Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, 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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 7 of 105
Found at i:1044341 original size:15 final size:15
Alignment explanation
Indices: 1044321--1044362 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
1044311 CTGCCATTTT
1044321 GAGAGAGAAGAGAGA
1 GAGAGAGAAGAGAGA
1044336 GAGAGAGAAGAGAGA
1 GAGAGAGAAGAGAGA
1044351 GAGAGAG-AGAGA
1 GAGAGAGAAGAGA
1044363 TTAATTGATC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 5 0.19
15 22 0.81
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (15 bp):
GAGAGAGAAGAGAGA
Found at i:1044706 original size:38 final size:38
Alignment explanation
Indices: 1044635--1044711 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
1044625 TATTCATGTG
* *
1044635 TTACGTATTATAAATATCATATATTATTTATATATTAT
1 TTACGTATTATAAATATCATATATTAATCATATATTAT
* * * *
1044673 TTACGTGTTATAAATATTATGTGTTAATCATATATTAT
1 TTACGTATTATAAATATCATATATTAATCATATATTAT
1044711 T
1 T
1044712 AAAATAATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.36, C:0.05, G:0.06, T:0.52
Consensus pattern (38 bp):
TTACGTATTATAAATATCATATATTAATCATATATTAT
Found at i:1052304 original size:60 final size:62
Alignment explanation
Indices: 1052166--1052306 Score: 162
Period size: 60 Copynumber: 2.3 Consensus size: 62
1052156 TTTTTTGGTA
* * *
1052166 AAAAATAACTTGAATAATCTTAAAAAAAATATTGAAGGAGATTATTAAATGCGTTTTTGGCC
1 AAAAATAACTTGAATAATCCTAAAAAAAATATTGAAGGAGATTATTAAAGGCGTTTTTAGCC
* * * * * *
1052228 AGAAATACCTTGAATAATCCT-AAAACAA-ATTGCGAGGA-ATTATTGAAGGTGTTTTTAGCC
1 AAAAATAACTTGAATAATCCTAAAAAAAATATTG-AAGGAGATTATTAAAGGCGTTTTTAGCC
*
1052288 AAAAATAACTTCAATAATC
1 AAAAATAACTTGAATAATC
1052307 ATACTTTCTA
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
60 38 0.58
61 10 0.15
62 18 0.27
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.30
Consensus pattern (62 bp):
AAAAATAACTTGAATAATCCTAAAAAAAATATTGAAGGAGATTATTAAAGGCGTTTTTAGCC
Found at i:1053285 original size:13 final size:14
Alignment explanation
Indices: 1053267--1053297 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1053257 TTAATCAATA
1053267 TTAAAA-AAATTTT
1 TTAAAATAAATTTT
1053280 TTAAAATAAATTTT
1 TTAAAATAAATTTT
1053294 TTAA
1 TTAA
1053298 TTTAGTGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTAAAATAAATTTT
Found at i:1053381 original size:34 final size:34
Alignment explanation
Indices: 1053337--1053421 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
1053327 TTAAATGTCA
* * *
1053337 AAATGTAGTGAC-TTTTTCTATTATAAATGCTGCT
1 AAATTTAGTGACATTTTT-TACTATAAACGCTGCT
* *
1053371 AAATTTAGTGACATTTTTTACTATAAACGTTTCT
1 AAATTTAGTGACATTTTTTACTATAAACGCTGCT
*
1053405 AAATTTAGTGGCATTTT
1 AAATTTAGTGACATTTT
1053422 ATAATTAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
34 39 0.89
35 5 0.11
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.46
Consensus pattern (34 bp):
AAATTTAGTGACATTTTTTACTATAAACGCTGCT
Found at i:1053913 original size:23 final size:24
Alignment explanation
Indices: 1053849--1053919 Score: 94
Period size: 23 Copynumber: 3.0 Consensus size: 24
1053839 ATGGTTATGA
1053849 TATGATGATTTCTAAAGATTGATT
1 TATGATGATTTCTAAAGATTGATT
*
1053873 TATGAT--TTTATATGAAGA-TGATT
1 TATGATGATTTCTA--AAGATTGATT
1053896 TATGATGATTTCTAAAGATTGATT
1 TATGATGATTTCTAAAGATTGATT
1053920 AATAATTTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
22 5 0.12
23 15 0.38
24 15 0.38
25 5 0.12
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (24 bp):
TATGATGATTTCTAAAGATTGATT
Found at i:1060515 original size:217 final size:219
Alignment explanation
Indices: 1059977--1060568 Score: 755
Period size: 217 Copynumber: 2.7 Consensus size: 219
1059967 TGTTTCTTAG
* * *
1059977 GCATTTCATATCGACCATGAAAGCAACTGCAAATATAATTGACTCAATCTAGCCTAGGTTGACAA
1 GCATTTCATATCGACTATGAAAGCAACTGCAAATATAATTGACTCAATCCAGCCTAGGTTGTCAA
* *
1060042 TGCGTAAAGTAGGGGAAGGATAGAACATTCTTCATAGTCATTTGTCGATTATTATTATATTATAT
66 TGCGTAAAGTACGGGAAGGGTAGAACATTCTTCATAGTCATTTGTCGA--ATTATTATATTATAT
* * *
1060107 TGGTGACGTTGGGATTGGGTAG-CAGGTAAAACGGGGGACCGTTTCTATAATTGTTGATTGTTGA
129 TGGTGACGTTGGGATTGGGTAGCCAGGTAAAA----GGACCATTTCTAGAATTGTCGATTGTTGA
* * *
1060171 CTGGTAACCTCCTGTAAACCAAATAATGAG
190 CCGGTAACCTCCGGTAAACCAAATAATGAA
* ** * *
1060201 GCTTTTCATA-AAAATATGAAAGCAACTGCAAATATAATTGACTCAATCCATCCTAGAGTTGTCA
1 GCATTTCATATCGACTATGAAAGCAACTGCAAATATAATTGACTCAATCCAGCCTAG-GTTGTCA
* *
1060265 ATGCGTATAGTACGGGAAAGGTAGAACATTCTTCATAGTCATTTGTCGAATTATTA-ATTATATT
65 ATGCGTAAAGTACGGGAAGGGTAGAACATTCTTCATAGTCATTTGTCGAATTATTATATTATATT
*
1060329 GGTGACGTTGGGATTGGTTAGCCA-GTAAAA-GACCATTTCTAGAATTGTCGATTGTTGACCGGT
130 GGTGACGTTGGGATTGGGTAGCCAGGTAAAAGGACCATTTCTAGAATTGTCGATTGTTGACCGGT
* * * **
1060392 AATCTGCGGTAAACCACATGCTGAA
195 AACCTCCGGTAAACCAAATAATGAA
* * *
1060417 GCATTTCATATCGACTATGAAAGCAACCGCAAACATAATTGACTGAATCCAGCCTATGGTTGTCA
1 GCATTTCATATCGACTATGAAAGCAACTGCAAATATAATTGACTCAATCCAGCCTA-GGTTGTCA
* * * * * *
1060482 ATGCGTAAAGTACAGGG-AGGGCAGAATATTCTTCATAATCGTTTCTCGAATTATTATATTATAC
65 ATGCGTAAAGTAC-GGGAAGGGTAGAACATTCTTCATAGTCATTTGTCGAATTATTATATTATAT
*
1060546 TGGCGACGTTGGGATTGGGTAGC
129 TGGTGACGTTGGGATTGGGTAGC
1060569 AAGAAAAACG
Statistics
Matches: 320, Mismatches: 42, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
216 56 0.17
217 90 0.28
218 31 0.10
221 34 0.11
222 9 0.03
223 40 0.12
224 60 0.19
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (219 bp):
GCATTTCATATCGACTATGAAAGCAACTGCAAATATAATTGACTCAATCCAGCCTAGGTTGTCAA
TGCGTAAAGTACGGGAAGGGTAGAACATTCTTCATAGTCATTTGTCGAATTATTATATTATATTG
GTGACGTTGGGATTGGGTAGCCAGGTAAAAGGACCATTTCTAGAATTGTCGATTGTTGACCGGTA
ACCTCCGGTAAACCAAATAATGAA
Found at i:1061012 original size:27 final size:27
Alignment explanation
Indices: 1060939--1061012 Score: 68
Period size: 27 Copynumber: 2.9 Consensus size: 27
1060929 AAATATACAT
* *
1060939 TAATATATATT-TTTAATAAAAATATAT
1 TAATTTATATTATTTAATAAAAA-ATAA
**
1060966 TAATTT-TA--A-TTAATCTAAAATAA
1 TAATTTATATTATTTAATAAAAAATAA
1060989 TAATTTATATTATTTAATAAAAAA
1 TAATTTATATTATTTAATAAAAAA
1061013 ATTATTTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
23 9 0.25
24 10 0.28
26 3 0.08
27 14 0.39
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (27 bp):
TAATTTATATTATTTAATAAAAAATAA
Found at i:1062783 original size:1 final size:1
Alignment explanation
Indices: 1062744--1062768 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1062734 TATTTAAAGT
1062744 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
1062769 CTCATAGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1062931 original size:10 final size:10
Alignment explanation
Indices: 1062918--1062990 Score: 59
Period size: 9 Copynumber: 7.7 Consensus size: 10
1062908 AAAAAACACA
1062918 AAATATATAT
1 AAATATATAT
1062928 AAATA-ATAT
1 AAATATATAT
1062937 ATAATATAT-T
1 A-AATATATAT
*
1062947 ATATAT-TAT
1 AAATATATAT
**
1062956 TTATATATATT
1 AAATATATA-T
1062967 AAA-ATATAT
1 AAATATATAT
1062976 AAATA-A-AT
1 AAATATATAT
1062984 AAATATA
1 AAATATA
1062991 AAGTACATGT
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
8 8 0.15
9 21 0.40
10 19 0.37
11 4 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
AAATATATAT
Found at i:1067829 original size:20 final size:21
Alignment explanation
Indices: 1067800--1067840 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1067790 TTTTTAATTA
1067800 TTGAAGAAGAAATT-TTATTT
1 TTGAAGAAGAAATTATTATTT
* *
1067820 TTGAATAAGATATTATTATTT
1 TTGAAGAAGAAATTATTATTT
1067841 ATAATAGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (21 bp):
TTGAAGAAGAAATTATTATTT
Found at i:1077625 original size:26 final size:26
Alignment explanation
Indices: 1077581--1077633 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1077571 ACCACAGACG
*
1077581 AGAGAAAAGTGCAAAGTCTCTGAGTA
1 AGAGAAAAGGGCAAAGTCTCTGAGTA
* *
1077607 AGAGAAAAGGGGAAGGTCTCTGAGTA
1 AGAGAAAAGGGCAAAGTCTCTGAGTA
1077633 A
1 A
1077634 TCATTCATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.09, G:0.32, T:0.17
Consensus pattern (26 bp):
AGAGAAAAGGGCAAAGTCTCTGAGTA
Found at i:1078922 original size:18 final size:18
Alignment explanation
Indices: 1078891--1078936 Score: 51
Period size: 21 Copynumber: 2.5 Consensus size: 18
1078881 AAAAATTTTA
1078891 TTAAA-AAATGATAA-AT
1 TTAAATAAATGATAATAT
1078907 TTAAATAAAGTGATAATAT
1 TTAAATAAA-TGATAATAT
1078926 TACTAAATAAA
1 T--TAAATAAA
1078937 AAATTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.20
17 3 0.12
18 6 0.24
19 3 0.12
21 8 0.32
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (18 bp):
TTAAATAAATGATAATAT
Found at i:1079108 original size:21 final size:21
Alignment explanation
Indices: 1079037--1079118 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 21
1079027 AATATATTAT
* * *
1079037 AAAGGTTATAAAAATTACATCA
1 AAAGATTATCAAAATTATAT-A
* *
1079059 AGAGATTATCAAAATTTTATA
1 AAAGATTATCAAAATTATATA
*
1079080 AAAAATTATCAAAATTATATA
1 AAAGATTATCAAAATTATATA
*
1079101 AATGATTAT-ATAAATTAT
1 AAAGATTATCA-AAATTAT
1079119 CAAAATTATA
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
20 1 0.02
21 33 0.67
22 15 0.31
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (21 bp):
AAAGATTATCAAAATTATATA
Found at i:1079159 original size:35 final size:33
Alignment explanation
Indices: 1079090--1079188 Score: 98
Period size: 33 Copynumber: 3.0 Consensus size: 33
1079080 AAAAATTATC
* * *
1079090 AAAATTAT-A-TA-AATGATTATATAAATTATC
1 AAAATTATAATTATAATAATTATATAAATGATT
*
1079120 AAAATTATATAAATTATAATTA-TATATAAATGATT
1 AAAA-T-TAT-AATTATAATAATTATATAAATGATT
*
1079155 AAAATTATAATTATCATAATTATATAAATGATT
1 AAAATTATAATTATAATAATTATATAAATGATT
1079188 A
1 A
1079189 TCAAAATTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
30 4 0.07
31 1 0.02
32 12 0.21
33 17 0.30
34 2 0.04
35 17 0.30
36 4 0.07
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (33 bp):
AAAATTATAATTATAATAATTATATAAATGATT
