Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008925.1 Hibiscus syriacus cultivar Beakdansim tig00112230_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: 2702387
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 11
Found at i:1012536 original size:20 final size:20
Alignment explanation
Indices: 1012511--1012556 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
1012501 AGGTACACTT
*
1012511 TCGCAATGCTAAA-CTCAAAA
1 TCGCAATGCGAAAGC-CAAAA
1012531 TCGCAATGCGAAAGCCAAAA
1 TCGCAATGCGAAAGCCAAAA
1012551 TCGCAA
1 TCGCAA
1012557 CACGAAAGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.43, C:0.26, G:0.15, T:0.15
Consensus pattern (20 bp):
TCGCAATGCGAAAGCCAAAA
Found at i:1012562 original size:20 final size:20
Alignment explanation
Indices: 1012526--1012564 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1012516 ATGCTAAACT
**
1012526 CAAAATCGCAATGCGAAAGC
1 CAAAATCGCAACACGAAAGC
1012546 CAAAATCGCAACACGAAAG
1 CAAAATCGCAACACGAAAG
1012565 TCAATTCGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.26, G:0.18, T:0.08
Consensus pattern (20 bp):
CAAAATCGCAACACGAAAGC
Found at i:1012665 original size:20 final size:20
Alignment explanation
Indices: 1012640--1012750 Score: 117
Period size: 20 Copynumber: 5.8 Consensus size: 20
1012630 GCGATTTTCT
*
1012640 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCA
*
1012660 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCA
*
1012680 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
**
1012700 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCA
*
1012714 TGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCA
*
1012734 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
1012751 GAATGTGTAA
Statistics
Matches: 75, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
14 11 0.15
16 1 0.01
18 1 0.01
20 62 0.83
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCA
Found at i:1012666 original size:34 final size:34
Alignment explanation
Indices: 1012606--1012742 Score: 134
Period size: 34 Copynumber: 3.9 Consensus size: 34
1012596 AGTCAATTCG
* *
1012606 CGTTGCGATAGTCTAATAT-ACTTTGCGATTTTCT
1 CGTTGCGATAGTCAAAT-TCACGTTGCGATTTTCT
* *
1012640 CGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCACGTTGCGAT--T----TTCT
*
1012680 CGTTGCGATAGTCAAATTCGCGTTGCGATTTT-T
1 CGTTGCGATAGTCAAATTCACGTTGCGATTTTCT
*
1012713 GTGTTGCGATAGTCAAATTCACGTTGCGAT
1 -CGTTGCGATAGTCAAATTCACGTTGCGAT
1012743 ATTCAAATGA
Statistics
Matches: 87, Mismatches: 8, Indels: 16
0.78 0.07 0.14
Matches are distributed among these distances:
33 1 0.01
34 53 0.61
36 1 0.01
38 1 0.01
40 31 0.36
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATTCACGTTGCGATTTTCT
Found at i:1012686 original size:54 final size:53
Alignment explanation
Indices: 1012575--1012688 Score: 131
Period size: 54 Copynumber: 2.1 Consensus size: 53
1012565 TCAATTCGCA
* * * * *
1012575 TTGCGATTTTCACGTTGTAAAAGTCAATTCGCGTTGCGATAGTCTAATATACT
1 TTGCGATTTTCACGTTGCAAAAGTCAATTCCCGTTGCGATAATCAAATATACG
* * *
1012628 TTGCGATTTTCTCGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAAT-TCACG
1 TTGCGATTTTCACGTTGCAAAAGTC-AATTCCCGTTGCGATAATCAAATAT-ACG
1012682 TTGCGAT
1 TTGCGAT
1012689 AGTCAAATTC
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
53 22 0.43
54 29 0.57
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (53 bp):
TTGCGATTTTCACGTTGCAAAAGTCAATTCCCGTTGCGATAATCAAATATACG
Found at i:1012721 original size:74 final size:74
Alignment explanation
Indices: 1012600--1012750 Score: 207
Period size: 74 Copynumber: 2.0 Consensus size: 74
1012590 TGTAAAAGTC
* * * *
1012600 AATTCGCGTTGCGATAGTCTAATATACTTTGCGATTTTCTCGTTGCGATAGTCAAATTCCCGTTG
1 AATTCACGTTGCGATAGTCAAATATACGTTGCGATTTTCTCGTTGCGATAGTCAAATTCACGTTG
1012665 CGATAATCA
66 CGATAATCA
* *
1012674 AATTCACGTTGCGATAGTCAAAT-TCGCGTTGCGATTTT-TGTGTTGCGATAGTCAAATTCACGT
1 AATTCACGTTGCGATAGTCAAATAT-ACGTTGCGATTTTCT-CGTTGCGATAGTCAAATTCACGT
*
1012737 TGCGATATTCA
64 TGCGATAATCA
1012748 AAT
1 AAT
1012751 GAATGTGTAA
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
73 2 0.03
74 66 0.97
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (74 bp):
AATTCACGTTGCGATAGTCAAATATACGTTGCGATTTTCTCGTTGCGATAGTCAAATTCACGTTG
CGATAATCA
Found at i:1015244 original size:24 final size:24
Alignment explanation
Indices: 1015217--1015263 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1015207 ATCATCAAAA
1015217 GTATTAACCAAGATCAAAGTTCGG
1 GTATTAACCAAGATCAAAGTTCGG
* * *
1015241 GTATTGACCAATATCAAATTTCG
1 GTATTAACCAAGATCAAAGTTCG
1015264 AATACTGACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (24 bp):
GTATTAACCAAGATCAAAGTTCGG
Found at i:1017688 original size:13 final size:13
Alignment explanation
Indices: 1017670--1017694 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1017660 TTGTTGTACT
1017670 TTTTGTTAATTTA
1 TTTTGTTAATTTA
1017683 TTTTGTTAATTT
1 TTTTGTTAATTT
1017695 TGTTTATTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (13 bp):
TTTTGTTAATTTA
Found at i:1028431 original size:16 final size:18
Alignment explanation
Indices: 1028399--1028433 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1028389 ATATAAAAAC
1028399 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
1028417 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
1028433 A
1 A
1028434 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:1028491 original size:18 final size:18
Alignment explanation
Indices: 1028438--1028491 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
1028428 TAAATAAATG
1028438 AGTAAAATATATAA-AA-A
1 AGTAAAATA-ATAATAATA
**
1028455 AGTAAAAGCAT-ATATATA
1 AGTAAAATAATAATA-ATA
1028473 AGTAAAATAATAATAATA
1 AGTAAAATAATAATAATA
1028491 A
1 A
1028492 AAAAAAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
15 1 0.03
16 3 0.10
17 8 0.28
18 14 0.48
19 3 0.10
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (18 bp):
AGTAAAATAATAATAATA
Found at i:1029055 original size:37 final size:36
Alignment explanation
Indices: 1029012--1029113 Score: 154
Period size: 34 Copynumber: 2.9 Consensus size: 36
1029002 ATAGTAGAAC
*
1029012 TCTATCCTTTTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
1029049 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
*
1029083 TCTATCATATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1029114 TAGGACGAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
34 32 0.54
37 27 0.46
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:1029967 original size:105 final size:105
Alignment explanation
Indices: 1029657--1030593 Score: 1461
Period size: 105 Copynumber: 9.0 Consensus size: 105
1029647 CATTGTTCCA
* * * ** * * *
1029657 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * * * *
1029722 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGATGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
1029763 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1029823 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1029863 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTTTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* * *
1029928 AGCGGTCCCTTCGTCGTGAAGTTGAACTAGCATTATCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1029968 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1030033 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1030073 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGT
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1030138 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
1030178 AGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1030243 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1030283 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1030348 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1030388 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1030453 AGCGGTCCCTTCGTCGTGAAGTTGAAATTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1030493 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * * * *
1030558 CAACCGTCCATTCGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1030594 CCTCGAGTGC
Statistics
Matches: 780, Mismatches: 45, Indels: 12
0.93 0.05 0.01
Matches are distributed among these distances:
100 83 0.11
101 1 0.00
102 4 0.01
103 4 0.01
104 3 0.00
105 611 0.78
106 74 0.09
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:1031326 original size:68 final size:65
Alignment explanation
Indices: 1031236--1031393 Score: 208
Period size: 68 Copynumber: 2.4 Consensus size: 65
1031226 AAGATATATG
* * ** *
1031236 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATT-TGTTTTAAGGGAAATAAATTCAAAG-G
1031301 TT
64 TT
* * *
1031303 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGGT
1031368 T
65 T
*
1031369 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
1031394 ATAGACGAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
65 22 0.28
66 3 0.04
67 23 0.29
68 32 0.40
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.32
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGGTT
Found at i:1031409 original size:65 final size:67
Alignment explanation
Indices: 1031237--1031629 Score: 241
Period size: 65 Copynumber: 5.7 Consensus size: 67
1031227 AGATATATGT
* * * * ** *
1031237 TGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGAGT
1031302 TTG
65 TTG
* * *
1031305 TGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAG-GTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
1031369 T-
66 TG
* * * * *
1031370 TGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACT--GTCTCAAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATTTGTTTTAAGGGAAA-TAAAT-TCAA-AG
*
1031432 AGACAAAACTT-
62 AG------TTTG
* * * * * * * * * * *
1031443 AGTTCCAAAAGAAACTGTCTCAAGGGAGACAGAATTTGTTTCAAAGAAAACATATTCAAATA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
1031507 T-
