Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, 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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 7 of 109
Found at i:1048265 original size:25 final size:25
Alignment explanation
Indices: 1048231--1048288 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 25
1048221 TAATATTTTA
1048231 TAAATATAATATTAAATTAAAAT-TAT
1 TAAAT-TAATATTAAA-TAAAATCTAT
* *
1048257 TAAATTAATTTTAGATAAAATCTAT
1 TAAATTAATATTAAATAAAATCTAT
1048282 TACAATT
1 TA-AATT
1048289 TATGAAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 6 0.21
25 13 0.46
26 9 0.32
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (25 bp):
TAAATTAATATTAAATAAAATCTAT
Found at i:1051122 original size:24 final size:24
Alignment explanation
Indices: 1051076--1051122 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1051066 AACATTGGTG
* *
1051076 TATAAATTTTATATATTATTAATA
1 TATAAATTTTATATACTAATAATA
1051100 TATAAATTTTATATACTAATAAT
1 TATAAATTTTATATACTAATAAT
1051123 TAATTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TATAAATTTTATATACTAATAATA
Found at i:1059726 original size:2 final size:2
Alignment explanation
Indices: 1059719--1059748 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1059709 TTCTAAATCT
1059719 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
1059749 AGTGACTACT
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):
TA
Found at i:1062721 original size:29 final size:29
Alignment explanation
Indices: 1062687--1062746 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
1062677 TAGGACATTG
1062687 TTTTTATGTGCATACATTCATAATAAACA
1 TTTTTATGTGCATACATTCATAATAAACA
1062716 TTTTTATGTGCATACATTCATAATAAACA
1 TTTTTATGTGCATACATTCATAATAAACA
1062745 TT
1 TT
1062747 CATACACACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (29 bp):
TTTTTATGTGCATACATTCATAATAAACA
Found at i:1065971 original size:305 final size:304
Alignment explanation
Indices: 1065402--1065996 Score: 834
Period size: 305 Copynumber: 2.0 Consensus size: 304
1065392 TATCTGAGGG
* *** * *
1065402 TTAAGTATACATAAAATATTCTTAGTTAATTATATAATTTGCAAAAGATATTCTACCTGATTCCA
1 TTAAGTATACATAAAATATTCTTAGTTAATTATACAATTAAAAAAAGATATTCCACCTAATTCCA
*
1065467 ACAGTTTGCATTGTCACATATCTCATTAGGAATACAAAATTAGACAAGCATCTCTACTTTAACCA
66 ACAGTTTGCATTGTCACATATCTCATTAGGAATACAAAATTAGACAAGCATCTATACTTTAACCA
* * *
1065532 GTGCATTATTATTGATCCTGGTTGCATAATTTTATTGACAAAACATCATGCATTAGAGGCTTCTA
131 GTGCATTAATAATGATCCTGGTTGCATAATTTCATTGACAAAACATCATGCATTAGAGGCTTCTA
* * * *
1065597 TATATAATTTTCTTGCATTACTGGCTACAATGACATCATATGAAACATTGCACAGGGTGGAACAT
196 CATATAATTTTCTTCCATTACTGGCTACAATAACAACATATGAAACATTGCACAGGGTGGAACAT
1065662 GAAAGTTTGCAAAGTCATGGGGGTTGCTCATGAAGGTTAAGACA
261 GAAAGTTTGCAAAGTCATGGGGGTTGCTCATGAAGGTTAAGACA
* * * *
1065706 TTAAGTATGCATAAAAATGTTCTTAGTTAATTATACAACTTAAAAAAAGATATTCCACTTAATTT
1 TTAAGTATACAT-AAAATATTCTTAGTTAATTATACAA-TTAAAAAAAGATATTCCACCTAATTC
* * * * **
1065771 CAACAGTTTGCGTTGTCATATA-CTCATTAGGAATACAAAATTGGACGAGCATCTATTGTTTAAC
64 CAACAGTTTGCATTGTCACATATCTCATTAGGAATACAAAATTAGACAAGCATCTATACTTTAAC
* * * *
1065835 CAGTGCTTTAATAATGATCCTGGTTGCATAATTTCATTGA-AAGAACATCATGCCTTGGAGGTTT
129 CAGTGCATTAATAATGATCCTGGTTGCATAATTTCATTGACAA-AACATCATGCATTAGAGGCTT
* * * *
1065899 CTACATGTAATTTTCTTCCATTATTGGCTACAATAACAAGATATGAAACATTGTACAGGGTGGAA
193 CTACATATAATTTTCTTCCATTACTGGCTACAATAACAACATATGAAACATTGCACAGGGTGGAA
***
1065964 CATGAAAGTTTGTGTAGTCATGGGGGTTGCTCA
258 CATGAAAGTTTGCAAAGTCATGGGGGTTGCTCA
1065997 ACTTCTCATT
Statistics
Matches: 253, Mismatches: 35, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
304 13 0.05
305 201 0.79
306 39 0.15
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (304 bp):
TTAAGTATACATAAAATATTCTTAGTTAATTATACAATTAAAAAAAGATATTCCACCTAATTCCA
ACAGTTTGCATTGTCACATATCTCATTAGGAATACAAAATTAGACAAGCATCTATACTTTAACCA
GTGCATTAATAATGATCCTGGTTGCATAATTTCATTGACAAAACATCATGCATTAGAGGCTTCTA
CATATAATTTTCTTCCATTACTGGCTACAATAACAACATATGAAACATTGCACAGGGTGGAACAT
GAAAGTTTGCAAAGTCATGGGGGTTGCTCATGAAGGTTAAGACA
Found at i:1070837 original size:18 final size:19
Alignment explanation
Indices: 1070811--1070846 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1070801 TTTTTATTGT
*
1070811 TATTTCCTAACTA-TTAAA
1 TATTACCTAACTACTTAAA
1070829 TATTACCTAACTACTTAA
1 TATTACCTAACTACTTAA
1070847 GCAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.42
Consensus pattern (19 bp):
TATTACCTAACTACTTAAA
Found at i:1075477 original size:15 final size:15
Alignment explanation
Indices: 1075457--1075487 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1075447 TCATGATTTA
1075457 TTGGGTTTATTGATT
1 TTGGGTTTATTGATT
*
1075472 TTGGGTTTCTTGATT
1 TTGGGTTTATTGATT
1075487 T
1 T
1075488 GGCTTATGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.03, G:0.26, T:0.61
Consensus pattern (15 bp):
TTGGGTTTATTGATT
Found at i:1075519 original size:17 final size:16
Alignment explanation
Indices: 1075497--1075545 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
1075487 TGGCTTATGC
1075497 ATTTTTGTCTTTTTTTA
1 ATTTTTGT-TTTTTTTA
*
1075514 ATTTTTTTTGTTTTTTA
1 ATTTTTGTT-TTTTTTA
*
1075531 TTTTGTTGTTTTTTT
1 ATTT-TTGTTTTTTT
1075546 ATCCTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 1 0.04
17 22 0.81
18 4 0.15
ACGTcount: A:0.08, C:0.02, G:0.08, T:0.82
Consensus pattern (16 bp):
ATTTTTGTTTTTTTTA
Found at i:1076393 original size:18 final size:18
Alignment explanation
Indices: 1076372--1076407 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1076362 TTTTAAAATT
1076372 TTAAAAT-ATTATAATTAA
1 TTAAAATAATTA-AATTAA
1076390 TTAAAATAATTAAATTAA
1 TTAAAATAATTAAATTAA
1076408 ATCTAACTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAAAATAATTAAATTAA
Found at i:1090805 original size:2 final size:2
Alignment explanation
Indices: 1090795--1090825 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1090785 TATGTGTGTG
*
1090795 TA TA AA 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 T
1090826 CCCTTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1092722 original size:15 final size:15
Alignment explanation
Indices: 1092697--1092732 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
1092687 GATCTAATCC
1092697 AAAATTTAA-TTTAA
1 AAAATTTAATTTTAA
1092711 AAAATATTAATTTTAA
1 AAAAT-TTAATTTTAA
1092727 AAAATT
1 AAAATT
1092733 CAGTCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 5 0.25
16 10 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAAATTTAATTTTAA
Found at i:1093253 original size:28 final size:29
Alignment explanation
Indices: 1093204--1093260 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
1093194 ATTAAATATT
*
1093204 AATTTTTTATGATTTTATA-TTTAAGTTA
1 AATTTTTTATGATTATATATTTTAAGTTA
*
1093232 AATTTTTTATTATTA-ATAATTTTAAGTTA
1 AATTTTTTATGATTATAT-ATTTTAAGTTA
1093261 GATAAGATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.08
28 14 0.56
29 9 0.36
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (29 bp):
AATTTTTTATGATTATATATTTTAAGTTA
Found at i:1093557 original size:24 final size:23
Alignment explanation
Indices: 1093517--1093562 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
1093507 TTATAAATAA
1093517 ATAAATAATTTTTATTTTTAAAC
1 ATAAATAATTTTTATTTTTAAAC
*
1093540 ATAAATATTTGTTTATTTTTAAA
1 ATAAATAATT-TTTATTTTTAAA
1093563 AAGATAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
ATAAATAATTTTTATTTTTAAAC
Found at i:1093923 original size:3 final size:3
Alignment explanation
Indices: 1093917--1093949 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1093907 CTCGTCGTCG
1093917 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1093950 ATCTTTGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1094006 original size:29 final size:28
Alignment explanation
Indices: 1093966--1094034 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
1093956 GAATTCCAAT
*
1093966 AAAATATTTAAAAT-TACTTATGAACTTTAA
1 AAAAT-TTTAAAATATA-TT-TAAACTTTAA