Found at i:1079339 original size:22 final size:22
Alignment explanation
Indices: 1079313--1079362 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1079303 ATTGATAATT
*
1079313 AGTTATTAGTTACT-TACTATTA
1 AGTTATTAGTGA-TATACTATTA
1079335 AGTTATTAGTGATATACTATTA
1 AGTTATTAGTGATATACTATTA
*
1079357 ATTTAT
1 AGTTAT
1079363 GAATAATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.34, C:0.06, G:0.10, T:0.50
Consensus pattern (22 bp):
AGTTATTAGTGATATACTATTA
Found at i:1079759 original size:101 final size:101
Alignment explanation
Indices: 1079654--1079837 Score: 271
Period size: 101 Copynumber: 1.8 Consensus size: 101
1079644 TAACTAAAAT
* * * * * *
1079654 CGCTGTTACTTTAGAGACGTTTGTATCTAAAAATATCTTTATATTAGCGGTGTTTGTATCTTTC-
1 CGCTGCTACTTTAGAGACATTTATATCTAAAAATACCTTTATATTAGCGATGTTTGTATATTTCA
**
1079718 AGATGCCGTTAATTTAGTGGCATTTTGTTAGTGAAAC
66 AG-TGCCACTAATTTAGTGGCATTTTGTTAGTGAAAC
*
1079755 CGCTGCTACTTTAGAGGCATTTATATCTAAAAATACCTTTATATTAGCGATGTTTGTATATTTCA
1 CGCTGCTACTTTAGAGACATTTATATCTAAAAATACCTTTATATTAGCGATGTTTGTATATTTCA
1079820 AGTGCCACTAATTTAGTG
66 AGTGCCACTAATTTAGTG
1079838 ATGTTTTTAT
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 71 0.97
102 2 0.03
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (101 bp):
CGCTGCTACTTTAGAGACATTTATATCTAAAAATACCTTTATATTAGCGATGTTTGTATATTTCA
AGTGCCACTAATTTAGTGGCATTTTGTTAGTGAAAC
Found at i:1081165 original size:21 final size:21
Alignment explanation
Indices: 1081139--1081186 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
1081129 CTATACAAAA
1081139 ACATATATTATTTGATATGAT
1 ACATATATTATTTGATATGAT
1081160 ACATATATTATTTGATATGAT
1 ACATATATTATTTGATATGAT
1081181 ACATAT
1 ACATAT
1081187 CAACCACAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (21 bp):
ACATATATTATTTGATATGAT
Found at i:1089143 original size:703 final size:694
Alignment explanation
Indices: 1087781--1090123 Score: 2785
Period size: 703 Copynumber: 3.4 Consensus size: 694
1087771 GAAAAACACT
* * * *
1087781 ATTTTTTCC-AGAAAAACGTCTTTCCTAATTCATTTGAACTTAGTACTTAATTACTGAAGGCGTT
1 ATTTTTTCCAAAAAAAATGCCTTTCCTAATTCATTTAAACTTAGTACTTAATTACTGAAGGCGTT
* * * *
1087845 TGTTATTCAGACACGCCTTTAATAATTTTCCTCT-AAAAATATTTTGGAATTATTAAAGGCATCT
66 TGTTATTAACACACGCCTTTAATAATTTTCCTCTAAAAAATTTTTTGAAATTATTAAAGGCATCT
* * * * * * *
1087909 TCCTCTAACAAACACCTTCAATAATTCCTTTTTAGTTGTCTTCATAAAAATTGAACGCGTTCCTT
131 TCCACTAACAAACACCTTCAATAATTTCTTTTAAATTATCTTCATAAAAATTAAAGGCGTTCCTT
* * * * *
1087974 GATTATAAATGCCTTTAATAATTTTCTTATAGAATTTGTTAGGATTAGTAAAGGCATATTCGACT
196 GATTATAAACGCCTTCAATAATTTTTTTATAGAATTTGTTAGGATTAGTAAAGGCATCTTCAACT
* * * * * *
1088039 ATTAAATG-CTTTCAAAAATTTCCTACTATTCAAGGCTTTTATACCAGAAAAACACCTTGACTAA
261 ATTAAACGCCTTT-AATAATTTTCTCCTATTCAAGGCTTTTATTCCAGAAAAATACCTTGACTAA
* * * * * *
1088103 TTCATTTTATTTTTTGAATCAGTTTGTTGAAGGCATCTTTTACTA-CAAAACGCCTTCAATGTTC
325 TTCATTTTATTTTTTGAATCAATTTATTGAAAGCATCTTCTGC-AGCAAAACGCCTTCAATATTC
* * ***
1088167 CACTACTCAAATTTT-ATG-GCAGATAGTGAAGGCATTTATTGTAGAAAAATGTTGCTACTAGAT
389 CACTACTCAAATTTTGA-GATC-GATAGTGAAGGC-GTTATTGTAGAAAAATGTCATTACTAGAT
*
1088230 GCTATTATTTTATTTTATGTACAAAAGATTGAACAATTTTCAATTGAAATTATTGGTGTTAGTAA
451 GCTATTATTTTATTTTATGTACAAAA-ATTGAACAATTTCCAATTGAAATTATTGGTGTTAGTAA
* *
1088295 TGGCATCTTT-TAACGAAAAATGCCTTCAATAATTTTCCTCTAAAAAATTT-GAGGATTACCAAA
515 TGGCAT-TTTCTAACGAAAAATACCTTCAATAATTTTTCTCTAAAAAATTTAG-GGATTACCAAA
* * *
1088358 AGCATCTTTTATTAGCAAAGGCCTTGAATATAGATGACATTTTTTTAAAGTAAATGCCTTTTATA
578 AGCGTCTTTTATGA-CAAAGGCCTTGAATATA-ATG--ATTTTTTTAAAGTAAACGCCTTTTATA
* *
1088423 AATTTAAGAATTATTAAATTCACCTTCAACTGAAAAATGCCATCAATATAGAAGGC
639 AATTTAAGAATTATTAAAGTCACCTTCAACTGAAAAATGTCATCAATATAGAAGGC
* *
1088479 ATTTTTTCCAAAAAAAATACCTTTCCTAATTTATTTAAACTTAGTACTTAATTACTGAAGGCGTT
1 ATTTTTTCCAAAAAAAATGCCTTTCCTAATTCATTTAAACTTAGTACTTAATTACTGAAGGCGTT
* * ** * *
1088544 TGTTATTAACACACG-TTTTCAATAATTTCCCTCTAAAATTTTTTTTGGAATGATTAAAGGCATC
66 TGTTATTAACACACGCCTTT-AATAATTTTCCTCTAAAAAATTTTTTGAAATTATTAAAGGCATC
* *
1088608 TTCCACTAACAAATACCTTCAATAATTTCTTTTAAATTATCTTCACAAAAATTAAAGGCGTTCCT
130 TTCCACTAACAAACACCTTCAATAATTTCTTTTAAATTATCTTCATAAAAATTAAAGGCGTTCCT
* * *
1088673 TGATTATAAATGCCTTCAATAATTTTTTTGATATATAATTTGTTGGGATTAGTAAAGGCATCTTC
195 TGATTATAAACGCCTTCAATAA-TTTTTT--TATAGAATTTGTTAGGATTAGTAAAGGCATCTTC
*
1088738 AACTATTAAACGCCTTTAATAATTTTCTCCTATTCAAGGCTTTTATTCCAGAAAAATGCCTTGAC
257 AACTATTAAACGCCTTTAATAATTTTCTCCTATTCAAGGCTTTTATTCCAGAAAAATACCTTGAC
* *
1088803 TAATTCATTTTATTTTTTGAATCAATTTATTGAATGCATCTTCTGCAGCAAAATGCCTTCAATAT
322 TAATTCATTTTATTTTTTGAATCAATTTATTGAAAGCATCTTCTGCAGCAAAACGCCTTCAATAT
* * * * *
1088868 TCCACCACACAAATTTTGAGATCGATAGTAAAGACGTT-TTCTAGAAAAATGTCATTACTAGATG
387 TCCACTACTCAAATTTTGAGATCGATAGTGAAGGCGTTATTGTAGAAAAATGTCATTACTAGATG
1088932 CTATTATTTTATTTTATGTACAAACAATTGAACAATTTCCAATTGAAATTATTGGTGTTAGTAAT
452 CTATTATTTTATTTTATGTACAAA-AATTGAACAATTTCCAATTGAAATTATTGGTGTTAGTAAT
** *
1088997 GGCATTTTCTAGTGAAAAATACCTTTAATAATTTTTCTCTAAAAAATTTAGGGATTACCAAAAGC
516 GGCATTTTCTAACGAAAAATACCTTCAATAATTTTTCTCTAAAAAATTTAGGGATTACCAAAAGC
*
1089062 GTCTTTTACTGACAAAAGGCCTTGAATATAAATGATGTTTTTTGAAAGTAAACGTCTTTTTATAA
581 GTCTTTTA-TGAC-AAAGGCCTTGAATAT-AATGAT-TTTTTT-AAAGTAAACG-CCTTTTATAA
* * **
1089127 ATTTAA-AGATTATTAAAGGCACCTTCAATTGAAAAACT-TTGTCAATATAGAAGGC
640 ATTTAAGA-ATTATTAAAGTCACCTTCAACTGAAAAA-TGTCATCAATATAGAAGGC
* *
1089182 A-TTTTTCCAAAAAAAATGCCTTTCTTAATTCATTTAAACTTTGTACTTAATTACTGAAGGCGTT
1 ATTTTTTCCAAAAAAAATGCCTTTCCTAATTCATTTAAACTTAGTACTTAATTACTGAAGGCGTT
* * * * *
1089246 TGTTGTTAACACACG-TTTTCAATATTTTTTCTCTAAAAAATTTTTTGAAATTATTAAAAGCATC
66 TGTTATTAACACACGCCTTT-AATAATTTTCCTCTAAAAAATTTTTTGAAATTATTAAAGGCATC
*** *
1089310 TTTTGCTAACAAACGCCTTCAATAA-TTCTTTTTAAATTATCTTCATAAAAATTGAAGGCGTTTA
130 TTCCACTAACAAACACCTTCAATAATTTC-TTTTAAATTATCTTCAT--AAA---AA------T-
* * *
1089374 TAATAGGTGTTCCTTGATTATAAACGCCTTCAATAA-TTTTTTATAGAATTTGTTGGGATTAATA
182 TAA-AGGCGTTCCTTGATTATAAACGCCTTCAATAATTTTTTTATAGAATTTGTTAGGATTAGTA
* * * * * * **
1089438 AAGGCCTCTTCCACTATTAAACACCTTCAATAATTTTTTCCTATTCAAGGTTTTTATTTTAGAAA
246 AAGGCATCTTCAACTATTAAACGCCTTTAATAATTTTCTCCTATTCAAGGCTTTTATTCCAGAAA
* * * *
1089503 AATACCTTCACTAATTCATTTTATTTTTTGATTCAATTTATTGAAAG-AGTCTTCAGCTGCAAAA
311 AATACCTTGACTAATTCATTTTATTTTTTGAATCAATTTATTGAAAGCA-TCTTCTGCAGCAAAA
*
1089567 CGCCTTCAATATTCCACTACTCAAATTTTTGAGATGGATAGTGAAGGCGTTTATTGTAGAAAAAT
375 CGCCTTCAATATTCCACTACTCAAA-TTTTGAGATCGATAGTGAAGGCG-TTATTGTAGAAAAAT
* * * ** *
1089632 GCCATTACTAGATGTTGTTATTTTATTTTATGTACAGATGATTGAACAATTTCCAATTAAAATT-
438 GTCATTACTAGATGCTATTATTTTATTTTATGTACA-AAAATTGAACAATTTCCAATTGAAATTA
* * * * * * *
1089696 TTGGTATTAGTAATGACGTCTTCTAACGAAAAACACCTTCAATAATTTCTCTCTAAAAAGTTTAG
502 TTGGTGTTAGTAATGGCATTTTCTAACGAAAAATACCTTCAATAATTTTTCTCTAAAAAATTTAG
* * * * *
1089761 GGATTAGCAAAAGCGTGTTCTATTGACAAA-G----G-------T-ATTTTTTTAAGGTAAACAC
567 GGATTACCAAAAGCGTCTTTTA-TGACAAAGGCCTTGAATATAATGATTTTTTTAAAGTAAACGC
* * * *
1089813 CTTCTATAAATTTAAGAATTATTAAAGGT-GCCTTCAACTGAAAAACGTCATCAATATAAAAGGC
631 CTTTTATAAATTTAAGAATTATTAAA-GTCACCTTCAACTGAAAAATGTCATCAATATAGAAGGC
* *
1089877 ATTTTTT-CTAGAAAAATGCCTTTCCTAATTCATTTAAACTTAGTACTTAATTACTGAAGGCGTT
1 ATTTTTTCCAAAAAAAATGCCTTTCCTAATTCATTTAAACTTAGTACTTAATTACTGAAGGCGTT
* * *
1089941 TGTTATTAACACATGCCTTTAATAATTTTCCTCTAAAAAAGTTTTTGAAATTATTAAAGGCGTCT
66 TGTTATTAACACACGCCTTTAATAATTTTCCTCTAAAAAATTTTTTGAAATTATTAAAGGCATCT
* * *
1090006 TCTACTAACAAACGCCTTTAATAATTT-TTTTAAAATTATCTTCATAAAAATTAAAGGCGTTCCT
131 TCCACTAACAAACACCTTCAATAATTTCTTTT-AAATTATCTTCATAAAAATTAAAGGCGTTCCT
* * * * * *
1090070 TAATTATAAACGCTTTTAATAATTTTCTTATAAAATTTGTTAGG-TTATTAAAGG
195 TGATTATAAACGCCTTCAATAATTTTTTTATAGAATTTGTTAGGATTAGTAAAGG
1090124 TGTCTACTAC
Statistics
Matches: 1430, Mismatches: 167, Indels: 112
0.84 0.10 0.07
Matches are distributed among these distances:
682 37 0.03
683 21 0.01
684 1 0.00
690 2 0.00
693 3 0.00
694 4 0.00
695 192 0.13
696 20 0.01
697 6 0.00
698 14 0.01
699 76 0.05
700 107 0.07
701 160 0.11
702 185 0.13
703 221 0.15
704 10 0.01
707 3 0.00
710 1 0.00
711 157 0.11
712 23 0.02
713 86 0.06
714 70 0.05
715 31 0.02
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (694 bp):
ATTTTTTCCAAAAAAAATGCCTTTCCTAATTCATTTAAACTTAGTACTTAATTACTGAAGGCGTT
TGTTATTAACACACGCCTTTAATAATTTTCCTCTAAAAAATTTTTTGAAATTATTAAAGGCATCT
TCCACTAACAAACACCTTCAATAATTTCTTTTAAATTATCTTCATAAAAATTAAAGGCGTTCCTT
GATTATAAACGCCTTCAATAATTTTTTTATAGAATTTGTTAGGATTAGTAAAGGCATCTTCAACT
ATTAAACGCCTTTAATAATTTTCTCCTATTCAAGGCTTTTATTCCAGAAAAATACCTTGACTAAT
TCATTTTATTTTTTGAATCAATTTATTGAAAGCATCTTCTGCAGCAAAACGCCTTCAATATTCCA
CTACTCAAATTTTGAGATCGATAGTGAAGGCGTTATTGTAGAAAAATGTCATTACTAGATGCTAT
TATTTTATTTTATGTACAAAAATTGAACAATTTCCAATTGAAATTATTGGTGTTAGTAATGGCAT
TTTCTAACGAAAAATACCTTCAATAATTTTTCTCTAAAAAATTTAGGGATTACCAAAAGCGTCTT
TTATGACAAAGGCCTTGAATATAATGATTTTTTTAAAGTAAACGCCTTTTATAAATTTAAGAATT
ATTAAAGTCACCTTCAACTGAAAAATGTCATCAATATAGAAGGC
Found at i:1091168 original size:80 final size:80
Alignment explanation
Indices: 1090997--1091236 Score: 306
Period size: 80 Copynumber: 3.0 Consensus size: 80
1090987 AATATTATGA
* * * * *
1090997 TTTACTAAACCTTGTTGTCTGATTTTTTTTTTGT-GAATGGTATTGTATGATATT-AGGGGCTGA
1 TTTACTGAACCTTGTTGTATGA-TATTATTTTGTCGAATGATATTGTATGATATTGAGGGGCTGA
* * *
1091060 ATCGTATACCGAATGG
65 ATCATATGCTGAATGG
* *
1091076 TTTACTGAACCTTGTTGTATGATATTGTATTGTCGAATGATATTGTATGATATTGAGGGGCTGAA
1 TTTACTGAACCTTGTTGTATGATATTATTTTGTCGAATGATATTGTATGATATTGAGGGGCTGAA
1091141 TCATATGCTGAATGG
66 TCATATGCTGAATGG
* * * *
1091156 TTTGCTGAACCTTGTTGTTTAATATTATTTTG-CTGAATGATTTTGTATGATATTGAGGGGCTGA
1 TTTACTGAACCTTGTTGTATGATATTATTTTGTC-GAATGATATTGTATGATATTGAGGGGCTGA
*
1091220 ATCATATGTTGAATGG
65 ATCATATGCTGAATGG
1091236 T
1 T
1091237 GTCTTTGAAT
Statistics
Matches: 142, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
78 8 0.06
79 40 0.28
80 94 0.66
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.43
Consensus pattern (80 bp):