66 TG
* * * *
1031508 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACT--GTCTCAAGATA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAA-TAAAT-TC-A-A-A
*
1031571 GACGAAATT-
61 GA-G--TTTG
*
1031580 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAA
1031630 CTGTCTCAAG
Statistics
Matches: 256, Mismatches: 46, Indels: 42
0.74 0.13 0.12
Matches are distributed among these distances:
64 2 0.01
65 87 0.34
66 11 0.04
67 24 0.09
68 34 0.13
72 55 0.21
73 42 0.16
74 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
TG
Found at i:1031420 original size:36 final size:35
Alignment explanation
Indices: 1031369--1031649 Score: 281
Period size: 36 Copynumber: 8.0 Consensus size: 35
1031359 TTCAAAGGTT
* *
1031369 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
1031405 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
1031440 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAGAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGACA-AAA
* * **
1031478 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
1031507 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
1031542 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
1031579 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
1031614 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1031650 CTCTTATAGT
Statistics
Matches: 205, Mismatches: 24, Indels: 32
0.79 0.09 0.12
Matches are distributed among these distances:
28 2 0.01
29 17 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 10 0.05
36 134 0.65
37 34 0.17
38 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:1031479 original size:138 final size:137
Alignment explanation
Indices: 1031317--1031630 Score: 441
Period size: 138 Copynumber: 2.3 Consensus size: 137
1031307 TTTCAAGAGT
* * * *
1031317 AACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* *
1031382 AACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
66 AACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGT
1031446 TCCAAAAGA
129 TCCAAAAGA
* * * * *
1031455 AACTGTCTCAAGGGAGACAGAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* * * * *
1031520 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTT
66 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
*
1031585 CAAGAGA
131 CAAAAGA
*
1031592 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
1031631 TGTCTCAAGA
Statistics
Matches: 154, Mismatches: 21, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
137 50 0.32
138 104 0.68
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (137 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
CAAAAGA
Found at i:1032606 original size:22 final size:22
Alignment explanation
Indices: 1032580--1032628 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
1032570 TTGTGTTTGG
* *
1032580 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
1032602 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
1032624 TCAAA
1 TCAAA
1032629 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:1032635 original size:22 final size:22
Alignment explanation
Indices: 1032592--1032635 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1032582 AAAGGTTTGG
* * *
1032592 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
1032614 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
1032636 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:1033298 original size:8 final size:8
Alignment explanation
Indices: 1033287--1033357 Score: 63
Period size: 8 Copynumber: 8.8 Consensus size: 8
1033277 ATTTTTGCTT
1033287 TTTTTTTC
1 TTTTTTTC
*
1033295 TTTTGTTC
1 TTTTTTTC
*
1033303 -TTGTTTC
1 TTTTTTTC
*
1033310 TCTTTTTC
1 TTTTTTTC
*
1033318 TTTGTTTTT
1 TTT-TTTTC
1033327 TTTTTTTGC
1 TTTTTTT-C
*
1033336 TTTTTTGC
1 TTTTTTTC
*
1033344 TTCTTTTC
1 TTTTTTTC
1033352 TTTTTT
1 TTTTTT
1033358 GTTCTTGATT
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
7 5 0.10
8 30 0.62
9 13 0.27
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (8 bp):
TTTTTTTC
Found at i:1033299 original size:23 final size:23
Alignment explanation
Indices: 1033264--1033320 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 23
1033254 CTTTTTGTCC
*
1033264 CTTTTTCTTTTTGATTTTTGCTTT-T
1 CTTTTTC-TTTTG-TTCTTG-TTTCT
1033289 -TTTTTCTTTTGTTCTTGTTTCT
1 CTTTTTCTTTTGTTCTTGTTTCT
1033311 CTTTTTCTTT
1 CTTTTTCTTT
1033321 GTTTTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 3 0.10
22 6 0.21
23 14 0.48
24 6 0.21
ACGTcount: A:0.02, C:0.14, G:0.07, T:0.77
Consensus pattern (23 bp):
CTTTTTCTTTTGTTCTTGTTTCT
Found at i:1036565 original size:16 final size:18
Alignment explanation
Indices: 1036533--1036567 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1036523 ATATAAAAAC
1036533 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
1036551 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
1036567 A
1 A
1036568 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:1036686 original size:2 final size:2
Alignment explanation
Indices: 1036673--1036709 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1036663 AAAATAGGAA
*
1036673 AT AT AT AA 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 AT A
1036710 ATAATACTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1037236 original size:34 final size:35
Alignment explanation
Indices: 1037154--1037251 Score: 153
Period size: 34 Copynumber: 2.8 Consensus size: 35
1037144 ATAGTAGAAA
1037154 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA--AAAAT
*
1037191 TTTATCCTATTTTTAGGAGTTTGAATCCT-AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAAT
*
1037225 TCTATCATATTTTTAGGAGTTTGAATC
1 TCTATCCTATTTTTAGGAGTTTGAATC
1037252 TTAGTAGGAC
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
34 30 0.52
37 28 0.48
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAAT
Found at i:1037355 original size:20 final size:20
Alignment explanation
Indices: 1037330--1037404 Score: 53
Period size: 20 Copynumber: 3.7 Consensus size: 20
1037320 TGGAATCCAA
1037330 GGGATCAATCCTTTTTCAAG
1 GGGATCAATCCTTTTTCAAG
* * * *
1037350 GGGATCGATCATTTGGTCAAC
1 GGGATCAATCCTTT-TTCAAG
* **
1037371 GCGATCAAT-CTTTTTGCTGG
1 GGGATCAATCCTTTTT-CAAG
*
1037391 GGGATCGATCCTTT
1 GGGATCAATCCTTT
1037405 GAGCAAAAAA
Statistics
Matches: 39, Mismatches: 13, Indels: 5
0.68 0.23 0.09
Matches are distributed among these distances:
19 1 0.03
20 23 0.59
21 15 0.38
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
GGGATCAATCCTTTTTCAAG
Found at i:1037956 original size:15 final size:16
Alignment explanation
Indices: 1037921--1037957 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1037911 GCATATAAGT
1037921 TCAAATATCCAACATA
1 TCAAATATCCAACATA
*
1037937 -AAAATATCCAA-ATA
1 TCAAATATCCAACATA
1037951 TCAAATA
1 TCAAATA
1037958 AACATAGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 3
0.78 0.09 0.13
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.57, C:0.19, G:0.00, T:0.24
Consensus pattern (16 bp):
TCAAATATCCAACATA
Found at i:1042687 original size:21 final size:21
Alignment explanation
Indices: 1042663--1042712 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1042653 TAGAGGAAGT
1042663 GATTGATCATTTTCATCAAGG
1 GATTGATCATTTTCATCAAGG
* * *
1042684 GATTGATCCTTTTGATTAAGG
1 GATTGATCATTTTCATCAAGG
*
1042705 GATCGATC
1 GATTGATC
1042713 TAAAACATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (21 bp):
GATTGATCATTTTCATCAAGG
Found at i:1043559 original size:12 final size:12
Alignment explanation
Indices: 1043542--1043567 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1043532 ACGAAAAATG
1043542 AATAAATAATAT
1 AATAAATAATAT
1043554 AATAAATAATAT
1 AATAAATAATAT
1043566 AA
1 AA
1043568 AATAAACATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATAAATAATAT
Found at i:1052011 original size:61 final size:61
Alignment explanation
Indices: 1051871--1052055 Score: 255
Period size: 61 Copynumber: 3.0 Consensus size: 61
1051861 GTGCTCAATA
* *
1051871 TAATACACATAAGGTCGTGCCCACCATATGCATTAAGTGTCC-TTATATACACTATAGTTC
1 TAATACACATAAGGTCGTGCCCACCATATACATTAAGTGTCCTTTATATACACTATAGTGC
*
1051931 TAATACACATAAGGTCGTGCCCACCATATCCATTAAGTGTCCTTTATATACACTATAGTGC
1 TAATACACATAAGGTCGTGCCCACCATATACATTAAGTGTCCTTTATATACACTATAGTGC
* * * * *** * *
1051992 TAATATACATAAGGACGTGCTCACTATATACACCCAGTGTCCTTTATTTACACTATAATGC
1 TAATACACATAAGGTCGTGCCCACCATATACATTAAGTGTCCTTTATATACACTATAGTGC
1052053 TAA
1 TAA
1052056 ACCAAATAAG
Statistics
Matches: 112, Mismatches: 12, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
60 41 0.37
61 71 0.63
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.32
Consensus pattern (61 bp):
TAATACACATAAGGTCGTGCCCACCATATACATTAAGTGTCCTTTATATACACTATAGTGC
Found at i:1061093 original size:14 final size:14
Alignment explanation
Indices: 1061060--1061093 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1061050 ATGAGCTCAT
1061060 AGATGATGTAAGAA
1 AGATGATGTAAGAA
* *
1061074 AAATGATGTAAGCA
1 AGATGATGTAAGAA
1061088 AGATGA
1 AGATGA
1061094 GATTATGGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.26, T:0.21
Consensus pattern (14 bp):
AGATGATGTAAGAA
Found at i:1064773 original size:26 final size:25
Alignment explanation
Indices: 1064744--1064796 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 25
1064734 AGTTCCAATA
1064744 CACAAAAGGTCGTGCACACCATAATG
1 CACAAAAGGTCGTGCACACCAT-ATG
* *
1064770 CACATAAGGTCGTGCCCACCATATG
1 CACAAAAGGTCGTGCACACCATATG
1064795 CA
1 CA
1064797 ATAAGTTTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.34, C:0.30, G:0.19, T:0.17
Consensus pattern (25 bp):
CACAAAAGGTCGTGCACACCATATG
Found at i:1064847 original size:61 final size:61
Alignment explanation
Indices: 1064769--1064950 Score: 274
Period size: 61 Copynumber: 3.0 Consensus size: 61
1064759 ACACCATAAT
* * *
1064769 GCACATAAGGTCGTGCCCACCATATGCAATAAGTTTCCTTTATATAAACTATAGTGCTAAC