*
1093996 AAAATTTTAAAATAATATTTAAATTTTAA
1 AAAATTTTAAAAT-ATATTTAAACTTTAA
1094025 AAAATTTTAA
1 AAAATTTTAA
1094035 TATGTCATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 26 0.74
30 7 0.20
31 2 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (28 bp):
AAAATTTTAAAATATATTTAAACTTTAA
Found at i:1094021 original size:19 final size:17
Alignment explanation
Indices: 1093997--1094034 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
1093987 GAACTTTAAA
1093997 AAATTTTAAAATAATATTT
1 AAATTTTAAAA-AAT-TTT
1094016 AAATTTTAAAAAATTTT
1 AAATTTTAAAAAATTTT
1094033 AA
1 AA
1094035 TATGTCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 3 0.16
19 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATTTTAAAAAATTTT
Found at i:1094180 original size:14 final size:14
Alignment explanation
Indices: 1094156--1094206 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1094146 CATTAATTAA
1094156 TAAAT-TTATATTT
1 TAAATATTATATTT
1094169 TAAATATTATATTAT
1 TAAATATTATATT-T
* * * *
1094184 AAAATTTTAAAATT
1 TAAATATTATATTT
1094198 TAAATATTA
1 TAAATATTA
1094207 CATTAAGTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 5 0.17
14 15 0.50
15 10 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TAAATATTATATTT
Found at i:1096092 original size:28 final size:28
Alignment explanation
Indices: 1096057--1096110 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
1096047 AAAGTAAGGT
* *
1096057 ATATAAAAGCAGATTTTTTTTTTGGTAA
1 ATATAAAAGCAGATTTGTTTGTTGGTAA
1096085 ATATAAAAGCAGATTTGTTTGTTGGT
1 ATATAAAAGCAGATTTGTTTGTTGGT
1096111 TTGGGTGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.19, T:0.44
Consensus pattern (28 bp):
ATATAAAAGCAGATTTGTTTGTTGGTAA
Found at i:1097649 original size:30 final size:30
Alignment explanation
Indices: 1097604--1097680 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
1097594 TTAATCAAAT
* *
1097604 TTTAAATTTTTTATTTTAAATCAATTGAATC
1 TTTAAA-TATTTATTTTAAATCAATTGAACC
* *
1097635 TTTAAATATTTATTTTTATTCAATTGAACC
1 TTTAAATATTTATTTTAAATCAATTGAACC
*
1097665 CTTATAA-ATTTATTTT
1 TTTA-AATATTTATTTT
1097681 TACTTAATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
30 32 0.80
31 8 0.20
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.56
Consensus pattern (30 bp):
TTTAAATATTTATTTTAAATCAATTGAACC
Found at i:1097681 original size:30 final size:30
Alignment explanation
Indices: 1097613--1097682 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
1097603 TTTTAAATTT
* * *
1097613 TTTATTTTAAATCAATTGAATCTTTAAATA
1 TTTATTTTTAATCAATTGAACCCTTAAATA
*
1097643 TTTATTTTTATTCAATTGAACCCTTATAA-A
1 TTTATTTTTAATCAATTGAACCCTTA-AATA
1097673 TTTATTTTTA
1 TTTATTTTTA
1097683 CTTAATTAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 33 0.94
31 2 0.06
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.54
Consensus pattern (30 bp):
TTTATTTTTAATCAATTGAACCCTTAAATA
Found at i:1098809 original size:2 final size:2
Alignment explanation
Indices: 1098802--1098828 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1098792 ATGAAGATTG
1098802 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 A
1098829 AAGAAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1099029 original size:24 final size:24
Alignment explanation
Indices: 1098980--1099030 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1098970 ACATATTTCT
* *
1098980 TGTGTGTATATATATATGTGTATG
1 TGTGTGTATATATATATATATATG
*
1099004 TGTGTGTATATATATATATATTTG
1 TGTGTGTATATATATATATATATG
1099028 TGT
1 TGT
1099031 TTGTGAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.53
Consensus pattern (24 bp):
TGTGTGTATATATATATATATATG
Found at i:1111944 original size:92 final size:92
Alignment explanation
Indices: 1111787--1111961 Score: 262
Period size: 92 Copynumber: 1.9 Consensus size: 92
1111777 TTGTTTCCTA
* * *
1111787 AGAAACTAACTAAAATTTACATAACAGTTATCCTGTAAGAATAGCTAAAATTAAAAATTCTTCCT
1 AGAAACTAACTAAAATTTAAATAACAGTTATCCTATAAGAATAACTAAAATTAAAAATTCTTCCT
* *
1111852 AATAGAATTGTTGATTCTTTCTACCCC
66 AAAAGAATTATTGATTCTTTCTACCCC
* * *
1111879 AGAAACTAACTACAATTTAAATAACAGTTATCCTATATGAATAACTATAA-TAAAAACTTCTTCC
1 AGAAACTAACTAAAATTTAAATAACAGTTATCCTATAAGAATAACTAAAATTAAAAA-TTCTTCC
1111943 TAAAAGAATTATTGATTCT
65 TAAAAGAATTATTGATTCT
1111962 CTATTCCACT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
91 6 0.08
92 68 0.92
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (92 bp):
AGAAACTAACTAAAATTTAAATAACAGTTATCCTATAAGAATAACTAAAATTAAAAATTCTTCCT
AAAAGAATTATTGATTCTTTCTACCCC
Found at i:1113916 original size:16 final size:17
Alignment explanation
Indices: 1113895--1113929 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1113885 GTTATTTCGA
*
1113895 TTCGGTT-TAATCGGTT
1 TTCGGTTGTAATCGATT
1113911 TTCGGTTGTAATCGATT
1 TTCGGTTGTAATCGATT
1113928 TT
1 TT
1113930 AAGATTGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.14, C:0.11, G:0.23, T:0.51
Consensus pattern (17 bp):
TTCGGTTGTAATCGATT
Found at i:1115046 original size:21 final size:21
Alignment explanation
Indices: 1115020--1115178 Score: 155
Period size: 21 Copynumber: 7.8 Consensus size: 21
1115010 AGCAAAGACA
* *
1115020 GCAGCAGACTACTGGTTTCTT
1 GCAGCAGACTGCTGGTTTCCT
*
1115041 GCAGCAGACTGTTGGTTTCCT
1 GCAGCAGACTGCTGGTTTCCT
* * * * **
1115062 ACAACAAACTACTGGTTTTTT
1 GCAGCAGACTGCTGGTTTCCT
** * *
1115083 ATAACAGACTACTGGTTTCCT
1 GCAGCAGACTGCTGGTTTCCT
*
1115104 ---GC-GTCTGCTGGTTTCCT
1 GCAGCAGACTGCTGGTTTCCT
1115121 GCAGCAGACTGCTGGTTTCCT
1 GCAGCAGACTGCTGGTTTCCT
*
1115142 GCAGCAGTCTGCTGGTTTCCT
1 GCAGCAGACTGCTGGTTTCCT
1115163 GCAGCAGACTGCTGGT
1 GCAGCAGACTGCTGGT
1115179 NNNNNNNNNN
Statistics
Matches: 114, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
17 13 0.11
18 1 0.01
20 2 0.02
21 98 0.86
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.33
Consensus pattern (21 bp):
GCAGCAGACTGCTGGTTTCCT
Found at i:1115171 original size:80 final size:80
Alignment explanation
Indices: 1115031--1115178 Score: 179
Period size: 80 Copynumber: 1.9 Consensus size: 80
1115021 CAGCAGACTA
* * ** *
1115031 CTGGTTTCTTGCAGCAGACTGTTGGTTTCCTACAACAAACTACTGGTTTTTTATAACAGACTACT
1 CTGGTTTCCTGCAGCAGACTGCTGGTTTCCTACAACAAACTACTGGTTTCCTACAACAGACTACT
1115096 GGTTTCCTGCGTCTG
66 GGTTTCCTGCGTCTG
* * ** * * * *
1115111 CTGGTTTCCTGCAGCAGACTGCTGGTTTCCTGCAGCAGTCTGCTGGTTTCCTGCAGCAGACTGCT
1 CTGGTTTCCTGCAGCAGACTGCTGGTTTCCTACAACAAACTACTGGTTTCCTACAACAGACTACT
1115176 GGT
66 GGT
1115179 NNNNNNNNNN
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
80 55 1.00
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.34
Consensus pattern (80 bp):
CTGGTTTCCTGCAGCAGACTGCTGGTTTCCTACAACAAACTACTGGTTTCCTACAACAGACTACT
GGTTTCCTGCGTCTG
Found at i:1116871 original size:92 final size:92
Alignment explanation
Indices: 1116775--1116949 Score: 253
Period size: 92 Copynumber: 1.9 Consensus size: 92
1116765 TTGTTCCCTA
* * *
1116775 AGAAACTAACTAAAATTTAAATAACAGTTATCCTGTAAGAATAGCTAAAATTAAAAA-TTCTTCC
1 AGAAACTAACTAAAATTTAAATAACAGTTATCCTATAAGAATAACCAAAA-TAAAAACTTCTTCC
* *
1116839 TAATAGAATTGCTGATTCTTTCTACCCC
65 TAAAAGAATTACTGATTCTTTCTACCCC
* * *
1116867 AGAAACTAACTACAATTTAAATAACAGTTATCCTATATGAATAACCATAATAAAAACTTCTTCCT
1 AGAAACTAACTAAAATTTAAATAACAGTTATCCTATAAGAATAACCAAAATAAAAACTTCTTCCT
*
1116932 AAAAGAATTATTGATTCT
66 AAAAGAATTACTGATTCT
1116950 CTATTCCACT
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
91 6 0.08
92 67 0.92
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (92 bp):
AGAAACTAACTAAAATTTAAATAACAGTTATCCTATAAGAATAACCAAAATAAAAACTTCTTCCT
AAAAGAATTACTGATTCTTTCTACCCC
Found at i:1118701 original size:20 final size:18
Alignment explanation
Indices: 1118660--1118702 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 18
1118650 TAAAATTTTG
*
1118660 ATAAAAAAAATAAAAATT
1 ATAATAAAAATAAAAATT
1118678 -TAATAAAAATAAAAAATAT
1 ATAATAAAAAT-AAAAAT-T
1118697 ATAATA
1 ATAATA
1118703 TTTGAAGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 9 0.43
