Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008105.1 Hibiscus syriacus cultivar Beakdansim tig00110637_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5962497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 30
Found at i:1150669 original size:30 final size:30
Alignment explanation
Indices: 1150635--1150692 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1150625 TTAAGGGTTT
* *
1150635 AATTTTTTTAATACTTGTTATTAGGGGCCC
1 AATTTCTTCAATACTTGTTATTAGGGGCCC
*
1150665 AATTTCTTCAATATTTGTTATTAGGGGC
1 AATTTCTTCAATACTTGTTATTAGGGGC
1150693 ATATTTCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (30 bp):
AATTTCTTCAATACTTGTTATTAGGGGCCC
Found at i:1151238 original size:14 final size:13
Alignment explanation
Indices: 1151214--1151254 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
1151204 AGTAATACGA
1151214 TTTTGAATTTAGGG
1 TTTT-AATTTAGGG
1151228 TTTATAATTTAGGG
1 TTT-TAATTTAGGG
*
1151242 TTTTAAGTTAGGG
1 TTTTAATTTAGGG
1151255 GAAGGGTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 9 0.36
14 15 0.60
15 1 0.04
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (13 bp):
TTTTAATTTAGGG
Found at i:1151254 original size:13 final size:14
Alignment explanation
Indices: 1151222--1151254 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1151212 GATTTTGAAT
*
1151222 TTAGGGTTTATAAT
1 TTAGGGTTTATAAG
1151236 TTAGGGTTT-TAAG
1 TTAGGGTTTATAAG
1151249 TTAGGG
1 TTAGGG
1151255 GAAGGGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.45
Consensus pattern (14 bp):
TTAGGGTTTATAAG
Found at i:1152335 original size:35 final size:34
Alignment explanation
Indices: 1152268--1152477 Score: 123
Period size: 34 Copynumber: 6.2 Consensus size: 34
1152258 CCTACTCAAA
** *
1152268 ATAAATATA-TTTTAATTTTCAA-ATTT-AAATAT
1 ATAAATA-ACTTTTAATTTGAAATATTTAAAAGAT
1152300 AT-AATAACTTTTAATTTGAAATATTTAAAAGAT
1 ATAAATAACTTTTAATTTGAAATATTTAAAAGAT
* * * *
1152333 ATAATTACCTTTTAATATT-TAA-ATTTAAGAGAT
1 ATAAATAACTTTTAAT-TTGAAATATTTAAAAGAT
* * * * * *
1152366 AATAAGTATCGTTTAAATTGAAATATTAAAAAACAT
1 -ATAAATAACTTTTAATTTGAAATATT-TAAAAGAT
* *
1152402 ATAATTATA-TTTTAATATTCAAA-A-TTAAATAGAT
1 ATAAATA-ACTTTTAAT-TTGAAATATTTAAA-AGAT
* * *
1152436 AGTAAATATCTTTTAATTTAAAATATTTAAAAAAT
1 A-TAAATAACTTTTAATTTGAAATATTTAAAAGAT
1152471 ATAAATA
1 ATAAATA
1152478 TCCTACTAAT
Statistics
Matches: 136, Mismatches: 26, Indels: 30
0.71 0.14 0.16
Matches are distributed among these distances:
30 1 0.01
31 15 0.11
32 6 0.04
33 22 0.16
34 43 0.32
35 34 0.25
36 15 0.11
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (34 bp):
ATAAATAACTTTTAATTTGAAATATTTAAAAGAT
Found at i:1152416 original size:69 final size:68
Alignment explanation
Indices: 1152268--1152537 Score: 251
Period size: 69 Copynumber: 4.0 Consensus size: 68
1152258 CCTACTCAAA
* * * *
1152268 ATAAATATATTTTAAT-TTTCAAATTTAA-ATAT-AT-AATAACTTTTAATTTGAAATATTTAAA
1 ATAAATATATTTTAATATTT-AAATTAAAGAGATAATAAATATCTTTTAATTTGAAATATTAAAA
*
1152329 AGAT
65 AAAT
* ** * * * *
1152333 ATAATTACCTTTTAATATTTAAATTTAAGAGATAATAAGTATCGTTTAAATTGAAATATTAAAAA
1 ATAAATATATTTTAATATTTAAATTAAAGAGATAATAAATATCTTTTAATTTGAAATATTAAAAA
1152398 ACAT
66 A-AT
* * * * * *
1152402 ATAATTATATTTTAATATTCAAAATTAAATAGATAGTAAATATCTTTTAATTTAAAATATTTAAA
1 ATAAATATATTTTAATATT-TAAATTAAAGAGATAATAAATATCTTTTAATTTGAAATATTAAAA
1152467 AAAT
65 AAAT
* ** * * **
1152471 ATAAATATCCTACTAATATTCAAATTAAAGAGATAATAAATATCTTCTAATTTGGGATATTAAAA
1 ATAAATAT-ATTTTAATATTTAAATTAAAGAGATAATAAATATCTTTTAATTTGAAATATTAAAA
1152536 AA
65 AA
1152538 GATGTGAATT