TTTACTGAACCTTGTTGTATGATATTATTTTGTCGAATGATATTGTATGATATTGAGGGGCTGAA
TCATATGCTGAATGG
Found at i:1094519 original size:35 final size:35
Alignment explanation
Indices: 1094488--1094556 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
1094478 TATACAATTG
* *
1094488 ACAATAAATGTTTTCTGCGCATAAACCTACAACTA
1 ACAACAAACGTTTTCTGCGCATAAACCTACAACTA
* * *
1094523 ACAGCAAACGTTTTTTGGGCATAAACCTACAACT
1 ACAACAAACGTTTTCTGCGCATAAACCTACAACT
1094557 GATTTGACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.28
Consensus pattern (35 bp):
ACAACAAACGTTTTCTGCGCATAAACCTACAACTA
Found at i:1096165 original size:22 final size:20
Alignment explanation
Indices: 1096102--1096165 Score: 56
Period size: 22 Copynumber: 3.0 Consensus size: 20
1096092 ATAATTAAAT
* *
1096102 ACTACTAATTATCAATGATTT
1 ACTATTAATTATC-ATGATTA
*
1096123 ACTATTAAGTTAACATCGATTA
1 ACTATTAA-TTATCAT-GATTA
1096145 ACTATTATATTATCGATGATT
1 ACTATTA-ATTATC-ATGATT
1096166 TAGCAATAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
21 9 0.26
22 23 0.66
23 3 0.09
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (20 bp):
ACTATTAATTATCATGATTA
Found at i:1096208 original size:21 final size:21
Alignment explanation
Indices: 1096161--1096209 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1096151 ATATTATCGA
1096161 TGATTTAGCAATAAGTTTTAC
1 TGATTTAGCAATAAGTTTTAC
* * *
1096182 TAATTTAGTAATAAGTTTTAT
1 TGATTTAGCAATAAGTTTTAC
1096203 TGATTTA
1 TGATTTA
1096210 TTTTTAAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (21 bp):
TGATTTAGCAATAAGTTTTAC
Found at i:1096256 original size:22 final size:21
Alignment explanation
Indices: 1096231--1096303 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 21
1096221 TCAATGATCA
1096231 ACTACTAAATTATCAATTATTT
1 ACTACTAAATTAT-AATTATTT
* * *
1096253 ACTATTAATTTATAGTTGATTT
1 ACTACTAAATTATAATT-ATTT
*
1096275 ACTACTAAATTATTTATTATTT
1 ACTACTAAATTA-TAATTATTT
1096297 ACTACTA
1 ACTACTA
1096304 TCAATTAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
21 3 0.07
22 36 0.86
23 3 0.07
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.49
Consensus pattern (21 bp):
ACTACTAAATTATAATTATTT
Found at i:1096392 original size:11 final size:11
Alignment explanation
Indices: 1096338--1096414 Score: 66
Period size: 11 Copynumber: 7.0 Consensus size: 11
1096328 ATCGATCTAC
1096338 TATTAAATTAT
1 TATTAAATTAT
* * *
1096349 TGTTAATTTAC
1 TATTAAATTAT
1096360 TATTAAATTAT
1 TATTAAATTAT
* * *
1096371 CATTGATTTAT
1 TATTAAATTAT
1096382 TATTAAATTAT
1 TATTAAATTAT
* *
1096393 CAAT-AATTAAT
1 TATTAAATT-AT
1096404 TATTAAATTAT
1 TATTAAATTAT
1096415 CACTTATTTT
Statistics
Matches: 48, Mismatches: 16, Indels: 4
0.71 0.24 0.06
Matches are distributed among these distances:
10 4 0.08
11 40 0.83
12 4 0.08
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.52
Consensus pattern (11 bp):
TATTAAATTAT
Found at i:1096431 original size:22 final size:21
Alignment explanation
Indices: 1096338--1096448 Score: 105
Period size: 22 Copynumber: 5.0 Consensus size: 21
1096328 ATCGATCTAC
** *
1096338 TATTAAATTATTGTTAATTTAC
1 TATTAAATTATCATT-ATTTAT
1096360 TATTAAATTATCATTGATTTAT
1 TATTAAATTATCATT-ATTTAT
* *
1096382 TATTAAATTATCAATAATTAAT
1 TATTAAATTATC-ATTATTTAT
*
1096404 TATTAAATTATCACTTATTTTT
1 TATTAAATTATCA-TTATTTAT
* *
1096426 TGTTAAGTTATCATTGATTTAT
1 TATTAAATTATCATT-ATTTAT
1096448 T
1 T
1096449 GCTATACCTT
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
21 3 0.04
22 69 0.93
23 2 0.03
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (21 bp):
TATTAAATTATCATTATTTAT
Found at i:1096576 original size:11 final size:11
Alignment explanation
Indices: 1096555--1096602 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
1096545 AACTATTAAC
*
1096555 TATTAAATTAT
1 TATTAATTTAT
*
1096566 CATTAATTTAT
1 TATTAATTTAT
* *
1096577 TGTTAAGTTAT
1 TATTAATTTAT
*
1096588 TATTAATTTAC
1 TATTAATTTAT
1096599 TATT
1 TATT
1096603 GAGTTATGCA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.56
Consensus pattern (11 bp):
TATTAATTTAT
Found at i:1096607 original size:22 final size:22
Alignment explanation
Indices: 1096523--1096617 Score: 70
Period size: 22 Copynumber: 4.3 Consensus size: 22
1096513 TTAGTGTATT
*
1096523 ATTAATTTTACTA-AAAGTTATC
1 ATTAA-TTTACTATTAAGTTATC
* * *
1096545 AACT-ATTAACTATTAAATTATC
1 -ATTAATTTACTATTAAGTTATC
* * *
1096567 ATTAATTTATTGTTAAGTTATT
1 ATTAATTTACTATTAAGTTATC
*
1096589 ATTAATTTACTATTGAGTTATGC
1 ATTAATTTACTATTAAGTTAT-C
1096612 A-TAATT
1 ATTAATT
1096618 AGTTCTAAGT
Statistics
Matches: 55, Mismatches: 14, Indels: 7
0.72 0.18 0.09
Matches are distributed among these distances:
21 8 0.15
22 44 0.80
23 3 0.05
ACGTcount: A:0.38, C:0.07, G:0.06, T:0.48
Consensus pattern (22 bp):
ATTAATTTACTATTAAGTTATC
Found at i:1098872 original size:18 final size:17
Alignment explanation
Indices: 1098849--1098891 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
1098839 TTAAAAACTT
* *
1098849 AAAATTTCTTTTATTTAA
1 AAAATTT-TATTATATAA
1098867 AAAATTTTATTATAT-A
1 AAAATTTTATTATATAA
1098883 AAAATTTTA
1 AAAATTTTA
1098892 AAAAACAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 10 0.43
17 6 0.26
18 7 0.30
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
AAAATTTTATTATATAA
Found at i:1098879 original size:17 final size:16
Alignment explanation
Indices: 1098857--1098891 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1098847 TTAAAATTTC
1098857 TTTTATT-TA-AAAAA
1 TTTTATTATATAAAAA
1098871 TTTTATTATATAAAAA
1 TTTTATTATATAAAAA
1098887 TTTTA
1 TTTTA
1098892 AAAAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.37
15 2 0.11
16 10 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTTATTATATAAAAA
Found at i:1111008 original size:12 final size:12
Alignment explanation
Indices: 1110991--1111015 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1110981 CATGAATATT
1110991 ATTCAAATCATC
1 ATTCAAATCATC
1111003 ATTCAAATCATC
1 ATTCAAATCATC
1111015 A
1 A
1111016 GATCTAGATC
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:0.24, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTCAAATCATC
Found at i:1115385 original size:32 final size:31
Alignment explanation
Indices: 1115342--1115415 Score: 85
Period size: 32 Copynumber: 2.4 Consensus size: 31
1115332 TAGATTTACG
* *
1115342 ATTTATGTATTTATATAATTTAATATATTAAA
1 ATTTATATATTTATATAATGTAATATA-TAAA
* **
1115374 ATTTATATATTTATATTATGTCTTATATAAA
1 ATTTATATATTTATATAATGTAATATATAAA
*
1115405 AATTATATATT
1 ATTTATATATT
1115416 ATAATATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 14 0.39
32 22 0.61
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (31 bp):
ATTTATATATTTATATAATGTAATATATAAA
Found at i:1115496 original size:22 final size:26
Alignment explanation
Indices: 1115454--1115511 Score: 79
Period size: 24 Copynumber: 2.4 Consensus size: 26
1115444 TATATTTTTT
*
1115454 TTATTTTATTAAATTTATAAA-TA-A
1 TTATTTTATAAAATTTATAAATTATA
1115478 TTATTTT-TAAAATTT-TAAATTATA
1 TTATTTTATAAAATTTATAAATTATA
1115502 TTATTTTATA
1 TTATTTTATA
1115512 TTTATTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 4 0.13
23 9 0.30
24 15 0.50
25 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
TTATTTTATAAAATTTATAAATTATA
Found at i:1115580 original size:2 final size:2
Alignment explanation
Indices: 1115573--1115619 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1115563 GAAAATTTAA
1115573 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1115615 AG AG A
1 AG AG A
1115620 TGTGTGTGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1120824 original size:23 final size:23
Alignment explanation
Indices: 1120794--1120843 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
1120784 CTTTGATTCT
1120794 TTTAAATGTTATTCCTTTCTTCC
1 TTTAAATGTTATTCCTTTCTTCC
1120817 TTTAAATGTTATTCCTTTCTTCC
1 TTTAAATGTTATTCCTTTCTTCC
1120840 TTTA
1 TTTA
1120844 TAAGCATCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.18, C:0.20, G:0.04, T:0.58
Consensus pattern (23 bp):
TTTAAATGTTATTCCTTTCTTCC
Found at i:1122410 original size:31 final size:32
Alignment explanation
Indices: 1122345--1122423 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 32
1122335 TATAATTTAT
* * *
1122345 ATTTTTATATTAACA-TAAATTATAATACTTA
1 ATTTTTATATTAATATTAAATTATAATAATAA
1122376 ATTTTTATATATAATATTAAA-TA-AATAATAA
1 ATTTTTATAT-TAATATTAAATTATAATAATAA
*
1122407 ATTTTAATATTTAATAT
1 ATTTTTATA-TTAATAT
1122424 GACACGAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
31 30 0.73
32 7 0.17
33 4 0.10
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (32 bp):
ATTTTTATATTAATATTAAATTATAATAATAA
Found at i:1132249 original size:5 final size:5
Alignment explanation
Indices: 1132239--1132266 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1132229 CGTCTGGTTT
1132239 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1132267 ATGAAAGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:1133908 original size:11 final size:11
Alignment explanation
Indices: 1133892--1133922 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
1133882 AAACTGCATT
1133892 GAGTCTTTATC
1 GAGTCTTTATC
1133903 GAGTCTTTATC
1 GAGTCTTTATC
1133914 GAGTCTTTA
1 GAGTCTTTA
1133923 CAAATTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.45
Consensus pattern (11 bp):
GAGTCTTTATC
Found at i:1135148 original size:15 final size:14
Alignment explanation
Indices: 1135124--1135161 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
1135114 ATTAAATTTA
1135124 AATAAAATTTATTC
1 AATAAAATTTATTC
1135138 AATATAAATTTATT-
1 AATA-AAATTTATTC
*
1135152 ATTAAAATTT
1 AATAAAATTT
1135162 TTTTAATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 6 0.27
14 7 0.32
15 9 0.41
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (14 bp):
AATAAAATTTATTC
Found at i:1140975 original size:2 final size:2
Alignment explanation
Indices: 1140968--1141000 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1140958 TTTAAAGTTG
