAATATA-TTTAA
*
1038238 ATTTTTAATTTATATTTAA
1 ATTTTTAA-ATATATTTAA
1038257 AT
1 AT
1038259 AAATTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTTAAATATATTTAA
Found at i:1038461 original size:20 final size:19
Alignment explanation
Indices: 1038436--1038486 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
1038426 AGGTACTTTC
1038436 TTTTTTTTAAATATGATTAT
1 TTTTTTTTAAAT-TGATTAT
* *
1038456 TTTTTTATATAATTTATTAT
1 TTTTTTTTA-AATTGATTAT
*
1038476 TTTTATTTAAA
1 TTTTTTTTAAA
1038487 AATATTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTTTTTAAATTGATTAT
Found at i:1038789 original size:2 final size:2
Alignment explanation
Indices: 1038782--1038825 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1038772 GCATATGCCT
* *
1038782 TC TC TC TC TC TC TC TC TC TC TC TC TC AC TC TC TC TC TC TT TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1038824 TC
1 TC
1038826 CTATCCATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.02, C:0.48, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1039623 original size:20 final size:20
Alignment explanation
Indices: 1039561--1039625 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
1039551 TTGTTTGGTG
*
1039561 TTTTTATTTTTATATTTTGCT
1 TTTTTA-TTTTATTTTTTGCT
**
1039582 ATTTTT-TCTTTATTTTCAGCT
1 -TTTTTAT-TTTATTTTTTGCT
1039603 TTTTTATTTTATTTTTTGCT
1 TTTTTATTTTATTTTTTGCT
1039623 TTT
1 TTT
1039626 CATTTTTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
20 20 0.56
21 11 0.31
22 5 0.14
ACGTcount: A:0.12, C:0.08, G:0.05, T:0.75
Consensus pattern (20 bp):
TTTTTATTTTATTTTTTGCT
Found at i:1039625 original size:19 final size:19
Alignment explanation
Indices: 1039561--1039631 Score: 61
Period size: 21 Copynumber: 3.5 Consensus size: 19
1039551 TTGTTTGGTG
*
1039561 TTTTTATTTTTATATTTTGC
1 TTTTTA-TTTTATTTTTTGC
* **
1039581 TATTTTTTCTTTATTTTCAGC
1 T-TTTTAT-TTTATTTTTTGC
1039602 TTTTTTATTTTATTTTTTGC
1 -TTTTTATTTTATTTTTTGC
*
1039622 TTTTCATTTT
1 TTTTTATTTT
1039632 TATTGAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
19 9 0.22
20 12 0.30
21 18 0.45
22 1 0.03
ACGTcount: A:0.13, C:0.08, G:0.04, T:0.75
Consensus pattern (19 bp):
TTTTTATTTTATTTTTTGC
Found at i:1039632 original size:20 final size:19
Alignment explanation
Indices: 1039562--1039635 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 19
1039552 TGTTTGGTGT
*
1039562 TTTTATTTTTATATTTTGC
1 TTTTATTTTTATTTTTTGC
* **
1039581 TATTTTTTCTTTATTTTCAGC
1 T-TTTATT-TTTATTTTTTGC
*
1039602 TTTTTTATTTTATTTTTTGC
1 TTTTAT-TTTTATTTTTTGC
1039622 TTTTCATTTTTATT
1 TTTT-ATTTTTATT
1039636 GAAAAAAGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.02
20 31 0.70
21 12 0.27
ACGTcount: A:0.14, C:0.08, G:0.04, T:0.74
Consensus pattern (19 bp):
TTTTATTTTTATTTTTTGC
Found at i:1040854 original size:2 final size:2
Alignment explanation
Indices: 1040847--1040896 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
1040837 ATGTTTTCAA
* * *
1040847 AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1040889 AT AT AT AT
1 AT AT AT AT
1040897 GTATGTACAC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1040875 original size:16 final size:16
Alignment explanation
Indices: 1040856--1040903 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
1040846 AATATATATA
1040856 TATATATATATGTATG
1 TATATATATATGTATG
1040872 TATATATATATGTA--
1 TATATATATATGTATG
1040886 TATATATATATGTATG
1 TATATATATATGTATG
1040902 TA
1 TA
1040904 CACACACATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 14 0.47
16 16 0.53
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (16 bp):
TATATATATATGTATG
Found at i:1042532 original size:2 final size:2
Alignment explanation
Indices: 1042525--1042553 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1042515 ATACCCTATT
1042525 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1042554 TATTGATGAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1044357 original size:17 final size:16
Alignment explanation
Indices: 1044331--1044373 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
1044321 ATTTAACTTA
1044331 AATATAAAATTATAAAT
1 AATATAAAATT-TAAAT
* *
1044348 AATTTAAAATTTAACT
1 AATATAAAATTTAAAT
1044364 AATATAAAAT
1 AATATAAAAT
1044374 AATATTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
AATATAAAATTTAAAT
Found at i:1044788 original size:14 final size:15
Alignment explanation
Indices: 1044761--1044790 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1044751 AGTCAATAAT
1044761 AAGACAAGTTTTTAC
1 AAGACAAGTTTTTAC
1044776 AAGACAA-TTTTTAC
1 AAGACAAGTTTTTAC
1044790 A
1 A
1044791 TTATGTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (15 bp):
AAGACAAGTTTTTAC
Found at i:1045155 original size:2 final size:2
Alignment explanation
Indices: 1045148--1045182 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1045138 CAATTGACAC
1045148 AT AT 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 AT AT A
1045183 GAAAAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1045384 original size:2 final size:2
Alignment explanation
Indices: 1045377--1045424 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1045367 CCTAATAATC
1045377 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1045419 AT AT AT
1 AT AT AT
1045425 CTCTTAACTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1049835 original size:13 final size:13
Alignment explanation
Indices: 1049817--1049843 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1049807 TTAGCCAACA
1049817 ACATTTGACTTTT
1 ACATTTGACTTTT
1049830 ACATTTGACTTTT