Statistics
Matches: 165, Mismatches: 33, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
65 21 0.13
66 6 0.04
67 2 0.01
68 23 0.14
69 67 0.41
70 46 0.28
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (68 bp):
ATAAATATATTTTAATATTTAAATTAAAGAGATAATAAATATCTTTTAATTTGAAATATTAAAAA
AAT
Found at i:1152531 original size:139 final size:134
Alignment explanation
Indices: 1152268--1152537 Score: 344
Period size: 139 Copynumber: 2.0 Consensus size: 134
1152258 CCTACTCAAA
* * * *
1152268 ATAAATATATTTTAATTTTCAAATTTAAATATATAATAACTTTTAATTTGAAATATTTAAAAGAT
1 ATAAATATATTTTAATATTCAAAATTAAATATATAATAACTTTTAATTTAAAATATTTAAAAAAT
* ** * * *
1152333 ATAATTACCTTTTAATATTTAAATTTAAGAGATAATAAGTATCGTTTAAATTGAAATATTAAAAA
66 ATAAATACCTACTAATATTCAAATTAAAGAGATAATAAATATCGTTTAAATTGAAATATTAAAAA
1152398 ACAT
131 ACAT
* *
1152402 ATAATTATATTTTAATATTCAAAATTAAATAGATAGTAAATATCTTTTAATTTAAAATATTTAAA
1 ATAAATATATTTTAATATTCAAAATTAAAT--ATA-T-AATAACTTTTAATTTAAAATATTTAAA
* **
1152467 AAATATAAATATCCTACTAATATTCAAATTAAAGAGATAATAAATATC-TTCTAATTTGGGATAT
62 AAATATAAATA-CCTACTAATATTCAAATTAAAGAGATAATAAATATCGTT-TAAATTGAAATAT
1152531 TAAAAAA
125 TAAAAAA
1152538 GATGTGAATT
Statistics
Matches: 115, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
134 27 0.23
136 3 0.03
137 1 0.01
138 36 0.31
139 48 0.42
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (134 bp):
ATAAATATATTTTAATATTCAAAATTAAATATATAATAACTTTTAATTTAAAATATTTAAAAAAT
ATAAATACCTACTAATATTCAAATTAAAGAGATAATAAATATCGTTTAAATTGAAATATTAAAAA
ACAT
Found at i:1156656 original size:100 final size:100
Alignment explanation
Indices: 1156460--1156649 Score: 353
Period size: 100 Copynumber: 1.9 Consensus size: 100
1156450 TTGTAGTCTG
* *
1156460 ACAATTAGTTATTCAACAATTATTTTCTTCCTTTTTTGCTTCAGATAATTCTTGAAGTCACTCTA
1 ACAATTAGTTATTCAACAATTATTTTCTTCCTTTTGTGCTTCAGATAATTCTTGAAGTCACTCCA
1156525 TCTGAGATATAATTTTTCAATAATAGCGGCTACTA
66 TCTGAGATATAATTTTTCAATAATAGCGGCTACTA
*
1156560 ACAATTAGTTATTCAACAATTATTTTCTTCCTTTTGTGCTTCGGATAATTCTTGAAGTCACTCCA
1 ACAATTAGTTATTCAACAATTATTTTCTTCCTTTTGTGCTTCAGATAATTCTTGAAGTCACTCCA
1156625 TCTGAGATATAATTTTTCAATAATA
66 TCTGAGATATAATTTTTCAATAATA
1156650 TTGGCTATTA
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 87 1.00
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (100 bp):
ACAATTAGTTATTCAACAATTATTTTCTTCCTTTTGTGCTTCAGATAATTCTTGAAGTCACTCCA
TCTGAGATATAATTTTTCAATAATAGCGGCTACTA
Found at i:1158053 original size:34 final size:34
Alignment explanation
Indices: 1158014--1158215 Score: 148
Period size: 34 Copynumber: 5.9 Consensus size: 34
1158004 ATATACTTAC
* *
1158014 CTTTTAATATTTAAATTTAAAGAAATAATAAATAT
1 CTTTTAATATTAAAAATTAAA-AAATAATAAATAT
* **
1158049 -TTTTAAT-TTAAAAATTGAAAAATATATAACCAT
1 CTTTTAATATTAAAAATTAAAAAATA-ATAAATAT
* * * *
1158082 GTTTTAATATTCAAAGTAAAATAAATAATAAATAT
1 CTTTTAATATTAAAAATTAAA-AAATAATAAATAT
* *
1158117 CTTTTAAT-TTAAAATATTTAAAAGAAT-ACAATTAT
1 CTTTTAATATTAAAA-A-TTAAAA-AATAATAAATAT
* *
1158152 CCTATTAATATT-CAAATTAAAAATATAATAAATAT
1 -CTTTTAATATTAAAAATTAAAAA-ATAATAAATAT
1158187 CTTTTAAT-TT-AAAATATATAAAAATAATA
1 CTTTTAATATTAAAAAT-TA-AAAAATAATA
1158216 TAAATTTAAT
Statistics
Matches: 131, Mismatches: 23, Indels: 27
0.72 0.13 0.15
Matches are distributed among these distances:
32 5 0.04
33 22 0.17
34 42 0.32
35 39 0.30
36 21 0.16
37 2 0.02
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (34 bp):
CTTTTAATATTAAAAATTAAAAAATAATAAATAT
Found at i:1158108 original size:68 final size:69
Alignment explanation
Indices: 1158013--1158218 Score: 240