1140968 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
1141001 GTGACAAACA
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:1145989 original size:18 final size:20
Alignment explanation
Indices: 1145958--1145995 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1145948 AAGTTTTGAG
1145958 AAAATTTTAATAAA-AAATT
1 AAAATTTTAATAAATAAATT
*
1145977 AAAA-TTTATTAAATAAATT
1 AAAATTTTAATAAATAAATT
1145996 TGATCATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAATTTTAATAAATAAATT
Found at i:1146016 original size:33 final size:31
Alignment explanation
Indices: 1145978--1146044 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
1145968 TAAAAAATTA
** *
1145978 AAATTTATTAAATAAATTTGATCATAATTTTTT
1 AAATTTATTAAA-AAATTAAATC-GAATTTTTT
*
1146011 AAATTTATTTAAAAATTAAATCGAATTTTTT
1 AAATTTATTAAAAAATTAAATCGAATTTTTT
1146042 AAA
1 AAA
1146045 AAATTAAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 11 0.37
32 8 0.27
33 11 0.37
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (31 bp):
AAATTTATTAAAAAATTAAATCGAATTTTTT
Found at i:1146091 original size:7 final size:7
Alignment explanation
Indices: 1146079--1146113 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
1146069 TTTAGTTAAA
1146079 ATAAAAT
1 ATAAAAT
1146086 ATAAAAT
1 ATAAAAT
1146093 -TAAAAT
1 ATAAAAT
1146099 ATAAAAT
1 ATAAAAT
1146106 -TAAAAT
1 ATAAAAT
1146112 AT
1 AT
1146114 TATAATTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 12 0.46
7 14 0.54
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
ATAAAAT
Found at i:1146098 original size:6 final size:6
Alignment explanation
Indices: 1146074--1146111 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
1146064 ATCAATTTAG
1146074 TTAAAA -TAAAA TATAAAA TTAAAA TATAAAA TTAAAA T
1 TTAAAA TTAAAA T-TAAAA TTAAAA T-TAAAA TTAAAA T
1146112 ATTATAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.17
6 12 0.41
7 12 0.41
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
TTAAAA
Found at i:1146098 original size:13 final size:13
Alignment explanation
Indices: 1146075--1146113 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
1146065 TCAATTTAGT
1146075 TAAAA-TAAAATA
1 TAAAATTAAAATA
1146087 TAAAATTAAAATA
1 TAAAATTAAAATA
1146100 TAAAATTAAAATA
1 TAAAATTAAAATA
1146113 T
1 T
1146114 TATAATTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 5 0.19
13 21 0.81
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAAATTAAAATA
Found at i:1146349 original size:2 final size:2
Alignment explanation
Indices: 1146342--1146373 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1146332 TTTCTTCATA
1146342 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1146374 GGGCTCCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1155202 original size:2 final size:2
Alignment explanation
Indices: 1155195--1155221 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1155185 ATAAGAAGGT
1155195 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1155222 TTATTTATTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1155307 original size:4 final size:4
Alignment explanation
Indices: 1155298--1155323 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1155288 ATACCAAATA
1155298 TATC TATC TATC TATC TATC TATC TA
1 TATC TATC TATC TATC TATC TATC TA
1155324 AAAGTAACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (4 bp):
TATC
Found at i:1163133 original size:4 final size:4
Alignment explanation
Indices: 1163124--1163151 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1163114 GTTATACGTG
1163124 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
1163152 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:1167323 original size:28 final size:29
Alignment explanation
Indices: 1167271--1167330 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 29
1167261 TCCATAAGAC
1167271 GATGGCAGTAAAAAAAACAAATGTTCAAAA
1 GATGGCAGT-AAAAAAACAAATGTTCAAAA
*
1167301 GATGGCAGT-AAAAAACAAGTGTTCAAAA
1 GATGGCAGTAAAAAAACAAATGTTCAAAA
1167329 GA
1 GA
1167331 CTTACCTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 20 0.69
30 9 0.31
ACGTcount: A:0.53, C:0.10, G:0.20, T:0.17
Consensus pattern (29 bp):
GATGGCAGTAAAAAAACAAATGTTCAAAA
Found at i:1169757 original size:21 final size:20
Alignment explanation
Indices: 1169720--1169758 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1169710 TAAATTTAAA
* *
1169720 TTTATTTAAATATATAAAAT
1 TTTATTTAAAAAAATAAAAT
1169740 TTTATATTAAAAAAATAAA
1 TTTAT-TTAAAAAAATAAA
1169759 TAAAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTATTTAAAAAAATAAAAT
Found at i:1171209 original size:254 final size:252
Alignment explanation
Indices: 1170757--1171258 Score: 905
Period size: 254 Copynumber: 2.0 Consensus size: 252
1170747 AAAAAAAAAA
* * *
1170757 AATATATATATATATATGTATTATAGAGGGAGGAACATGTCTGAGCCTGGTGAAGTGAATGCCAA
1 AATATATATATATATATATATTATAGAGGGAGGAACATGGCTGAGCATGGTGAAGTGAATGCCAA
*
1170822 TGACATATAGTTCCAGATTAGAAGAACTGTCTCAATGCAGTACAAAAGTACAAGGTTTCTGAGGT
66 TGACATATAGTTCCAGATTAGAAGAACTGTCTCAATGCAGTACAAAAGTACAAGGTTTCCGAGGT
1170887 TTTCTAACTGGCAAGAGGGATCATTGGTTGGCATCATAGGCCGAAACTCCTCCCAGTTAGAGGAC
131 TTTCTAACTGGCAAGAGGGATCATTGGTTGGCATCATAGGCCGAAACTCCTCCCAGTTAGAGGAC
1170952 CACTTTGACATGCTATTTTGGTCAAATTTTGGTTTGGGAATTGTGAAATATTATTAT
196 CACTTTGACATGCTATTTTGGTCAAATTTTGGTTTGGGAATTGTGAAATATTATTAT
*
1171009 AATATATATATATATATATATTTTAGAGGGAGGAACATGGCTGAGCATGGTGAAGTGAATGCCAA
1 AATATATATATATATATATATTATAGAGGGAGGAACATGGCTGAGCATGGTGAAGTGAATGCCAA
*
1171074 TGACATATATAGTTCCAGATTAGAAGAACTGTTTCAATGCAGTACAAAAGTACAAGGTTTCCGAG
66 TGAC--ATATAGTTCCAGATTAGAAGAACTGTCTCAATGCAGTACAAAAGTACAAGGTTTCCGAG
* * *
1171139 GTTTTCTAACTGGCAAGAGGGATCATTGGTTGGCATCATCGGCCGAAGCTCCTCCCAGTTAGATG
129 GTTTTCTAACTGGCAAGAGGGATCATTGGTTGGCATCATAGGCCGAAACTCCTCCCAGTTAGAGG
1171204 ACCACTTTGACATGCTATTTTGGTCAAATTTTGGTTTGGGAATTGTGAAATATTA
194 ACCACTTTGACATGCTATTTTGGTCAAATTTTGGTTTGGGAATTGTGAAATATTA
1171259 CTCTAGAGTT
Statistics
Matches: 239, Mismatches: 9, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
252 65 0.27
254 174 0.73
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.31
Consensus pattern (252 bp):
AATATATATATATATATATATTATAGAGGGAGGAACATGGCTGAGCATGGTGAAGTGAATGCCAA
TGACATATAGTTCCAGATTAGAAGAACTGTCTCAATGCAGTACAAAAGTACAAGGTTTCCGAGGT
TTTCTAACTGGCAAGAGGGATCATTGGTTGGCATCATAGGCCGAAACTCCTCCCAGTTAGAGGAC
CACTTTGACATGCTATTTTGGTCAAATTTTGGTTTGGGAATTGTGAAATATTATTAT
Found at i:1172684 original size:20 final size:18
Alignment explanation
Indices: 1172642--1172676 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1172632 TCGAACCAAA
1172642 TTATATATTTTTATTAAT
1 TTATATATTTTTATTAAT
1172660 TTATATATATTTT-TTAA
1 TTATATAT-TTTTATTAA
1172677 GTTTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTATATATTTTTATTAAT
Found at i:1176826 original size:87 final size:87
Alignment explanation
Indices: 1176723--1177003 Score: 499
Period size: 87 Copynumber: 3.2 Consensus size: 87
1176713 CATCATCATC
* * *
1176723 ATCATTATCATTACTATCAATTTTCTCTTCATCATCAACATATTCTTCAATCTCTTTCTCGTGTA
1 ATCATTATCATCACTATCAATTTTGTCTTCATCATCAACATATTCTTCAATCTCTTTCTCATGTA
1176788 GAGACCAAAAAATTGCCATAAA
66 GAGACCAAAAAATTGCCATAAA
1176810 ATCATTATCATCACTATCAATTTTGTCTTCATCATCAACATATTCTTCAATCTCTTTCTCATGTA
1 ATCATTATCATCACTATCAATTTTGTCTTCATCATCAACATATTCTTCAATCTCTTTCTCATGTA
1176875 GAGACCAAAAAATTGCCATAAA
66 GAGACCAAAAAATTGCCATAAA
*
1176897 ATCATTGTCATCACTATCAATTTTGTCTTCATCATCAACATATTCTTCAATCTCTTTCTCATGTA
1 ATCATTATCATCACTATCAATTTTGTCTTCATCATCAACATATTCTTCAATCTCTTTCTCATGTA
* *
1176962 GAGACCAAAAATTTGCCATGAA
66 GAGACCAAAAAATTGCCATAAA
*
1176984 ATCATTATCATCACCATCAA
1 ATCATTATCATCACTATCAA
1177004 CAAGAGCACA
Statistics
Matches: 186, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 186 1.00
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.37
Consensus pattern (87 bp):
ATCATTATCATCACTATCAATTTTGTCTTCATCATCAACATATTCTTCAATCTCTTTCTCATGTA
GAGACCAAAAAATTGCCATAAA
Found at i:1177828 original size:160 final size:161
Alignment explanation
Indices: 1177521--1177838 Score: 451
Period size: 160 Copynumber: 2.0 Consensus size: 161
1177511 TCGTAAATGA
* * **
1177521 CTTTATAGAGCATAGAATTGGGACCGTAAGCTTGGGTTGCAAGGATTTTGTCTGGTCGTGATCCT
1 CTTTATAGAACATAGAATTGGGACCATAAGCTTGGGAAGCAAGGATTTTGTCTGGTCGTGATCCT
* *
1177586 TGTTGGCCAAGGAGTTTATCAGTTTGACTAACAAGTCACTTTTGTGAACAGCATTACGAAAATAG
66 TGTTGGCCAAGGAGTTAATCAGTTTGACTAACAAGTCACTTTTGCGAACAGCATTACGAAAATAG
* *
1177651 AAAGCCAATGGCTCTTTCCTTCTTTAGCCGT
131 AAAGCCAACGACTCTTTCCTTCTTTAGCCGT
** * * *
1177682 CTTTATAGAACATAGAATTGGGACCATGTGCTTTGGAAGCGA-GATTTTGTCTTGTCGTGATCCT
1 CTTTATAGAACATAGAATTGGGACCATAAGCTTGGGAAGCAAGGATTTTGTCTGGTCGTGATCCT
* * * *
1177746 TGTTGTCCAAGGAGTTAATCAGTTTGACTAACAAGTCATTTTTGCGAACAG-ATTATGAAAGTAG
66 TGTTGGCCAAGGAGTTAATCAGTTTGACTAACAAGTCACTTTTGCGAACAGCATTACGAAAATAG
*
1177810 AAAAGTCAACGACTCTTTCCTTCTTTAGC
131 -AAAGCCAACGACTCTTTCCTTCTTTAGC
1177839 TGTTGACCTG
Statistics
Matches: 138, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
159 11 0.08
160 93 0.67
161 34 0.25
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (161 bp):
CTTTATAGAACATAGAATTGGGACCATAAGCTTGGGAAGCAAGGATTTTGTCTGGTCGTGATCCT
TGTTGGCCAAGGAGTTAATCAGTTTGACTAACAAGTCACTTTTGCGAACAGCATTACGAAAATAG
AAAGCCAACGACTCTTTCCTTCTTTAGCCGT
Found at i:1178725 original size:19 final size:18
Alignment explanation
Indices: 1178701--1178754 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
1178691 CAGGTATCAC
1178701 TTTTTATTGTAATTCTTTG
1 TTTTTATTGTAATT-TTTG
* *
1178720 TTTTTAGTTTTACTTTTTG
1 TTTTTA-TTGTAATTTTTG
1178739 TGTTTTATTGT-ATTTT
1 T-TTTTATTGTAATTTT
1178755 ATTTCTTGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 4 0.14
19 14 0.48
20 11 0.38
ACGTcount: A:0.13, C:0.04, G:0.11, T:0.72
Consensus pattern (18 bp):
TTTTTATTGTAATTTTTG
Found at i:1183955 original size:16 final size:16
Alignment explanation
Indices: 1183936--1183968 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1183926 TGCCCCAGTC