1 GCACATAAGGTCGTGCCCACCATATGCACTAAGTGTCCTTTATATACACTATAGTGCTAAC
* * * *
1064830 GTACATAAGATCGTGCCCACCATATGCACTAAGTGTCCTTTATATACACTATAGTGGTAAT
1 GCACATAAGGTCGTGCCCACCATATGCACTAAGTGTCCTTTATATACACTATAGTGCTAAC
* * *
1064891 GCACATAAGGTCGTGCCCACCATATGTACTAAGTGTCCTGTATATACATTATAGTGCTAA
1 GCACATAAGGTCGTGCCCACCATATGCACTAAGTGTCCTTTATATACACTATAGTGCTAA
1064951 ACCGATTATG
Statistics
Matches: 108, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 108 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.30
Consensus pattern (61 bp):
GCACATAAGGTCGTGCCCACCATATGCACTAAGTGTCCTTTATATACACTATAGTGCTAAC
Found at i:1065449 original size:2 final size:2
Alignment explanation
Indices: 1065405--1065439 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1065395 ATAAAAAATC
*
1065405 AT AT AA 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
1065440 ACACATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1065909 original size:20 final size:20
Alignment explanation
Indices: 1065869--1065910 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1065859 AATTTGATCC
* *
1065869 AAATCAACATTCTAACCTTA
1 AAATCAACATTCCAACATTA
*
1065889 AAATCAACATTCCAATATTA
1 AAATCAACATTCCAACATTA
1065909 AA
1 AA
1065911 TTCCATCATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATCAACATTCCAACATTA
Found at i:1082065 original size:21 final size:20
Alignment explanation
Indices: 1082041--1082080 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
1082031 TAGATACCAA
1082041 CTAGCTACCTAAGCTACCTAG
1 CTAGCTACCTAAG-TACCTAG
1082062 CTAGCTACCTAAGTACCTA
1 CTAGCTACCTAAGTACCTA
1082081 CCTTGGCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.30, C:0.33, G:0.12, T:0.25
Consensus pattern (20 bp):
CTAGCTACCTAAGTACCTAG
Found at i:1082190 original size:20 final size:20
Alignment explanation
Indices: 1082153--1082191 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1082143 CTTGGCGTGG
*
1082153 AAAGTCATGTGTCTTCAAGA
1 AAAGTCATGTGACTTCAAGA
1082173 AAAGTCATGT-ACTATCAAG
1 AAAGTCATGTGACT-TCAAG
1082192 GGAGGTTCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (20 bp):
AAAGTCATGTGACTTCAAGA
Found at i:1087442 original size:18 final size:18
Alignment explanation
Indices: 1087419--1087453 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1087409 ATAGCCCATC
*
1087419 CATACTTCCATTTTTCTT
1 CATACTTCCATATTTCTT
*
1087437 CATACTTTCATATTTCT
1 CATACTTCCATATTTCT
1087454 AACTCACCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.26, G:0.00, T:0.54
Consensus pattern (18 bp):
CATACTTCCATATTTCTT
Found at i:1091625 original size:143 final size:143
Alignment explanation
Indices: 1091364--1091656 Score: 394
Period size: 143 Copynumber: 2.0 Consensus size: 143
1091354 CATCTTCAAC
* * *
1091364 AACTTTTTAGTACCCAATTAATCATCTTCATAAACTTTTCAGTGATATATAAACTCATTTCAAAA
1 AACTTTTCAGTACCCAATTAATCATCTTCAGAAACTTTTAAGTGATATATAAACTCATTTCAAAA
* * * *
1091429 AACTTTTTCAGTGGTGATATATCACTTCATATCAGAAAAACGTGCATTCTCATAGGTAAAATAAT
66 AACTTTTTCAATGGTGATAGATCACTTCATATCAGAAAAACGTGCATTATCATAGGCAAAATAAT
*
1091494 GTACCATGAA-AGA
131 GCACCAT-AATAGA
* * * * * *
1091507 AACTTTTCAGTGCCCAATTAATCATCTTCAGCAACTTTTAATTGATATATCAACTCATTTTAGAA
1 AACTTTTCAGTACCCAATTAATCATCTTCAGAAACTTTTAAGTGATATATAAACTCATTTCAAAA
*
1091572 AAC-TTTTCAAT-GTCGATAGATCACTTCATATCAGAAAAATGTGCATTTATCATAGGCAAAATA
66 AACTTTTTCAATGGT-GATAGATCACTTCATATCAGAAAAACGTGCA-TTATCATAGGCAAAATA
*
1091635 ATGCACCCTAATAGA
129 ATGCACCATAATAGA
1091650 AACTTTT
1 AACTTTT
1091657 TAGTTCACAA
Statistics
Matches: 131, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
141 2 0.02
142 38 0.29
143 91 0.69
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (143 bp):
AACTTTTCAGTACCCAATTAATCATCTTCAGAAACTTTTAAGTGATATATAAACTCATTTCAAAA
AACTTTTTCAATGGTGATAGATCACTTCATATCAGAAAAACGTGCATTATCATAGGCAAAATAAT
GCACCATAATAGA
Found at i:1093500 original size:24 final size:24
Alignment explanation
Indices: 1093457--1093517 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
1093447 AATCTACACA
*
1093457 TAAATTTAAAAATTAAAATT-T-AT
1 TAAATTT-AAAATAAAAATTATAAT
1093480 TAAAATTTAAAATAAAGAATTATAAT
1 T-AAATTTAAAATAAA-AATTATAAT
*
1093506 TAAATTTCAAAT
1 TAAATTTAAAAT
1093518 GTTTTGAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 8 0.25
24 10 0.31
25 11 0.34
26 3 0.09
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (24 bp):
TAAATTTAAAATAAAAATTATAAT
Found at i:1093600 original size:39 final size:39
Alignment explanation
Indices: 1093547--1093624 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
1093537 TAATTTAAAA
*
1093547 AATAATTTAGAATGTTAATGG-GA-AATAATTTAAGAAATT
1 AATAATTTAAAATGTT-ATGGTGAGAA-AATTTAAGAAATT
* *
1093586 AATAGTTTAAAATGTTATGGTGAGAAATTTTAAGAAATT
1 AATAATTTAAAATGTTATGGTGAGAAAATTTAAGAAATT
1093625 CGGAATTTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 4 0.12
39 28 0.82
40 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (39 bp):
AATAATTTAAAATGTTATGGTGAGAAAATTTAAGAAATT
Found at i:1093698 original size:17 final size:18
Alignment explanation
Indices: 1093665--1093705 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1093655 TGAGAATTAT
*
1093665 AATAAAAAATTTAATAAA
1 AATAAAAAATATAATAAA
*
1093683 AATAAAAAATAT-ATAAT
1 AATAAAAAATATAATAAA
1093700 AATAAA
1 AATAAA
1093706 TTGGGTGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AATAAAAAATATAATAAA
Found at i:1102464 original size:14 final size:14
Alignment explanation
Indices: 1102445--1102474 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1102435 TTCAGATTTT
*
1102445 TTAAAATTACATTA
1 TTAAAAATACATTA
1102459 TTAAAAATACATTA
1 TTAAAAATACATTA
1102473 TT
1 TT
1102475 GATGAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:1103353 original size:17 final size:17
Alignment explanation
Indices: 1103316--1103354 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1103306 GTAAAGAAAA
**
1103316 AAAAAAGAAATATTGAC
1 AAAAAAGAAATATAAAC
*
1103333 AAAAAAGAAATATAAAG
1 AAAAAAGAAATATAAAC
1103350 AAAAA
1 AAAAA
1103355 GATAAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.74, C:0.03, G:0.10, T:0.13
Consensus pattern (17 bp):
AAAAAAGAAATATAAAC
Found at i:1104118 original size:2 final size:2
Alignment explanation
Indices: 1104111--1104196 Score: 172
Period size: 2 Copynumber: 43.0 Consensus size: 2
1104101 CTGAAAGAAT
1104111 TA TA TA 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
1104153 TA TA TA 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
1104195 TA
1 TA
1104197 GATACTATAA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1105011 original size:2 final size:2
Alignment explanation
Indices: 1105004--1105036 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1104994 AAATACTTTC
1105004 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 A
1105037 ATTACACAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1107948 original size:17 final size:17
Alignment explanation
Indices: 1107926--1107997 Score: 117
Period size: 17 Copynumber: 4.2 Consensus size: 17
1107916 AAATTCGAGT
*
1107926 TCGAGTTTGAGCTTGAA
1 TCGAGTTCGAGCTTGAA
*
1107943 TCGAGTTCGAGTTTGAA
1 TCGAGTTCGAGCTTGAA
1107960 TCGAGTTCGAGCTTGAA
1 TCGAGTTCGAGCTTGAA
*
1107977 TCGAGCTCGAGCTTGAA
1 TCGAGTTCGAGCTTGAA
1107994 TCGA
1 TCGA
1107998 ACTCAAAATC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.31
Consensus pattern (17 bp):
TCGAGTTCGAGCTTGAA
Found at i:1107969 original size:23 final size:23
Alignment explanation
Indices: 1107918--1107970 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1107908 GAAGGTTCAA
* *
1107918 ATTCGAGTTCGAGTTTGAGCTTG
1 ATTCGAGTTCGAGTTTGAGATCG
*
1107941 AATCGAGTTCGAGTTTGA-ATCG
1 ATTCGAGTTCGAGTTTGAGATCG
1107963 AGTTCGAG
1 A-TTCGAG
1107971 CTTGAATCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.23, C:0.13, G:0.30, T:0.34
Consensus pattern (23 bp):
ATTCGAGTTCGAGTTTGAGATCG
Found at i:1108075 original size:31 final size:31
Alignment explanation
Indices: 1108040--1108098 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1108030 GTTCGAGCCT
*
1108040 TTTCGAGTTCGAGTCGAGTTTCAATATTATC
1 TTTCGAGTTCGAGTCGAGCTTCAATATTATC
*
1108071 TTTCGAGTTCGAGTCGAGCTTGAATATT
1 TTTCGAGTTCGAGTCGAGCTTCAATATT
1108099 TTAGGCTCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (31 bp):
TTTCGAGTTCGAGTCGAGCTTCAATATTATC
Found at i:1108124 original size:41 final size:41
Alignment explanation
Indices: 1108071--1108171 Score: 184
Period size: 41 Copynumber: 2.4 Consensus size: 41
1108061 CAATATTATC
1108071 TTTCGAGTTCGAGTCGAGCTTGAATATTTTAGGCTCGCGAGT
1 TTTCGAG-TCGAGTCGAGCTTGAATATTTTAGGCTCGCGAGT
*
1108113 TTTTGAGTCGAGTCGAGCTTGAATATTTTAGGCTCGCGAGT
1 TTTCGAGTCGAGTCGAGCTTGAATATTTTAGGCTCGCGAGT
1108154 TTTCGAGTCGAGTCGAGC
1 TTTCGAGTCGAGTCGAGC
1108172 CTACATATAA
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
41 51 0.89
42 6 0.11
ACGTcount: A:0.19, C:0.17, G:0.30, T:0.35
Consensus pattern (41 bp):
TTTCGAGTCGAGTCGAGCTTGAATATTTTAGGCTCGCGAGT
Found at i:1110686 original size:21 final size:23
Alignment explanation
Indices: 1110648--1110690 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1110638 ATAGAATTTT
1110648 TATTATTTAATGACAAAATAAAAA
1 TATTATTTAATGACAAAA-AAAAA
1110672 TATT-TTTAA-GA-AAAAAAAA
1 TATTATTTAATGACAAAAAAAA
1110691 TTAACGACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.21
21 4 0.21
22 2 0.11
23 5 0.26
24 4 0.21
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (23 bp):
TATTATTTAATGACAAAAAAAAA
Found at i:1112058 original size:29 final size:27
Alignment explanation
Indices: 1111995--1112065 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 27
1111985 AATTTTAGCA
* * * *
1111995 TTTTTATTTTATTTTAGTATTTTACTT
1 TTTTTTTTTTATTTTAGCACTTTAATT
1112022 TTTGTTTTTTTATGTTTAGCACTTTAATT
1 TTT-TTTTTTTAT-TTTAGCACTTTAATT
*
1112051 TTCTTTTTTATATTT
1 TT-TTTTTTTTATTT
1112066 CGGTACATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