Period size: 70 Copynumber: 2.9 Consensus size: 69
1158003 AATATACTTA
* *
1158013 CCTTTTAATATTTAAATTTAAAGAAATAATAAATAT-TTTTAATTTAAAA-ATTGAAAAATATAT
1 CCTTTTAATATTCAAA-TTAAAAAAATAATAAATATCTTTTAATTTAAAATATT-AAAAATATAT
1158076 AACCAT
64 AACCAT
* *
1158082 -GTTTTAATATTCAAAGTAAAATAAATAATAAATATCTTTTAATTTAAAATATTTAAAAGA-ATA
1 CCTTTTAATATTCAAATTAAAA-AAATAATAAATATCTTTTAATTTAAAATA-TTAAAA-ATATA
* **
1158145 CAATTAT
63 TAACCAT
* *
1158152 CCTATTAATATTCAAATTAAAAATATAATAAATATCTTTTAATTTAAAATATATAAAAATAATAT
1 CCTTTTAATATTCAAATTAAAAAAATAATAAATATCTTTTAATTTAAAATAT-TAAAAAT-ATAT
1158217 AA
64 AA
1158219 ATTTAATTTA
Statistics
Matches: 116, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
67 4 0.03
68 26 0.22
69 15 0.13
70 45 0.39
71 26 0.22
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (69 bp):
CCTTTTAATATTCAAATTAAAAAAATAATAAATATCTTTTAATTTAAAATATTAAAAATATATAA
CCAT
Found at i:1165059 original size:190 final size:190
Alignment explanation
Indices: 1164736--1165094 Score: 578
Period size: 190 Copynumber: 1.9 Consensus size: 190
1164726 ATATATAAAA
* * *
1164736 AAATGGTTGTCCCTTGTTCCCATATGTAATGAGGTAAGGGGGAGGTAAGATAGTAGACTGACCCA
1 AAATGGTTATCCCTTGTTCCCATATGTAATGAGGTAAGAGGGAGGTAAAATAGTAGACTGACCCA
*
1164801 ACACTAGGTTGAGAGCAGCTTCCGTAGAAGACCTCCAAATTATGAAATGCCCTCCATAGGACTCG
66 ACACCAGGTTGAGAGCAGCTTCCGTAGAAGACCTCCAAATTATGAAATGCCCTCCATAGGACTCG
*
1164866 ATCCCAATACCTCAAGGTTAAAAACCTTGTGCTCTACCAACTGAGCTAGATGGTCATTTC
131 ATCCCAAGACCTCAAGGTTAAAAACCTTGTGCTCTACCAACTGAGCTAGATGGTCATTTC
* * *
1164926 AAATGGTTATCCCTTGTTCCCATATGTAATGGGGTAAGAGGGAGGTAAAATAGTAGGCTGCCCCC
1 AAATGGTTATCCCTTGTTCCCATATGTAATGAGGTAAGAGGGAGGTAAAATAGTAGACTG-ACCC
* *
1164991 AACACCA-GTTGAGAGCAGCTTCCGTAGAAGACCTCCGAATTATGAAATGCCCTCCGT-GAGACT
65 AACACCAGGTTGAGAGCAGCTTCCGTAGAAGACCTCCAAATTATGAAATGCCCTCCATAG-GACT
* *
1165054 CGATCCCACGACCTCAAGGTTAAGAACCTTGTGCTCTACCA
129 CGATCCCAAGACCTCAAGGTTAAAAACCTTGTGCTCTACCA
1165095 TATATATAAT
Statistics
Matches: 155, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
189 1 0.01
190 145 0.94
191 9 0.06
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (190 bp):
AAATGGTTATCCCTTGTTCCCATATGTAATGAGGTAAGAGGGAGGTAAAATAGTAGACTGACCCA
ACACCAGGTTGAGAGCAGCTTCCGTAGAAGACCTCCAAATTATGAAATGCCCTCCATAGGACTCG
ATCCCAAGACCTCAAGGTTAAAAACCTTGTGCTCTACCAACTGAGCTAGATGGTCATTTC
Found at i:1167859 original size:21 final size:21
Alignment explanation
Indices: 1167833--1167900 Score: 127
Period size: 21 Copynumber: 3.2 Consensus size: 21
1167823 GATTCGGAAC
*
1167833 GCGAACTTCGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
1167854 GCGAACTTGGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
1167875 GCGAACTTGGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
1167896 GCGAA
1 GCGAA
1167901 TATGTAAATC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22
Consensus pattern (21 bp):
GCGAACTTGGACTATCGCAAT
Found at i:1167939 original size:21 final size:21
Alignment explanation
Indices: 1167915--1167978 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
1167905 TAAATCGCAA
1167915 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
*
1167936 TGCGATAGTCGAAGTTCGCAT
1 TGCGATAGTCGAAGTTCGCGT
*
1167957 TGCGATAGTCGCAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
1167978 T
1 T
1167979 CCGTTTTTCC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.30
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTCGCGT
Found at i:1168239 original size:21 final size:21
Alignment explanation