1 ACATTTGACTTTT
1049843 A
1 A
1049844 TTCAAATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.52
Consensus pattern (13 bp):
ACATTTGACTTTT
Found at i:1050152 original size:18 final size:19
Alignment explanation
Indices: 1050131--1050169 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1050121 AAATTAAGTT
*
1050131 ATTTATTTTA-ATTTAAAA
1 ATTTATTTAATATTTAAAA
1050149 ATTTATTTAATATTTAAAA
1 ATTTATTTAATATTTAAAA
1050168 AT
1 AT
1050170 ATTTAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTATTTAATATTTAAAA
Found at i:1050163 original size:19 final size:18
Alignment explanation
Indices: 1050131--1050177 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1050121 AAATTAAGTT
*
1050131 ATTTATTTTAATTTAAAA
1 ATTTATTTAAATTTAAAA
1050149 ATTTATTTAATATTTAAAA
1 ATTTATTTAA-ATTTAAAA
1050168 A--TATTTAAAT
1 ATTTATTTAAAT
1050178 AAAAATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 2 0.07
17 7 0.26
18 9 0.33
19 9 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTATTTAAATTTAAAA
Found at i:1050172 original size:17 final size:16
Alignment explanation
Indices: 1050134--1050186 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 16
1050124 TTAAGTTATT
*
1050134 TATTTTAATTTAAAAA
1 TATTTAAATTTAAAAA
1050150 TTTATTTAATATTTAAAAA
1 --TATTTAA-ATTTAAAAA
1050169 TATTTAAA--TAAAAA
1 TATTTAAATTTAAAAA
1050183 TATT
1 TATT
1050187 AGATTTAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.30
16 1 0.03
17 7 0.21
18 6 0.18
19 9 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TATTTAAATTTAAAAA
Found at i:1050364 original size:14 final size:14
Alignment explanation
Indices: 1050345--1050372 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1050335 GTAATAAATA
1050345 TATAATATTATAAT
1 TATAATATTATAAT
1050359 TATAATATTATAAT
1 TATAATATTATAAT
1050373 ATGATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATAATATTATAAT
Found at i:1050368 original size:8 final size:8
Alignment explanation
Indices: 1050341--1050380 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
1050331 TAAAGTAATA
1050341 AATA-TAT
1 AATATTAT
1050348 AATATTAT
1 AATATTAT
1050356 -A-ATTAT
1 AATATTAT
1050362 AATATTAT
1 AATATTAT
*
1050370 AATATGAT
1 AATATTAT
1050378 AAT
1 AAT
1050381 GTATCTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
6 5 0.17
7 6 0.21
8 18 0.62
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (8 bp):
AATATTAT
Found at i:1051424 original size:2 final size:2
Alignment explanation
Indices: 1051417--1051441 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1051407 AATTTTAGTT
1051417 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1051442 TAATATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1052499 original size:18 final size:18
Alignment explanation
Indices: 1052478--1052513 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1052468 AAAAACTGAC
*
1052478 AAAAGAAAAAATAAAATT
1 AAAAAAAAAAATAAAATT
1052496 AAAAAAAAAAATAAAATT
1 AAAAAAAAAAATAAAATT
1052514 TACCTAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.17
Consensus pattern (18 bp):
AAAAAAAAAAATAAAATT
Found at i:1053016 original size:41 final size:41
Alignment explanation
Indices: 1052896--1053035 Score: 113
Period size: 41 Copynumber: 3.4 Consensus size: 41
1052886 GGCATTTTTG
* * *
1052896 TAAAAAAACTGTTAATAGAAAAAATTTAGTGACATTTA-ATT
1 TAAAAACACCGTTAATAGAAAAAATTTAGTGACATTCACA-T
* ** * *** *
1052937 TATAAACGTCGCTAATA-AGAAAAATTTAGTGGTGTTCACCT
1 TAAAAACACCGTTAATAGA-AAAAATTTAGTGACATTCACAT
* *
1052978 TAAAAACACCGTTAATAGAAAAAATTTAGCGACATTCACAG
1 TAAAAACACCGTTAATAGAAAAAATTTAGTGACATTCACAT
**
1053019 TAAAAACGTCGTTAATA
1 TAAAAACACCGTTAATA
1053036 TAACTGATTA
Statistics
Matches: 73, Mismatches: 23, Indels: 6
0.72 0.23 0.06
Matches are distributed among these distances:
40 1 0.01
41 71 0.97
42 1 0.01
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (41 bp):
TAAAAACACCGTTAATAGAAAAAATTTAGTGACATTCACAT
Found at i:1053881 original size:13 final size:14
Alignment explanation
Indices: 1053856--1053884 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1053846 ACATTAAATA
1053856 TAAATTATATATTT
1 TAAATTATATATTT
1053870 TAAATT-TATATTT
1 TAAATTATATATTT
1053883 TA
1 TA
1053885 TACATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAAATTATATATTT
Found at i:1053892 original size:20 final size:20
Alignment explanation
Indices: 1053844--1053892 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
1053834 TAGTATGCTA
1053844 ATACATTAAATATAAATTAT
1 ATACATTAAATATAAATTAT
** * * *
1053864 ATATTTTAAATTTATATTTT
1 ATACATTAAATATAAATTAT
1053884 ATACATTAA
1 ATACATTAA
1053893 TAATATATAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (20 bp):
ATACATTAAATATAAATTAT
Found at i:1054968 original size:3 final size:3
Alignment explanation
Indices: 1054960--1054999 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1054950 AAATTTGTAA
1054960 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1055000 TTTGGAGTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1062675 original size:62 final size:62
Alignment explanation
Indices: 1062578--1062698 Score: 181
Period size: 62 Copynumber: 2.0 Consensus size: 62
1062568 CAAACTACTG
*
1062578 ACGTGAAAGACTTTCAATCAGACAGCTCAAATCATATTACTTGGTTTCATTGTTAAGTAATA
1 ACGTGAAAGACTTTCAATCAGACAGCTCAAATCATATGACTTGGTTTCATTGTTAAGTAATA
* * * *
1062640 ACGTGAAAGGCTTTCAATTAGAC-GACTGAAATCATATGATTTGGTTTCATTGTTAAGTA
1 ACGTGAAAGACTTTCAATCAGACAG-CTCAAATCATATGACTTGGTTTCATTGTTAAGTA
1062699 GTACACTTTG
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
61 1 0.02