27 3 0.08
28 10 0.28
29 22 0.61
30 1 0.03
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.72
Consensus pattern (27 bp):
TTTTTTTTTTATTTTAGCACTTTAATT
Found at i:1112155 original size:22 final size:20
Alignment explanation
Indices: 1112098--1112155 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 20
1112088 AATATTTCAG
1112098 TATTTTTACTTTTTTATTTA
1 TATTTTTACTTTTTTATTTA
* * *
1112118 CATGTTTATCTCTTTTACTTTA
1 TATTTTTA-CTTTTTTA-TTTA
1112140 TATTATTTACTTTTTT
1 TATT-TTTACTTTTTT
1112156 TTAGTAATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
20 6 0.21
21 7 0.24
22 12 0.41
23 4 0.14
ACGTcount: A:0.19, C:0.10, G:0.02, T:0.69
Consensus pattern (20 bp):
TATTTTTACTTTTTTATTTA
Found at i:1119495 original size:21 final size:20
Alignment explanation
Indices: 1119447--1119485 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1119437 GGAAGAAAAA
1119447 TTGTAAAATTTATATTTTTT
1 TTGTAAAATTTATATTTTTT
1119467 TTGTAAAATTTATATTTTT
1 TTGTAAAATTTATATTTTT
1119486 GGTTTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (20 bp):
TTGTAAAATTTATATTTTTT
Found at i:1126483 original size:28 final size:28
Alignment explanation
Indices: 1126433--1126858 Score: 201
Period size: 28 Copynumber: 15.7 Consensus size: 28
1126423 CTTATGTTTA
*
1126433 TATATATATAC-T-TATGT-AA-ATACT
1 TATATATATACTTATATATAAATATACT
*
1126457 TATGTATATACTTATATATAAATATACT
1 TATATATATACTTATATATAAATATACT
*
1126485 TATGTATATACTTATATATAAATATACT
1 TATATATATACTTATATATAAATATACT
* *
1126513 TATGTATATACTTATATAT-ACT-TA--
1 TATATATATACTTATATATAAATATACT
* *
1126537 -AGTATATATGCTTATATACTTATATATATAGT
1 TA-TATATATACTTATATA--TA-A-ATATACT
* **
1126569 TATATATATACTTATATATACATATGGT
1 TATATATATACTTATATATAAATATACT
* * * *
1126597 TATATATATTCTTTTATATATATATTCTTT
1 TATATATATACTTATATATAAATATAC--T
* *
1126627 TATATATATA-TATATATTTATATATA-T
1 TATATATATACT-TATATATAAATATACT
* *
1126654 T-TA-AT-TACATATATACTTAAGTATA--
1 TATATATATACTTATATA--TAAATATACT
* *
1126679 TATGCTTATATAC-T-TATAT--ATATAGT
1 TAT--ATATATACTTATATATAAATATACT
*
1126705 TATATATATAC-T-TATAT--ATATAGT
1 TATATATATACTTATATATAAATATACT
* **
1126729 TATATATATACTTATATATACATATGGT
1 TATATATATACTTATATATAAATATACT
* *
1126757 TATATATATTCTTTTATATATATATATACT
1 TATATATATAC--TTATATATAAATATACT
* * * *
1126787 TATCTACATA--TGTATATACATATA-T
1 TATATATATACTTATATATAAATATACT
* *
1126812 TAAACT-TATA-TTATATATATATATA-T
1 TATA-TATATACTTATATATAAATATACT
*
1126838 ATATATATATATTTATATATA
1 -TATATATATACTTATATATA
1126859 TTTAATTACA
Statistics
Matches: 323, Mismatches: 41, Indels: 72
0.74 0.09 0.17
Matches are distributed among these distances:
23 1 0.00
24 66 0.20
25 11 0.03
26 52 0.16
27 13 0.04
28 110 0.34
29 5 0.02
30 49 0.15
32 15 0.05
33 1 0.00
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (28 bp):
TATATATATACTTATATATAAATATACT
Found at i:1126494 original size:20 final size:20
Alignment explanation
Indices: 1126422--1126876 Score: 123
Period size: 20 Copynumber: 22.9 Consensus size: 20
1126412 TATTTTTTTC
*
1126422 ACTTATGTTTATATATATAT
1 ACTTATGTATATATATATAT
*
1126442 ACTTATGTAAATACTTATGTATAT
1 ACTTATGT--ATA--TATATATAT
1126466 ACTTA--TATATA-A-ATAT
1 ACTTATGTATATATATATAT
1126482 ACTTATGTATATACT-TATAT
1 ACTTATGTATATA-TATATAT
** *
1126502 A--TAAATATACTTATGTATAT
1 ACTTATGTATA--TATATATAT
*
1126522 ACTTATATATACTTAAGTATATAT
1 ACTTATGTATA--T-A-TATATAT
* *
1126546 GCTTATATACT-TATATATAT
1 ACTTATGTA-TATATATATAT
* *
1126566 AGTTATATATATACTTATATAT
1 ACTTATGTATATA--TATATAT
*
1126588 ACATATGGT-TATATATAT-T
1 ACTTAT-GTATATATATATAT
1126607 -CTT-T-TATATATATAT-T
1 ACTTATGTATATATATATAT
* *
1126623 -CTTTTATATATATATATAT
1 ACTTATGTATATATATATAT
* *
1126642 ATTTATATATATTTAATTACATATAT
1 ACTTATGTATA--T-A-T--ATATAT
* *
1126668 ACTTAAGTATATATGCTTATAT
1 ACTTATGTATATAT--ATATAT
1126690 ACTTA--TATATATAGT-TAT
1 ACTTATGTATATATA-TATAT
*
1126708 A--TATATACT-TATATATAT
1 ACTTATGTA-TATATATATAT
* *
1126726 AGTTATATATATACTTATATAT
1 ACTTATGTATATA--TATATAT
*
1126748 ACATATGGT-TATATATAT-T
1 ACTTAT-GTATATATATATAT
1126767 -CTT-T-TATATATATATAT
1 ACTTATGTATATATATATAT
* * *
1126784 ACTTATCTACATATGTATAT
1 ACTTATGTATATATATATAT
* *
1126804 AC--ATATAT-TAAACT-TAT
1 ACTTATGTATATATA-TATAT
*
1126821 A-TTATATATATATATATAT
1 ACTTATGTATATATATATAT
* *
1126840 A--TATATATATTTATATAT
1 ACTTATGTATATATATATAT
* *
1126858 ATTTAAT-TACATATATATA
1 ACTT-ATGTATATATATATA
1126877 AAAGTATATT
Statistics
Matches: 343, Mismatches: 36, Indels: 112
0.70 0.07 0.23
Matches are distributed among these distances:
15 2 0.01
16 33 0.10
17 11 0.03
18 75 0.22
19 16 0.05
20 97 0.28
21 3 0.01
22 57 0.17
23 5 0.01
24 29 0.08
25 1 0.00
26 14 0.04
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (20 bp):
ACTTATGTATATATATATAT
Found at i:1126532 original size:12 final size:12
Alignment explanation
Indices: 1126433--1126859 Score: 242
Period size: 12 Copynumber: 34.8 Consensus size: 12
1126423 CTTATGTTTA
1126433 TATATATATACT
1 TATATATATACT
* *
1126445 TATGTAAATACT
1 TATATATATACT
*
1126457 TATGTATATACTT
1 TATATATATAC-T
1126470 ATATATAAATATACT
1 -TATAT--ATATACT
*
1126485 TATGTATATACTT
1 TATATATATAC-T
1126498 ATATATAAATATACT
1 -TATAT--ATATACT
*
1126513 TATGTATATAC-
1 TATATATATACT
1126524 T-TATATATACT
1 TATATATATACT
1126535 TA-AGTATATA-T
1 TATA-TATATACT
**
1126546 GCT-TATATACT
1 TATATATATACT
*
1126557 TATATATATAGT
1 TATATATATACT
1126569 TATATATATACT
1 TATATATATACT
*
1126581 TATATATACATATGGT
1 TATATAT--ATA--CT
*
1126597 TATATATATTCTTT
1 TATATATATAC--T
1126611 TATATATATATTCT
1 TATATATATA--CT
1126625 T-T-TATATA--
1 TATATATATACT
*
1126633 TATATATATATT
1 TATATATATACT
*
1126645 TATATATATTTAAT
1 TATATATA--TACT
*
1126659 TACATATATACT
1 TATATATATACT
1126671 TA-AGTATATA-T
1 TATA-TATATACT
**
1126682 GCT-TATATACT
1 TATATATATACT
*
1126693 TATATATATAGT
1 TATATATATACT
1126705 TATATATATACT
1 TATATATATACT
*
1126717 TATATATATAGT
1 TATATATATACT
1126729 TATATATATACT
1 TATATATATACT
*
1126741 TATATATACATATGGT
1 TATATAT--ATA--CT
*
1126757 TATATATATTCT
1 TATATATATACT
*
1126769 TTTATATATA-T
1 TATATATATACT
* *
1126780 ATATACTTATCTACA
1 -TATA--TATATACT
* *
1126795 TATGTATATACA
1 TATATATATACT
*
1126807 TATAT-TAAACT
1 TATATATATACT
1126818 TATAT-TATA--
1 TATATATATACT
1126827 TATATATATA-T
1 TATATATATACT
*
1126838 ATATATATATATT
1 -TATATATATACT
1126851 TATATATAT
1 TATATATAT
1126860 TTAATTACAT
Statistics
Matches: 328, Mismatches: 43, Indels: 88
0.71 0.09 0.19
Matches are distributed among these distances:
8 1 0.00
9 6 0.02
10 30 0.09
11 23 0.07
12 177 0.54
13 4 0.01
14 56 0.17
15 2 0.01
16 29 0.09
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (12 bp):
TATATATATACT
Found at i:1126576 original size:16 final size:15
Alignment explanation
Indices: 1126461--1126876 Score: 169
Period size: 16 Copynumber: 26.3 Consensus size: 15
1126451 AATACTTATG
1126461 TATATACTTATATATA
1 TATATA-TTATATATA
* *
1126477 AATATACTTATGTATA
1 TATATA-TTATATATA
*
1126493 TACT-TA-TATATAAA
1 TA-TATATTATATATA
1126507 TATACTTATGTATATACTTA
1 TATA--TAT-TATATA--TA
1126527 TATATACTTA-AGTATA
1 TATATA-TTATA-TATA
**
1126543 TAT-GCTTATATACT-
1 TATATATTATATA-TA
1126557 TATATA-TATAGTTATA
1 TATATATTATA--TATA
1126573 TATATACTTATATATA
1 TATATA-TTATATATA
* *
1126589 CATATGGTTATATATA
1 TATAT-ATTATATATA
* *
1126605 T-TCTTTTATATATA
1 TATATATTATATATA
* *
1126619 TAT-TCTTTTATATA
1 TATATATTATATATA
*
1126633 TATATA-TATATTTA
1 TATATATTATATATA
*
1126647 TATATATT-TAATTACA
1 TATATATTAT-A-TATA
1126663 TATATACTTA-AGTATA
1 TATATA-TTATA-TATA
*
1126679 TATGCT-TATATACTTATA
1 TAT-ATAT-TATA--TATA
1126697 TATATAGTTATATATA
1 TATATA-TTATATATA
1126713 TACTTATATATATAGTTATA
1 TA--TATAT-TATA--TATA
1126733 TATATACTTATATATA
1 TATATA-TTATATATA
* *
1126749 CATATGGTTATATATA
1 TATAT-ATTATATATA
* *
1126765 T-TCTTTTATATATA
1 TATATATTATATATA
* *
1126779 TATATACTTATCTACA
1 TATATA-TTATATATA
* *
1126795 TATGTA-TATACATA
1 TATATATTATATATA
*
1126809 TATTAAACTTATATTATA
1 TA-TATA-TTATA-TATA
1126827 TATATATATATATATA
1 TATATAT-TATATATA
1126843 TATATATT-TATATA
1 TATATATTATATATA
* *
1126857 TATTTAATTACATATA
1 TATAT-ATTATATATA
1126873 TATA
1 TATA
1126877 AAAGTATATT
Statistics
Matches: 305, Mismatches: 47, Indels: 96
0.68 0.10 0.21
Matches are distributed among these distances:
13 1 0.00
14 82 0.27
15 20 0.07
16 121 0.40
17 19 0.06
18 48 0.16
19 3 0.01
20 11 0.04
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.50
Consensus pattern (15 bp):
TATATATTATATATA
Found at i:1126941 original size:19 final size:20
Alignment explanation
Indices: 1126902--1126941 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1126892 ATGTATTTTG
*
1126902 TAATACAAATGGGCTTATAT
1 TAATACAAATGGACTTATAT
*
1126922 TAATA-AAATGGACTTGTAT
1 TAATACAAATGGACTTATAT
1126941 T
1 T
1126942 TATTTTAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (20 bp):
TAATACAAATGGACTTATAT
Found at i:1127061 original size:13 final size:15
Alignment explanation
Indices: 1127032--1127061 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1127022 CCGTTATACT
1127032 TATAATATACATATA
1 TATAATATACATATA
*
1127047 TATAATATACTTATA
1 TATAATATACATATA
1127062 ATTATATTTA
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (15 bp):
TATAATATACATATA
Found at i:1133060 original size:24 final size:24
Alignment explanation
Indices: 1133033--1133090 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
1133023 AAAATGAAGC
1133033 AAATATAAATTCA-AGAATATATAA
1 AAATATAAATTCATA-AATATATAA
*
1133057 AAATATCAAA-TCATAAATATATTA
1 AAATAT-AAATTCATAAATATATAA
*
1133081 ATATATAAAT
1 AAATATAAAT
1133091 GTATCTCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 3 0.10
24 22 0.76
25 4 0.14
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATATAAATTCATAAATATATAA
Found at i:1133088 original size:16 final size:16
Alignment explanation
Indices: 1133048--1133095 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1133038 TAAATTCAAG