Indices: 1168215--1168281 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
1168205 TTTGGAATAA
1168215 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * **
1168236 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
*
1168255 ATCGCAACGCGAACTTCTACT
1 ATCGCAACGCGAACTTCGACT
1168276 ATCGCA
1 ATCGCA
1168282 TTGCGATTTA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
19 15 0.43
21 20 0.57
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:1168258 original size:19 final size:19
Alignment explanation
Indices: 1168194--1168263 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
1168184 ATGCAATACT
*
1168194 ATCGCAAAGAATTTGGAATAA
1 ATCGCAACGAATTTGG-A-AA
* * **
1168215 ATCGCAACGCGAACTTCGACT
1 ATCGCAA--CGAATTTGGAAA
1168236 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
1168255 ATCGCAACG
1 ATCGCAACG
1168264 CGAACTTCTA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 17 0.45
21 14 0.37
22 1 0.03
23 6 0.16
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:1168268 original size:40 final size:42
Alignment explanation
Indices: 1168191--1168281 Score: 150
Period size: 40 Copynumber: 2.2 Consensus size: 42
1168181 CAAATGCAAT
1168191 ACTATCGCAAAGAATTTGGAATAAATCGCAACGCGAACTTCG
1 ACTATCGCAAAGAATTTGGAATAAATCGCAACGCGAACTTCG
* *
1168233 ACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTCT
1 ACTATCGCAAAGAATTTGGAATAAATCGCAACGCGAACTTCG
1168273 ACTATCGCA
1 ACTATCGCA
1168282 TTGCGATTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 28 0.60
41 1 0.02
42 18 0.38
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (42 bp):
ACTATCGCAAAGAATTTGGAATAAATCGCAACGCGAACTTCG
Found at i:1168347 original size:21 final size:21
Alignment explanation
Indices: 1168296--1168349 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
1168286 GATTTACATA
*
1168296 TTCGCATTACGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
1168317 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
1168338 TTCGCGTTGCGA
1 TTCGCATTGCGA
1168350 ATCTGGAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:1168569 original size:28 final size:28
Alignment explanation
Indices: 1168499--1168588 Score: 99
Period size: 28 Copynumber: 3.1 Consensus size: 28
1168489 ATTTTACCTA
* *
1168499 ATTTTTTGTCAAAATAAATACTTAAAGTTAT
1 ATTTTTAGTCAAAATAAGTACTTAAAG---T
* *
1168530 ATTTTTAATCAAAATAAGTACCTAAAGT
1 ATTTTTAGTCAAAATAAGTACTTAAAGT
* *
1168558 ATTTTTGGTCAAAATAGGTACTTAAAGT
1 ATTTTTAGTCAAAATAAGTACTTAAAGT
1168586 ATT
1 ATT
1168589 CAATTTTTGT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
28 28 0.55
31 23 0.45
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (28 bp):
ATTTTTAGTCAAAATAAGTACTTAAAGT
Found at i:1168713 original size:28 final size:29
Alignment explanation
Indices: 1168672--1168750 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 29
1168662 AAAAAGTTTG
* * *
1168672 AATAGTTTAAGTACCTATTTTGA-CATAA
1 AATACTTTAGGTACCTATTTTGACCAAAA
*
1168700 AATACTTTAGGTA-CTTTTTTGACCAAAA
1 AATACTTTAGGTACCTATTTTGACCAAAA
* *
1168728 AGATAATTTTAGATACCTATTTT
1 A-AT-ACTTTAGGTACCTATTTT
1168751 TGATGGAGAG
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
27 8 0.20
28 16 0.40
29 2 0.05
30 8 0.20
31 6 0.15
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (29 bp):
AATACTTTAGGTACCTATTTTGACCAAAA
Found at i:1170293 original size:31 final size:30
Alignment explanation
Indices: 1170193--1170297 Score: 88
Period size: 31 Copynumber: 3.4 Consensus size: 30
1170183 AATTAGGGTT
1170193 TAATATTTATAAATAAGTTCAAATAAGGATC
1 TAATATTT-TAAATAAGTTCAAATAAGGATC
* * * *