1183936 AAATAATAATTGGGTT
1 AAATAATAATTGGGTT
1183952 AAATAATAATTGGGTT
1 AAATAATAATTGGGTT
1183968 A
1 A
1183969 GATTAATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.36
Consensus pattern (16 bp):
AAATAATAATTGGGTT
Found at i:1185660 original size:29 final size:27
Alignment explanation
Indices: 1185642--1185695 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
1185632 ATTTGAATGA
1185642 TAACATATTTTGTAATGATTTATGAAG
1 TAACATATTTTGTAATGATTTATGAAG
* *
1185669 TGACATATTTTGATATTGATTTATGAA
1 TAACATATTTTG-TAATGATTTATGAA
1185696 ATTTATGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (27 bp):
TAACATATTTTGTAATGATTTATGAAG
Found at i:1191614 original size:23 final size:24
Alignment explanation
Indices: 1191580--1191625 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
1191570 GTTATTTAGT
* *
1191580 TATTATATATAATTTTTTAAATAA
1 TATTATATATAATTATTAAAATAA
1191604 TATTA-ATATAATTATTAAAATA
1 TATTATATATAATTATTAAAATA
1191626 TTAAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TATTATATATAATTATTAAAATAA
Found at i:1191653 original size:10 final size:9
Alignment explanation
Indices: 1191613--1191685 Score: 75
Period size: 9 Copynumber: 8.4 Consensus size: 9
1191603 ATATTAATAT
1191613 AATTATTAA
1 AATTATTAA
1191622 AA-TATTAAA
1 AATTATT-AA
*
1191631 AATTATT-T
1 AATTATTAA
1191639 AA-TATTAA
1 AATTATTAA
1191647 AATATATTAA
1 AAT-TATTAA
1191657 AATTATT--
1 AATTATTAA
*
1191664 TATTATTAA
1 AATTATTAA
1191673 AATTATTAA
1 AATTATTAA
1191682 AATT
1 AATT
1191686 TAAAAATAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
7 10 0.19
8 8 0.15
9 22 0.42
10 13 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
AATTATTAA
Found at i:1191658 original size:26 final size:26
Alignment explanation
Indices: 1191616--1191685 Score: 108
Period size: 25 Copynumber: 2.8 Consensus size: 26
1191606 TTAATATAAT
*
1191616 TATTAAAATAT-TAAAAATTATTTAA
1 TATTAAAATATATTAAAATTATTTAA
*
1191641 TATTAAAATATATTAAAATTATTTAT
1 TATTAAAATATATTAAAATTATTTAA
1191667 TATTAAAAT-TATTAAAATT
1 TATTAAAATATATTAAAATT
1191686 TAAAAATAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
25 21 0.50
26 21 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TATTAAAATATATTAAAATTATTTAA
Found at i:1191685 original size:25 final size:25
Alignment explanation
Indices: 1191614--1191685 Score: 110
Period size: 26 Copynumber: 2.8 Consensus size: 25
1191604 TATTAATATA
1191614 ATTATTAAAA-TATTAAAAATTATTT
1 ATTATTAAAATTATT-AAAATTATTT
*
1191639 AATATTAAAATATATTAAAATTATTT
1 ATTATTAAAAT-TATTAAAATTATTT
1191665 ATTATTAAAATTATTAAAATT
1 ATTATTAAAATTATTAAAATT
1191686 TAAAAATAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.44
26 20 0.47
27 4 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTATTAAAATTATTAAAATTATTT
Found at i:1191729 original size:19 final size:19
Alignment explanation
Indices: 1191685--1191748 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
1191675 TTATTAAAAT
* *
1191685 TTAAAAATAAT-TGT-ATT
1 TTAAAAATAATATTTAATA
*
1191702 TTAATAATAATATTTAATA
1 TTAAAAATAATATTTAATA
*
1191721 TTAAAAATATTATATTAATA
1 TTAAAAATAATAT-TTAATA
1191741 -TAAAAATA
1 TTAAAAATA
1191749 CTTTAAATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
17 10 0.26
18 2 0.05
19 21 0.54
20 6 0.15
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
TTAAAAATAATATTTAATA
Found at i:1191731 original size:16 final size:16
Alignment explanation
Indices: 1191622--1191772 Score: 61
Period size: 16 Copynumber: 9.4 Consensus size: 16
1191612 TAATTATTAA
1191622 AATATTAAAAATTATTT
1 AATATTAAAAA-TATTT
1191639 AATATT--AAA-A--T
1 AATATTAAAAATATTT
*
1191650 -ATATTAAAATTATTT
1 AATATTAAAAATATTT
* *
1191665 ATTATTAAAATTA-TT
1 AATATTAAAAATATTT
*
1191680 AAAATTTAAAAATAATTGT
1 AATA-TTAAAAAT-ATT-T
*
1191699 -ATTTTAATAATAATATTT
1 AATATT-A-AA-AATATTT
1191717 AATATTAAAAATATTAT
1 AATATTAAAAATATT-T
*
1191734 ATTAATATAAAAATACTTT
1 AAT-AT-TAAAAATA-TTT
*
1191753 AA-A-TAAAACTATTT
1 AATATTAAAAATATTT
*
1191767 ATTATT
1 AATATT
1191773 TTTTATATTA
Statistics
Matches: 102, Mismatches: 12, Indels: 41
0.66 0.08 0.26
Matches are distributed among these distances:
10 5 0.05
11 1 0.01
12 2 0.02
13 2 0.02
14 4 0.04
15 16 0.16
16 25 0.25
17 15 0.15
18 7 0.07
19 20 0.20
20 5 0.05
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (16 bp):
AATATTAAAAATATTT
Found at i:1191770 original size:33 final size:35
Alignment explanation
Indices: 1191650--1191770 Score: 87
Period size: 36 Copynumber: 3.6 Consensus size: 35
1191640 ATATTAAAAT
* *
1191650 ATATTAAAATTATT-TATT-AT-TAAAATTA-TTA
1 ATATTAAAAATATTATATTAATATAAAAATATTTA
* * * *
1191681 AAATTTAAAAATAATTGTATT-TTAATAATAATATTTA
1 ATA-TTAAAAAT-ATTATATTAAT-ATAAAAATATTTA
1191718 ATATTAAAAATATTATATTAATATAAAAATACTTTA
1 ATATTAAAAATATTATATTAATATAAAAATA-TTTA
*
1191754 A-A-TAAAACTATT-TATTA
1 ATATTAAAAATATTATATTA
1191771 TTTTTTATAT
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
31 2 0.03
32 7 0.10
33 8 0.11
34 14 0.19
35 16 0.22
36 20 0.28
37 5 0.07
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (35 bp):
ATATTAAAAATATTATATTAATATAAAAATATTTA
Found at i:1191838 original size:31 final size:33
Alignment explanation
Indices: 1191800--1191880 Score: 114
Period size: 31 Copynumber: 2.5 Consensus size: 33
1191790 ATAAATTATA
* *
1191800 ATATTATTTATTAATATATTCT-AT-TAATGGT
1 ATATTATTTATTAATATATTATAATATAATAGT
*
1191831 ATATTATTTATTAATATATTATAATATAATATT
1 ATATTATTTATTAATATATTATAATATAATAGT
1191864 AT-TTATTTATTAATATA
1 ATATTATTTATTAATATA
1191881 ACATTATTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
31 21 0.47
32 17 0.38
33 7 0.16
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (33 bp):
ATATTATTTATTAATATATTATAATATAATAGT
Found at i:1192030 original size:22 final size:22
Alignment explanation
Indices: 1191994--1192041 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1191984 AAATAATCTC
* * *
1191994 ATTTTTTATTGATTAATGAATT
1 ATTTTTAATTAATTAATCAATT
1192016 ATTTTTAATTAATTAATCAATT
1 ATTTTTAATTAATTAATCAATT
1192038 -TTTT
1 ATTTT
1192042 ATCAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (22 bp):
ATTTTTAATTAATTAATCAATT
Found at i:1192083 original size:13 final size:14
Alignment explanation
Indices: 1192058--1192085 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1192048 TAAATACCCA
1192058 AAAAATTATTTTTC
1 AAAAATTATTTTTC
1192072 AAAAATTATTTTTC
1 AAAAATTATTTTTC
1192086 GCCAAACAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
AAAAATTATTTTTC
Found at i:1192413 original size:31 final size:31
Alignment explanation
Indices: 1192375--1192448 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 31
1192365 TATATTTTTT
1192375 ATTTTTATATTAATATAAATTATAATATAT-A
1 ATTTTTATATTAATATAAATTA-AATATATAA
* * *
1192406 ATTTTTATATAAAATATTATTTAAATATATAA
1 ATTTTTATAT-TAATATAAATTAAATATATAA
*
1192438 ATTTTAATATT
1 ATTTTTATATT
1192449 TTATTAGACA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 17 0.47
32 19 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
ATTTTTATATTAATATAAATTAAATATATAA
Found at i:1204143 original size:6 final size:6
Alignment explanation
Indices: 1204134--1204159 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1204124 TATTACAAAT
1204134 ATTAAA ATTAAA ATTAAA ATTAAA AT
1 ATTAAA ATTAAA ATTAAA ATTAAA AT
1204160 ATTATTGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATTAAA
Found at i:1204574 original size:8 final size:8
Alignment explanation
Indices: 1204556--1204590 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
1204546 TCATGCTCTC
1204556 TAAACATAA
1 TAAA-ATAA
1204565 TAAAATAA
1 TAAAATAA
1204573 TAAAATAA
1 TAAAATAA
1204581 TAATAATAA
1 TAA-AATAA
1204590 T
1 T
1204591 TATTATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 15 0.60
9 10 0.40
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (8 bp):
TAAAATAA
Found at i:1205117 original size:43 final size:43
Alignment explanation
Indices: 1205056--1205142 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
1205046 AGATAAAAAA
*
1205056 AAAGATTGTCGGATTTGACATTTGAATATCATATATGTTGGAT
1 AAAGATTGTCGGAGTTGACATTTGAATATCATATATGTTGGAT
1205099 AAAGATTGTCGGAGTTGACATTTGAATATCATATATGTTGGAT
1 AAAGATTGTCGGAGTTGACATTTGAATATCATATATGTTGGAT
1205142 A
1 A
1205143 CTATTTGTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.38
Consensus pattern (43 bp):
AAAGATTGTCGGAGTTGACATTTGAATATCATATATGTTGGAT
Found at i:1208849 original size:2 final size:2
Alignment explanation
Indices: 1208842--1208870 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1208832 GTTTCTCCAA
1208842 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1208871 GGGATTTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1209912 original size:18 final size:18
Alignment explanation
Indices: 1209874--1209913 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1209864 ATCGCTGGCT
* **
1209874 GCAGCATCAGGGCCATCA
1 GCAGCAGCAGGGCCAGAA
1209892 GCAGCAGCAGGGCCAGAA
1 GCAGCAGCAGGGCCAGAA
1209910 GCAG
1 GCAG
1209914 GGGCGTTAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.35, T:0.05
Consensus pattern (18 bp):
GCAGCAGCAGGGCCAGAA
Found at i:1212302 original size:32 final size:32
Alignment explanation
Indices: 1212265--1212332 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
1212255 ACAAGCGAGT
*
1212265 TCTTTTATCCCTTATTTTGTTTCAGTATAAAA
1 TCTTTTACCCCTTATTTTGTTTCAGTATAAAA
1212297 TCTTTTACCCCTTATTTTGTTTCAGTATAAAA
1 TCTTTTACCCCTTATTTTGTTTCAGTATAAAA
1212329 -CTTT
1 TCTTT
1212333 AGATTTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 4 0.11
32 31 0.89
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.53
Consensus pattern (32 bp):
TCTTTTACCCCTTATTTTGTTTCAGTATAAAA
Found at i:1218352 original size:18 final size:17
Alignment explanation
Indices: 1218328--1218431 Score: 59
Period size: 19 Copynumber: 5.8 Consensus size: 17
1218318 CAAATATTTT
1218328 TAAAAATTATAAATAATTA
1 TAAAAATTA-AAA-AATTA