*
1133048 AATATATAAAAATATC
1 AATATATAAATATATC
*
1133064 AA-ATCATAAATATATT
1 AATAT-ATAAATATATC
*
1133080 AATATATAAATGTATC
1 AATATATAAATATATC
1133096 TCTAAACCTG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 2 0.08
16 22 0.85
17 2 0.08
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.35
Consensus pattern (16 bp):
AATATATAAATATATC
Found at i:1134397 original size:6 final size:6
Alignment explanation
Indices: 1134386--1134414 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1134376 CACGTATTAT
1134386 CACGAC CACGAC CACGAC CACGAC CACGA
1 CACGAC CACGAC CACGAC CACGAC CACGA
1134415 GCCGAGCCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.48, G:0.17, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:1140301 original size:5 final size:5
Alignment explanation
Indices: 1140291--1140333 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
1140281 CCGCGACCAT
* * *
1140291 GAGCC GAGCC GAGCC GAGCC GTGCC GTGCC GAGCC GAGAC GAG
1 GAGCC GAGCC GAGCC GAGCC GAGCC GAGCC GAGCC GAGCC GAG
1140334 ACGGACGGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.19, C:0.35, G:0.42, T:0.05
Consensus pattern (5 bp):
GAGCC
Found at i:1145770 original size:13 final size:13
Alignment explanation
Indices: 1145749--1145781 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1145739 ATCGTCCATA
*
1145749 AAATTTCAGGATT
1 AAATCTCAGGATT
1145762 AAATCTCAGGATT
1 AAATCTCAGGATT
1145775 AAATCTC
1 AAATCTC
1145782 TTCTTTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (13 bp):
AAATCTCAGGATT
Found at i:1149645 original size:6 final size:6
Alignment explanation
Indices: 1149634--1149661 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1149624 ATCTTTCACA
1149634 ACGACC ACGACC ACGACC ACGACC ACGA
1 ACGACC ACGACC ACGACC ACGACC ACGA
1149662 GCCGAGACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.46, G:0.18, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:1151276 original size:5 final size:5
Alignment explanation
Indices: 1151268--1151332 Score: 53
Period size: 5 Copynumber: 12.0 Consensus size: 5
1151258 AAAGAGAGAG
1151268 TAAAA TAAAA TAAAA TAAAA TAAAGA -AAATA TTAAAA TAAAA -AACGAA
1 TAAAA TAAAA TAAAA TAAAA TAAA-A TAAA-A -TAAAA TAAAA TAA--AA
1151316 TAAAAAA TAAAA TAAAA
1 T--AAAA TAAAA TAAAA
1151333 ACGTTAAATT
Statistics
Matches: 51, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
4 2 0.04
5 37 0.73
6 4 0.08
7 6 0.12
9 2 0.04
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (5 bp):
TAAAA
Found at i:1151396 original size:12 final size:13
Alignment explanation
Indices: 1151364--1151395 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1151354 AAATAGAAAG
1151364 GAAAAAATGTTAA
1 GAAAAAATGTTAA
1151377 GAAAAAATGTTAA
1 GAAAAAATGTTAA
*
1151390 TAAAAA
1 GAAAAA
1151396 TACAAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (13 bp):
GAAAAAATGTTAA
Found at i:1152590 original size:19 final size:19
Alignment explanation
Indices: 1152566--1152615 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1152556 AATTAAATTA
1152566 AATAAATAAGTAATA-AAAT
1 AATAAATAA-TAATAGAAAT
*
1152585 AATAAATAATAATAGAATT
1 AATAAATAATAATAGAAAT
*
1152604 AATATATAATAA
1 AATAAATAATAA
1152616 AAACTATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 5 0.18
19 23 0.82
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (19 bp):
AATAAATAATAATAGAAAT
Found at i:1152640 original size:24 final size:26
Alignment explanation
Indices: 1152587--1152670 Score: 77
Period size: 26 Copynumber: 3.3 Consensus size: 26
1152577 AATAAAATAA
* * **
1152587 TAAATAATAATAGA-ATTAATATATAA
1 TAAAAAATAATATATATT-ATATATGT
*
1152613 TAAAAACT-ATATAATATTATAT-T-T
1 TAAAAAATAATAT-ATATTATATATGT
1152637 TAAAAAATAATATATATTATATATGT
1 TAAAAAATAATATATATTATATATGT
1152663 TAAAAAAT
1 TAAAAAAT
1152671 CATTTTAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
24 16 0.33
25 9 0.19
26 20 0.42
27 3 0.06
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.39
Consensus pattern (26 bp):
TAAAAAATAATATATATTATATATGT
Found at i:1152736 original size:85 final size:83
Alignment explanation
Indices: 1152646--1152815 Score: 213
Period size: 85 Copynumber: 2.0 Consensus size: 83
1152636 TTAAAAAATA
*
1152646 ATATATAT-TATATATGTTAAAAAATCATTTT-AAA-AAACT-ATATATATGTTTTCAAAAAAAT
1 ATATATATATATATATATTAAAAAATCATTTTCAAACAAA-TAATATATATGTTTTC-AAAAAAT
*
1152707 CATTTTTAAAACTATATAAT
64 CATTTTCAAAACTATATAAT
* * * *
1152727 ATATATATATATATATATTCAAAAATTATTTTCGAAACTATATAATATATATGTTTTCAAAAATT
1 ATATATATATATATATATTAAAAAATCATTTTC-AAAC-AAATAATATATATGTTTTCAAAAAAT
*
1152792 GATTTTCAAAACTATATAAT
64 CATTTTCAAAACTATATAAT
1152812 ATAT
1 ATAT
1152816 CTTCAAAAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
81 8 0.11
82 20 0.26
84 3 0.04
85 29 0.38
86 16 0.21
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (83 bp):
ATATATATATATATATATTAAAAAATCATTTTCAAACAAATAATATATATGTTTTCAAAAAATCA
TTTTCAAAACTATATAAT
Found at i:1152744 original size:120 final size:118
Alignment explanation
Indices: 1152603--1152925 Score: 262
Period size: 111 Copynumber: 2.8 Consensus size: 118
1152593 ATAATAGAAT
* *
1152603 TAATATATAATAAAAACTATA-T-AATATTATATTTTAAAAAATAATATATATTATATATG-TT-
1 TAATATATAATAAAAACTATATTCAAAAAT-TATTTTAAAAAAT-ATATA-A-TATATATGTTTC
* * *
1152664 AAAAAATCATTTTAAAAAACTATAT-ATATGTTTTCAAAAAAATCATTTTTAAAACTATA
62 AAAAAATCATTTT-AAAAACTATATAATATATCTTC--AAAAATCATTTTCAAAACTATA
* * ** *
1152723 TAATATATATATATATA-TATATTCAAAAATTATTTTCGAAACTATATAATATATATGTTTTCAA
1 TAATATATA-ATAAAAACTATATTCAAAAATTATTTTAAAAAATATATAATATATATG-TTTCAA
* * *
1152787 AAATTGATTTTCAAAACTATATAATATATCTTCAAAAATCATTTTCAAAACTATA
64 AAAATCATTTTAAAAACTATATAATATATCTTCAAAAATCATTTTCAAAACTATA
* * * * * *
1152842 TAATATAT-GT----A-T-T-TTCAAAAGTTGTTTTCAAAATTATATAATATATATATTTTC-AA
1 TAATATATAATAAAAACTATATTCAAAAATTATTTTAAAAAATATATAATATATAT-GTTTCAAA
* *
1152898 AAATCGTTTTCAAAACTATATAATATAT
65 AAATCATTTTAAAAACTATATAATATAT
1152926 ATATTTTTCA
Statistics
Matches: 173, Mismatches: 22, Indels: 26
0.78 0.10 0.12
Matches are distributed among these distances:
110 27 0.16
111 35 0.20
112 1 0.01
113 2 0.01
117 1 0.01
118 8 0.05
119 30 0.17
120 30 0.17
121 35 0.20
122 4 0.02
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (118 bp):
TAATATATAATAAAAACTATATTCAAAAATTATTTTAAAAAATATATAATATATATGTTTCAAAA
AATCATTTTAAAAACTATATAATATATCTTCAAAAATCATTTTCAAAACTATA
Found at i:1152778 original size:38 final size:38
Alignment explanation
Indices: 1152726--1153028 Score: 315
Period size: 38 Copynumber: 8.1 Consensus size: 38
1152716 AACTATATAA
* *
1152726 TATATATATATATATATATTCAAAAATTATTTTCGAAAC
1 TATATA-ATATATATATTTTCAAAAATTATTTTCAAAAC
*
1152765 TATATAATATATATGTTTTCAAAAATTGATTTTCAAAAC
1 TATATAATATATATATTTTCAAAAATT-ATTTTCAAAAC
* *
1152804 --TAT-ATA-ATATATCTTCAAAAATCATTTTCAAAAC
1 TATATAATATATATATTTTCAAAAATTATTTTCAAAAC
* * * *
1152838 TATATAATATATGTATTTTCAAAAGTTGTTTTCAAAAT
1 TATATAATATATATATTTTCAAAAATTATTTTCAAAAC
**
1152876 TATATAATATATATATTTTCAAAAATCGTTTTCAAAAC
1 TATATAATATATATATTTTCAAAAATTATTTTCAAAAC
* *
1152914 TATATAATATATATATTTTTCAAAAAATTGTTTTAAAAAC
1 TATATAATATATATA-TTTTC-AAAAATTATTTTCAAAAC
* * *
1152954 --TAT-ATA-ATATATTTTCAAAAATCGATTTTTAAAAGG
1 TATATAATATATATATTTTCAAAAAT-TATTTTCAAAA-C
1152990 TATAT-AT-TATAT-TTTTCAAAAA-TATTTTCAAAAAC
1 TATATAATATATATATTTTCAAAAATTATTTTC-AAAAC
1153025 TATA
1 TATA
1153029 CTATATTAAT
Statistics
Matches: 226, Mismatches: 25, Indels: 30
0.80 0.09 0.11
Matches are distributed among these distances:
34 17 0.08
35 36 0.16
36 15 0.07
37 19 0.08
38 102 0.45
39 21 0.09
40 16 0.07
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.44
Consensus pattern (38 bp):
TATATAATATATATATTTTCAAAAATTATTTTCAAAAC
Found at i:1152870 original size:111 final size:111
Alignment explanation
Indices: 1152726--1152925 Score: 312
Period size: 111 Copynumber: 1.8 Consensus size: 111
1152716 AACTATATAA
* *
1152726 TATATATATATATATATATTCAAAAATTATTTTCGAAACTATATAATATATATGTTTTCAAAAAT
1 TATATATATATATATATATTCAAAAATTATTTTCAAAACTATATAATATATATATTTTCAAAAAT
*
1152791 TGATTTTCAAAACTATATAATATATCTTCAAAAATCATTTTCAAAAC
66 CG-TTTTCAAAACTATATAATATATCTTCAAAAATCATTTTCAAAAC
* * * * *
1152838 TATATA-ATATATGTATTTTCAAAAGTTGTTTTCAAAATTATATAATATATATATTTTCAAAAAT
1 TATATATATATATATATATTCAAAAATTATTTTCAAAACTATATAATATATATATTTTCAAAAAT
1152902 CGTTTTCAAAACTATATAATATAT
66 CGTTTTCAAAACTATATAATATAT
1152926 ATATTTTTCA
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
110 22 0.28
111 52 0.65
112 6 0.08
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.43
Consensus pattern (111 bp):
TATATATATATATATATATTCAAAAATTATTTTCAAAACTATATAATATATATATTTTCAAAAAT
CGTTTTCAAAACTATATAATATATCTTCAAAAATCATTTTCAAAAC
Found at i:1152912 original size:76 final size:72
Alignment explanation
Indices: 1152729--1153028 Score: 349
Period size: 73 Copynumber: 4.1 Consensus size: 72
1152719 TATATAATAT
* * * *
1152729 ATATATATATATATATTCAAAAATTATTTTCGAAACTATATAATATATATGTTTTCAAAAATTGA
1 ATATATA-ATATATTTTCAAAAATCATTTTCAAAACTATATAATATATATATTTTCAAAAATTG-
1152794 TTTTCAAAA
64 TTTTCAAAA
* * * *
1152803 CTATATAATATATCTTCAAAAATCATTTTCAAAACTATATAATATATGTATTTTCAAAAGTTGTT
1 ATATATAATATATTTTCAAAAATCATTTTCAAAACTATATAATATATATATTTTCAAAAATTGTT
1152868 TTCAAAA
66 TTCAAAA
*
1152875 TTATATAATATATATATTTTCAAAAATCGTTTTCAAAACTATATAATATATATATTTTTCAAAAA
1 --ATAT-ATA-ATATATTTTCAAAAATCATTTTCAAAACTATATAATATATATA-TTTTC-AAAA
1152940 ATTGTTTT-AAAA
60 ATTGTTTTCAAAA
* *
1152952 ACTATATAATATATTTTCAAAAATCGATTTTTAAAAGGTATAT-AT-TATAT-TTTTCAAAAA-T
1 A-TATATAATATATTTTCAAAAATC-ATTTTCAAAA-CTATATAATATATATATTTTCAAAAATT
*
1153013 ATTTTCAAAA
63 GTTTTCAAAA
1153023 ACTATA
1 A-TATA
1153029 CTATATTAAT
Statistics
Matches: 200, Mismatches: 16, Indels: 23
0.84 0.07 0.10
Matches are distributed among these distances:
70 5 0.03
71 15 0.08
72 14 0.07
73 50 0.25
74 31 0.16
75 17 0.09
76 48 0.24