1170224 TAATCTTTTAAA-AAGGTCAAATAA-AAGCC
1 TAATATTTTAAATAAGTTCAAATAAGGA-TC
*** *
1170253 TAGCCTTTTCAAATATGTTCAAATAAGGATC
1 TAATATTTT-AAATAAGTTCAAATAAGGATC
1170284 TAATATTTTCAAAT
1 TAATATTTT-AAAT
1170298 GTTGAATGCA
Statistics
Matches: 57, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
28 1 0.02
29 19 0.33
30 7 0.12
31 29 0.51
32 1 0.02
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (30 bp):
TAATATTTTAAATAAGTTCAAATAAGGATC
Found at i:1173488 original size:20 final size:21
Alignment explanation
Indices: 1173443--1173485 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1173433 TATGGTTTCG
*
1173443 AACCCCTTGATTGGTTTCTAA
1 AACCCCTTGACTGGTTTCTAA
* *
1173464 AACCCCTTGCCTGGTTTTTAA
1 AACCCCTTGACTGGTTTCTAA
1173485 A
1 A
1173486 CCCTCGGTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (21 bp):
AACCCCTTGACTGGTTTCTAA
Found at i:1174936 original size:22 final size:21
Alignment explanation
Indices: 1174874--1174944 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 21
1174864 ATATCAATAT
* *
1174874 TAATATTAAATATATAAATTAA
1 TAATATTATATTTAT-AATTAA
* *
1174896 TATTATTCATTATTAATAATTGAA
1 TAATATT-A-TATTTATAATT-AA
*
1174920 TAATATTATATTTATAA-AAA
1 TAATATTATATTTATAATTAA
1174940 TAATA
1 TAATA
1174945 AATAATATGA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
20 7 0.18
22 14 0.36
23 6 0.15
24 12 0.31
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (21 bp):
TAATATTATATTTATAATTAA
Found at i:1174997 original size:57 final size:57
Alignment explanation
Indices: 1174870--1174998 Score: 135
Period size: 54 Copynumber: 2.3 Consensus size: 57
1174860 TATTATATCA
* *
1174870 ATATTAATATTAAATAT-ATAAATTAATATTATTCATTATTAATAATTGAATAATATT
1 ATATTAA-ATTAAAAATAATAAATTAATATAATTCATTATTAATAATTGAATAATATT
* * *
1174927 ATATT-TA-TAAAAATAATAAA-TAATATGAATT-A-TATTAATAATTTATTATATATT
1 ATATTAAATTAAAAATAATAAATTAATAT-AATTCATTATTAATAATTGAATA-ATATT
1174981 ATTATTAAATTAAAAATA
1 A-TATTAAATTAAAAATA
1174999 TAATATCATA
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
53 14 0.23
54 19 0.32
55 13 0.22
56 1 0.02
57 13 0.22
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.46
Consensus pattern (57 bp):
ATATTAAATTAAAAATAATAAATTAATATAATTCATTATTAATAATTGAATAATATT
Found at i:1178067 original size:18 final size:18
Alignment explanation
Indices: 1178024--1178067 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
1178014 GGAAATGACG
*
1178024 AGTTTGAAACATATGAGT
1 AGTTTGATACATATGAGT
1178042 AGTTTGATACATATGAGT
1 AGTTTGATACATATGAGT
1178060 AGTTTGAT
1 AGTTTGAT
1178068 GACTATTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.39
Consensus pattern (18 bp):
AGTTTGATACATATGAGT
Found at i:1178654 original size:27 final size:27
Alignment explanation
Indices: 1178624--1178686 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
1178614 TTTCTACTGA
*
1178624 AAATATTAATATTGGACACTTTATCGG
1 AAATGTTAATATTGGACACTTTATCGG
1178651 AAATGTTAATATTGGACACTTTATCGG
1 AAATGTTAATATTGGACACTTTATCGG
1178678 AAATGTTAA
1 AAATGTTAA
1178687 AAAACATTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.37
Consensus pattern (27 bp):
AAATGTTAATATTGGACACTTTATCGG
Found at i:1178712 original size:22 final size:22
Alignment explanation
Indices: 1178684--1178730 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1178674 TCGGAAATGT
* * *
1178684 TAAAAAACATTAATGTTTTAGG
1 TAAAAAAAAATAATGGTTTAGG
1178706 TAAAAAAAAATAATGGTTTAGG
1 TAAAAAAAAATAATGGTTTAGG
1178728 TAA
1 TAA
1178731 TTTTTTACCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.02, G:0.15, T:0.32