* * * *
1218347 -AAAAATGAAATATTTT
1 TAAAAATTAAAAAATTA
* *
1218363 TAAAAAATATAAAATT-
1 TAAAAATTAAAAAATTA
*
1218379 GAAAAATTATAAAAATTTA
1 TAAAAATTA-AAAAA-TTA
*
1218398 TAAAAATCTAAAAATTTTAA
1 TAAAAAT-TAAAAA-ATT-A
1218418 TAAAAATTAAAAAA
1 TAAAAATTAAAAAA
1218432 ATGAAAAATT
Statistics
Matches: 63, Mismatches: 15, Indels: 15
0.68 0.16 0.16
Matches are distributed among these distances:
16 10 0.16
17 16 0.25
18 9 0.14
19 18 0.29
20 10 0.16
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (17 bp):
TAAAAATTAAAAAATTA
Found at i:1218398 original size:10 final size:10
Alignment explanation
Indices: 1218380--1218425 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
1218370 TATAAAATTG
1218380 AAAAA-TTAT
1 AAAAATTTAT
1218389 AAAAATTTAT
1 AAAAATTTAT
*
1218399 AAAAATCTA-
1 AAAAATTTAT
*
1218408 AAAATTTTAAT
1 AAAAATTT-AT
1218419 AAAAATT
1 AAAAATT
1218426 AAAAAAATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
9 11 0.37
10 13 0.43
11 6 0.20
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAAATTTAT
Found at i:1218420 original size:20 final size:17
Alignment explanation
Indices: 1218323--1218430 Score: 67
Period size: 18 Copynumber: 6.1 Consensus size: 17
1218313 AATTTCAAAT
*
1218323 ATTTTTAAAAATTATAAA
1 ATTTATAAAAATTA-AAA
* * *
1218341 TAATTA-AAAAATGAAAT
1 -ATTTATAAAAATTAAAA
* *
1218358 ATTTTTAAAAAATATAAA
1 ATTTATAAAAATTA-AAA
* *
1218376 ATTGA-AAAATTATAAAA
1 ATTTATAAAAAT-TAAAA
1218393 ATTTATAAAAATCTAAAA
1 ATTTATAAAAAT-TAAAA
1218411 ATTTTAATAAAAATTAAAA
1 A-TTT-ATAAAAATTAAAA
1218430 A
1 A
1218431 AATGAAAAAT
Statistics
Matches: 67, Mismatches: 16, Indels: 12
0.71 0.17 0.13
Matches are distributed among these distances:
16 3 0.04
17 19 0.28
18 25 0.37
19 12 0.18
20 8 0.12
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (17 bp):
ATTTATAAAAATTAAAA
Found at i:1218431 original size:20 final size:18
Alignment explanation
Indices: 1218380--1218431 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 18
1218370 TATAAAATTG
1218380 AAAAATTATAAAAATTTAT
1 AAAAATTA-AAAAATTTAT
*
1218399 AAAAATCTAAAAATTTTAAT
1 AAAAAT-TAAAAAATTT-AT
1218419 AAAAATTAAAAAA
1 AAAAATTAAAAAA
1218432 ATGAAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAATTAAAAAATTTAT
Found at i:1218431 original size:28 final size:30
Alignment explanation
Indices: 1218347--1218449 Score: 82
Period size: 26 Copynumber: 3.7 Consensus size: 30
1218337 TAAATAATTA
* *
1218347 AAAAATGAAATATTTT--TAAAAA-AT-AT
1 AAAAATGAAAAATTTTAATAAAAATTTAAT
*
1218373 AAAATTGAAAAA--TT-ATAAAAATTT-AT
1 AAAAATGAAAAATTTTAATAAAAATTTAAT
*
1218399 AAAAATCTAAAAATTTTAATAAAAA-TTAA-
1 AAAAAT-GAAAAATTTTAATAAAAATTTAAT
*
1218428 AAAAATGAAAAATTTTAGTAAA
1 AAAAATGAAAAATTTTAATAAA
1218450 GATGAAATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
24 2 0.03
25 6 0.10
26 18 0.29
27 5 0.08
28 14 0.22
29 10 0.16
30 8 0.13
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (30 bp):
AAAAATGAAAAATTTTAATAAAAATTTAAT
Found at i:1218542 original size:38 final size:37
Alignment explanation
Indices: 1218500--1218596 Score: 90
Period size: 37 Copynumber: 2.6 Consensus size: 37
1218490 TTAACAAAAC
* ** *
1218500 TGAAAATTAAAAAAATCT-AAATTGTTTTTGAAAATTTT
1 TGAAAATTAAAAAAAT-TAAAAAT-TTTTCAAAAAATTT
* *
1218538 TGAAATTTTAAAAAATTAAAAATTTTTCAAAAAATTT
1 TGAAAATTAAAAAAATTAAAAATTTTTCAAAAAATTT
*
1218575 TGAAAA-TCAAAAAATTCAAAAA
1 TGAAAATTAAAAAAATT-AAAAA
1218597 ATCTAAAACA
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
36 9 0.18
37 22 0.45
38 18 0.37
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (37 bp):
TGAAAATTAAAAAAATTAAAAATTTTTCAAAAAATTT
Found at i:1218644 original size:56 final size:57
Alignment explanation
Indices: 1218584--1218716 Score: 132
Period size: 56 Copynumber: 2.3 Consensus size: 57
1218574 TTGAAAATCA
* *
1218584 AAAAATTCAAAAAATCTAAAACATT-GT-AAAA-AAATATAAAAAAT-TAAAAATATTCT
1 AAAAATT-AAAAAAT-TAAAACATTAATAAAAATAAAAATAAAAAATCTAAAAA-ATTCT
* **
1218640 AAAAA-TAAAAACTTAAAATTTTAATAAAAATAAAAATAAAAAATCTAAAAAATTCT
1 AAAAATTAAAAAATTAAAACATTAATAAAAATAAAAATAAAAAATCTAAAAAATTCT
1218696 AAAAATATATAAAAAATTAAA
1 -AAAA-AT-TAAAAAATTAAA
1218717 TCTGTAAGAT
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
53 7 0.11
54 7 0.11
55 5 0.08
56 22 0.35
57 10 0.16
58 1 0.02
60 11 0.17
ACGTcount: A:0.68, C:0.05, G:0.01, T:0.26
Consensus pattern (57 bp):
AAAAATTAAAAAATTAAAACATTAATAAAAATAAAAATAAAAAATCTAAAAAATTCT
Found at i:1218655 original size:25 final size:24
Alignment explanation
Indices: 1218622--1218690 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
1218612 AAAAAATATA
1218622 AAAAATTAAAAATATTCTAAAAAT
1 AAAAATTAAAAATATTCTAAAAAT
* *
1218646 AAAAACTT-AAAATTTTAATAAAAAT
1 AAAAA-TTAAAAATATT-CTAAAAAT
1218671 AAAAA-TAAAAA-A-TCTAAAAA
1 AAAAATTAAAAATATTCTAAAAA
1218691 ATTCTAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
21 6 0.16
22 1 0.03
23 1 0.03
24 16 0.42
25 14 0.37
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (24 bp):
AAAAATTAAAAATATTCTAAAAAT
Found at i:1218931 original size:37 final size:37
Alignment explanation
Indices: 1218860--1218931 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
1218850 AGAAAATTTA
**
1218860 ATTTTTATTAAGAATTTTTGAATTTTTCTTTTTTTGT
1 ATTTTTATTAAGAATTTTTGAATTTTTCAGTTTTTGT
* *
1218897 ATTTTTATTAA-AATTTTTAGATTTTTTGAGTTTTT
1 ATTTTTATTAAGAATTTTT-GAATTTTTCAGTTTTT
1218932 TAAGTTTTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 7 0.23
37 23 0.77
ACGTcount: A:0.24, C:0.01, G:0.08, T:0.67
Consensus pattern (37 bp):
ATTTTTATTAAGAATTTTTGAATTTTTCAGTTTTTGT
Found at i:1219024 original size:30 final size:30
Alignment explanation
Indices: 1218988--1219061 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
1218978 TTTTTATAAT
1218988 TTTTTAAATATTTCAG-ATTTTTTAAAAAAA
1 TTTTTAAATATTTCAGAATTTTTT-AAAAAA
* * *
1219018 TTTTTAAA-ATTTTTAGAATTTTTTATAACA
1 TTTTTAAATA-TTTCAGAATTTTTTAAAAAA
1219048 TTTTTAAATATTTC
1 TTTTTAAATATTTC
1219062 TTTTAATGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
29 1 0.03
30 28 0.76
31 8 0.22
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.55
Consensus pattern (30 bp):
TTTTTAAATATTTCAGAATTTTTTAAAAAA
Found at i:1224272 original size:19 final size:21
Alignment explanation
Indices: 1224238--1224279 Score: 70
Period size: 19 Copynumber: 2.1 Consensus size: 21
1224228 TAAAATTAAT
1224238 AAATATTAATTTTTTAATATA
1 AAATATTAATTTTTTAATATA
1224259 AAATATT-A-TTTTTAATATA
1 AAATATTAATTTTTTAATATA
1224278 AA
1 AA
1224280 TATAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 13 0.62
20 1 0.05
21 7 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATATTAATTTTTTAATATA
Found at i:1224301 original size:17 final size:17
Alignment explanation
Indices: 1224270--1224303 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1224260 AATATTATTT
1224270 TTAATATAAATATAAAA
1 TTAATATAAATATAAAA
1224287 TTAA-ATAAATAATAAAA
1 TTAATATAAAT-ATAAAA
1224304 AATAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TTAATATAAATATAAAA
Found at i:1224786 original size:11 final size:11
Alignment explanation
Indices: 1224772--1224839 Score: 55
Period size: 11 Copynumber: 5.6 Consensus size: 11
1224762 ATTATGTTAA
*
1224772 ATTTATATATT
1 ATTTTTATATT
1224783 ATTTTTTTATATT
1 A--TTTTTATATT
1224796 ATTTTTATATTTT
1 ATTTTTATA--TT
*
1224809 ATTATCTTATTTT
1 ATT-T-TTATATT
1224822 ATTTTTATATT
1 ATTTTTATATT
*
1224833 ATATTTA
1 ATTTTTA
1224840 AAAATGCACA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
11 21 0.45
12 1 0.02
13 20 0.43
14 1 0.02
15 4 0.09
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (11 bp):
ATTTTTATATT
Found at i:1224808 original size:21 final size:20
Alignment explanation
Indices: 1224782--1224837 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
1224772 ATTTATATAT
1224782 TATTTTTTTATATTATTTTTA
1 TATTTTTTTATATTA-TTTTA
* *
1224803 TATTTTATTATCTTATTTTA
1 TATTTTTTTATATTATTTTA
1224823 T-TTTTATATTATATT
1 TATTTT-T-TTATATT
1224838 TAAAAATGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 4 0.14
20 6 0.21
21 19 0.66
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (20 bp):
TATTTTTTTATATTATTTTA
Found at i:1224832 original size:13 final size:13
Alignment explanation
Indices: 1224773--1224838 Score: 71
Period size: 13 Copynumber: 5.1 Consensus size: 13
1224763 TTATGTTAAA
*
1224773 TTTATATATTATT
1 TTTATATTTTATT
* *
1224786 TTTTTATATTATT
1 TTTATATTTTATT
1224799 TTTATATTTTATT
1 TTTATATTTTATT
*
1224812 ATCT-TATTTTATT
1 -TTTATATTTTATT
*
1224825 TTTATATTATATT
1 TTTATATTTTATT
1224838 T
1 T
1224839 AAAAATGCAC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
12 2 0.04
13 41 0.91
14 2 0.04
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTATATTTTATT
Found at i:1224832 original size:26 final size:26
Alignment explanation
Indices: 1224773--1224837 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
1224763 TTATGTTAAA
* * *
1224773 TTTATATATTATTTTTTTATATTATT
1 TTTATATTTTATTATCTTATATTATT
*
1224799 TTTATATTTTATTATCTTATTTTATT
1 TTTATATTTTATTATCTTATATTATT
*
1224825 TTTATATTATATT
1 TTTATATTTTATT
1224838 TAAAAATGCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (26 bp):
TTTATATTTTATTATCTTATATTATT
Found at i:1229367 original size:36 final size:35
Alignment explanation
Indices: 1229288--1229367 Score: 97
Period size: 37 Copynumber: 2.2 Consensus size: 35
1229278 AAATATTATA
*
1229288 TTTAAATTAAAATTAAAAAAAAATATTTTGAAAAT
1 TTTAAAATAAAATTAAAAAAAAATATTTTGAAAAT
* * * *
1229323 TTTGAAAATAAAATTATACAAATATTATTTTTAAAAT
1 TTT-AAAATAAAATTA-AAAAAAAATATTTTGAAAAT
1229360 TTTAAAAT
1 TTTAAAAT
1229368 TTATTATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
35 3 0.08
36 16 0.42
37 19 0.50
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (35 bp):
TTTAAAATAAAATTAAAAAAAAATATTTTGAAAAT
Found at i:1230911 original size:18 final size:18
Alignment explanation
Indices: 1230873--1230912 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1230863 ATCACTGCCT