62 52 0.98
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (62 bp):
ACGTGAAAGACTTTCAATCAGACAGCTCAAATCATATGACTTGGTTTCATTGTTAAGTAATA
Found at i:1067317 original size:21 final size:21
Alignment explanation
Indices: 1067277--1067319 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1067267 TTGCTGGTTG
* **
1067277 AAACTCCACCTGTTTTGGAGT
1 AAACTCCACCTGCTGCGGAGT
1067298 AAACTCCACCTGCTGCGGAGT
1 AAACTCCACCTGCTGCGGAGT
1067319 A
1 A
1067320 CTACTTGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (21 bp):
AAACTCCACCTGCTGCGGAGT
Found at i:1069637 original size:26 final size:25
Alignment explanation
Indices: 1069570--1069638 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 25
1069560 ATATCATCAT
*
1069570 TTTTAATAAATAAAAAAAATACTATT
1 TTTTAATAAATAAAAAAAATACTA-A
* *
1069596 TTTTACA-AACATAAAATAATTACTAA
1 TTTTA-ATAA-ATAAAAAAAATACTAA
1069622 TTTTAATAAATAAAAAA
1 TTTTAATAAATAAAAAA
1069639 TAACTTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
25 8 0.22
26 14 0.39
27 14 0.39
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (25 bp):
TTTTAATAAATAAAAAAAATACTAA
Found at i:1069638 original size:27 final size:26
Alignment explanation
Indices: 1069570--1069641 Score: 83
Period size: 27 Copynumber: 2.8 Consensus size: 26
1069560 ATATCATCAT
*
1069570 TTTTAATAAATAAAAAA-AATACTAT
1 TTTTAATAAATAAAAAATAATACTAA
* * * *
1069595 TTTTTACAAACATAAAATAATTACTAA
1 TTTTAATAAATAAAAAATAA-TACTAA
1069622 TTTTAATAAATAAAAAATAA
1 TTTTAATAAATAAAAAATAA
1069642 CTTTTATTGA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
25 13 0.36
26 2 0.06
27 21 0.58
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (26 bp):
TTTTAATAAATAAAAAATAATACTAA
Found at i:1080172 original size:15 final size:17
Alignment explanation
Indices: 1080139--1080179 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
1080129 TAAAATATAA
*
1080139 ATATTAAATATGAATAT
1 ATATTTAATATGAATAT
1080156 ATATTTAATAT-AA-AT
1 ATATTTAATATGAATAT
1080171 ATATTTAAT
1 ATATTTAAT
1080180 TTTTTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.48
16 2 0.09
17 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
ATATTTAATATGAATAT
Found at i:1085761 original size:86 final size:86
Alignment explanation
Indices: 1085589--1085761 Score: 285
Period size: 86 Copynumber: 2.0 Consensus size: 86
1085579 CATAAATAAG
*
1085589 AAAAGTTAAATAAATATTGGTGAAATGAAGTTGACAAACTAAAACTTCATTCAAATGTTAGAAAT
1 AAAAGTTAAATAAATATTGGTGAAACGAAGTTGACAAACTAAAACTTCATTCAAATGTTAGAAAT
*
1085654 AATGAATGAAAATTGACCAAA
66 AATGAAAGAAAATTGACCAAA
* *
1085675 AAAAGTTTAATAAATATTGGTGAACCGAAGTTGACAAACTAAAACTTGCATTCAAATGTTAGAAA
1 AAAAGTTAAATAAATATTGGTGAAACGAAGTTGACAAACTAAAACTT-CATTCAAATGTTAGAAA
*
1085740 TAATGAAAGACAATTGA-CAAA
65 TAATGAAAGAAAATTGACCAAA
1085761 A
1 A
1085762 CCTGGGAATA
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
86 49 0.60
87 32 0.40
ACGTcount: A:0.50, C:0.09, G:0.14, T:0.26
Consensus pattern (86 bp):
AAAAGTTAAATAAATATTGGTGAAACGAAGTTGACAAACTAAAACTTCATTCAAATGTTAGAAAT
AATGAAAGAAAATTGACCAAA
Found at i:1087503 original size:36 final size:35
Alignment explanation
Indices: 1087454--1087525 Score: 94
Period size: 35 Copynumber: 2.0 Consensus size: 35
1087444 TAATAAAAAA
*
1087454 TTATTATAATAAACTCTAAATTTATAA-TATTTTATT
1 TTATTATAATAAACTAT-AA-TTATAATTATTTTATT
1087490 TTATTA-AATTAAACTATAATTATAATTATTTTATT
1 TTATTATAA-TAAACTATAATTATAATTATTTTATT
1087525 T
1 T
1087526 AATTTTCATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
34 6 0.18
35 14 0.42
36 13 0.39
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (35 bp):
TTATTATAATAAACTATAATTATAATTATTTTATT
Found at i:1088499 original size:2 final size:2
Alignment explanation
Indices: 1088492--1088525 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1088482 GAATATCCCA
1088492 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1088526 GTCTGTTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1088911 original size:22 final size:22
Alignment explanation
Indices: 1088883--1088924 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1088873 ATTAAAAAAT
1088883 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
1088905 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
1088925 ATTAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:1088952 original size:26 final size:25
Alignment explanation
Indices: 1088906--1088959 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
1088896 ATATTTATAT
*
1088906 ATTTTTATAATTAAATTTAATTAAA
1 ATTTTTATAATTAAATATAATTAAA
* *
1088931 ATTTTTATTATTAAATAATAATTCAA
1 ATTTTTATAATTAAAT-ATAATTAAA
1088957 ATT
1 ATT
1088960 AATCCGAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTTTTATAATTAAATATAATTAAA
Found at i:1094153 original size:505 final size:502
Alignment explanation
Indices: 1093206--1094199 Score: 1713
Period size: 505 Copynumber: 2.0 Consensus size: 502
1093196 ACAATTTAGC
*
1093206 AAATTACGTCATCATCCCGTTGAAGCGCATTATTAAAATAACTACTTACGGATTCTTAAGATTTA
1 AAATTACGTCATCATCACGTTGAAGCGCATTATTAAAATAACTACTTACGGATTCTTAAGATTTA
* *
1093271 TCTCAAAAGATAAAATAAATTAAAATACTTTAAAAAAAAGTATGCACCGTCTAAAGTACAAAAAA
66 TCTCAAAAGATAAAATAAATTAAAATACTTTAAAAAAAAGTATACACCATCTAAAGTACAAAAAA
* * ***
1093336 TTAAGAATTTGGATGTCTAAGATTGAACGATACATATTTTTCACAATATATATATAAATGAGGGA
131 TTAAGAATTTGGATGTCTAAGATTGAACAATACATATTTTTCACAATATATATATAAACGAAAAA
* *
1093401 TTTATTTATACATGTATAAAATTAAATTTTTAAATTTTTTATATAATTTATATCTGTTTAATTTA
196 TTTACTTATACATGTATAAAATTAAATTTTTAAATTTTTTATATAATTTATATCTATTTAATTTA
* * *
1093466 TATGTTGTATTTCATTGTATATTCACATAAATTATGAACGTTAAATTTTTAATAAATAAAAAATA