Consensus pattern (22 bp):
TAAAAAAAAATAATGGTTTAGG
Found at i:1179144 original size:31 final size:32
Alignment explanation
Indices: 1179082--1179150 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
1179072 TAGTTAAGGA
* * *
1179082 TCATTATTTTGGGTGACGTAACATATTTCATG
1 TCATTATTTTGGGTGACATAACACATGTCATG
* *
1179114 TCATTATTTT-GGTTATATAACACATGTCATG
1 TCATTATTTTGGGTGACATAACACATGTCATG
1179145 TCATTA
1 TCATTA
1179151 ATTATATACA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 22 0.69
32 10 0.31
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.45
Consensus pattern (32 bp):
TCATTATTTTGGGTGACATAACACATGTCATG
Found at i:1181625 original size:21 final size:21
Alignment explanation
Indices: 1181601--1181648 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1181591 ACCTTAATAG
1181601 CCTCCACCACCACCTTTCCCT
1 CCTCCACCACCACCTTTCCCT
* *
1181622 CCTCCACCGCCACCTTTTCCT
1 CCTCCACCACCACCTTTCCCT
1181643 CCTCCA
1 CCTCCA
1181649 TGTCCGCCGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.12, C:0.60, G:0.02, T:0.25
Consensus pattern (21 bp):
CCTCCACCACCACCTTTCCCT
Found at i:1181737 original size:30 final size:30
Alignment explanation
Indices: 1181703--1181797 Score: 93
Period size: 30 Copynumber: 3.2 Consensus size: 30
1181693 ACTGCTACTT
1181703 CCACCACCACCATATCCGCCTCCGCCACTA
1 CCACCACCACCATATCCGCCTCCGCCACTA
* ** * * * *
1181733 CCACCGCTTCC-TTTGCCTCCTCCGCTACTT
1 CCACCACCACCATAT-CCGCCTCCGCCACTA
* *
1181763 CCACCACCACCATGTCCGCCTCCCCCACTA
1 CCACCACCACCATATCCGCCTCCGCCACTA
1181793 CCACC
1 CCACC
1181798 GCTTCCTTTA
Statistics
Matches: 48, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
29 2 0.04
30 44 0.92
31 2 0.04
ACGTcount: A:0.17, C:0.57, G:0.07, T:0.19
Consensus pattern (30 bp):
CCACCACCACCATATCCGCCTCCGCCACTA
Found at i:1181770 original size:60 final size:60
Alignment explanation
Indices: 1181696--1181831 Score: 236
Period size: 60 Copynumber: 2.3 Consensus size: 60
1181686 GTCCCCCACT
* *
1181696 GCTACTTCCACCACCACCATATCCGCCTCCGCCACTACCACCGCTTCCTTTGCCTCCTCC
1 GCTACTTCCACCACCACCATATCCGCCTCCCCCACTACCACCGCTTCCTTTACCTCCTCC
*
1181756 GCTACTTCCACCACCACCATGTCCGCCTCCCCCACTACCACCGCTTCCTTTACCTCCTCC
1 GCTACTTCCACCACCACCATATCCGCCTCCCCCACTACCACCGCTTCCTTTACCTCCTCC
*
1181816 GCCACTTCCACCACCA
1 GCTACTTCCACCACCA
1181832 TCACCGCCAT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 72 1.00
ACGTcount: A:0.16, C:0.54, G:0.07, T:0.22
Consensus pattern (60 bp):
GCTACTTCCACCACCACCATATCCGCCTCCCCCACTACCACCGCTTCCTTTACCTCCTCC
Found at i:1181815 original size:30 final size:29
Alignment explanation
Indices: 1181721--1181827 Score: 106
Period size: 30 Copynumber: 3.6 Consensus size: 29
1181711 ACCATATCCG
1181721 CCTCCGCCACTACCACCGCTTCCTTTGCCT
1 CCTCCGCCACTACCACCGCTTCCTTT-CCT
* * * ** * *
1181751 CCTCCGCTACTTCCACCACCACCATGTCCG
1 CCTCCGCCACTACCACCGCTTCC-TTTCCT
*
1181781 CCTCCCCCACTACCACCGCTTCCTTTACCT
1 CCTCCGCCACTACCACCGCTTCCTTT-CCT
*
1181811 CCTCCGCCACTTCCACC
1 CCTCCGCCACTACCACC
1181828 ACCATCACCG
Statistics
Matches: 58, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
29 2 0.03
30 54 0.93
31 2 0.03
ACGTcount: A:0.13, C:0.56, G:0.07, T:0.23
Consensus pattern (29 bp):
CCTCCGCCACTACCACCGCTTCCTTTCCT
Found at i:1181967 original size:147 final size:145
Alignment explanation
Indices: 1181817--1182184 Score: 330
Period size: 147 Copynumber: 2.5 Consensus size: 145
1181807 ACCTCCTCCG
* * *
1181817 CCACTTCCACCACCATCACCGCCATGTCCGCCACCGCTACCTCCTCCAGCACTTCCGCCACCACC
1 CCACTTCCACCACCACCACCACCA---CCGCCACCGCTACCTCCTCCACCACTTCCGCCACCACC