* **
1230873 GCAGCATCAGGGCCATCA
1 GCAGCAGCAGGGCCAGAA
1230891 GCAGCAGCAGGGCCAGAA
1 GCAGCAGCAGGGCCAGAA
1230909 GCAG
1 GCAG
1230913 GGGCGTCAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.35, T:0.05
Consensus pattern (18 bp):
GCAGCAGCAGGGCCAGAA
Found at i:1232292 original size:5 final size:5
Alignment explanation
Indices: 1232282--1232310 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1232272 CCAACCTACC
1232282 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1232311 TGTTAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:1233501 original size:21 final size:21
Alignment explanation
Indices: 1233491--1233531 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1233481 CTTTAATAAT
1233491 AATAAATTAAAAATTAAAAAA
1 AATAAATTAAAAATTAAAAAA
1233512 AATAAATTAAAAATTAAAAA
1 AATAAATTAAAAATTAAAAA
1233532 TGAACTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (21 bp):
AATAAATTAAAAATTAAAAAA
Found at i:1233506 original size:7 final size:7
Alignment explanation
Indices: 1233494--1233532 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
1233484 TAATAATAAT
1233494 AAATTAA
1 AAATTAA
1233501 AAATTAA
1 AAATTAA
*
1233508 AAA-AAA
1 AAATTAA
1233514 TAAATTAA
1 -AAATTAA
1233522 AAATTAA
1 AAATTAA
1233529 AAAT
1 AAAT
1233533 GAACTTTCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 2 0.07
7 24 0.86
8 2 0.07
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAATTAA
Found at i:1245397 original size:130 final size:130
Alignment explanation
Indices: 1245164--1245424 Score: 495
Period size: 130 Copynumber: 2.0 Consensus size: 130
1245154 TCGATTCAAA
*
1245164 CACTTTTGTTGTCATACACTTATTATTAGTTTAATGAAATATGTTAGCTTTCTTTTGGAAATAAT
1 CACTTTTGTTGTCATACACTTATTATCAGTTTAATGAAATATGTTAGCTTTCTTTTGGAAATAAT
1245229 GCCTATCCATTTTTTTACCTCATTTGATATCTTTGTTCACCTTATAAACGAATGAGAGAAATGTG
66 GCCTATCCATTTTTTTACCTCATTTGATATCTTTGTTCACCTTATAAACGAATGAGAGAAATGTG
1245294 CACTTTTGTTGTCATACACTTATTATCAGTTTAATGAAATATGTTAGCTTTCTTTTGGAAATAAT
1 CACTTTTGTTGTCATACACTTATTATCAGTTTAATGAAATATGTTAGCTTTCTTTTGGAAATAAT
* *
1245359 GCCTATCCATTTTTTTACCTCATTTGGTATCTTTGTTCACCTTATAAATGAATGAGAGAAATGTG
66 GCCTATCCATTTTTTTACCTCATTTGATATCTTTGTTCACCTTATAAACGAATGAGAGAAATGTG
1245424 C
1 C
1245425 GATTGCATTT
Statistics
Matches: 128, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 128 1.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (130 bp):
CACTTTTGTTGTCATACACTTATTATCAGTTTAATGAAATATGTTAGCTTTCTTTTGGAAATAAT
GCCTATCCATTTTTTTACCTCATTTGATATCTTTGTTCACCTTATAAACGAATGAGAGAAATGTG
Found at i:1245954 original size:50 final size:50
Alignment explanation
Indices: 1245892--1246382 Score: 327
Period size: 51 Copynumber: 9.6 Consensus size: 50
1245882 GAGACTTTTT
* * * *
1245892 TTTTAAAATTATTGAGCATCTACTGAGAGAAACCTTTTTCAGATTTTAAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGAAACCTTTTTCAGATTTTAAA
* * * *
1245942 TTTTAAAGTTATTGAGCCTCTGCTGAGATG--AGCTTTTTCA-ATATAAAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGA-GAAACCTTTTTCAGATTTTAAA
* *
1245990 CTTTTAAAGTTGTTGAGCTTCTGTTGAGAGAAGCAGATAAGCCTTTTTCAGATTTTAAA
1 -TTTTAAAGTTGTTGAGCCTCTGCT----G-AG-AGA-AA-CCTTTTTCAGATTTTAAA
* * * * * **
1246049 TTTTAAAGTTGTTGAGCCTTTACTGATATG-AGCCTTTTTTAAGA-TGAAAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGA-GAAACC-TTTTTCAGATTTTAAA
* *
1246099 TTTTTAAAATTGTTGAGTCTCTGCTG-GAGAAACCTTTTTCAGATTTTAAA
1 -TTTTAAAGTTGTTGAGCCTCTGCTGAGAGAAACCTTTTTCAGATTTTAAA
* ** ** *
1246149 TTTTAAAGTTATTGAGCCTCTATTGA-A-AAGAGCCTTTTTCAAGATGATAAT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGAA-A-CCTTTTTC-AGATTTTAAA
* * * * * **
1246200 TTTTAAAGTTGTTGAGACTCTGTTGAGAGGAGCCTTTATCA-ATATAAAAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGAAACCTTTTTCAGAT-TTTAAA
* * * * **
1246250 TTTCTTTAAAGTTGTTAAGCCTTTGCTTAGAGGAACCTTTTTCAAGA-TGAAAA
1 --T-TTTAAAGTTGTTGAGCCTCTGCTGAGAGAAACCTTTTTC-AGATTTTAAA
* * * *
1246303 TTTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCCTTTTTTAGATTTTAAA
1 -TTTTAAAGTTGTTGAGCCTCTGCTGAGAGAAACCTTTTTCAGATTTTAAA
*
1246354 TTTTAAAGTTGTTGAACCTCTGCTGAGAG
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAG
1246383 GAGCTTTTTT
Statistics
Matches: 345, Mismatches: 65, Indels: 62
0.73 0.14 0.13
Matches are distributed among these distances:
48 8 0.02
49 63 0.18
50 81 0.23
51 105 0.30
52 5 0.01
53 41 0.12
54 5 0.01
55 2 0.01
57 1 0.00
58 28 0.08
59 6 0.02
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (50 bp):
TTTTAAAGTTGTTGAGCCTCTGCTGAGAGAAACCTTTTTCAGATTTTAAA
Found at i:1246165 original size:100 final size:101
Alignment explanation
Indices: 1246029--1246395 Score: 423
Period size: 100 Copynumber: 3.6 Consensus size: 101
1246019 GAAGCAGATA
* * *
1246029 AGCCTTTTTCAGATTTTAAATTTTAAAGTTGTTGAGCCTTTACTGATATGAGCCTTTTTTAAGAT
1 AGCCTTTTTCAGATTTTAAATTTTAAAGTTGTTGAGCCTTTACTGAAAAGAGCCTTTTTCAAGAT
* * * *
1246094 GAAAATTTTTAAAATTGTTGAGTCTCTGCTG-GAGA
66 GAAAATTTTTAAAGTTGTTGAGACTCTGTTGAGAGG
* * * *
1246129 AACCTTTTTCAGATTTTAAATTTTAAAGTTATTGAGCCTCTATTGAAAAGAGCCTTTTTCAAGAT
1 AGCCTTTTTCAGATTTTAAATTTTAAAGTTGTTGAGCCTTTACTGAAAAGAGCCTTTTTCAAGAT
*
1246194 GATAATTTTTAAAGTTGTTGAGACTCTGTTGAGAGG
66 GAAAATTTTTAAAGTTGTTGAGACTCTGTTGAGAGG
* ** * * * * * *
1246230 AGCCTTTATCA-ATATAAAAATTTCTTTAAAGTTGTTAAGCCTTTGCTTAGAGGAACCTTTTTCA
1 AGCCTTTTTCAGAT-TTTAAA--T-TTTAAAGTTGTTGAGCCTTTACTGAAAAGAGCCTTTTTCA
*
1246294 AGATGAAAATTTTTAAAGTTGTTGAGCCTCTGTTGAGAGG
62 AGATGAAAATTTTTAAAGTTGTTGAGACTCTGTTGAGAGG
* * * * * * *
1246334 AGCCTTTTTTAGATTTTAAATTTTAAAGTTGTTGAACCTCTGCTGAGAGGAGCTTTTTTCAA
1 AGCCTTTTTCAGATTTTAAATTTTAAAGTTGTTGAGCCTTTACTGAAAAGAGCCTTTTTCAA
1246396 CTGAGAGGAG
Statistics
Matches: 224, Mismatches: 37, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
100 87 0.39
101 51 0.23
102 1 0.00
103 1 0.00
104 82 0.37
105 2 0.01
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (101 bp):
AGCCTTTTTCAGATTTTAAATTTTAAAGTTGTTGAGCCTTTACTGAAAAGAGCCTTTTTCAAGAT
GAAAATTTTTAAAGTTGTTGAGACTCTGTTGAGAGG
Found at i:1246401 original size:20 final size:20
Alignment explanation
Indices: 1246376--1246415 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1246366 TGAACCTCTG
1246376 CTGAGAGGAGCTTTTTTCAA
1 CTGAGAGGAGCTTTTTTCAA
1246396 CTGAGAGGAGCTTTTTTCAA
1 CTGAGAGGAGCTTTTTTCAA
1246416 GATAGAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (20 bp):
CTGAGAGGAGCTTTTTTCAA
Found at i:1246441 original size:119 final size:119
Alignment explanation
Indices: 1246278--1246512 Score: 298
Period size: 117 Copynumber: 2.0 Consensus size: 119
1246268 GCCTTTGCTT
* ** *
1246278 AGAGGAACCTTTTTCAAGATGAAAATTTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCCTTTTT
1 AGAGGAACCTTTTTCAAGATGAAAATTTTTAAAGTTGTTAAGCCTCTACTGAGAGGA-ACTTTTT
* * *
1246343 -TAGATTTTAAATTTTAAAGTTGTTGAA-CCTCTGCTGAGAGGAGCTTTTTTCAACTG
65 CAAGA--TAAAATTTTAAAGTTGTT-AAGCCTCTGCTGAGAGGAGCATTTTTCAACTG
* * *
1246399 AGAGGAGCTTTTTTCAAGAT-AGAA-TTTTAAAGTTGTTAAGCCTCTACTGAGAGGAACTTTTTC
1 AGAGGAACCTTTTTCAAGATGAAAATTTTTAAAGTTGTTAAGCCTCTACTGAGAGGAACTTTTTC
* *
1246462 AAGATAAAATTTTAAAGTTGTTAAGCTTCTGTTGAGAGGAGCATTTTTCAA
66 AAGATAAAATTTTAAAGTTGTTAAGCCTCTGCTGAGAGGAGCATTTTTCAA
1246513 GATAAGACTT
Statistics
Matches: 100, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
116 2 0.02
117 40 0.40
118 6 0.06
119 31 0.31
120 3 0.03
121 18 0.18
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (119 bp):
AGAGGAACCTTTTTCAAGATGAAAATTTTTAAAGTTGTTAAGCCTCTACTGAGAGGAACTTTTTC
AAGATAAAATTTTAAAGTTGTTAAGCCTCTGCTGAGAGGAGCATTTTTCAACTG
Found at i:1246535 original size:50 final size:50
Alignment explanation
Indices: 1246396--1246612 Score: 280
Period size: 48 Copynumber: 4.4 Consensus size: 50
1246386 CTTTTTTCAA
*
1246396 CTGAGAGGAGCTTTTTTCAAGAT-AGAATTTTAAAGTTGTTAAGCCTCTA
1 CTGAGAGGAGCTTTTTTCAAGATAAGAATTTTAAAGTTGTTAAGCCTCTG
* *
1246445 CTGAGAGGAAC-TTTTTCAAGATAA-AATTTTAAAGTTGTTAAGCTTCTG
1 CTGAGAGGAGCTTTTTTCAAGATAAGAATTTTAAAGTTGTTAAGCCTCTG
* * * *
1246493 TTGAGAGGAGCATTTTTCAAGATAAGACTTTTAAAATTGTTAAGCCTCTG
1 CTGAGAGGAGCTTTTTTCAAGATAAGAATTTTAAAGTTGTTAAGCCTCTG
* **
1246543 CTGAGAGGAGCTTTTTTCAAGATTAA-AATTTTTAAAGTTGTTGAGTTTCTG
1 CTGAGAGGAGCTTTTTTCAAGA-TAAGAA-TTTTAAAGTTGTTAAGCCTCTG
* *
1246594 CTAAGAAGAGCTTTTTTCA
1 CTGAGAGGAGCTTTTTTCA
1246613 TATTTTAAAT
Statistics
Matches: 146, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
48 42 0.29
49 24 0.16
50 42 0.29
51 38 0.26
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (50 bp):
CTGAGAGGAGCTTTTTTCAAGATAAGAATTTTAAAGTTGTTAAGCCTCTG
Found at i:1246543 original size:167 final size:168
Alignment explanation
Indices: 1246254--1246562 Score: 457
Period size: 167 Copynumber: 1.8 Consensus size: 168
1246244 TAAAAATTTC
* * * *
1246254 TTTAAAGTTGTTAAGCCTTTGCTTAGAGGAACCTTTTTCAAGATGAAAATTTTTAAAGTTGTTGA
1 TTTAAAGTTGTTAAGCCTCTACTGAGAGGAACCTTTTTCAAGATGAAAATTTTTAAAGTTGTTAA
* * *
1246319 GCCTCTGTTGAGAGGAGCCTTTTTTAGATTTTAAATTTTAAAGTTGTTGAACCTCTGCTGAGAGG
66 GCCTCTGTTGAGAGGAGCATTTTTAAGA--TTAAATTTTAAAATTGTTGAACCTCTGCTGAGAGG
1246384 AGCTTTTTTCAACTGAGAGGAGCTTTTTTCAAGATAGAAT
129 AGCTTTTTTCAACTGAGAGGAGCTTTTTTCAAGATAGAAT
1246424 TTTAAAGTTGTTAAGCCTCTACTGAGAGGAA-CTTTTTCAAGAT-AAAA-TTTTAAAGTTGTTAA
1 TTTAAAGTTGTTAAGCCTCTACTGAGAGGAACCTTTTTCAAGATGAAAATTTTTAAAGTTGTTAA
*
1246486 GCTTCTGTTGAGAGGAGCATTTTTCAAGA-TAAGACTTTTAAAATTGTT-AAGCCTCTGCTGAGA
66 GCCTCTGTTGAGAGGAGCATTTTT-AAGATTAA-A-TTTTAAAATTGTTGAA-CCTCTGCTGAGA
1246549 GGAGCTTTTTTCAA
127 GGAGCTTTTTTCAA
1246563 GATTAAAATT
Statistics
Matches: 127, Mismatches: 8, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
165 3 0.02
166 3 0.02
167 74 0.58
168 7 0.06
169 12 0.09
170 28 0.22
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (168 bp):
TTTAAAGTTGTTAAGCCTCTACTGAGAGGAACCTTTTTCAAGATGAAAATTTTTAAAGTTGTTAA
GCCTCTGTTGAGAGGAGCATTTTTAAGATTAAATTTTAAAATTGTTGAACCTCTGCTGAGAGGAG
CTTTTTTCAACTGAGAGGAGCTTTTTTCAAGATAGAAT
Found at i:1246580 original size:268 final size:275
Alignment explanation