18 6 0.29
19 1 0.05
20 5 0.24
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
ATAATAAAAATAAAAATT
Found at i:1119137 original size:28 final size:29
Alignment explanation
Indices: 1119088--1119155 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 29
1119078 TATGATTCAA
*
1119088 TATTGAAATTTTTAATTTTATTTCT-A-TT
1 TATTG-AATTTTTAATTATATTTCTAATTT
* *
1119116 TATTGAATTTTATTATTATATTTTTAATTT
1 TATTGAATTTT-TAATTATATTTCTAATTT
1119146 TATTG-ATTTT
1 TATTGAATTTT
1119156 GAATAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 6 0.18
28 15 0.44
29 6 0.18
30 7 0.21
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.66
Consensus pattern (29 bp):
TATTGAATTTTTAATTATATTTCTAATTT
Found at i:1119144 original size:20 final size:20
Alignment explanation
Indices: 1119095--1119149 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
1119085 CAATATTGAA
1119095 ATTTTTAATTTTATTTCTAT
1 ATTTTTAATTTTATTTCTAT
*
1119115 -TTATTGAATTTTATTAT-TAT
1 ATT-TTTAATTTTATT-TCTAT
1119135 ATTTTTAATTTTATT
1 ATTTTTAATTTTATT
1119150 GATTTTGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 2 0.07
20 25 0.83
21 3 0.10
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (20 bp):
ATTTTTAATTTTATTTCTAT
Found at i:1121170 original size:23 final size:23
Alignment explanation
Indices: 1121133--1121209 Score: 82
Period size: 23 Copynumber: 3.2 Consensus size: 23
1121123 TTCAATTAAG
* * *
1121133 TTAAATAAATTTATTTATGAATA
1 TTAAATGAATATATTCATGAATA
1121156 TTAAATGAATATATTCATGAATATA
1 TTAAATGAATATATTCATG-A-ATA
*
1121181 TATAAATGAACATATTCATGAATA
1 T-TAAATGAATATATTCATGAATA
*
1121205 ATAAA
1 TTAAA
1121210 CAAATCATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
23 20 0.43
24 4 0.09
25 5 0.11
26 17 0.37
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (23 bp):
TTAAATGAATATATTCATGAATA
Found at i:1121177 original size:12 final size:12
Alignment explanation
Indices: 1121160--1121204 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
1121150 TGAATATTAA
1121160 ATGAATATATTC
1 ATGAATATATTC
*
1121172 ATGAATATATATAA
1 ATGAATATAT-T-C
*
1121186 ATGAACATATTC
1 ATGAATATATTC
1121198 ATGAATA
1 ATGAATA
1121205 ATAAACAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 16 0.59
13 2 0.07
14 9 0.33
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.36
Consensus pattern (12 bp):
ATGAATATATTC
Found at i:1121195 original size:26 final size:25
Alignment explanation
Indices: 1121153--1121204 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
1121143 TTATTTATGA
*
1121153 ATATTAAATGAATATATTCATGAAT
1 ATATTAAATGAACATATTCATGAAT
1121178 ATATATAAATGAACATATTCATGAAT
1 ATAT-TAAATGAACATATTCATGAAT
1121204 A
1 A
1121205 ATAAACAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.37
Consensus pattern (25 bp):
ATATTAAATGAACATATTCATGAAT
Found at i:1121234 original size:25 final size:25
Alignment explanation
Indices: 1121206--1121253 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1121196 TCATGAATAA
1121206 TAAACAAATCATAAC-TAAACAAATT
1 TAAACAAAT-ATAACTTAAACAAATT
*
1121231 TAAACAAATATATCTTAAACAAA
1 TAAACAAATATAACTTAAACAAA
1121254 CCCAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (25 bp):
TAAACAAATATAACTTAAACAAATT
Found at i:1128013 original size:10 final size:10
Alignment explanation
Indices: 1127998--1128024 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1127988 CCTCAGTGTG
1127998 AGAGAGAGAA
1 AGAGAGAGAA
1128008 AGAGAGAGAA
1 AGAGAGAGAA
1128018 AGAGAGA
1 AGAGAGA
1128025 ATTTGTTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (10 bp):
AGAGAGAGAA
Found at i:1130058 original size:33 final size:33
Alignment explanation
Indices: 1130011--1130083 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
1130001 ATAATCAAAC
*
1130011 AAAGCTATGGATCAGAATTCTCGAGTATCCATA
1 AAAGATATGGATCAGAATTCTCGAGTATCCATA
1130044 AAAGATATGGATCAGAATTCTCGAGTATCCATA
1 AAAGATATGGATCAGAATTCTCGAGTATCCATA
1130077 AAAGATA
1 AAAGATA
1130084 ATCAAACAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (33 bp):
AAAGATATGGATCAGAATTCTCGAGTATCCATA
Found at i:1137408 original size:34 final size:34
Alignment explanation
Indices: 1137302--1137408 Score: 119
Period size: 34 Copynumber: 3.1 Consensus size: 34
1137292 AAGTTACTGG
* * *
1137302 AAATGGATTTCCGGAAAGTCATAAACCTGTCTGA
1 AAATGGATTTCCGGAAAGTCATAAACTTTTCCGA
** *
1137336 AAATGGATTTCCAAAAAGTCATATAACTTTT-CGG
1 AAATGGATTTCCGGAAAGTCATA-AACTTTTCCGA
*
1137370 AAATGGATTTCCGG-AAGATTATAAACTTTTCCGA
1 AAATGGATTTCCGGAAAG-TCATAAACTTTTCCGA
1137404 AAATG
1 AAATG
1137409 AATGTAAATT
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
33 10 0.17
34 45 0.75
35 5 0.08
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (34 bp):
AAATGGATTTCCGGAAAGTCATAAACTTTTCCGA
Found at i:1137646 original size:34 final size:33
Alignment explanation
Indices: 1137603--1137725 Score: 131
Period size: 34 Copynumber: 3.6 Consensus size: 33
1137593 AAGTTACTGG
* *
1137603 AAATGGATTTCCGGAAAGTCATAAACCTGTCTGA
1 AAATGGATTTCCGGAAAGTCATAAACTTTTC-GA
** *
1137637 AAATGGATTTCCAAAAAGTCATATAACTTTTCGG
1 AAATGGATTTCCGGAAAGTCATA-AACTTTTCGA
*
1137671 AAATGGATTTCCGG-AAGATTATAAACTTTTCCGA
1 AAATGGATTTCCGGAAAG-TCATAAACTTTT-CGA
* *
1137705 AAATGAATTTTCGGAAAGTCA
1 AAATGGATTTCCGGAAAGTCA
1137726 AATTTTCGTA
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
33 10 0.14
34 54 0.74
35 9 0.12
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (33 bp):
AAATGGATTTCCGGAAAGTCATAAACTTTTCGA
Found at i:1137650 original size:301 final size:301
Alignment explanation
Indices: 1137108--1137712 Score: 1210
Period size: 301 Copynumber: 2.0 Consensus size: 301
1137098 TTTTTCTTAA
1137108 AATGTAAATTAGGCACCACACAAGCAACATGAAAAGAATTAACATTGTAAAAGATGTTTTAGATG
1 AATGTAAATTAGGCACCACACAAGCAACATGAAAAGAATTAACATTGTAAAAGATGTTTTAGATG
1137173 CACTCATATGATAATAGAGTGCTGTTAAATGCACCCCAGCCTTTTCTCTTCACAACCAGCTTTTT
66 CACTCATATGATAATAGAGTGCTGTTAAATGCACCCCAGCCTTTTCTCTTCACAACCAGCTTTTT
1137238 TTTTCCAAAATTTTTTGCAAATGAAATTATTTAATTATTTTTTCTTTTTCACACAAGTTACTGGA
131 TTTTCCAAAATTTTTTGCAAATGAAATTATTTAATTATTTTTTCTTTTTCACACAAGTTACTGGA
1137303 AATGGATTTCCGGAAAGTCATAAACCTGTCTGAAAATGGATTTCCAAAAAGTCATATAACTTTTC
196 AATGGATTTCCGGAAAGTCATAAACCTGTCTGAAAATGGATTTCCAAAAAGTCATATAACTTTTC
1137368 GGAAATGGATTTCCGGAAGATTATAAACTTTTCCGAAAATG
261 GGAAATGGATTTCCGGAAGATTATAAACTTTTCCGAAAATG
1137409 AATGTAAATTAGGCACCACACAAGCAACATGAAAAGAATTAACATTGTAAAAGATGTTTTAGATG
1 AATGTAAATTAGGCACCACACAAGCAACATGAAAAGAATTAACATTGTAAAAGATGTTTTAGATG
1137474 CACTCATATGATAATAGAGTGCTGTTAAATGCACCCCAGCCTTTTCTCTTCACAACCAGCTTTTT
66 CACTCATATGATAATAGAGTGCTGTTAAATGCACCCCAGCCTTTTCTCTTCACAACCAGCTTTTT
1137539 TTTTCCAAAATTTTTTGCAAATGAAATTATTTAATTATTTTTTCTTTTTCACACAAGTTACTGGA
131 TTTTCCAAAATTTTTTGCAAATGAAATTATTTAATTATTTTTTCTTTTTCACACAAGTTACTGGA
1137604 AATGGATTTCCGGAAAGTCATAAACCTGTCTGAAAATGGATTTCCAAAAAGTCATATAACTTTTC
196 AATGGATTTCCGGAAAGTCATAAACCTGTCTGAAAATGGATTTCCAAAAAGTCATATAACTTTTC
1137669 GGAAATGGATTTCCGGAAGATTATAAACTTTTCCGAAAATG
261 GGAAATGGATTTCCGGAAGATTATAAACTTTTCCGAAAATG
1137710 AAT
1 AAT
1137713 TTTCGGAAAG
Statistics
Matches: 304, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
301 304 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (301 bp):
AATGTAAATTAGGCACCACACAAGCAACATGAAAAGAATTAACATTGTAAAAGATGTTTTAGATG
CACTCATATGATAATAGAGTGCTGTTAAATGCACCCCAGCCTTTTCTCTTCACAACCAGCTTTTT
TTTTCCAAAATTTTTTGCAAATGAAATTATTTAATTATTTTTTCTTTTTCACACAAGTTACTGGA
AATGGATTTCCGGAAAGTCATAAACCTGTCTGAAAATGGATTTCCAAAAAGTCATATAACTTTTC
GGAAATGGATTTCCGGAAGATTATAAACTTTTCCGAAAATG
Found at i:1139489 original size:23 final size:23
Alignment explanation
Indices: 1139459--1139504 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1139449 ATACACGAAT
*
1139459 TGCCAGGTTTACCTAATGCTTTC
1 TGCCAGGTTTAACTAATGCTTTC
*
1139482 TGCCAGGTTTAACTTATGCTTTC
1 TGCCAGGTTTAACTAATGCTTTC
1139505 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.41