261 TACGTTATATTTCATTGTATATTCACATAAATTATGAACGTCAAATTTTTAATAAATAAAAAATA
* *
1093531 TTTAAATATTTATTTAACGTAAAAAACTTTCAATTGTTAAATATATATTAAAAATATCAGTATCC
326 TTTAAATATTTATTTAACGTAAAAAACTTTCAACTGTTAAATATATATTAAAAATATCAATATCC
*
1093596 TTGATCAATATGATTAAAAAATTATATTGATTATTTGTATGACGAGTAAAATTATAATTTTTTAA
391 TTGATCAATATAATTAAAAAATTATATTGATTATTTGTATGACGAGTAAAATTATAATTTTTTAA
1093661 TATAACAATTAATTTAGTAATATATTAATTATATCTATTTAGACGGT
456 TATAACAATTAATTTAGTAATATATTAATTATATCTATTTAGACGGT
* *
1093708 AAATTACGTCATCATCACGTTGAAGTGCATTATTAAAATAACTAGTTACGGATTCTTAAGATTTA
1 AAATTACGTCATCATCACGTTGAAGCGCATTATTAAAATAACTACTTACGGATTCTTAAGATTTA
* *
1093773 TCTCAAAAGATAAAATAAATTAAAATACTTTAAAAAAAAGTATACGCCATCTAAAGTACCAAAAA
66 TCTCAAAAGATAAAATAAATTAAAATACTTTAAAAAAAAGTATACACCATCTAAAGTACAAAAAA
*
1093838 TTAAGAATTTGGATGTCTAAGATTGAATAATACATA-TTTTCTACAATATATATATATAAACGAA
131 TTAAGAATTTGGATGTCTAAGATTGAACAATACATATTTTTC-AC-A-ATATATATATAAACGAA
*
1093902 AAATTTACTTATATATGTATAAAATTAAATTTTTATAATTTTTTATATAATTTATATCTATTTAA
193 AAATTTACTTATACATGTATAAAATTAAATTTTTA-AATTTTTTATATAATTTATATCTATTTAA
1093967 TTTATACGTTATATTTCATTGTATATTCACATAAATTATGAACGTCAAATTTTTAATAAATAAAA
257 TTTATACGTTATATTTCATTGTATATTCACATAAATTATGAACGTCAAATTTTTAATAAATAAAA
*
1094032 AATATTTAAATATTTATTTAACGTAAAAAATTTTCAACTGTTAAATATATATTAAAAATATCAAT
322 AATATTTAAATATTTATTTAACGTAAAAAACTTTCAACTGTTAAATATATATTAAAAATATCAAT
1094097 AT-CTTCGATCAATATAATTAAAAAATTATATTGATTATTTGTATGACGAGTAAAATTATAATTT
387 ATCCTT-GATCAATATAATTAAAAAATTATATTGATTATTTGTATGACGAGTAAAATTATAATTT
*
1094161 TTTAATATAACAATTAATTTATTAATATATTAATTATAT
451 TTTAATATAACAATTAATTTAGTAATATATTAATTATAT
1094200 ATAAAACTAT
Statistics
Matches: 463, Mismatches: 24, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
501 5 0.01
502 159 0.34
503 1 0.00
504 49 0.11
505 249 0.54
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (502 bp):
AAATTACGTCATCATCACGTTGAAGCGCATTATTAAAATAACTACTTACGGATTCTTAAGATTTA
TCTCAAAAGATAAAATAAATTAAAATACTTTAAAAAAAAGTATACACCATCTAAAGTACAAAAAA
TTAAGAATTTGGATGTCTAAGATTGAACAATACATATTTTTCACAATATATATATAAACGAAAAA
TTTACTTATACATGTATAAAATTAAATTTTTAAATTTTTTATATAATTTATATCTATTTAATTTA
TACGTTATATTTCATTGTATATTCACATAAATTATGAACGTCAAATTTTTAATAAATAAAAAATA
TTTAAATATTTATTTAACGTAAAAAACTTTCAACTGTTAAATATATATTAAAAATATCAATATCC
TTGATCAATATAATTAAAAAATTATATTGATTATTTGTATGACGAGTAAAATTATAATTTTTTAA
TATAACAATTAATTTAGTAATATATTAATTATATCTATTTAGACGGT
Found at i:1094495 original size:20 final size:20
Alignment explanation
Indices: 1094458--1094496 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1094448 TTTAATTTTT
**
1094458 TATTAATTATATTCTTAAAA
1 TATTAATTATATAATTAAAA
*
1094478 TATTAATTTTATAATTAAA
1 TATTAATTATATAATTAAA
1094497 TTTAAATAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTAATTATATAATTAAAA
Found at i:1094653 original size:3 final size:3
Alignment explanation
Indices: 1094641--1094669 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1094631 GTACCGCACA
1094641 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1094670 TAGTTAGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1095239 original size:22 final size:21
Alignment explanation
Indices: 1095214--1095254 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1095204 TATTAAAAAT
*
1095214 TATTTTTAAATTAATATTTATA
1 TATTTTAAAATTAA-ATTTATA
1095236 TATTTTAAAATTAAATTTA
1 TATTTTAAAATTAAATTTA
1095255 AATAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTTTAAAATTAAATTTATA
Found at i:1096356 original size:83 final size:83
Alignment explanation
Indices: 1096234--1096388 Score: 197
Period size: 83 Copynumber: 1.9 Consensus size: 83
1096224 ATATTGATAT
* * * ** *
1096234 AATACCAATAATCATAAAAATATTAAAAGTAATACAATCAAATTTTCTTACTAATTATAATTGAA
1 AATACCAATAACCATAAAAATATTAAAAGCAATAAAATCAAAAGTTATTACTAATTATAATT-AA
1096299 AAT-TATAACCTCCAATAA
65 AATATATAACCTCCAATAA
* * *
1096317 AATACCGATAACCATTAAAAA-ATTAGAAGCAATAAAATCAAAAGTTATTATTAATTATAATTAA
1 AATACCAATAACCA-TAAAAATATTAAAAGCAATAAAATCAAAAGTTATTACTAATTATAATTAA
1096381 AATATATA
65 AATATATA
1096389 TATAACCAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
82 5 0.08
83 50 0.82
84 6 0.10
ACGTcount: A:0.54, C:0.11, G:0.04, T:0.32
Consensus pattern (83 bp):
AATACCAATAACCATAAAAATATTAAAAGCAATAAAATCAAAAGTTATTACTAATTATAATTAAA
ATATATAACCTCCAATAA
Found at i:1097071 original size:12 final size:13
Alignment explanation
Indices: 1097056--1097085 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1097046 TTCTTTGGGG
1097056 TTTTTTTTTCTT-
1 TTTTTTTTTCTTC
1097068 TTTTTTTTTCTTC
1 TTTTTTTTTCTTC
1097081 TTTTT
1 TTTTT
1097086 ATTTGTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTTTTTCTTC
Found at i:1097074 original size:15 final size:15
Alignment explanation
Indices: 1097056--1097097 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1097046 TTCTTTGGGG
1097056 TTTTTTTTTCTTTTT
1 TTTTTTTTTCTTTTT
*
1097071 TTTTTTCTTCTTTTT
1 TTTTTTTTTCTTTTT
* *
1097086 ATTTGTTTTCTT
1 TTTTTTTTTCTT
1097098 GGAATCAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.02, C:0.10, G:0.02, T:0.86
Consensus pattern (15 bp):
TTTTTTTTTCTTTTT
Found at i:1106337 original size:21 final size:22
Alignment explanation
Indices: 1106313--1106359 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
1106303 GACACAAAAT
1106313 AATTAAATAT-AATATAATATA
1 AATTAAATATAAATATAATATA
* *
1106334 AATT-ATTATAAATTTAATATA
1 AATTAAATATAAATATAATATA
1106355 AATTA
1 AATTA
1106360 TTATCATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTAAATATAAATATAATATA
Found at i:1106343 original size:10 final size:10
Alignment explanation
Indices: 1106330--1106363 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1106320 TATAATATAA
1106330 TATAAATTAT
1 TATAAATTAT
*
1106340 TATAAATTTAA
1 TATAAA-TTAT
1106351 TATAAATTAT
1 TATAAATTAT
1106361 TAT
1 TAT
1106364 CATTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TATAAATTAT
Found at i:1108922 original size:26 final size:26
Alignment explanation
Indices: 1108893--1108967 Score: 74
Period size: 26 Copynumber: 3.2 Consensus size: 26
1108883 TAATAATGTG
*
1108893 ATTTAAATAATAATTAAATATATTTT
1 ATTTAAATAATAATTAAATATATTTA
*
1108919 ATTT-AAT--T--TTTAAT-T-TTTA
1 ATTTAAATAATAATTAAATATATTTA
*
1108938 ATTCAAATAATAATTAAATATATTTA
1 ATTTAAATAATAATTAAATATATTTA
1108964 ATTT
1 ATTT
1108968 GATTTTTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 14
0.66 0.09 0.25
Matches are distributed among these distances:
19 6 0.16
20 4 0.11
21 5 0.14
22 1 0.03
23 1 0.03
24 5 0.14
25 4 0.11
26 11 0.30
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (26 bp):
ATTTAAATAATAATTAAATATATTTA
Found at i:1108948 original size:45 final size:45
Alignment explanation
Indices: 1108897--1109028 Score: 147
Period size: 45 Copynumber: 2.8 Consensus size: 45
1108887 AATGTGATTT
* *
1108897 AAATAATAATTAAATATATTTTATTTAATTTTTAATTTTTAATTC
1 AAATAATAATTAAATATATTTAATTTAATTTTTAATTCTTAATTC
* * *
1108942 AAATAATAATTAAATATATTTAATTTGATTTTTAATTCTTAACTA
1 AAATAATAATTAAATATATTTAATTTAATTTTTAATTCTTAATTC
* * *
1108987 AAATCAATTATCAAATATCAAATTCTAATTTTATTTTTAATT
1 AAAT-AATAATTAAATAT---ATT-TAATTTAATTTTTAATT
1109029 AATTTTTAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
45 44 0.59
46 11 0.15
49 3 0.04
50 16 0.22
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.51
Consensus pattern (45 bp):
AAATAATAATTAAATATATTTAATTTAATTTTTAATTCTTAATTC
Found at i:1119007 original size:3 final size:3
Alignment explanation
Indices: 1119001--1119039 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
1118991 GATGATGGAC
*
1119001 GAG GAG GCG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1119040 CCATGGACGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.31, C:0.03, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:1119745 original size:5 final size:5
Alignment explanation
Indices: 1119735--1119791 Score: 57
Period size: 5 Copynumber: 11.6 Consensus size: 5
1119725 AATAAATAAA
* *
1119735 TTAAT TTAAT TT-AT TTAATT TTAAT TTTAT TTAA- TTAA- ATAAT TTAATT
1 TTAAT TTAAT TTAAT TTAA-T TTAAT TTAAT TTAAT TTAAT TTAAT TTAA-T
1119784 TTAAT TTA
1 TTAAT TTA
1119792 CTTATTTGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 11 0.25
5 23 0.52
6 10 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTAAT
Found at i:1119748 original size:43 final size:44
Alignment explanation
Indices: 1119692--1119791 Score: 125
Period size: 43 Copynumber: 2.3 Consensus size: 44
1119682 TGTTTTATTC
*
1119692 AATTTTAATTTTATTTGATTAATT-ATTTTA-TTAAATAAATAAATT
1 AATTTTAA-TTTATTTAATT--TTAATTTTATTTAAATAAATAAATT
* *
1119737 AA-TTTAATTTATTTAATTTTAATTTTATTTAATTAAATAATTT
1 AATTTTAATTTATTTAATTTTAATTTTATTTAAATAAATAAATT
1119780 AATTTTAATTTA
1 AATTTTAATTTA
1119792 CTTATTTGAT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
41 2 0.04
42 6 0.12
43 25 0.51
44 14 0.29
45 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (44 bp):
AATTTTAATTTATTTAATTTTAATTTTATTTAAATAAATAAATT
Found at i:1119767 original size:10 final size:10
Alignment explanation
Indices: 1119735--1119791 Score: 57
Period size: 9 Copynumber: 5.8 Consensus size: 10
1119725 AATAAATAAA
1119735 TTAATTTAAT
1 TTAATTTAAT
1119745 TT-ATTTAATT
1 TTAATTTAA-T
*
1119755 TTAATTTTAT
1 TTAATTTAAT
1119765 TTAA-TTAA-
1 TTAATTTAAT
*
1119773 ATAATTTAATT
1 TTAATTTAA-T
1119784 TTAATTTA
1 TTAATTTA
1119792 CTTATTTGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
8 3 0.08
9 13 0.34
10 10 0.26
11 12 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TTAATTTAAT
Found at i:1120125 original size:13 final size:13
Alignment explanation
Indices: 1120106--1120195 Score: 55
Period size: 12 Copynumber: 7.2 Consensus size: 13
1120096 TACTCGTATA
1120106 ATATTTATATTAT
1 ATATTTATATTAT
* *
1120119 TTATTTATATCAT
1 ATATTTATATTAT
1120132 AT-TTTATATTAT
1 ATATTTATATTAT
* *
1120144 AAAAATTT-TAATAT
1 --ATATTTATATTAT
*
1120158 ATTTTTATATT-T
1 ATATTTATATTAT
* *
1120170 ATA-TCATATCAT
1 ATATTTATATTAT
*
1120182 AT-TTTTTATTAT
1 ATATTTATATTAT
1120194 AT
1 AT
1120196 TTAATTTTTT
Statistics
Matches: 56, Mismatches: 15, Indels: 13
0.67 0.18 0.15
Matches are distributed among these distances:
11 5 0.09
12 27 0.48
13 15 0.27
14 6 0.11
15 3 0.05
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (13 bp):
ATATTTATATTAT
Found at i:1120424 original size:2 final size:2
Alignment explanation
Indices: 1120419--1120523 Score: 147
Period size: 2 Copynumber: 52.5 Consensus size: 2
1120409 GTGTGTTTGC
* * * *
1120419 AT AT AT AA AT AT AT AT AT AT AT AT AT AT TT GT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1120461 AT AT AT AT AT AT AT AT TT GT AT AT AT TT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1120503 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
1120524 ATCTAAATTA
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 91 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1121115 original size:6 final size:6
Alignment explanation
Indices: 1121106--1121139 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
1121096 TTTACTTAAA
1121106 ATATTT ATATTT AATATTT ATATTT AATATTT AT