77 9 0.05
78 11 0.05
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (72 bp):
ATATATAATATATTTTCAAAAATCATTTTCAAAACTATATAATATATATATTTTCAAAAATTGTT
TTCAAAA
Found at i:1161809 original size:7 final size:7
Alignment explanation
Indices: 1161791--1161828 Score: 58
Period size: 7 Copynumber: 5.1 Consensus size: 7
1161781 ATTGTGAAAT
1161791 ATAAAAA
1 ATAAAAA
1161798 TATAAAAA
1 -ATAAAAA
1161806 ATAAAAA
1 ATAAAAA
1161813 ATTAAAAA
1 A-TAAAAA
1161821 ATAAAAA
1 ATAAAAA
1161828 A
1 A
1161829 ATAGATAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 15 0.52
8 14 0.48
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (7 bp):
ATAAAAA
Found at i:1161809 original size:15 final size:15
Alignment explanation
Indices: 1161787--1161828 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
1161777 TTAAATTGTG
1161787 AAATATAAAAATATAAA
1 AAATA-AAAAAT-TAAA
1161804 AAATAAAAAATTAAA
1 AAATAAAAAATTAAA
1161819 AAATAAAAAA
1 AAATAAAAAA
1161829 ATAGATAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 14 0.56
16 6 0.24
17 5 0.20
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
AAATAAAAAATTAAA
Found at i:1161829 original size:8 final size:8
Alignment explanation
Indices: 1161787--1161831 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
1161777 TTAAATTGTG
*
1161787 AAATATAA
1 AAATAAAA
1161795 AAATATAAA
1 AAATA-AAA
1161804 AAAT-AAA
1 AAATAAAA
*
1161811 AAATTAAA
1 AAATAAAA
1161819 AAATAAAA
1 AAATAAAA
1161827 AAATA
1 AAATA
1161832 GATAAGTTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 7 0.21
8 20 0.61
9 6 0.18
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (8 bp):
AAATAAAA
Found at i:1161890 original size:22 final size:22
Alignment explanation
Indices: 1161865--1161936 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
1161855 AAGAGCGAAA
*
1161865 AAAAGAGAGAGAAAAATAAAAT
1 AAAAGAAAGAGAAAAATAAAAT
* * *
1161887 AAAATAAAGAGAATATTAAAAT
1 AAAAGAAAGAGAAAAATAAAAT
*
1161909 AAAA-AAACGAATAAAAAGTAAAAT
1 AAAAGAAA-G-AGAAAAA-TAAAAT
1161933 AAAA
1 AAAA
1161937 ACTTTAAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 3 0.08
22 23 0.57
23 4 0.10
24 10 0.25
ACGTcount: A:0.74, C:0.01, G:0.11, T:0.14
Consensus pattern (22 bp):
AAAAGAAAGAGAAAAATAAAAT
Found at i:1161981 original size:14 final size:14
Alignment explanation
Indices: 1161951--1161998 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 14
1161941 TAAATTTTGA
* *
1161951 AAGAAAAAATAG-A
1 AAGAAAAAATTGTT
1161964 AAGAAAAAATTGTT
1 AAGAAAAAATTGTT
1161978 AAGAAAAAA-TGTT
1 AAGAAAAAATTGTT
*
1161991 AATAAAAA
1 AAGAAAAA
1161999 TACAAAACAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
13 22 0.71
14 9 0.29
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (14 bp):
AAGAAAAAATTGTT
Found at i:1163219 original size:16 final size:16
Alignment explanation
Indices: 1163162--1163243 Score: 62
Period size: 16 Copynumber: 4.9 Consensus size: 16
1163152 TAAAAAAATA
1163162 AAAAATAAA-AATAA-
1 AAAAATAAATAATAAT
1163176 AATTAAATAAATAAGTAAT
1 AA--AAATAAATAA-TAAT
1163195 AAAATAATAAATAATAAT
1 -AAA-AATAAATAATAAT
*
1163213 AGAAAT-AATATATAAT
1 AAAAATAAATA-ATAAT
*
1163229 AAAAACTATATAATA
1 AAAAA-TAAATAATA
1163244 TTATATTTTC
Statistics
Matches: 55, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
14 2 0.04
15 4 0.07
16 19 0.35
17 8 0.15
18 11 0.20
19 9 0.16
20 2 0.04
ACGTcount: A:0.70, C:0.01, G:0.02, T:0.27
Consensus pattern (16 bp):
AAAAATAAATAATAAT
Found at i:1163219 original size:19 final size:18
Alignment explanation
Indices: 1163156--1163230 Score: 87
Period size: 19 Copynumber: 3.9 Consensus size: 18
1163146 TTCTTTTAAA
* *
1163156 AAAATAAAAAATAAAAAT
1 AAAATAATAAATAATAAT
1163174 AAAATTAAATAAATAAGTAAT
1 AAAA-T-AATAAATAA-TAAT
1163195 AAAATAATAAATAATAAT
1 AAAATAATAAATAATAAT
*
1163213 AGAAATAATATATAATAA
1 A-AAATAATAAATAATAA
1163231 AAACTATATA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
18 9 0.18
19 25 0.50
20 9 0.18
21 7 0.14
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (18 bp):
AAAATAATAAATAATAAT
Found at i:1163229 original size:34 final size:31
Alignment explanation
Indices: 1163158--1163232 Score: 82
Period size: 34 Copynumber: 2.3 Consensus size: 31
1163148 CTTTTAAAAA
*
1163158 AATAA-AAAATAAAAATAAAATTAAATAAAT
1 AATAATAAAATAAAAATAAAATGAAATAAAT
1163188 AAGTAATAAAATAATAAATAATAATAGAAAT-AAT
1 AA-TAATAAAATAA-AAATAA-AAT-GAAATAAAT
1163222 ATATAATAAAA
1 A-ATAATAAAA
1163233 ACTATATAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
30 2 0.05
31 3 0.08
32 7 0.18
33 6 0.16
34 15 0.39
35 5 0.13
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (31 bp):
AATAATAAAATAAAAATAAAATGAAATAAAT
Found at i:1163285 original size:26 final size:24
Alignment explanation
Indices: 1163228--1163285 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 24
1163218 TAATATATAA
*
1163228 TAAAAACTATATAATATTATATTT
1 TAAAAAATATATAATATTATATTT
*
1163252 TCAAAAATA-ATATATATTATATATGT
1 TAAAAAATATATA-ATATTATAT-T-T
1163278 TAAAAAAT
1 TAAAAAAT
1163286 CATTTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 3 0.11
24 16 0.57
25 1 0.04
26 8 0.29
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (24 bp):
TAAAAAATATATAATATTATATTT
Found at i:1163358 original size:38 final size:37
Alignment explanation
Indices: 1163248--1163653 Score: 347
Period size: 38 Copynumber: 11.0 Consensus size: 37
1163238 ATAATATTAT
* * *
1163248 ATTTTCAAAAATAATATATATTATATATGTTAAAAAATC
1 ATTTTCAAAACT-ATATATA-TATATATTTTCAAAAATC
* * *
1163287 ATTTT-TAAA--ATCTATATATATGTTTTCAAAAAAATC
1 ATTTTCAAAACTATATATATATATATTTTC--AAAAATC
* *
1163323 ATTTTTAAAACTATATAATATATATATTTTCAAAAATT
1 ATTTTCAAAACTATAT-ATATATATATTTTCAAAAATC
* * *
1163361 ATTTTCGAAACTATATAATATATATGTTTTCAAAAATTG
1 ATTTTCAAAACTATAT-ATATATATATTTTCAAAAA-TC
*
1163400 ATTTTCAAAACTATATA-ATATAT-CTTT-AAAAATC
1 ATTTTCAAAACTATATATATATATATTTTCAAAAATC
* *
1163434 GTTTTCAAAACTATATAATATATATATTTTCAAAAATT
1 ATTTTCAAAACTATAT-ATATATATATTTTCAAAAATC
* *
1163472 GTTTTCAAAATTATATAATATATATATTTTCAAAAATC
1 ATTTTCAAAACTATAT-ATATATATATTTTCAAAAATC
*
1163510 GTTTTCAAAACTATATA-ATATATATTTTCAAAAAAT-
1 ATTTTCAAAACTATATATATATATATTTTC-AAAAATC
* *
1163546 ATTTTTCAAAAC--TATATA-ATATATTTTCTAAAACTG
1 A-TTTTCAAAACTATATATATATATATTTTC-AAAAATC
* * * *
1163582 ATTTTTTAAAAGGTATATAT-TATATGTTTTCAAAAACC
1 A-TTTTCAAAA-CTATATATATATATATTTTCAAAAATC
* *
1163620 GTTTTCTAAAAAT-TATAT-TATAT-TTTTCAAAAAT
1 ATTTTC-AAAACTATATATATATATATTTTCAAAAAT
1163654 ATATATACTA
Statistics
Matches: 312, Mismatches: 35, Indels: 44
0.80 0.09 0.11
Matches are distributed among these distances:
34 24 0.08
35 41 0.13
36 54 0.17
37 34 0.11
38 108 0.35
39 38 0.12
40 13 0.04
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (37 bp):
ATTTTCAAAACTATATATATATATATTTTCAAAAATC
Found at i:1163462 original size:111 final size:112
Alignment explanation
Indices: 1163247--1163569 Score: 399
Period size: 111 Copynumber: 2.9 Consensus size: 112
1163237 TATAATATTA
* * * * * *
1163247 TATTTTCAAAAATA-ATATATATTATATATGTTAAAAAATCATTTTTAAAATCTATAT-ATATGT
1 TATTTTCAAAACTATATA-ATA-TATATATTTTCAAAAATCGTTTTCAAAA-CTATATAATATAT
*
1163310 --TTTCAAAAAAATCATTTTTAAAACTATATAATATATATATTTTCAAAAAT
63 ACTTT--AAAAAATCATTTTCAAAACTATATAATATATATATTTTCAAAAAT
* * *
1163360 TATTTTCGAAACTATATAATATATATGTTTTCAAAAATTGATTTTCAAAACTATATAATATAT-C
1 TATTTTCAAAACTATATAATATATATATTTTCAAAAATCG-TTTTCAAAACTATATAATATATAC
*
1163424 TTT-AAAAATCGTTTTCAAAACTATATAATATATATATTTTCAAAAAT
65 TTTAAAAAATCATTTTCAAAACTATATAATATATATATTTTCAAAAAT
* * *
1163471 TGTTTTCAAAATTATATAATATATATATTTTCAAAAATCGTTTTCAAAACTATATAATATATATT
1 TATTTTCAAAACTATATAATATATATATTTTCAAAAATCGTTTTCAAAACTATATAATATATACT
1163536 TTCAAAAAAT-ATTTTTCAAAACTATATAATATAT
66 TT-AAAAAATCA-TTTTCAAAACTATATAATATAT
1163570 TTTCTAAAAC
Statistics
Matches: 184, Mismatches: 18, Indels: 16
0.84 0.08 0.07
Matches are distributed among these distances:
110 22 0.12
111 80 0.43
112 20 0.11
113 56 0.30
114 6 0.03
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (112 bp):
TATTTTCAAAACTATATAATATATATATTTTCAAAAATCGTTTTCAAAACTATATAATATATACT
TTAAAAAATCATTTTCAAAACTATATAATATATATATTTTCAAAAAT
Found at i:1163562 original size:15 final size:15
Alignment explanation
Indices: 1163526--1163563 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1163516 AAAACTATAT
1163526 AATATATATTTTCAA
1 AATATATATTTTCAA
*
1163541 AAAATAT-TTTTCAA
1 AATATATATTTTCAA
1163555 AACTATATA
1 AA-TATATA
1163564 ATATATTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATATATTTTCAA
Found at i:1164445 original size:22 final size:23
Alignment explanation
Indices: 1164383--1164461 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 23
1164373 TTTTAATCAA
* *
1164383 AATATTAATTATTAAAATATCTAA-
1 AATA-TAA-TATTAATATTTCTAAT
*
1164407 AATATATTTATTAATATTTCTAAT
1 AATATA-ATATTAATATTTCTAAT
*
1164431 AATATAATATT-ATATTTTTAAT
1 AATATAATATTAATATTTCTAAT
*
1164453 ATTATAATA
1 AATATAATA
1164462 AAATAATCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
22 18 0.38
23 19 0.40
24 10 0.21
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (23 bp):
AATATAATATTAATATTTCTAAT
Found at i:1164475 original size:32 final size:32
Alignment explanation
Indices: 1164409--1164488 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
1164399 ATATCTAAAA
* *
1164409 TATATTTATTAATATTTCTAATAATATAATAT
1 TATATTTATTAATATTTATAATAAAATAATAT
1164441 TATATTT-TTAATA-TTATAATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAAAATAAT--AT
*
1164473 TATATTATAATAATAT
1 TATATT-TATTAATAT
1164489 AAGATATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 13 0.32
31 6 0.15
32 15 0.38
33 1 0.03
34 5 0.12
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAAAATAATAT
Found at i:1164774 original size:29 final size:29
Alignment explanation
Indices: 1164712--1164788 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
1164702 AATATAATTT
* *