Consensus pattern (23 bp):
TGCCAGGTTTAACTAATGCTTTC
Found at i:1141453 original size:6 final size:6
Alignment explanation
Indices: 1141434--1141471 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
1141424 TTTTTTTTTT
* *
1141434 TGGAGG GGGGGG TGGAGG TGGAGG TGGAGG TGGAGG TG
1 TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG TG
1141472 TTTGCTGTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.13, C:0.00, G:0.71, T:0.16
Consensus pattern (6 bp):
TGGAGG
Found at i:1149507 original size:61 final size:60
Alignment explanation
Indices: 1149433--1149549 Score: 180
Period size: 61 Copynumber: 1.9 Consensus size: 60
1149423 TTAGTGTATG
*
1149433 ACAAATAGAAAATCTCCATTGTTTAAAGTTGAGCCTGCAAAAAGAACAGGTTCATGATAAA
1 ACAAATAGAAAATCTCCATTGTTTAAAGTTGAGCCTACAAAAAGAACAGGTT-ATGATAAA
* * * *
1149494 ACAAATAGAAAATCTTCATTGTTTAAAGTTGAGCTTACAAAAGGAACATGTTATGA
1 ACAAATAGAAAATCTCCATTGTTTAAAGTTGAGCCTACAAAAAGAACAGGTTATGA
1149550 AACATATGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 4 0.08
61 47 0.92
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (60 bp):
ACAAATAGAAAATCTCCATTGTTTAAAGTTGAGCCTACAAAAAGAACAGGTTATGATAAA
Found at i:1152239 original size:16 final size:16
Alignment explanation
Indices: 1152201--1152245 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1152191 TTATGTAAAA
*
1152201 ATAAATTAATAAATGT
1 ATAAATTAATAAAAGT
1152217 AGT-AATTAATAAAAGT
1 A-TAAATTAATAAAAGT
1152233 ATAAATTTAATAA
1 ATAAA-TTAATAA
1152246 CTCAAACCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 1 0.04
16 16 0.64
17 8 0.32
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (16 bp):
ATAAATTAATAAAAGT
Found at i:1155776 original size:21 final size:21
Alignment explanation
Indices: 1155727--1155777 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1155717 AAGTGAACAT
1155727 AATAATAAGAATAAAAAATAA
1 AATAATAAGAATAAAAAATAA
* * **
1155748 AATTATAAGTATAAAATCTAA
1 AATAATAAGAATAAAAAATAA
*
1155769 CATAATAAG
1 AATAATAAG
1155778 GATATCATAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.25
Consensus pattern (21 bp):
AATAATAAGAATAAAAAATAA
Found at i:1160694 original size:45 final size:45
Alignment explanation
Indices: 1160630--1160722 Score: 168
Period size: 45 Copynumber: 2.1 Consensus size: 45
1160620 ATAGTTATAC
*
1160630 TAAAAATCTAGGATGGAATTCCCTTTTCAATTGGGAATTGGTGGT
1 TAAAAATCTAGGATGGAATTCCCTTTTCAATTGCGAATTGGTGGT
*
1160675 TAAAAATCTGGGATGGAATTCCCTTTTCAATTGCGAATTGGTGGT
1 TAAAAATCTAGGATGGAATTCCCTTTTCAATTGCGAATTGGTGGT
1160720 TAA
1 TAA
1160723 GGGTTTGCTT
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:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (45 bp):
TAAAAATCTAGGATGGAATTCCCTTTTCAATTGCGAATTGGTGGT
Found at i:1165843 original size:19 final size:19
Alignment explanation
Indices: 1165786--1165832 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
1165776 TCGGTGAAAA
1165786 TATTTTATTATAAAATAAT
1 TATTTTATTATAAAATAAT
1165805 TATTTTATTATAAAATAAT
1 TATTTTATTATAAAATAAT
1165824 TATTTTATT
1 TATTTTATT
1165833 CAAATTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTTATTATAAAATAAT
Found at i:1171324 original size:10 final size:10
Alignment explanation
Indices: 1171309--1171339 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1171299 TAAATATAAA
1171309 ATTTTAATAT
1 ATTTTAATAT
1171319 ATTTTAATAT
1 ATTTTAATAT
*
1171329 ATTTTGATAT
1 ATTTTAATAT
1171339 A
1 A
1171340 AAATTACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (10 bp):
ATTTTAATAT
Found at i:1171674 original size:16 final size:18
Alignment explanation
Indices: 1171653--1171685 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1171643 ATAATGAATG
1171653 AAATAAT-TTTT-TTATA
1 AAATAATATTTTATTATA
1171669 AAATAATATTTTATTAT
1 AAATAATATTTTATTAT
1171686 TTTAATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AAATAATATTTTATTATA
Found at i:1174827 original size:12 final size:13
Alignment explanation
Indices: 1174789--1174818 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1174779 AATATCAAAC
*
1174789 AATAATCATACAA
1 AATAATTATACAA
1174802 AATAATTATACAA
1 AATAATTATACAA
1174815 AATA
1 AATA
1174819 TGTTACAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (13 bp):
AATAATTATACAA
Found at i:1174950 original size:16 final size:16
Alignment explanation
Indices: 1174912--1174970 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 16
1174902 TCAAAATCAA
1174912 AATTAAGAAGAAAATAG
1 AATTAA-AAGAAAATAG
*
1174929 ATTTAAAAGAGAAA-AG
1 AATTAAAAGA-AAATAG
*
1174945 AATTAAAAATAAAAATAG
1 AATT-AAAA-GAAAATAG
1174963 AATTAAAA
1 AATTAAAA
1174971 ATAAAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
16 9 0.26
17 19 0.54
18 7 0.20
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (16 bp):
AATTAAAAGAAAATAG
Found at i:1174960 original size:34 final size:33
Alignment explanation
Indices: 1174922--1174991 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
1174912 AATTAAGAAG
* * *
1174922 AAAATAGATTTAAAAGAGAAAAGAATTAAAAATA
1 AAAATAGAATTAAAA-AGAAAAAAATAAAAAATA
*
1174956 AAAATAGAATTAAAAATAAAAAAATAAAAAATA
1 AAAATAGAATTAAAAAGAAAAAAATAAAAAATA
1174989 AAA
1 AAA
1174992 TAAAAACATA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 18 0.56
34 14 0.44
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (33 bp):
AAAATAGAATTAAAAAGAAAAAAATAAAAAATA
Found at i:1174971 original size:18 final size:18
Alignment explanation
Indices: 1174922--1174977 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
1174912 AATTAAGAAG
* *
1174922 AAAATAG-ATTTAAAAGA
1 AAAATAGAATTAAAAATA
*
1174939 GAAA-AGAATTAAAAATA
1 AAAATAGAATTAAAAATA
1174956 AAAATAGAATTAAAAATA
1 AAAATAGAATTAAAAATA
1174974 AAAA
1 AAAA
1174978 AATAAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
16 2 0.06
17 14 0.42
18 17 0.52
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (18 bp):
AAAATAGAATTAAAAATA
Found at i:1175149 original size:12 final size:11
Alignment explanation
Indices: 1175132--1175174 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
1175122 GGTTTTCAAG
1175132 TTTTTTTTCT-
1 TTTTTTTTCTC
*
1175142 TTTGTTTTCTC
1 TTTTTTTTCTC
1175153 TTTTTTTTCTC
1 TTTTTTTTCTC
*
1175164 TCTCTTTTTCT
1 T-TTTTTTTCT
1175175 TCCTAAAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 11 0.39
12 8 0.29
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTTTTTTCTC
Found at i:1175175 original size:21 final size:21
Alignment explanation
Indices: 1175132--1175175 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1175122 GGTTTTCAAG
* *
1175132 TTTTTTTTCTTTTGTTTTCTC
1 TTTTTTTTCTTCTCTTTTCTC
1175153 TTTTTTTTCTCTCTCTTTT-TC
1 TTTTTTTTCT-TCTCTTTTCTC
1175174 TT
1 TT
1175176 CCTAAAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTTTTTCTTCTCTTTTCTC
Found at i:1175946 original size:21 final size:20
Alignment explanation
Indices: 1175904--1175946 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1175894 ACTTGACTAC
*
1175904 AAATAAAAATAAAATTAAAG
1 AAATAAAAATAAAATAAAAG
1175924 AAATAAACAA-AAATATAAAAG
1 AAATAAA-AATAAA-ATAAAAG
1175945 AA
1 AA
1175947 GAAAGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (20 bp):
AAATAAAAATAAAATAAAAG
Found at i:1181780 original size:29 final size:29
Alignment explanation
Indices: 1181747--1181805 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1181737 TTGTACTATG
* * *
1181747 TATGATTGTGCTGTGAGTTTCTTTATAAT
1 TATGATTATGCTATAAGTTTCTTTATAAT
* *
1181776 TATGATTATGTTATAAGTTTCTTTGTAAT
1 TATGATTATGCTATAAGTTTCTTTATAAT
1181805 T
1 T
1181806 TTGTATAAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.24, C:0.05, G:0.17, T:0.54
Consensus pattern (29 bp):
TATGATTATGCTATAAGTTTCTTTATAAT
Found at i:1184304 original size:16 final size:16
Alignment explanation
Indices: 1184266--1184310 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1184256 TTATGTAAAA
*
1184266 ATAAATTAATAAATGT
1 ATAAATTAATAAAAGT
1184282 AGT-AATTAATAAAAGT
1 A-TAAATTAATAAAAGT
1184298 ATAAATTTAATAA