1 ATATTT ATATTT -ATATTT ATATTT -ATATTT AT
1121140 TTAAACAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 14 0.54
7 12 0.46
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
ATATTT
Found at i:1121124 original size:7 final size:7
Alignment explanation
Indices: 1121105--1121138 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
1121095 TTTTACTTAA
1121105 AATATTT
1 AATATTT
1121112 -ATATTT
1 AATATTT
1121118 AATATTT
1 AATATTT
1121125 -ATATTT
1 AATATTT
1121131 AATATTT
1 AATATTT
1121138 A
1 A
1121139 TTTAAACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AATATTT
Found at i:1121143 original size:11 final size:13
Alignment explanation
Indices: 1121105--1121139 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
1121095 TTTTACTTAA
1121105 AATATTTATATTT
1 AATATTTATATTT
1121118 AATATTTATATTT
1 AATATTTATATTT
1121131 AATATTTAT
1 AATATTTAT
1121140 TTAAACAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:1121568 original size:19 final size:19
Alignment explanation
Indices: 1121523--1121560 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1121513 TTTTTTTTAA
1121523 AAAAAGAATTAACTTATTT
1 AAAAAGAATTAACTTATTT
1121542 AAAAAGAATTAACTTATTT
1 AAAAAGAATTAACTTATTT
1121561 TTGAAGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (19 bp):
AAAAAGAATTAACTTATTT
Found at i:1122720 original size:2 final size:2
Alignment explanation
Indices: 1122713--1122744 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1122703 GCCTTCCATA
1122713 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1122745 TCTGGGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1123729 original size:20 final size:19
Alignment explanation
Indices: 1123701--1123752 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
1123691 TTTTTTTTTT
*
1123701 TTTTTAATTTAAATTATTA
1 TTTTTAATTTAAATTAATA
*
1123720 TTTATTAA-TTAAAATAATA
1 TTT-TTAATTTAAATTAATA
1123739 TTTTT-ATTTAAATT
1 TTTTTAATTTAAATT
1123753 TAATTATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 1 0.04
18 8 0.29
19 15 0.54
20 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTTAATTTAAATTAATA
Found at i:1125756 original size:2 final size:2
Alignment explanation
Indices: 1125749--1125776 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1125739 CTGTAGAATC
1125749 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1125777 TCCTTGACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1127944 original size:2 final size:2
Alignment explanation
Indices: 1127937--1127969 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1127927 ACGAAATTAT
1127937 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1127970 TTCTAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1132315 original size:7 final size:7
Alignment explanation
Indices: 1132300--1132329 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1132290 ATTAATTAAG
*
1132300 TTTACAA
1 TTTAAAA
1132307 TTTAAAA
1 TTTAAAA
1132314 TTTAAAA
1 TTTAAAA
1132321 TTTAAAA
1 TTTAAAA
1132328 TT
1 TT
1132330 ATTATTTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (7 bp):
TTTAAAA
Found at i:1141778 original size:2 final size:2
Alignment explanation
Indices: 1141771--1141798 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1141761 ATACTGGAGT
1141771 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1141799 GATAGATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1148682 original size:16 final size:16
Alignment explanation
Indices: 1148657--1148689 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1148647 TAAATACTTG
*
1148657 AGTTGGCATGTCCAAT
1 AGTTGACATGTCCAAT
1148673 AGTTGACATGTCCAAT
1 AGTTGACATGTCCAAT
1148689 A
1 A
1148690 TATATATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (16 bp):
AGTTGACATGTCCAAT
Found at i:1151854 original size:2 final size:2
Alignment explanation
Indices: 1151847--1151876 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1151837 CTTGTTGACA
1151847 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1151877 CAAATTATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1153031 original size:26 final size:26
Alignment explanation
Indices: 1152964--1153031 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 26
1152954 TTCTTTATAT
1152964 TATAGTTAAAAATATATTTTAATTTTA
1 TATA-TTAAAAATATATTTTAATTTTA
*
1152991 T-TATTAAATTTAATAT-TTTTATTTTTA
1 TATATTAAA---AATATATTTTAATTTTA
1153018 TATATTTAAAAATA
1 TATA-TTAAAAATA
1153032 GAATATACGA
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
25 5 0.14
26 6 0.17
27 12 0.34
28 7 0.20
29 5 0.14
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (26 bp):
TATATTAAAAATATATTTTAATTTTA
Found at i:1156812 original size:20 final size:20
Alignment explanation
Indices: 1156773--1156812 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1156763 TTTTTAATAA
* *
1156773 TTTTTATCAATTAAATTATT
1 TTTTTACCAATTAAAGTATT
*
1156793 TTTTTACCAATTCAAGTATT
1 TTTTTACCAATTAAAGTATT
1156813 ATCTTACTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTTTACCAATTAAAGTATT
Found at i:1159076 original size:16 final size:19
Alignment explanation
Indices: 1159057--1159097 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1159047 AGATTAAAAA
1159057 AATTT-AATT-ATA-ATAT
1 AATTTAAATTAATATATAT
1159073 AATTTTAAATTAATATATAT
1 AA-TTTAAATTAATATATAT
1159093 AATTT
1 AATTT
1159098 TAAAAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.10
17 3 0.14
18 4 0.19
19 6 0.29
20 6 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTTAAATTAATATATAT
Found at i:1159104 original size:22 final size:24