Indices: 1246147--1246643 Score: 661
Period size: 268 Copynumber: 1.8 Consensus size: 275
1246137 TCAGATTTTA
* * * *
1246147 AATTTTAAAGTTATTGAGCCTCTATTGAAAAGAGCCTTTTTCAAGATGATAATTTTTAAAGTTGT
1 AATTTTAAAGTTATTAAGCCTCTACTGAAAAGAGACTTTTTCAAGATGATAAATTTTAAAGTTGT
* * * * * *
1246212 TGAGACTCTGTTGAGAGGAGCCTTTATCAATATAAAAATTTCTTTAAAGTTGTTAAGCCTTTGCT
66 TAAGACTCTGTTGAGAGGAGCATTTATCAAGATAAAAATCTCTTTAAAATTGTTAAGCCTCTGCT
* * * *
1246277 TAGAGGAACCTTTTTCAAGATGAAAATTTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCCTTTT
131 GAGAGGAACCTTTTTCAAGATGAAAATTTTTAAAGTTGTTGAGCCTCTGCTAAGAAGAG-CTTTT
* *
1246342 TT-AGATTTTAAATTTT-AAAGTTGTTGAACCTCTGCTGAGAGGAGCTTTTTTCAACTGAGAGGA
195 TTCAGATTTTAAATTTTAAAAGTTATCGAACCTCTGCTGAGAGGAGCTTTTTTCAACTGAGAGGA
1246405 GCTTTTTTCAAGATAG
260 GCTTTTTTCAAGATAG
* * *
1246421 AATTTTAAAGTTGTTAAGCCTCTACTGAGAGGA-ACTTTTTCAAGAT-A-AAATTTTAAAGTTGT
1 AATTTTAAAGTTATTAAGCCTCTACTGAAAAGAGACTTTTTCAAGATGATAAATTTTAAAGTTGT
* *
1246483 TAAG-CTTCTGTTGAGAGGAGCATTTTTCAAGAT-AAGA-CT-TTTAAAATTGTTAAGCCTCTGC
66 TAAGAC-TCTGTTGAGAGGAGCATTTATCAAGATAAAAATCTCTTTAAAATTGTTAAGCCTCTGC
* * * **
1246544 TGAGAGGAGCTTTTTTCAAGATTAAAATTTTTAAAGTTGTTGAGTTTCTGCTAAGAAGAGCTTTT
130 TGAGAGGAACCTTTTTCAAGATGAAAATTTTTAAAGTTGTTGAGCCTCTGCTAAGAAGAGCTTTT
*
1246609 TTCATATTTTAAATTTTCAAAAGTTATCGAACCTC
195 TTCAGATTTTAAATTTT-AAAAGTTATCGAACCTC
1246644 GAGTAAAAAG
Statistics
Matches: 192, Mismatches: 27, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
267 7 0.04
268 84 0.44
269 1 0.01
270 18 0.09
271 41 0.21
272 1 0.01
273 12 0.06
274 28 0.15
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.39
Consensus pattern (275 bp):
AATTTTAAAGTTATTAAGCCTCTACTGAAAAGAGACTTTTTCAAGATGATAAATTTTAAAGTTGT
TAAGACTCTGTTGAGAGGAGCATTTATCAAGATAAAAATCTCTTTAAAATTGTTAAGCCTCTGCT
GAGAGGAACCTTTTTCAAGATGAAAATTTTTAAAGTTGTTGAGCCTCTGCTAAGAAGAGCTTTTT
TCAGATTTTAAATTTTAAAAGTTATCGAACCTCTGCTGAGAGGAGCTTTTTTCAACTGAGAGGAG
CTTTTTTCAAGATAG
Found at i:1248167 original size:16 final size:14
Alignment explanation
Indices: 1248144--1248178 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1248134 ATAAAACTTT
1248144 AATAATAAT-AAAA
1 AATAATAATAAAAA
*
1248157 AATAATGATAAAAA
1 AATAATAATAAAAA
1248171 AATAATAA
1 AATAATAA
1248179 ATTTAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (14 bp):
AATAATAATAAAAA
Found at i:1248406 original size:18 final size:18
Alignment explanation
Indices: 1248383--1248418 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1248373 TTTCTTGTTA
1248383 AAAAATTAAATAATAAAT
1 AAAAATTAAATAATAAAT
*
1248401 AAAAATTAACTAATAAAT
1 AAAAATTAAATAATAAAT
1248419 TAAGAATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAAATTAAATAATAAAT
Found at i:1250036 original size:15 final size:15
Alignment explanation
Indices: 1249998--1250037 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
1249988 CGAAGTATTC
*
1249998 AGGGTTCAGGGTTTA
1 AGGGTTCTGGGTTTA
*
1250013 AGGGTTTCTGGGTTTT
1 AGGG-TTCTGGGTTTA
1250029 AGGGTTCTG
1 AGGGTTCTG
1250038 TTTTTAATCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.12, C:0.07, G:0.40, T:0.40
Consensus pattern (15 bp):
AGGGTTCTGGGTTTA
Found at i:1256966 original size:18 final size:18
Alignment explanation
Indices: 1256920--1256985 Score: 73
Period size: 18 Copynumber: 3.7 Consensus size: 18
1256910 TTTAAATTTG
*
1256920 AAATATTTTTAAAAAGTA
1 AAATATTTTTAAAAAATA
*
1256938 TAAATA--ATTAAAAAATA
1 -AAATATTTTTAAAAAATA
1256955 AAATATTTTTAAAAAATA
1 AAATATTTTTAAAAAATA
* *
1256973 AAAAATTGTTAAA
1 AAATATTTTTAAA
1256986 TTATAAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
16 5 0.12
17 9 0.22
18 21 0.52
19 5 0.12
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
AAATATTTTTAAAAAATA
Found at i:1256992 original size:36 final size:35
Alignment explanation
Indices: 1256911--1256993 Score: 87
Period size: 35 Copynumber: 2.4 Consensus size: 35
1256901 AATTTTTTTT
* * *
1256911 TTAAATT-TGAAATATTTTTAAAAAGTATAAATAA
1 TTAAATTATAAAATATTTTTAAAAAATAAAAATAA
** **
1256945 TTAAAAAATAAAATATTTTTAAAAAATAAAAAATTG
1 TTAAATTATAAAATATTTTTAAAAAAT-AAAAATAA
1256981 TTAAATTATAAAA
1 TTAAATTATAAAA
1256994 ATTCAAAAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
34 5 0.13
35 17 0.45
36 16 0.42
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (35 bp):
TTAAATTATAAAATATTTTTAAAAAATAAAAATAA
Found at i:1257116 original size:16 final size:17
Alignment explanation
Indices: 1257081--1257126 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
1257071 TTAAAATGTA
*
1257081 AAAAAATCACAAAAACTT
1 AAAAAATC-TAAAAACTT
1257099 AACAAAA-CTAAAAA-TT
1 AA-AAAATCTAAAAACTT
1257115 AAAAAATCTAAA
1 AAAAAATCTAAA
1257127 TTTTTTGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
15 4 0.16
16 9 0.36
17 5 0.20
18 3 0.12
19 4 0.16
ACGTcount: A:0.70, C:0.13, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAAAATCTAAAAACTT
Found at i:1257163 original size:36 final size:38
Alignment explanation
Indices: 1257113--1257193 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 38
1257103 AAACTAAAAA
** *
1257113 TTAAAAAATCTAAA-TTTTTTGAAAATTTTTTGAAACT
1 TTAAAAAATCTAAATTTTTTTGAAAAAATCTTGAAACT
*
1257150 TTAAAAAAT-TAAATTTTTTTGAAAAAATCTTGAAATT
1 TTAAAAAATCTAAATTTTTTTGAAAAAATCTTGAAACT
1257187 TTAAAAA
1 TTAAAAA
1257194 TTTCAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 4 0.10
37 35 0.90
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (38 bp):
TTAAAAAATCTAAATTTTTTTGAAAAAATCTTGAAACT
Found at i:1257225 original size:30 final size:30
Alignment explanation
Indices: 1257189--1257252 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 30
1257179 TTGAAATTTT
1257189 AAAAATT-TCAAAAAAATCT-AAAACATTCTA
1 AAAAATTAT-AAAAAAAT-TAAAAACATTCTA
*
1257219 AAAAATTATAAAAAAATTAAAAATATTCTA
1 AAAAATTATAAAAAAATTAAAAACATTCTA
1257249 AAAA
1 AAAA
1257253 TAAAAACTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 1 0.03
30 29 0.94
31 1 0.03
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.27
Consensus pattern (30 bp):
AAAAATTATAAAAAAATTAAAAACATTCTA
Found at i:1257254 original size:11 final size:10
Alignment explanation
Indices: 1257182--1257252 Score: 65
Period size: 10 Copynumber: 7.2 Consensus size: 10
1257172 AAAAATCTTG
*
1257182 AAATTTTAAA
1 AAATTCTAAA
*
1257192 AATTTC-AAA
1 AAATTCTAAA
*
1257201 AAAATCTAAA
1 AAATTCTAAA
*
1257211 ACATTCTAAA
1 AAATTCTAAA
*
1257221 AAATTATAAA
1 AAATTCTAAA
*
1257231 AAAAT-TAAA
1 AAATTCTAAA
1257240 AATATTCTAAA
1 AA-ATTCTAAA
1257251 AA
1 AA
1257253 TAAAAACTTA
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
9 13 0.27
10 29 0.60
11 6 0.12
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (10 bp):
AAATTCTAAA
Found at i:1257575 original size:21 final size:20
Alignment explanation
Indices: 1257551--1257618 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
1257541 CGTTTTCATA
1257551 ATTTTTTCAAAATTTTTAAAT
1 ATTTTTT-AAAATTTTTAAAT
***
1257572 ATTTATTTTTTTATTTTTAAAAT
1 A-TT-TTTTAAAATTTTT-AAAT
* *
1257595 ATATTTTAAAATTTTTAAAA
1 ATTTTTTAAAATTTTTAAAT
1257615 ATTT
1 ATTT
1257619 CTTTTAATAC
Statistics
Matches: 35, Mismatches: 9, Indels: 7
0.69 0.18 0.14
Matches are distributed among these distances:
20 6 0.17
21 11 0.31
22 9 0.26
23 9 0.26
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTTTTAAAATTTTTAAAT
Found at i:1262728 original size:18 final size:16
Alignment explanation
Indices: 1262678--1262744 Score: 62
Period size: 18 Copynumber: 3.9 Consensus size: 16
1262668 CGATGCAAAT
1262678 ATAATATAAATATTTAA
1 ATAATATAAATATTT-A
*
1262695 ATAATGTAAATCATTTA
1 ATAATATAAAT-ATTTA
1262712 ATGAATATAATATATTTA
1 AT-AATATAA-ATATTTA
* *
1262730 TTATATATATATATT
1 ATA-ATATAAATATT
1262745 ATATGTGATA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
17 19 0.45
18 21 0.50
19 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (16 bp):
ATAATATAAATATTTA
Found at i:1262987 original size:23 final size:20
Alignment explanation
Indices: 1262961--1263021 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
1262951 TTCGTAATTA
1262961 ATTAGATTTGAAATTAATAAAAT
1 ATTA-ATTTGAAA-T-ATAAAAT
**
1262984 ATTAATTTTTAATATAAAAT
1 ATTAATTTGAAATATAAAAT
* *
1263004 ATTATTTTTAAATATAAA
1 ATTAATTTGAAATATAAA
1263022 TATAAAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 23 0.68
21 1 0.03
22 6 0.18
23 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
ATTAATTTGAAATATAAAAT
Found at i:1262997 original size:18 final size:18
Alignment explanation
Indices: 1262976--1263024 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 18
1262966 ATTTGAAATT
1262976 AATAAAATATTAATTTTTA
1 AATAAAATATT-ATTTTTA
1262995 ATATAAAATATTATTTTTA
1 A-ATAAAATATTATTTTTA
1263014 AATATAAATAT
1 AATA-AAATAT
1263025 AAAATTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.11
19 15 0.54
20 10 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATAAAATATTATTTTTA
Found at i:1263012 original size:19 final size:21
Alignment explanation
Indices: 1262977--1263021 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
1262967 TTTGAAATTA
1262977 ATAAAATATTAATTTTT-AAT
1 ATAAAATATTAATTTTTAAAT
1262997 ATAAAATATT-ATTTTTAAAT
1 ATAAAATATTAATTTTTAAAT
1263017 ATAAA
1 ATAAA
1263022 TATAAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATAAAATATTAATTTTTAAAT
Found at i:1272570 original size:2 final size:2
Alignment explanation
Indices: 1272563--1272593 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1272553 CGCCGGTTTA
1272563 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1272594 ACTTTTCTGT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1274209 original size:22 final size:22
Alignment explanation
Indices: 1274175--1274216 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1274165 AGAAACGCTA
*
1274175 TATTTGTTCAATAAAAAATAAT
1 TATTTGTTAAATAAAAAATAAT
* *
1274197 TATTTTTTAAATAATAAATA
1 TATTTGTTAAATAAAAAATA
1274217 TCATGTTTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
TATTTGTTAAATAAAAAATAAT
Done.