1 ATAAA-TTAATAA
1184311 CTCAAACCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 1 0.04
16 16 0.64
17 8 0.32
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (16 bp):
ATAAATTAATAAAAGT
Found at i:1190066 original size:22 final size:23
Alignment explanation
Indices: 1190025--1190069 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1190015 GCTTTTCTAT
1190025 GATGCAGGAGATGCAGTATTTGA
1 GATGCAGGAGATGCAGTATTTGA
1190048 GATGCAGGAGAT-CAGTATTTGA
1 GATGCAGGAGATGCAGTATTTGA
1190070 TGCATCACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.31, C:0.09, G:0.33, T:0.27
Consensus pattern (23 bp):
GATGCAGGAGATGCAGTATTTGA
Found at i:1192671 original size:45 final size:45
Alignment explanation
Indices: 1192607--1192699 Score: 168
Period size: 45 Copynumber: 2.1 Consensus size: 45
1192597 ATAGTTATAC
*
1192607 TAAAAATCTAGGATGGAATTCCCTTTTCAATTGGGAATTGGTGGT
1 TAAAAATCTAGGATGGAATTCCCTTTTCAATTGCGAATTGGTGGT
*
1192652 TAAAAATCTGGGATGGAATTCCCTTTTCAATTGCGAATTGGTGGT
1 TAAAAATCTAGGATGGAATTCCCTTTTCAATTGCGAATTGGTGGT
1192697 TAA
1 TAA
1192700 GGGTTTGCTT
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:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (45 bp):
TAAAAATCTAGGATGGAATTCCCTTTTCAATTGCGAATTGGTGGT
Found at i:1201665 original size:2 final size:2
Alignment explanation
Indices: 1201658--1201696 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1201648 CACAATCACA
*
1201658 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1201697 TAATATTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1203291 original size:10 final size:10
Alignment explanation
Indices: 1203276--1203306 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1203266 TAAATATAAA
1203276 ATTTTAATAT
1 ATTTTAATAT
1203286 ATTTTAATAT
1 ATTTTAATAT
*
1203296 ATTTTGATAT
1 ATTTTAATAT
1203306 A
1 A
1203307 AAATTACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (10 bp):
ATTTTAATAT
Found at i:1204437 original size:20 final size:20
Alignment explanation
Indices: 1204399--1204453 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
1204389 ATTTTTATTA
*
1204399 TCAAAAATAAAAAATAAAAT
1 TCAAAAATAAAAAACAAAAT
* *
1204419 TCAAATATAAAAAGCAAAAAT
1 TCAAAAATAAAAAAC-AAAAT
1204440 AT-AAAAATAAAAAA
1 -TCAAAAATAAAAAA
1204454 GATTTAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 12 0.43
21 15 0.54
22 1 0.04
ACGTcount: A:0.75, C:0.05, G:0.02, T:0.18
Consensus pattern (20 bp):
TCAAAAATAAAAAACAAAAT
Found at i:1206786 original size:12 final size:13
Alignment explanation
Indices: 1206748--1206777 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1206738 AATATCAAAC
*
1206748 AATAATCATACAA
1 AATAATTATACAA
1206761 AATAATTATACAA
1 AATAATTATACAA
1206774 AATA
1 AATA
1206778 TGTTACAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (13 bp):
AATAATTATACAA
Found at i:1206909 original size:16 final size:16
Alignment explanation
Indices: 1206871--1206929 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 16
1206861 TCAAAATCAA
1206871 AATTAAGAAGAAAATAG
1 AATTAA-AAGAAAATAG
*
1206888 ATTTAAAAGAGAAA-AG
1 AATTAAAAGA-AAATAG
*
1206904 AATTAAAAATAAAAATAG
1 AATT-AAAA-GAAAATAG
1206922 AATTAAAA
1 AATTAAAA
1206930 ATATAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
16 9 0.26
17 19 0.54
18 7 0.20
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (16 bp):
AATTAAAAGAAAATAG
Found at i:1206919 original size:34 final size:33
Alignment explanation
Indices: 1206881--1206950 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
1206871 AATTAAGAAG
* *
1206881 AAAATAGATTTAAAAGAGA-AAAGAATTAAAAATA
1 AAAATAGAATTAAAA-AGATAAA-AATAAAAAATA
*
1206915 AAAATAGAATTAAAAATATAAAAATAAAAAATA
1 AAAATAGAATTAAAAAGATAAAAATAAAAAATA
1206948 AAA
1 AAA
1206951 TAAAAACATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 15 0.47
34 17 0.53
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (33 bp):
AAAATAGAATTAAAAAGATAAAAATAAAAAATA
Found at i:1206940 original size:20 final size:18
Alignment explanation
Indices: 1206881--1206937 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 18
1206871 AATTAAGAAG
* *
1206881 AAAATAG-ATTTAAAAGA
1 AAAATAGAATTAAAAATA
*
1206898 GAAA-AGAATTAAAAATA
1 AAAATAGAATTAAAAATA
1206915 AAAATAGAATTAAAAATA
1 AAAATAGAATTAAAAATA
1206933 TAAAA
1 -AAAA
1206938 ATAAAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 2 0.06
17 14 0.42
18 13 0.39
19 4 0.12
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
AAAATAGAATTAAAAATA
Found at i:1206950 original size:12 final size:12
Alignment explanation
Indices: 1206909--1206956 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
1206899 AAAAGAATTA
1206909 AAAAT-AAAAAT
1 AAAATAAAAAAT
*
1206920 AGAATTAAAAATAT
1 A-AAATAAAAA-AT
1206934 AAAAATAAAAAAT
1 -AAAATAAAAAAT
1206947 AAAATAAAAA
1 AAAATAAAAA
1206957 CATACAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 1 0.03
12 13 0.42
13 6 0.19
14 10 0.32
15 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:1206954 original size:26 final size:26
Alignment explanation
Indices: 1206907--1206956 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
1206897 AGAAAAGAAT
*
1206907 TAAAAATAAAAATAGAATTAAAAATA
1 TAAAAATAAAAATAGAAATAAAAATA
1206933 TAAAAATAAAAAATA-AAATAAAAA
1 TAAAAAT-AAAAATAGAAATAAAAA
1206957 CATACAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (26 bp):
TAAAAATAAAAATAGAAATAAAAATA
Found at i:1207004 original size:22 final size:22
Alignment explanation
Indices: 1206979--1207033 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1206969 TCAAATCAGA
1206979 AAATAAGATAACACACGAATCC
1 AAATAAGATAACACACGAATCC
1207001 AAATAAGATAACACACGAATCC
1 AAATAAGATAACACACGAATCC
**
1207023 TTATAAGATAA
1 AAATAAGATAA
1207034 AGTGTGGATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.55, C:0.18, G:0.09, T:0.18
Consensus pattern (22 bp):
AAATAAGATAACACACGAATCC
Found at i:1207140 original size:25 final size:25
Alignment explanation
Indices: 1207112--1207159 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
1207102 GTTTTTCAAG
* *
1207112 TTTTTTTTCT-TCTGT-TTTCTCTT
1 TTTTTTTTCTCTCTCTCTTTTTCTT
1207135 TTTTTTTTCTCTCTCTCTTTTTCTT
1 TTTTTTTTCTCTCTCTCTTTTTCTT
1207160 CCTAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 10 0.48
24 4 0.19
25 7 0.33
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (25 bp):
TTTTTTTTCTCTCTCTCTTTTTCTT
Found at i:1207931 original size:19 final size:21
Alignment explanation
Indices: 1207899--1207941 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
1207889 TTTGACTAAC
1207899 AAATAAAAATAAAT-T-AAAG
1 AAATAAAAATAAATATAAAAG
1207918 AAATAAACAA-AAATATAAAAG
1 AAATAAA-AATAAATATAAAAG
1207939 AAA
1 AAA
1207942 AAGAAAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 11 0.52
20 3 0.14
21 7 0.33
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (21 bp):
AAATAAAAATAAATATAAAAG
Found at i:1208330 original size:49 final size:49
Alignment explanation
Indices: 1208235--1208330 Score: 111
Period size: 49 Copynumber: 2.0 Consensus size: 49
1208225 AACAGAGGTA
* ** * *
1208235 TTGAAACTTTAAAAATTCAAAACTAAAAAGTTTTTTCTCAACAAAGGAG
1 TTGAAACTTTAAAAATTCAAAACTAAAAAGCTACTCCCCAACAAAGGAG
* * * *
1208284 TTGAAAGTTTAAAAATTCAAAATTGAAAAGCTACTCCCCAATAAAGG
1 TTGAAACTTTAAAAATTCAAAACTAAAAAGCTACTCCCCAACAAAGG
1208331 CATTCGAAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
49 38 1.00
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (49 bp):
TTGAAACTTTAAAAATTCAAAACTAAAAAGCTACTCCCCAACAAAGGAG
Found at i:1209446 original size:15 final size:15
Alignment explanation
Indices: 1209419--1209452 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1209409 TTAATTTAAG
1209419 TCTTCCTTTTTTTTT
1 TCTTCCTTTTTTTTT
1209434 TCTT-CTTTATTTTTT
1 TCTTCCTTT-TTTTTT
1209449 TCTT
1 TCTT
1209453 TCAAACAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (15 bp):
TCTTCCTTTTTTTTT
Found at i:1225052 original size:13 final size:12
Alignment explanation