Alignment explanation
Indices: 1159054--1159104 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 24
1159044 TTAAGATTAA
1159054 AAAAATTTAATTATAATATAATTTT
1 AAAAA-TTAATTATAATATAATTTT
1159079 --AAATTAA-TAT-ATATAATTTT
1 AAAAATTAATTATAATATAATTTT
1159099 AAAAAT
1 AAAAAT
1159105 ATTTTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
20 10 0.42
21 3 0.12
22 8 0.33
23 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
AAAAATTAATTATAATATAATTTT
Found at i:1159132 original size:14 final size:15
Alignment explanation
Indices: 1159102--1159149 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 15
1159092 TAATTTTAAA
*
1159102 AATATTTTATTATTT
1 AATATTTTATAATTT
1159117 AATATTTTA-AATTT
1 AATATTTTATAATTT
1159131 AATATTTT-T-ATTT
1 AATATTTTATAATTT
1159144 AA-ATTT
1 AATATTT
1159150 ATTAGAACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
12 4 0.13
13 6 0.19
14 12 0.39
15 9 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AATATTTTATAATTT
Found at i:1165336 original size:13 final size:12
Alignment explanation
Indices: 1165319--1165367 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
1165309 TTTAAATTTC
1165319 ATAATATTAAAT
1 ATAATATTAAAT
1165331 ATTAATATATAAAT
1 A-TAATAT-TAAAT
1165345 ATAATA-TAAAT
1 ATAATATTAAAT
*
1165356 AAAATAATTAAA
1 ATAAT-ATTAAA
1165368 ATATGATATC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
11 9 0.28
12 2 0.06
13 15 0.47
14 6 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATAATATTAAAT
Found at i:1165345 original size:14 final size:14
Alignment explanation
Indices: 1165320--1165443 Score: 54
Period size: 15 Copynumber: 9.0 Consensus size: 14
1165310 TTAAATTTCA
1165320 TAATAT-TAAATAT
1 TAATATATAAATAT
1165333 TAATATATAAATA-
1 TAATATATAAATAT
1165346 TAATATAAATAAA-A-
1 TAATAT--ATAAATAT
1165360 TAAT-TA-AAATA-
1 TAATATATAAATAT
* *
1165371 TGATATCATAAAAAT
1 TAATAT-ATAAATAT
* *
1165386 TTATATTTTAAA-ATT
1 TAATA-TATAAATA-T
1165401 TATATAATATAAATTAT
1 TA-AT-ATATAAA-TAT
1165418 TAATATATTAAAT-T
1 TAATATA-TAAATAT
1165432 T--TATATAAATAT
1 TAATATATAAATAT
1165444 AAAATATTTT
Statistics
Matches: 89, Mismatches: 6, Indels: 33
0.70 0.05 0.26
Matches are distributed among these distances:
10 3 0.03
11 10 0.11
12 6 0.07
13 14 0.16
14 18 0.20
15 19 0.21
16 14 0.16
17 4 0.04
18 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.44
Consensus pattern (14 bp):
TAATATATAAATAT
Found at i:1165413 original size:16 final size:16
Alignment explanation
Indices: 1165359--1165448 Score: 59
Period size: 14 Copynumber: 5.8 Consensus size: 16
1165349 TATAAATAAA
*
1165359 ATAAT-TAAAATATGAT
1 ATAATATAAAAT-TTAT
*
1165375 ATCATA-AAAATTTAT
1 ATAATATAAAATTTAT
*
1165390 AT--TTTAAAATTTAT
1 ATAATATAAAATTTAT
1165404 ATAATAT-AAA-TTAT
1 ATAATATAAAATTTAT
1165418 -TAATATATTAAATTTTAT
1 ATAATATA--AAA-TTTAT
1165436 ATAAATATAAAAT
1 AT-AATATAAAAT
1165449 ATTTTAAATA
Statistics
Matches: 59, Mismatches: 4, Indels: 21
0.70 0.05 0.25
Matches are distributed among these distances:
13 7 0.12
14 15 0.25
15 8 0.14
16 14 0.24
17 1 0.02
18 7 0.12
19 1 0.02
20 6 0.10
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (16 bp):
ATAATATAAAATTTAT
Found at i:1165435 original size:18 final size:18
Alignment explanation
Indices: 1165394--1165448 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
1165384 ATTTATATTT
1165394 TAAAA-TTTATAT-AATA
1 TAAAATTTTATATAAATA
1165410 T-AAA--TTAT-TAATATA
1 TAAAATTTTATATAA-ATA
*
1165425 TTAAATTTTATATAAATA
1 TAAAATTTTATATAAATA
1165443 TAAAAT
1 TAAAAT
1165449 ATTTTAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 7 0.22
16 4 0.12
18 12 0.38
19 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAAATTTTATATAAATA
Found at i:1165435 original size:32 final size:33
Alignment explanation
Indices: 1165322--1165451 Score: 99
Period size: 32 Copynumber: 3.9 Consensus size: 33
1165312 AAATTTCATA
* * *
1165322 ATATTAAATATTAATATATAAATATAATATAAATAAA
1 ATATTAAA-ATT--TATATAAATATAAAAT-ATTAAT
* *
1165359 ATAATTAAAATATGATAT-CATA-AAAAT-TT-AT
1 AT-ATTAAAAT-TTATATAAATATAAAATATTAAT
* *
1165390 ATTTTAAAATTTATAT-AATATAAATTATTAAT
1 ATATTAAAATTTATATAAATATAAAATATTAAT
*
1165422 ATATTAAATTTTATATAAATATAAAATATT
1 ATATTAAAATTTATATAAATATAAAATATT
1165452 TTAAATATCT
Statistics
Matches: 75, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
29 8 0.11
30 11 0.15
31 5 0.07
32 17 0.23
33 12 0.16
34 4 0.05
35 3 0.04
36 4 0.05
37 4 0.05
38 7 0.09
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (33 bp):
ATATTAAAATTTATATAAATATAAAATATTAAT
Found at i:1166736 original size:24 final size:24
Alignment explanation
Indices: 1166694--1166739 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1166684 GCTCCTCATC
*
1166694 AGCAAATTGGAAGCAAAGAAACTG
1 AGCAAATTGAAAGCAAAGAAACTG
**
1166718 AGCAAATTGAAAGTGAAGAAAC
1 AGCAAATTGAAAGCAAAGAAAC
1166740 ACCGAGTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.11, G:0.24, T:0.13
Consensus pattern (24 bp):
AGCAAATTGAAAGCAAAGAAACTG
Found at i:1182474 original size:17 final size:16
Alignment explanation
Indices: 1182427--1182474 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
1182417 TAATATTAAA
*
1182427 AATTAAAAAAAAATTT
1 AATTAAATAAAAATTT
**
1182443 AATTAATATTTAAATTT
1 AATTAA-ATAAAAATTT
1182460 AATTTAAATAAAAAT
1 AA-TTAAATAAAAAT
1182475 AAATTTTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 6 0.24
17 15 0.60
18 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTAAATAAAAATTT
Found at i:1182511 original size:27 final size:27
Alignment explanation