* ** *
1181882 ATGTCCGCTTCCGCCACTACCACCGCTTCCTTTGCCTCCTCCGCCACTTCCTCCACTGCTACCAC
63 ATGTCCGCCTCCAACACTACCACCGCTTCCTTTGCCTCCTCCGCCACTTCCACCACTGCTACCAC
1181947 CTCCACCATGTCTACTGCC
128 CTCCACCATGTCTACTG-C
* * ** *** * * * *
1181966 ACCACTTCCGCCACCACCACTACCACCGCTTCTTTTGCCTCCTCCTCCACTTCCTCCACCGCCAT
1 -CCACTTCCACCACCACCACCACCACCGCCACCGCTACCTCCTCCACCACTTCCGCCACCACCAT
*
1182031 GTCCGCCTCCAACACTACCACCGCTTCCTTTGCCTCCTCCGCCACTTCCACCAC--C-ACCACTT
65 GTCCGCCTCCAACACTACCACCGCTTCCTTTGCCTCCTCCGCCACTTCCACCACTGCTACCACCT
* * **
1182093 CCTCCACCG-CTACCACC
130 CCACCA-TGTCTA-CTGC
** * ** * * *
1182110 TCCACCATGTCCACCACCACCACTTCCACCGCTACCTTTGCCTCCTCCACCGCTTCCACCACCAC
1 -CCA-C-T-TCCACCACCACCACCACCACCGCCACCGCTACCTCCTCCACCACTTCCGCCACCAC
1182175 CATGTCCGCC
62 CATGTCCGCC
1182185 GCCACCGCTT
Statistics
Matches: 181, Mismatches: 32, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
144 18 0.10
145 4 0.02
146 1 0.01
147 138 0.76
150 20 0.11
ACGTcount: A:0.16, C:0.54, G:0.08, T:0.21
Consensus pattern (145 bp):
CCACTTCCACCACCACCACCACCACCGCCACCGCTACCTCCTCCACCACTTCCGCCACCACCATG
TCCGCCTCCAACACTACCACCGCTTCCTTTGCCTCCTCCGCCACTTCCACCACTGCTACCACCTC
CACCATGTCTACTGC
Found at i:1182047 original size:60 final size:60
Alignment explanation
Indices: 1181972--1182085 Score: 183
Period size: 60 Copynumber: 1.9 Consensus size: 60
1181962 TGCCACCACT
* * * *
1181972 TCCGCCACCACCACTACCACCGCTTCTTTTGCCTCCTCCTCCACTTCCTCCACCGCCATG
1 TCCGCCACCAACACTACCACCGCTTCCTTTGCCTCCTCCGCCACTTCCACCACCGCCATG
*
1182032 TCCGCCTCCAACACTACCACCGCTTCCTTTGCCTCCTCCGCCACTTCCACCACC
1 TCCGCCACCAACACTACCACCGCTTCCTTTGCCTCCTCCGCCACTTCCACCACC
1182086 ACCACTTCCT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.14, C:0.54, G:0.08, T:0.24
Consensus pattern (60 bp):
TCCGCCACCAACACTACCACCGCTTCCTTTGCCTCCTCCGCCACTTCCACCACCGCCATG
Found at i:1182082 original size:30 final size:30
Alignment explanation
Indices: 1181979--1182082 Score: 84
Period size: 30 Copynumber: 3.5 Consensus size: 30
1181969 ACTTCCGCCA
*
1181979 CCACCACTACCACCGCTTCTTTTGCCTCCT
1 CCACCACTACCACCGCTTCCTTTGCCTCCT
* * * * ** * *
1182009 CCTCCACTTCCTCCACCGCC-ATGTCCGCCT
1 CCACCACTACCACCGCTTCCTTTG-CCTCCT
*
1182039 CCAACACTACCACCGCTTCCTTTGCCTCCT
1 CCACCACTACCACCGCTTCCTTTGCCTCCT
* *
1182069 CCGCCACTTCCACC
1 CCACCACTACCACC
1182083 ACCACCACTT
Statistics
Matches: 51, Mismatches: 21, Indels: 4
0.67 0.28 0.05
Matches are distributed among these distances:
29 2 0.04
30 47 0.92
31 2 0.04
ACGTcount: A:0.13, C:0.54, G:0.08, T:0.25
Consensus pattern (30 bp):
CCACCACTACCACCGCTTCCTTTGCCTCCT
Found at i:1182092 original size:15 final size:15
Alignment explanation
Indices: 1182072--1182230 Score: 89
Period size: 15 Copynumber: 10.8 Consensus size: 15
1182062 GCCTCCTCCG
1182072 CCACTTCCACCACCA
1 CCACTTCCACCACCA
*
1182087 CCACTT---CCTCCA
1 CCACTTCCACCACCA
* * *
1182099 CCGCTACCACCTCCA
1 CCACTTCCACCACCA
1182114 CCA-TGTCCACCACCA
1 CCACT-TCCACCACCA
* *
1182129 CCACTTCCACCGCTA
1 CCACTTCCACCACCA
* * *
1182144 CC-TTTGCCTCCTCCA
1 CCACTT-CCACCACCA
*
1182159 CCGCTTCCACCACCA
1 CCACTTCCACCACCA
* *
1182174 CCA-TGTCCGCCGCCA
1 CCACT-TCCACCACCA
* *
1182189 CCGCTTCCACCACCT
1 CCACTTCCACCACCA
*
1182204 CCA-TATCCACCGCCA
1 CCACT-TCCACCACCA
*
1182219 CTACTTCCACCA
1 CCACTTCCACCA
1182231 TGATTAGTTC
Statistics
Matches: 106, Mismatches: 27, Indels: 22
0.68 0.17 0.14
Matches are distributed among these distances:
12 9 0.08
14 5 0.05
15 87 0.82
16 5 0.05
ACGTcount: A:0.19, C:0.56, G:0.06, T:0.18
Consensus pattern (15 bp):
CCACTTCCACCACCA