Indices: 1225035--1225075 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
1225025 AAATTTTAAA
1225035 TTATAT-ATTTT
1 TTATATAATTTT
*
1225046 TTATATAA-TAT
1 TTATATAATTTT
1225057 TTATATAATATTT
1 TTATATAAT-TTT
1225070 TTATAT
1 TTATAT
1225076 CATATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 16 0.64
12 1 0.04
13 8 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTATATAATTTT
Found at i:1225070 original size:24 final size:22
Alignment explanation
Indices: 1225035--1225082 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 22
1225025 AAATTTTAAA
1225035 TTATATATTTTTTATATAATAT
1 TTATATATTTTTTATATAATAT
*
1225057 TTATATAATATTTTTATATCATAT
1 TTATAT-AT-TTTTTATATAATAT
1225081 TT
1 TT
1225083 TAAATTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.26
23 2 0.09
24 15 0.65
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATATATTTTTTATATAATAT
Found at i:1225080 original size:13 final size:12
Alignment explanation
Indices: 1225035--1225083 Score: 57
Period size: 13 Copynumber: 4.1 Consensus size: 12
1225025 AAATTTTAAA
1225035 TTATATAT-TTT
1 TTATATATATTT
*
1225046 TTATATA-ATAT
1 TTATATATATTT
1225057 TTATATAATATTT
1 TTATAT-ATATTT
1225070 TTATATCATATTT
1 TTATAT-ATATTT
1225083 T
1 T
1225084 AAATTTCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 15 0.47
12 1 0.03
13 16 0.50
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (12 bp):
TTATATATATTT
Found at i:1226118 original size:21 final size:20
Alignment explanation
Indices: 1226072--1226115 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1226062 AATAAAAAGA
1226072 TTAATTTGAAATTAATTAAT
1 TTAATTTGAAATTAATTAAT
*
1226092 TTAATTTTAAATTTAA-TAAT
1 TTAATTTGAAA-TTAATTAAT
1226112 TTAA
1 TTAA
1226116 ATTCAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TTAATTTGAAATTAATTAAT
Found at i:1226124 original size:21 final size:21
Alignment explanation
Indices: 1226083--1226124 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1226073 TAATTTGAAA
**
1226083 TTAATTAATTTAATTTTAAAT
1 TTAATTAATTTAATTCAAAAT
1226104 TTAA-TAATTTAAATTCAAAAT
1 TTAATTAATTT-AATTCAAAAT
1226125 AATTTGAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAATTAATTTAATTCAAAAT
Found at i:1226948 original size:20 final size:20
Alignment explanation
Indices: 1226923--1226963 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1226913 AAATAAATTG
1226923 AATAAACTTTATCATTTATT
1 AATAAACTTTATCATTTATT
* *
1226943 AATAAATTTTATTATTTATT
1 AATAAACTTTATCATTTATT
1226963 A
1 A
1226964 GCAAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (20 bp):
AATAAACTTTATCATTTATT
Found at i:1226969 original size:20 final size:20
Alignment explanation
Indices: 1226930--1226974 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1226920 TTGAATAAAC
*
1226930 TTTATCATTTATTAATAAAT
1 TTTATCATTTATTAACAAAT
* *
1226950 TTTATTATTTATTAGCAAAT
1 TTTATCATTTATTAACAAAT
1226970 TTTAT
1 TTTAT
1226975 AAATATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTATCATTTATTAACAAAT
Found at i:1232858 original size:26 final size:27
Alignment explanation
Indices: 1232818--1232872 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
1232808 AAAATTTAAA
1232818 ATAATATCTATTTTTA-TTTTCATATTT
1 ATAATATCTATTTTTACTTTT-ATATTT
*
1232845 ATAATAT-TATTTTTACTTTTATTTTT
1 ATAATATCTATTTTTACTTTTATATTT
1232871 AT
1 AT
1232873 TAGAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.65
Consensus pattern (27 bp):
ATAATATCTATTTTTACTTTTATATTT
Found at i:1233194 original size:56 final size:54
Alignment explanation
Indices: 1233134--1233308 Score: 162
Period size: 56 Copynumber: 3.2 Consensus size: 54
1233124 AATAAATTTT
*
1233134 TTATTGATATGAATTATAATATATAATTTTATGAAAATATAATCTAAATATATAAA
1 TTATTAATAT-AATTATAATATATAATTTTATGAAAATATAAT-TAAATATATAAA
* * * * ***
1233190 TTATTAATAT-TTTA-AATATATATGGATTTAAT-AAAAAATTAA-AAAATA-ATTTT
1 TTATTAATATAATTATAATATATA---ATTTTATGAAAATA-TAATTAAATATATAAA
*
1233243 TTATTGATATAAATTATAATATATAATTTTATGAAAATATAATATAAATATATAAA
1 TTATTAATAT-AATTATAATATATAATTTTATGAAAATATAAT-TAAATATATAAA
1233299 TTATTAATAT
1 TTATTAATAT
1233309 TTTTATATGA
Statistics
Matches: 91, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
53 28 0.31
54 13 0.14
55 13 0.14
56 37 0.41
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.45
Consensus pattern (54 bp):
TTATTAATATAATTATAATATATAATTTTATGAAAATATAATTAAATATATAAA
Found at i:1233288 original size:28 final size:28
Alignment explanation
Indices: 1233148--1233297 Score: 75
Period size: 28 Copynumber: 5.4 Consensus size: 28
1233138 TGATATGAAT
1233148 TATAATATATAATTTTATGAAAATATAA
1 TATAATATATAATTTTATGAAAATATAA
* * * * *
1233176 TCTAAATATATAA-ATTATTAATATTTTAA
1 TAT-AATATATAATTTTATGAA-AATATAA
* * *
1233205 -AT-ATATATGGATTTAAT-AAAAAATTAA
1 TATAATATAT-AATTTTATGAAAATA-TAA
* * *
1233232 -AAAATA-AT-TTTTTATTG-ATATA-AA
1 TATAATATATAATTTTA-TGAAAATATAA
1233256 TTATAATATATAATTTTATGAAAATATAA
1 -TATAATATATAATTTTATGAAAATATAA
1233285 TATAAATATATAA
1 TAT-AATATATAA
1233298 ATTATTAATA
Statistics
Matches: 87, Mismatches: 20, Indels: 29
0.64 0.15 0.21
Matches are distributed among these distances:
24 2 0.02
25 4 0.05
26 16 0.18
27 13 0.15
28 27 0.31
29 25 0.29
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (28 bp):
TATAATATATAATTTTATGAAAATATAA
Found at i:1233306 original size:21 final size:22
Alignment explanation
Indices: 1233140--1233308 Score: 77
Period size: 23 Copynumber: 7.7 Consensus size: 22
1233130 TTTTTTATTG
*
1233140 ATATGAATTATAATATATAATT
1 ATATAAATTATAATATATAATT
* * *
1233162 TTATGAAAATATAATCTA-AA-T
1 ATAT-AAATTATAATATATAATT
*
1233183 ATATAAATTATTAATATTTTAAATAT
1 ATATAAATTA-TAATA-TAT-AAT-T
** * *
1233209 ATATGGATT-TAATAAAAAATT
1 ATATAAATTATAATATATAATT
* * *
1233230 A-A-AAA--ATAATTTTTTATT
1 ATATAAATTATAATATATAATT
1233248 GATATAAATTATAATATATAATT
1 -ATATAAATTATAATATATAATT
* *
1233271 TTATGAAAATATAATATA-AA-T
1 ATAT-AAATTATAATATATAATT
1233292 ATATAAATTATTAATAT
1 ATATAAATTA-TAATAT
1233309 TTTTATATGA
Statistics
Matches: 105, Mismatches: 27, Indels: 31
0.64 0.17 0.19
Matches are distributed among these distances:
18 7 0.07
19 2 0.02
20 12 0.11
21 23 0.22
22 14 0.13
23 32 0.30
24 7 0.07
26 8 0.08
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.44
Consensus pattern (22 bp):
ATATAAATTATAATATATAATT
Found at i:1233322 original size:109 final size:112
Alignment explanation
Indices: 1233082--1233311 Score: 414
Period size: 109 Copynumber: 2.1 Consensus size: 112
1233072 ATAATATGAG
*
1233082 TTAA-ATTTTAAATATATATGGATTTAATAAAAAATTTAAAAAAATAAATTTTTTATTGATATGA
1 TTAATATTTTAAATATATATGGATTTAATAAAAAATTTAAAAAAATAAATTTTTTATTGATATAA
*
1233146 ATTATAATATATAATTTTATGAAAATATAATCTAAATATATAAATTA
66 ATTATAATATATAATTTTATGAAAATATAATATAAATATATAAATTA
1233193 TTAATATTTTAAATATATATGGATTTAATAAAAAA-TT-AAAAAAT-AATTTTTTATTGATATAA
1 TTAATATTTTAAATATATATGGATTTAATAAAAAATTTAAAAAAATAAATTTTTTATTGATATAA
1233255 ATTATAATATATAATTTTATGAAAATATAATATAAATATATAAATTA
66 ATTATAATATATAATTTTATGAAAATATAATATAAATATATAAATTA
1233302 TTAATATTTT
1 TTAATATTTT
1233312 TATATGATAT
Statistics
Matches: 116, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
109 73 0.63
110 7 0.06
111 6 0.05
112 30 0.26
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (112 bp):
TTAATATTTTAAATATATATGGATTTAATAAAAAATTTAAAAAAATAAATTTTTTATTGATATAA
ATTATAATATATAATTTTATGAAAATATAATATAAATATATAAATTA
Found at i:1238825 original size:21 final size:22
Alignment explanation
Indices: 1238799--1238839 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1238789 TATATATAAA
*
1238799 AATATATATTTTA-ATATTTAT
1 AATATAAATTTTACATATTTAT
1238820 AATATAAATTTTACATATTT
1 AATATAAATTTTACATATTT
1238840 TAACTTTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
AATATAAATTTTACATATTTAT
Found at i:1238893 original size:23 final size:23
Alignment explanation
Indices: 1238854--1238912 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
1238844 TTTTGTGTGC