Indices: 1182461--1182512 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1182451 TTTAAATTTA
*
1182461 ATTTAAATAAAAATAAATTTTATTTTT
1 ATTTAAATAAAAATAAATTATATTTTT
*
1182488 ATTTAAATTAAAA-AAATTCATATTT
1 ATTTAAATAAAAATAAATT-ATATTT
1182513 AAGTTCAGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
ATTTAAATAAAAATAAATTATATTTTT
Found at i:1188090 original size:41 final size:40
Alignment explanation
Indices: 1188009--1188092 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 40
1187999 ACTGTAATTA
* *
1188009 TAATATAATATTATCATTATTATTTTATAATTTTAATTTTT
1 TAATATAATATTATAATAATTATTTTATAATTTT-ATTTTT
1188050 TAATATAATATTATAATAATTATTTTATATATATTT-TTTTT
1 TAATATAATATTATAATAATTATTTTATA-AT-TTTATTTTT
1188091 TA
1 TA
1188093 CTGTCGATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
41 34 0.87
42 2 0.05
43 3 0.08
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (40 bp):
TAATATAATATTATAATAATTATTTTATAATTTTATTTTT
Found at i:1189235 original size:23 final size:24
Alignment explanation
Indices: 1189183--1189243 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
1189173 TTGACTGATT
*
1189183 TATTA-TAAAAAAATTATTTATAA
1 TATTATTAAAATAATTATTTATAA
* *
1189206 AAATATTAAAATAATTATTT-TAA
1 TATTATTAAAATAATTATTTATAA
*
1189229 TATTATTTAAATAAT
1 TATTATTAAAATAAT
1189244 AAAATCAATC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
23 18 0.58
24 13 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TATTATTAAAATAATTATTTATAA
Found at i:1190183 original size:22 final size:23
Alignment explanation
Indices: 1190141--1190188 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
1190131 ATTTAATATT
*
1190141 TAAAATAATTGAATAATATACAA
1 TAAAATAATTGAATAAAATACAA
*
1190164 TAAAA-AATTG-ATCAAAATACTA
1 TAAAATAATTGAAT-AAAATACAA
1190186 TAA
1 TAA
1190189 TATTATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 15 0.68
23 5 0.23
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.29
Consensus pattern (23 bp):
TAAAATAATTGAATAAAATACAA
Found at i:1190441 original size:2 final size:2
Alignment explanation
Indices: 1190429--1190472 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1190419 TGCACGGCAT
*
1190429 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1190471 TA
1 TA
1190473 AAATTATGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1190745 original size:20 final size:21
Alignment explanation
Indices: 1190699--1190742 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1190689 TAATCAAAAC
1190699 TTTAAAAAATTTTCATATATT
1 TTTAAAAAATTTTCATATATT
* *
1190720 TTTAAAAATTTTTTATATATT
1 TTTAAAAAATTTTCATATATT
1190741 TT
1 TT
1190743 AAAGATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTAAAAAATTTTCATATATT
Found at i:1194393 original size:24 final size:23
Alignment explanation
Indices: 1194357--1194403 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
1194347 ATAATAATCG
*
1194357 AAAATAAATGGTT-ATTTATTTAA
1 AAAATAAAAGGTTAATTT-TTTAA
1194380 AAAATTAAAAGGTTAATTTTTTAA
1 AAAA-TAAAAGGTTAATTTTTTAA
1194404 TGGATAGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (23 bp):
AAAATAAAAGGTTAATTTTTTAA
Found at i:1196408 original size:32 final size:33
Alignment explanation
Indices: 1196334--1196471 Score: 118
Period size: 32 Copynumber: 4.0 Consensus size: 33
1196324 ATTTTACATA
* * *
1196334 ATTAAAAAACTAATATTTATATAATAT-AATAT
1 ATTAAAATATTAAAATTTATATAATATAAATAT
1196366 ATTAAAATATTAAAATTTATATAATATAAAT-T
1 ATTAAAATATTAAAATTTATATAATATAAATAT
* * *
1196398 ATTAATATATTAAATTTTTTATAAATATATAATAT
1 ATTAAAATATTAAAATTTATAT-AATATA-AATAT
* * *
1196433 TTTAAATAAAATTATAATATATATATAAATATAAATAT
1 ATT-AA-AATATTA-AA-ATTTATAT-AATATAAATAT
1196471 A
1 A
1196472 AAATAAATAT
Statistics
Matches: 85, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
32 44 0.52
33 9 0.11
34 3 0.04
35 3 0.04
36 2 0.02
37 5 0.06
38 7 0.08
39 12 0.14
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (33 bp):
ATTAAAATATTAAAATTTATATAATATAAATAT
Found at i:1196425 original size:18 final size:18
Alignment explanation
Indices: 1196370--1196435 Score: 50
Period size: 17 Copynumber: 3.8 Consensus size: 18
1196360 TAATATATTA
* *
1196370 AAATATTAAAATTTATAT
1 AAATATTAAATTTTTTAT
*
1196388 -AATA-TAAA-TTATTA-
1 AAATATTAAATTTTTTAT
*
1196402 ATATATTAAATTTTTTAT
1 AAATATTAAATTTTTTAT
1196420 AAATATATAATATTTT
1 AAATAT-TAA-ATTTT
1196436 AAATAAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
15 7 0.19
16 8 0.22
17 9 0.24
18 5 0.14
19 3 0.08
20 5 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATATTAAATTTTTTAT
Found at i:1196434 original size:20 final size:20
Alignment explanation
Indices: 1196401--1196470 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
1196391 ATAAATTATT
*
1196401 AATATATTAA-ATTTTTTATA
1 AATATA-TAATATTTTATATA
*
1196421 AATATATAATATTTTAAATA
1 AATATATAATATTTTATATA
*
1196441 AA-ATTATAATA-TATATATA
1 AATA-TATAATATTTTATATA
1196460 AATATA-AATAT
1 AATATATAATAT
1196471 AAAATAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
18 4 0.10
19 14 0.33
20 24 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATATAATATTTTATATA
Found at i:1196464 original size:6 final size:6
Alignment explanation
Indices: 1196435--1196481 Score: 55
Period size: 6 Copynumber: 8.2 Consensus size: 6
1196425 TATAATATTT
*
1196435 TAAATA -AAAT- TATAATA TATATA TAAATA TAAATA TAAA-A TAAATA
1 TAAATA TAAATA TA-AATA TAAATA TAAATA TAAATA TAAATA TAAATA
1196481 T
1 T
1196482 TTTTGTCAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
5 10 0.29
6 23 0.66
7 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TAAATA
Done.