1164712 ATAATATTTT-TCAATAAAATATACCAATA
1 ATAATATTTTATTAATAAAATATA-CAAAA
*
1164741 TTAATATTTTATTAATAAAATTATA-AAAA
1 ATAATATTTTATTAATAAAA-TATACAAAA
*
1164770 ATAATATTTTAATAATAAA
1 ATAATATTTTATTAATAAA
1164789 TAAATTATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 29 0.71
30 8 0.20
31 4 0.10
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (29 bp):
ATAATATTTTATTAATAAAATATACAAAA
Found at i:1164784 original size:18 final size:20
Alignment explanation
Indices: 1164763--1164803 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1164753 TAATAAAATT
1164763 ATAAAAAAT-AA-TATTTTA
1 ATAAAAAATAAATTATTTTA
*
1164781 ATAATAAATAAATTATTTTA
1 ATAAAAAATAAATTATTTTA
1164801 ATA
1 ATA
1164804 TTTTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 2 0.10
20 10 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATAAAAAATAAATTATTTTA
Found at i:1172592 original size:18 final size:18
Alignment explanation
Indices: 1172566--1172603 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1172556 GTAATATTTA
1172566 AATAATTAAATCGAATAT
1 AATAATTAAATCGAATAT
*
1172584 AATATTTAAATCGAATAT
1 AATAATTAAATCGAATAT
1172602 AA
1 AA
1172604 AATCTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (18 bp):
AATAATTAAATCGAATAT
Found at i:1175029 original size:21 final size:21
Alignment explanation
Indices: 1175003--1175075 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
1174993 CGATACCAGG
1175003 GTATCGATACTCGTTGAAGCA
1 GTATCGATACTCGTTGAAGCA
*
1175024 GTATCGGTACT-GTT-AAGAACA
1 GTATCGATACTCGTTGAAG--CA
*
1175045 GTATCGATACTCATTGAAGCA
1 GTATCGATACTCGTTGAAGCA
1175066 GTATCGATAC
1 GTATCGATAC
1175076 GATGCTAGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
19 3 0.07
20 3 0.07
21 34 0.76
22 2 0.04
23 3 0.07
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29
Consensus pattern (21 bp):
GTATCGATACTCGTTGAAGCA
Found at i:1177267 original size:30 final size:30
Alignment explanation
Indices: 1177233--1177289 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
1177223 ATTTTCAAAT
1177233 TTTCAACACCTACCATCCCACCATCCCATA
1 TTTCAACACCTACCATCCCACCATCCCATA
1177263 TTTCAACACCTACCATCCCACCATCCC
1 TTTCAACACCTACCATCCCACCATCCC
1177290 GTGTTTCCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.49, G:0.00, T:0.23
Consensus pattern (30 bp):
TTTCAACACCTACCATCCCACCATCCCATA
Found at i:1177766 original size:2 final size:2
Alignment explanation
Indices: 1177759--1177819 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
1177749 CTTATAATAG
1177759 TA TA TA 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
1177801 TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA
1177820 ACCAAAACTA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1183919 original size:75 final size:74
Alignment explanation
Indices: 1183829--1184066 Score: 284
Period size: 76 Copynumber: 3.1 Consensus size: 74
1183819 ATCTCACTTG
* *
1183829 AGATTGTTTTCCTTAAAAC-AGACTTTGTCTCGCTTGAGATTATTTTACTCGAAAGAAGACATTG
1 AGATTGTTTTTCTTAAAACAAGA-TTTGTCTCGCTTGAGA-TATTTTACTCGAAAGAAGACATTT
*
1183893 CATTTGACTCA
64 CATTTCACTCA
* * *
1183904 AGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACAGTTTTTACTCGAAACAAGA-ATAT
1 AGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGATA--TTTTACTCGAAAGAAGACAT-T
* *
1183968 TTATTTCACTTA
63 TCATTTCACTCA
* *
1183980 AGATTGATTTTCTTAAAACAAGATTTGTCTCGCTTGAGACGGT-TTTTACTCGAAAGAAGGCATT
1 AGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGA---TATTTTACTCGAAAGAAGACATT
*
1184044 TCATTTCACCCA
63 TCATTTCACTCA
1184056 AGATTGTTTTT
1 AGATTGTTTTT
1184067 AAAGAAGATT
Statistics
Matches: 138, Mismatches: 17, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
74 1 0.01
75 35 0.25
76 100 0.72
77 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (74 bp):
AGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGATATTTTACTCGAAAGAAGACATTTCA
TTTCACTCA
Found at i:1183949 original size:36 final size:36
Alignment explanation
Indices: 1183909--1184026 Score: 110
Period size: 36 Copynumber: 3.2 Consensus size: 36
1183899 ACTCAAGATT
1183909 GTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACA
1 GTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACA
** * * * **
1183945 GTTTTTACTCGAAACAAGAATATTTATTTCACTTAAGATT
1 GTTTTT-CTTAAAACAAG---ATTTGTCTCACTTGAGACA
* * *
1183985 GATTTTCTTAAAACAAGATTTGTCTCGCTTGAGACG
1 GTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACA
1184021 GTTTTT
1 GTTTTT
1184027 ACTCGAAAGA
Statistics
Matches: 61, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
36 24 0.39
37 9 0.15
39 9 0.15
40 19 0.31
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (36 bp):
GTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACA
Found at i:1184123 original size:39 final size:39
Alignment explanation
Indices: 1184069--1184617 Score: 830
Period size: 39 Copynumber: 14.3 Consensus size: 39
1184059 TTGTTTTTAA
*
1184069 AGAAGATTTTATCTCGCTTTAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1184108 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
1184147 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1184186 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTC-AAACC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAA-C
*
1184225 AGAATATTTTATCTCGCTT--G--A-----CCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1184255 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
1184294 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
1184333 AGAAAATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
1184372 AGAAGATTTTATCTTGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
1184411 ATAAGAATTTGTCTGGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
1184450 AGAAGATTTTGTCTGGCTTGAGATAATTTCCCTCGAAAT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1184489 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
1184528 AGAAAATTTTGTCTCGCATGAGATCGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
1184567 AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1184606 AGAAGATTTTAT
1 AGAAGATTTTAT
1184618 AAGAAACTAA
Statistics
Matches: 464, Mismatches: 35, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
30 23 0.05
31 3 0.01
32 1 0.00
34 1 0.00
35 1 0.00
37 1 0.00
38 3 0.01
39 431 0.93
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (39 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:1184264 original size:30 final size:30
Alignment explanation
Indices: 1184216--1184275 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1184206 AGATAGTTTC
*
1184216 CCTCAAACCAGAATATTTTATCTCGCTTGA
1 CCTCAAACCAGAAGATTTTATCTCGCTTGA
1184246 CCTCGAAA-CAGAAGATTTTATCTCGCTTGA
1 CCTC-AAACCAGAAGATTTTATCTCGCTTGA
1184276 GATAGTTTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 25 0.89
31 3 0.11
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (30 bp):
CCTCAAACCAGAAGATTTTATCTCGCTTGA
Found at i:1184762 original size:41 final size:41
Alignment explanation
Indices: 1184650--1184762 Score: 104
Period size: 42 Copynumber: 2.7 Consensus size: 41
1184640 AGGTTTTCTT
* * *
1184650 GATGAGTAAGTCCTTTGGGCCAT-CAGTAAGTCTTTCGAACAT
1 GATGA-TAAGACCTTCGGGCCATCCA-TAAGTCTTTCGAACAG
* * * * *
1184692 AATGCTTAA-ATCCTTCGGGTCATCTATAAGTCTTTCGAGCAG
1 GATG-ATAAGA-CCTTCGGGCCATCCATAAGTCTTTCGAACAG
1184734 GATGATAAGACCTTCGGGCCATCCATAAG
1 GATGATAAGACCTTCGGGCCATCCATAAG
1184763 ACCTTCCGGC
Statistics
Matches: 55, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
41 20 0.36
42 34 0.62
43 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.29
Consensus pattern (41 bp):
GATGATAAGACCTTCGGGCCATCCATAAGTCTTTCGAACAG
Found at i:1191373 original size:14 final size:15
Alignment explanation
Indices: 1191354--1191382 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1191344 AAAAAGTGAG
1191354 TTAAA-TATTTTTAT
1 TTAAATTATTTTTAT
1191368 TTAAATTATTTTTAT
1 TTAAATTATTTTTAT
1191383 AATTATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTAAATTATTTTTAT
Found at i:1191572 original size:27 final size:29
Alignment explanation
Indices: 1191518--1191574 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
1191508 AAGAATATAT
1191518 AATTATATTAAAAAATAAAATTATATTAA
1 AATTATATTAAAAAATAAAATTATATTAA
*
1191547 AATTAT-TTAAAGAATCAAAA-TA-ATTAA
1 AATTATATTAAAAAAT-AAAATTATATTAA
1191574 A
1 A
1191575 TAAAAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 6 0.23
28 10 0.38
29 10 0.38
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (29 bp):
AATTATATTAAAAAATAAAATTATATTAA
Found at i:1191582 original size:14 final size:14
Alignment explanation
Indices: 1191563--1191589 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1191553 TTAAAGAATC
1191563 AAAATAATTAAATA
1 AAAATAATTAAATA
1191577 AAAATAATTAAAT
1 AAAATAATTAAAT
1191590 TTAAAATAAA
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATAATTAAATA
Found at i:1194202 original size:18 final size:18
Alignment explanation
Indices: 1194179--1194218 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1194169 CGGAAACCAT
1194179 GGTGAGAAGTAATTTAAC
1 GGTGAGAAGTAATTTAAC
1194197 GGTGAGAAGTAATTTAAC
1 GGTGAGAAGTAATTTAAC
1194215 GGTG
1 GGTG
1194219 TTCGCTGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.05, G:0.33, T:0.28
Consensus pattern (18 bp):
GGTGAGAAGTAATTTAAC
Found at i:1194716 original size:42 final size:42
Alignment explanation
Indices: 1194669--1194768 Score: 173
Period size: 42 Copynumber: 2.4 Consensus size: 42
1194659 TACACGTGTG
* *
1194669 TATAGCGCGTGTCAGGGGTCGCGCCTGACCTTTATAATTATA
1 TATAGCGCGGGTCAGGGGCCGCGCCTGACCTTTATAATTATA
1194711 TATAGCGCGGGTCAGGGGCCGCGCCTGACCTTTATAATTATA
1 TATAGCGCGGGTCAGGGGCCGCGCCTGACCTTTATAATTATA
*
1194753 TATAGCGCGGGGCAGG
1 TATAGCGCGGGTCAGG
1194769 TATCGCGTCT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.21, C:0.22, G:0.31, T:0.26
Consensus pattern (42 bp):
TATAGCGCGGGTCAGGGGCCGCGCCTGACCTTTATAATTATA