** *
1238854 TTTTTTAAATTCACTTTT-TTTT
1 TTTTTTAAATTTTCTTTTCATTT
1238876 ATTTTTTAAATTTTCTTTTCATTT
1 -TTTTTTAAATTTTCTTTTCATTT
*
1238900 TTTTTTACATTTT
1 TTTTTTAAATTTT
1238913 TTCTTCTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 28 0.90
24 3 0.10
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTTTAAATTTTCTTTTCATTT
Found at i:1238901 original size:12 final size:12
Alignment explanation
Indices: 1238877--1238914 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1238867 CTTTTTTTTA
*
1238877 TTTTTTAAATTT
1 TTTTTTACATTT
*
1238889 TCTTTT-CATTT
1 TTTTTTACATTT
1238900 TTTTTTACATTT
1 TTTTTTACATTT
1238912 TTT
1 TTT
1238915 CTTCTTTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTTACATTT
Found at i:1241431 original size:18 final size:18
Alignment explanation
Indices: 1241397--1241431 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1241387 TGACTGAATA
*
1241397 ATAATAATAATAATAGTG
1 ATAATAATAACAATAGTG
*
1241415 ATAATAATAACAGTAGT
1 ATAATAATAACAATAGT
1241432 AAAGAGAGAT
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:0.54, C:0.03, G:0.11, T:0.31
Consensus pattern (18 bp):
ATAATAATAACAATAGTG
Found at i:1246062 original size:2 final size:2
Alignment explanation
Indices: 1246055--1246085 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1246045 CTGGTCGTTT
1246055 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1246086 AGAAAGCCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1248849 original size:12 final size:12
Alignment explanation
Indices: 1248832--1248856 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1248822 AAAATAAAAA
1248832 ATATATATATGT
1 ATATATATATGT
1248844 ATATATATATGT
1 ATATATATATGT
1248856 A
1 A
1248857 CGTGCATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATATATATATGT
Found at i:1249985 original size:3 final size:3
Alignment explanation
Indices: 1249977--1250006 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1249967 AAGCATAAGC
1249977 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1250007 GAAATAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1254959 original size:28 final size:28
Alignment explanation
Indices: 1254920--1254977 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
1254910 AACTGCCAAG
1254920 AATTAAAAGAAGATAAAAAGTGAATAGA
1 AATTAAAAGAAGATAAAAAGTGAATAGA
* *
1254948 AATTAAATGAAGATAAAAAGTTAATAGA
1 AATTAAAAGAAGATAAAAAGTGAATAGA
1254976 AA
1 AA
1254978 AGAGTCATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.16, T:0.21
Consensus pattern (28 bp):
AATTAAAAGAAGATAAAAAGTGAATAGA
Found at i:1257702 original size:2 final size:2
Alignment explanation
Indices: 1257695--1257725 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1257685 ATTTTGAATG
1257695 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1257726 GATTGAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1259516 original size:38 final size:38
Alignment explanation
Indices: 1259467--1259551 Score: 110
Period size: 32 Copynumber: 2.4 Consensus size: 38
1259457 TGAATATGAT
*
1259467 TCGAATAAAATTTAAATTT--G--ATTTAA-TTATT-A
1 TCGAATCAAATTTAAATTTAAGTAATTTAATTTATTAA
*
1259499 TCGAGTCAAATTTAAATTTAAGTAATTTAATTTATTAA
1 TCGAATCAAATTTAAATTTAAGTAATTTAATTTATTAA
1259537 TCGAATCAAATTTAA
1 TCGAATCAAATTTAA
1259552 GTATTTTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
32 17 0.39
34 1 0.02
36 6 0.14
37 5 0.11
38 15 0.34
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.44
Consensus pattern (38 bp):
TCGAATCAAATTTAAATTTAAGTAATTTAATTTATTAA
Found at i:1260167 original size:20 final size:21
Alignment explanation
Indices: 1260134--1260172 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1260124 ATTATAAAAA
1260134 ATATTAATAATTTATATATTT
1 ATATTAATAATTTATATATTT
*
1260155 ATATT-ATATTTTATATAT
1 ATATTAATAATTTATATAT
1260173 AATTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTAATAATTTATATATTT
Found at i:1260683 original size:29 final size:28
Alignment explanation
Indices: 1260651--1260746 Score: 79
Period size: 29 Copynumber: 3.3 Consensus size: 28
1260641 ATATTTTATT
1260651 ATTTATATAATTATATATTATATTAATAA
1 ATTTATAT-ATTATATATTATATTAATAA
* *
1260680 ATTTAT-TATTAAATATTTTAATTTAATAAA
1 ATTTATATATTATATATTAT-A-TTAAT-AA
* **
1260710 ATATTATAT-TTATATATAATAAAAATATA
1 AT-TTATATATTATATATTATATTAATA-A
1260739 ATTTATAT
1 ATTTATAT
1260747 TAAAAAATAA
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
27 10 0.19
28 9 0.17
29 17 0.31
30 5 0.09
31 12 0.22
32 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
ATTTATATATTATATATTATATTAATAA
Found at i:1260742 original size:22 final size:22
Alignment explanation
Indices: 1260702--1260763 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 22
1260692 ATATTTTAAT
1260702 TTAAT-AAAATATTATATTTATA
1 TTAATAAAAATA-TATATTTATA
1260724 TATAATAAAAATATA-ATTTATA
1 T-TAATAAAAATATATATTTATA
1260746 TT-A-AAAAATA-ATATTTAT
1 TTAATAAAAATATATATTTAT
1260764 TCTCCCTTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
18 1 0.03
19 13 0.35
20 1 0.03
21 1 0.03
22 9 0.24
23 6 0.16
24 6 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAATAAAAATATATATTTATA
Found at i:1260761 original size:19 final size:21
Alignment explanation
Indices: 1260690--1260763 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 21
1260680 ATTTATTATT
*
1260690 AAATAT-TTTA-ATTTAATAA
1 AAATATATTTATATATAATAA
1260709 AATATTATATTTATATATAATAA
1 AA-A-TATATTTATATATAATAA
1260732 AAATATAATTTATAT-T-A-AA
1 AAATAT-ATTTATATATAATAA
1260751 AAATAATATTTAT
1 AAAT-ATATTTAT
1260764 TCTCCCTTCT
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
19 14 0.29
20 4 0.08
21 7 0.15
22 13 0.27
23 10 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATATATTTATATATAATAA
Found at i:1260764 original size:17 final size:18
Alignment explanation
Indices: 1260724--1260757 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1260714 TATATTTATA
*
1260724 TATAATAAAAATATAATT
1 TATATTAAAAATATAATT
1260742 TATATTAAAAA-ATAAT
1 TATATTAAAAATATAAT
1260758 ATTTATTCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TATATTAAAAATATAATT
Found at i:1262698 original size:13 final size:14
Alignment explanation
Indices: 1262667--1262699 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1262657 ATCAAATTAT
1262667 TTAAATTTATTTGA
1 TTAAATTTATTTGA
1262681 TTAAATTTATTT-A
1 TTAAATTTATTTGA
1262694 TTAAAT
1 TTAAAT
1262700 AAAAAGAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (14 bp):
TTAAATTTATTTGA
Found at i:1263687 original size:30 final size:30
Alignment explanation
Indices: 1263652--1263715 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
1263642 GCGTAGCCAA
*
1263652 GCATTAAAGAATTGGGATTGGGATACCTTT
1 GCATTAAAGAATTAGGATTGGGATACCTTT
*
1263682 GCATTAAAGAATTAGGATTGGGATATCTTT
1 GCATTAAAGAATTAGGATTGGGATACCTTT
1263712 GCAT
1 GCAT
1263716 CTGTCAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.31, C:0.09, G:0.25, T:0.34
Consensus pattern (30 bp):
GCATTAAAGAATTAGGATTGGGATACCTTT
Found at i:1264210 original size:35 final size:35
Alignment explanation
Indices: 1264133--1264212 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
1264123 TTTATCAAAT
* **
1264133 ATATTTTAAAAAATAAAAAATAGAAAATAAAAACG
1 ATATTTTAAAAAATAAAAAATAAAAAATAAAAAAA
* *
1264168 ATTTTTTAAAAAAT-GAAAATAAAAAATAAAAAAAA
1 ATATTTTAAAAAATAAAAAATAAAAAAT-AAAAAAA
1264203 ATATTTTAAA
1 ATATTTTAAA
1264213 GATTCCCTCT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 11 0.29
35 27 0.71
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.28
Consensus pattern (35 bp):
ATATTTTAAAAAATAAAAAATAAAAAATAAAAAAA
Found at i:1276340 original size:13 final size:14
Alignment explanation
Indices: 1276309--1276341 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1276299 ATCAAATTAT
1276309 TTAAATTTATTTGA
1 TTAAATTTATTTGA
1276323 TTAAATTTATTT-A
1 TTAAATTTATTTGA
1276336 TTAAAT
1 TTAAAT
1276342 AAAAAGAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (14 bp):