Found at i:1198420 original size:35 final size:34
Alignment explanation
Indices: 1198335--1198421 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 34
1198325 AAAATAATTT
*
1198335 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
*
1198369 TAAATGATAATC-AAATTACAATAACTGCTATTAAATGG
1 TAAAT-ACAA-CAAAATTACAATAA--G-TATTAAATGG
1198407 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
1198422 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
34 6 0.13
35 22 0.49
36 2 0.04
37 4 0.09
38 11 0.24
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.29
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:1201537 original size:21 final size:21
Alignment explanation
Indices: 1201513--1201559 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
1201503 TCTTTAAACC
1201513 TATAAAAGATT-ATAATTATTT
1 TATAAAAG-TTAATAATTATTT
*
1201534 TAT-AACGTTCAATAATTATTT
1 TATAAAAGTT-AATAATTATTT
1201555 TATAA
1 TATAA
1201560 TATTCTAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 2 0.09
20 3 0.14
21 16 0.73
22 1 0.05
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (21 bp):
TATAAAAGTTAATAATTATTT
Found at i:1204455 original size:17 final size:17
Alignment explanation
Indices: 1204433--1204468 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1204423 AAATGATTGT
1204433 TTTGATATATTAAATAA
1 TTTGATATATTAAATAA
*
1204450 TTTGATATATTTAATAA
1 TTTGATATATTAAATAA
1204467 TT
1 TT
1204469 AAAACAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TTTGATATATTAAATAA
Found at i:1205410 original size:45 final size:45
Alignment explanation
Indices: 1205346--1205438 Score: 168
Period size: 45 Copynumber: 2.1 Consensus size: 45
1205336 ATGGATTATT
1205346 TATTTATTTATTTTTGCACTAGCTTCATCAACCTTTACAAAATTC
1 TATTTATTTATTTTTGCACTAGCTTCATCAACCTTTACAAAATTC
* *
1205391 TATTTTTTTTTTTTTGCACTAGCTTCATCAACCTTTACAAAATTC
1 TATTTATTTATTTTTGCACTAGCTTCATCAACCTTTACAAAATTC
1205436 TAT
1 TAT
1205439 CTTTCCAATG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.27, C:0.19, G:0.04, T:0.49
Consensus pattern (45 bp):
TATTTATTTATTTTTGCACTAGCTTCATCAACCTTTACAAAATTC
Found at i:1206902 original size:26 final size:26
Alignment explanation
Indices: 1206841--1206903 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
1206831 CACAATTCAC
** * *
1206841 ATCATAATCCAAATGAACCAGTAATA
1 ATCATAATCTGAATCAAACAGTAATA
1206867 ATCATAATCTGAATCAAACAGTAATA
1 ATCATAATCTGAATCAAACAGTAATA
1206893 ATCATAATCTG
1 ATCATAATCTG
1206904 GATATTATGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.48, C:0.17, G:0.08, T:0.27
Consensus pattern (26 bp):
ATCATAATCTGAATCAAACAGTAATA
Found at i:1206962 original size:13 final size:13
Alignment explanation
Indices: 1206944--1206972 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1206934 GCCTTACACA
1206944 ATGTTCGAATAGT
1 ATGTTCGAATAGT
1206957 ATGTTCGAATAGT
1 ATGTTCGAATAGT
1206970 ATG
1 ATG
1206973 CACCCCGTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.38
Consensus pattern (13 bp):
ATGTTCGAATAGT
Found at i:1211993 original size:26 final size:26
Alignment explanation
Indices: 1211964--1212018 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
1211954 ATGATTTTAA
* *
1211964 AAAAATGAAAATA-AAAACTATTTTCT
1 AAAAATAAAAACATAAAA-TATTTTCT
1211990 AAAAATAAAAACATAAAATATTTTCT
1 AAAAATAAAAACATAAAATATTTTCT
1212016 AAA
1 AAA
1212019 CTCAAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (26 bp):
AAAAATAAAAACATAAAATATTTTCT
Found at i:1217766 original size:22 final size:22
Alignment explanation
Indices: 1217734--1217793 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
1217724 CGATACCGTA
1217734 AGGGAGTATCGATACCATTG-T
1 AGGGAGTATCGATACCATTGTT
*
1217755 AGGGTAGTATCGATATCA-TGTT
1 AGGG-AGTATCGATACCATTGTT
*
1217777 AAGG-GTATCGATACCAT
1 AGGGAGTATCGATACCAT
1217794 GAAACATCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 11 0.33
21 6 0.18
22 16 0.48
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (22 bp):
AGGGAGTATCGATACCATTGTT
Found at i:1217859 original size:95 final size:95
Alignment explanation
Indices: 1217685--1217860 Score: 223
Period size: 95 Copynumber: 1.8 Consensus size: 95
1217675 CATTGAGGCA
* * *
1217685 GTATCGATACCAAGCAAACATCGAATCTAATTTCGGTATCGATACCGTAAGGGAGTATCGATACC
1 GTATCGATACCAAGCAAACATCGAACCTAATTTCGGTATCAATACCGGAAGGGAGTATCGATACC
* *
1217750 ATTGTAGGGTAGTATCGATATCATGTTAAGG
66 AGTGTA-GGAAGTATCGATATCATGTTAAGG
* **
1217781 GTATCGATACCATG-AAACATCGAACCTAATTTTTGTATCAATACCAGGAAGGG-GTATCGATAC
1 GTATCGATACCAAGCAAACATCGAACCTAATTTCGGTATCAATACC-GGAAGGGAGTATCGATA-
1217844 CCTAGTGTA-GAAGTATC
64 CC-AGTGTAGGAAGTATC
1217861 AGTACTAGGG
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
95 43 0.62
96 21 0.30
97 5 0.07
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.28
Consensus pattern (95 bp):
GTATCGATACCAAGCAAACATCGAACCTAATTTCGGTATCAATACCGGAAGGGAGTATCGATACC
AGTGTAGGAAGTATCGATATCATGTTAAGG
Found at i:1217886 original size:20 final size:20
Alignment explanation
Indices: 1217834--1217886 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
1217824 CCAGGAAGGG
*
1217834 GTATCGATACCCTAGTGTAGAA
1 GTATCGATA--CTAGGGTAGAA
*
1217856 GTATC-AGTACTAGGGTAGTA
1 GTATCGA-TACTAGGGTAGAA
1217876 GTATCGATACT
1 GTATCGATACT
1217887 TTGGAACCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 18 0.67
21 2 0.07
22 7 0.26
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (20 bp):
GTATCGATACTAGGGTAGAA
Found at i:1218378 original size:45 final size:45
Alignment explanation
Indices: 1218297--1218726 Score: 630
Period size: 45 Copynumber: 9.6 Consensus size: 45
1218287 TGAAAATAAT
* * * *
1218297 AATGCATATGGGTGCATTATCATCATG-AAAGGATGCCATAGTTGA
1 AATGCATATGGGTGCATTATCAACA-GAAAAGTATACTATAGTTGA
* * * * *
1218342 AATGTATATAGGTACATTATCAACAGAAAAGTATGCCATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
* * * * *
1218387 AAAGTATATGGGTACATTATCAACAGAAAAATATAATATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
* *
1218432 AATGTATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
1218477 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
*
1218522 AATGCATATGGGTGCATTATCAACATAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
1218567 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
*
1218612 AATGCATATGGGTGCATTATCAACA-TAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
* *
1218656 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAATTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
* *
1218701 AACTGCATATTGGTGCATTATAAACA
1 AA-TGCATATGGGTGCATTATCAACA
1218727 TGAATGGAGG
Statistics
Matches: 358, Mismatches: 24, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
44 44 0.12
45 293 0.82
46 21 0.06
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAGTTGA
Found at i:1219560 original size:22 final size:22
Alignment explanation
Indices: 1219529--1219593 Score: 103
Period size: 22 Copynumber: 2.9 Consensus size: 22
1219519 ATGGATACAC
*
1219529 TGCATGGTGCATCGATGCACTAG
1 TGCA-GGTGCATGGATGCACTAG
1219552 TGCAGGTGCATGGATGCACTAG
1 TGCAGGTGCATGGATGCACTAG
*
1219574 TGCAAGTGCATGGATGCACT
1 TGCAGGTGCATGGATGCACT
1219594 GCAGGGGTGC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 36 0.90
23 4 0.10
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (22 bp):
TGCAGGTGCATGGATGCACTAG
Found at i:1219715 original size:29 final size:29
Alignment explanation
Indices: 1219683--1219745 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
1219673 CAAACCTTTT
1219683 AAAACTTTGAATAAATTCAATT-AAGTCCAA
1 AAAACTTTG--TAAATTCAATTCAAGTCCAA
*
1219713 AAATATTTTGTAAATTCAATTCAAGTCCAA
1 AAA-ACTTTGTAAATTCAATTCAAGTCCAA
1219743 AAA
1 AAA
1219746 CCATTTTGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 11 0.37
30 14 0.47
31 5 0.17
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (29 bp):
AAAACTTTGTAAATTCAATTCAAGTCCAA
Found at i:1219762 original size:34 final size:29
Alignment explanation
Indices: 1219694--1219753 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
1219684 AAACTTTGAA
*
1219694 TAAATTCAATTAAGTCCAAAAATATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
1219723 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1219754 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:1221067 original size:19 final size:20
Alignment explanation
Indices: 1221024--1221071 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1221014 TCTAAATCCT
*
1221024 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1221044 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1221063 TTTTCAAAA
1 TTTTCAAAA
1221072 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1222373 original size:20 final size:21
Alignment explanation
Indices: 1222344--1222417 Score: 89
Period size: 20 Copynumber: 3.6 Consensus size: 21
1222334 GCAGCCTTCG
*
1222344 TGCATGGATGCACA-ACAGGA
1 TGCATCGATGCACAGACAGGA
* * **
1222364 TGCATCGATGCATAGCCTTGA
1 TGCATCGATGCACAGACAGGA
1222385 TGCATCGATGCACAGA-AGGA
1 TGCATCGATGCACAGACAGGA
1222405 TGCATCGATGCAC
1 TGCATCGATGCAC
1222418 TAATTGCATT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 27 0.61
21 17 0.39
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (21 bp):
TGCATCGATGCACAGACAGGA
Found at i:1222381 original size:41 final size:41
Alignment explanation
Indices: 1222336--1222416 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
1222326 TAGCCGTTGC
*
1222336 AGCCTTCG-TGCATGGATGCACA-ACAGGATGCATCGATGCAT
1 AGCCTT-GATGCATCGATGCACAGA-AGGATGCATCGATGCAT
1222377 AGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGCA
1 AGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGCA
1222417 CTAATTGCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
40 1 0.03
41 35 0.95
42 1 0.03
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.21
Consensus pattern (41 bp):
AGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGCAT
Done.