TTAAATTTATTTGA
Found at i:1277342 original size:29 final size:30
Alignment explanation
Indices: 1277296--1277358 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 30
1277286 GCGTAGCCAA
*
1277296 GCATTAAAGAATTGGGATTGGGATACCTTT
1 GCATTAAAGAATTAGGATTGGGATACCTTT
*
1277326 GCATT-AAGAATTAGGATTGGGATATCTTT
1 GCATTAAAGAATTAGGATTGGGATACCTTT
1277355 GCAT
1 GCAT
1277359 CTGTCAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 26 0.84
30 5 0.16
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (30 bp):
GCATTAAAGAATTAGGATTGGGATACCTTT
Found at i:1277835 original size:13 final size:12
Alignment explanation
Indices: 1277819--1277851 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1277809 AACGATTTTT
1277819 TAAAAAATGAAAA
1 TAAAAAAT-AAAA
1277832 TAAAAAATAAAA
1 TAAAAAATAAAA
1277844 -AAAAAATA
1 TAAAAAATA
1277852 TTTTAAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.40
12 4 0.20
13 8 0.40
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (12 bp):
TAAAAAATAAAA
Found at i:1278068 original size:19 final size:20
Alignment explanation
Indices: 1278034--1278073 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1278024 AAAAAAATAT
* *
1278034 ATTTTTATTAATAATATTTA
1 ATTTTTATTAAAAATACTTA
1278054 ATTTTTA-TAAAAATACTTA
1 ATTTTTATTAAAAATACTTA
1278073 A
1 A
1278074 AATACATTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTTTATTAAAAATACTTA
Found at i:1288249 original size:32 final size:32
Alignment explanation
Indices: 1288190--1288250 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
1288180 TGCAATTCCT
* *
1288190 CAAATGGGTATTTTTTATTTTTCATAAATAAG
1 CAAATGGGTATTATTTATTTCTCATAAATAAG
*
1288222 CAAATGGGTATTAATTT-TTTCTGATAAAT
1 CAAATGGGTATT-ATTTATTTCTCATAAAT
1288251 TAACTAATGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 22 0.88
33 3 0.12
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.46
Consensus pattern (32 bp):
CAAATGGGTATTATTTATTTCTCATAAATAAG
Found at i:1293749 original size:2 final size:2
Alignment explanation
Indices: 1293742--1293787 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1293732 AGAACAGTAG
1293742 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1293784 AC AC
1 AC AC
1293788 TTCTACAAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1302154 original size:19 final size:19
Alignment explanation
Indices: 1302130--1302169 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1302120 GATATAACTA
*
1302130 TTACATATACCAACAGCAT
1 TTACATATAACAACAGCAT
1302149 TTACATATAACAACAGCAT
1 TTACATATAACAACAGCAT
1302168 TT
1 TT
1302170 TTTATAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.30
Consensus pattern (19 bp):
TTACATATAACAACAGCAT
Found at i:1304756 original size:65 final size:66
Alignment explanation
Indices: 1304681--1304814 Score: 261
Period size: 65 Copynumber: 2.0 Consensus size: 66
1304671 ACAAGCATTA
1304681 TAAGTTTTTATATAGTTAACTAAAGGGTAAAATAGAAAATTAAAATCTTTCTAAAACTGATCTTT
1 TAAGTTTTTATATAGTTAACTAAAGGGTAAAATAGAAAATTAAAATCTTTCTAAAACTGATCTTT
1304746 G
66 G
1304747 TAAG-TTTTATATAGTTAACTAAAGGGTAAAATAGAAAATTAAAATCTTTCTAAAACTGATCTTT
1 TAAGTTTTTATATAGTTAACTAAAGGGTAAAATAGAAAATTAAAATCTTTCTAAAACTGATCTTT
1304811 G
66 G
1304812 TAA
1 TAA
1304815 TTAAGGAATT
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
65 64 0.94
66 4 0.06
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.37
Consensus pattern (66 bp):
TAAGTTTTTATATAGTTAACTAAAGGGTAAAATAGAAAATTAAAATCTTTCTAAAACTGATCTTT
G
Found at i:1306847 original size:126 final size:126
Alignment explanation
Indices: 1306622--1306877 Score: 485
Period size: 126 Copynumber: 2.0 Consensus size: 126
1306612 CAGAGATTGT
*
1306622 AGTTACTTTATTTTCAAAGTTAGGATCAAGTTCTTGGACTTGCATTGGTTTAGGAGTTGAAACTT
1 AGTTACTTTATTTTCAAAGTTAGGATCAAGTTCTTAGACTTGCATTGGTTTAGGAGTTGAAACTT
1306687 TTCTTCTTGAGTACACCTATAATTCCTTCATAAAATCAAGAATAGTATTACCTTTAGTCAC
66 TTCTTCTTGAGTACACCTATAATTCCTTCATAAAATCAAGAATAGTATTACCTTTAGTCAC
1306748 AGTTACTTTATTTTCAAAGTTAGGATCAAGTTCTTAGACTTGCATTGGTTTAGGAGTTGAAACTT
1 AGTTACTTTATTTTCAAAGTTAGGATCAAGTTCTTAGACTTGCATTGGTTTAGGAGTTGAAACTT
* *
1306813 TTTTTCTTGAGTACACCTATAATTCTTTCATAAAATCAAGAATAGTATTACCTTTAGTCAC
66 TTCTTCTTGAGTACACCTATAATTCCTTCATAAAATCAAGAATAGTATTACCTTTAGTCAC
1306874 AGTT
1 AGTT
1306878 TTTGTGTTTG
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 127 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (126 bp):
AGTTACTTTATTTTCAAAGTTAGGATCAAGTTCTTAGACTTGCATTGGTTTAGGAGTTGAAACTT
TTCTTCTTGAGTACACCTATAATTCCTTCATAAAATCAAGAATAGTATTACCTTTAGTCAC
Found at i:1309862 original size:22 final size:22
Alignment explanation
Indices: 1309837--1309878 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1309827 TTTTTATCCT
*
1309837 TAATTCTAGGGATATAAATACA
1 TAATTCTAGGGATACAAATACA
*
1309859 TAATTTTAGGGATACAAATA
1 TAATTCTAGGGATACAAATA
1309879 TATACAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.33
Consensus pattern (22 bp):
TAATTCTAGGGATACAAATACA
Found at i:1310930 original size:5 final size:5
Alignment explanation
Indices: 1310920--1310951 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
1310910 AAATTTACAC
1310920 AAATA AAAT- AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAA
1310952 AGTATCACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:1310942 original size:19 final size:18
Alignment explanation
Indices: 1310920--1311014 Score: 75
Period size: 19 Copynumber: 5.1 Consensus size: 18
1310910 AAATTTACAC
1310920 AAATAAAATAAATAAAATA
1 AAATAAAATAAATAAAA-A
**
1310939 AAATAAAATAAA-AAGTATC
1 AAATAAAATAAATAA--AAA
**
1310958 ACTTAAAATCAAATAAAAA
1 AAATAAAAT-AAATAAAAA
* *
1310977 AATTTAAATAAATAAAAA
1 AAATAAAATAAATAAAAA
*
1310995 ACAATAAAACAAATAAAAA
1 A-AATAAAATAAATAAAAA
1311014 A
1 A
1311015 TTTTACCAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
18 12 0.20
19 42 0.70
20 4 0.07
21 2 0.03
ACGTcount: A:0.74, C:0.05, G:0.01, T:0.20
Consensus pattern (18 bp):
AAATAAAATAAATAAAAA
Found at i:1311110 original size:11 final size:11
Alignment explanation
Indices: 1311087--1311120 Score: 54
Period size: 10 Copynumber: 3.3 Consensus size: 11
1311077 TGAAAATATG
1311087 AAATTTT-TAA
1 AAATTTTCTAA
1311097 AAATTTTCTAA
1 AAATTTTCTAA
1311108 AAA-TTTCTAA
1 AAATTTTCTAA
1311118 AAA
1 AAA
1311121 CACATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 17 0.74
11 6 0.26
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (11 bp):
AAATTTTCTAA
Found at i:1312027 original size:12 final size:11
Alignment explanation
Indices: 1312012--1312049 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
1312002 TTGATAGTAT
1312012 TTTAATATAATA
1 TTTAATAT-ATA
1312024 TTTAATATATA
1 TTTAATATATA
*
1312035 TCTAAT-TATA
1 TTTAATATATA
1312045 TTTAA
1 TTTAA
1312050 GTAAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 8 0.33
11 8 0.33
12 8 0.33
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (11 bp):
TTTAATATATA
Found at i:1319038 original size:2 final size:2
Alignment explanation
Indices: 1318999--1319023 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1318989 GTTCTCTAAT
1318999 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
1319024 TAACCAGCAA
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:1319227 original size:2 final size:2
Alignment explanation
Indices: 1319220--1319255 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1319210 TACATATGTA
*
1319220 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1319256 CCTAGGTGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1340293 original size:19 final size:18
Alignment explanation
Indices: 1340266--1340303 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
1340256 ACAATTTGGG
1340266 ATATAAGCTTACATCCTCA
1 ATATAAGCTTACAT-CTCA
*
1340285 ATATCAGCTTACATCTCA
1 ATATAAGCTTACATCTCA
1340303 A
1 A
1340304 ATGACATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (18 bp):
ATATAAGCTTACATCTCA
Done.