Found at i:1182096 original size:87 final size:87
Alignment explanation
Indices: 1182005--1182176 Score: 227
Period size: 87 Copynumber: 2.0 Consensus size: 87
1181995 TTCTTTTGCC
* * * * * * *
1182005 TCCTCCTCCACTTCCTCCACCGCCATGTCCGCCTCCAACACTACCACCGCTTCCTTTGCCTCCTC
1 TCCTCCACCACTACCACCACCACCATGTCCACCACCAACACTACCACCGCTACCTTTGCCTCCTC
*
1182070 CGCCACTTCCACCACCACCACT
66 CACCACTTCCACCACCACCACT
* * * *
1182092 TCCTCCACCGCTACCACCTCCACCATGTCCACCACCACCACTTCCACCGCTACCTTTGCCTCCTC
1 TCCTCCACCACTACCACCACCACCATGTCCACCACCAACACTACCACCGCTACCTTTGCCTCCTC
*
1182157 CACCGCTTCCACCACCACCA
66 CACCACTTCCACCACCACCA
1182177 TGTCCGCCGC
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.17, C:0.56, G:0.06, T:0.21
Consensus pattern (87 bp):
TCCTCCACCACTACCACCACCACCATGTCCACCACCAACACTACCACCGCTACCTTTGCCTCCTC
CACCACTTCCACCACCACCACT
Found at i:1182097 original size:30 final size:30
Alignment explanation
Indices: 1182063--1182230 Score: 112
Period size: 30 Copynumber: 5.7 Consensus size: 30
1182053 GCTTCCTTTG
* *
1182063 CCTCCTCCGCCACTTCCACCACCACCACT-T
1 CCTCCACCACCACTTCCACCACCACCA-TGT
* * *
1182093 CCT---CCACCGCTACCACCTCCACCATGT
1 CCTCCACCACCACTTCCACCACCACCATGT
* * * *
1182120 CCACCACCACCACTTCCACCGCTACC-TTT
1 CCTCCACCACCACTTCCACCACCACCATGT
* *
1182149 GCCTCCTCCACCGCTTCCACCACCACCATGT
1 -CCTCCACCACCACTTCCACCACCACCATGT
* * * * *
1182180 CCGCCGCCACCGCTTCCACCACCTCCATAT
1 CCTCCACCACCACTTCCACCACCACCATGT
* * *
1182210 CCACCGCCACTACTTCCACCA
1 CCTCCACCACCACTTCCACCA
1182231 TGATTAGTTC
Statistics
Matches: 109, Mismatches: 23, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
26 1 0.01
27 20 0.18
29 2 0.02
30 84 0.77
31 2 0.02
ACGTcount: A:0.18, C:0.57, G:0.07, T:0.18
Consensus pattern (30 bp):
CCTCCACCACCACTTCCACCACCACCATGT
Found at i:1182157 original size:45 final size:44
Alignment explanation
Indices: 1182043--1182176 Score: 139
Period size: 45 Copynumber: 3.0 Consensus size: 44
1182033 CCGCCTCCAA
* * *
1182043 CACTACCACCGCTTCCTTTGCCTCCTCCGCCACTTCCACCACCAC
1 CACTTCCACCGCTACCTTTGCCTCCTCCACCA-TTCCACCACCAC
* ** * *
1182088 CACTTCC-TC-C-ACCGCTACCACCTCCACCATGTCCACCACCAC
1 CACTTCCACCGCTACCTTTGCCTCCTCCACCAT-TCCACCACCAC
*
1182130 CACTTCCACCGCTACCTTTGCCTCCTCCACCGCTTCCACCACCAC
1 CACTTCCACCGCTACCTTTGCCTCCTCCACC-ATTCCACCACCAC
1182175 CA
1 CA
1182177 TGTCCGCCGC
Statistics
Matches: 70, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
41 1 0.01
42 31 0.44
43 2 0.03
44 2 0.03
45 33 0.47
46 1 0.01
ACGTcount: A:0.18, C:0.56, G:0.06, T:0.20
Consensus pattern (44 bp):
CACTTCCACCGCTACCTTTGCCTCCTCCACCATTCCACCACCAC
Found at i:1182199 original size:147 final size:146
Alignment explanation
Indices: 1181856--1182199 Score: 417
Period size: 147 Copynumber: 2.3 Consensus size: 146
1181846 GCCACCGCTA
* * * *
1181856 CCTCCTCCAGCACTTCCGCCACCACCATGTCCGCTTCCGCCACTACCACCGCTTCCTTTGCCTCC
1 CCTCCTCCACCACTTCCACCACCACCATGTCCGCCTCCACCACTACCACCGCTTCCTTTGCCTCC
* * * *
1181921 TCCGCCACTTCCTCCACTGCTACCACCTCCACCATGTCTACTGCCACCACTTCCGCCACCACCAC
66 TCCGCCACTTCCACCAC-GCTACCACCTCCACCACGTCCACTGCCACCACTTCCACCACCACCAC
* *
1181986 TACCACCGCTTCTTTTG
130 TACCACCGCTACCTTTG
* * * *
1182003 CCTCCTCCTCCACTTCCTCCACCGCCATGTCCGCCTCCAACACTACCACCGCTTCCTTTGCCTCC
1 CCTCCTCCACCACTTCCACCACCACCATGTCCGCCTCCACCACTACCACCGCTTCCTTTGCCTCC
* *
1182068 TCCGCCACTTCCACCAC-C-ACCACTTCCTCCACCGCTACCACCT-CCACCA-TGTCCACCACCA
66 TCCGCCACTTCCACCACGCTACCACCTCCACCA-CG-T-CCA-CTGCCACCACT-TCCACCACCA
*
1182129 CCACTTCCACCGCTACCTTTG
126 CCACTACCACCGCTACCTTTG
* * * *
1182150 CCTCCTCCACCGCTTCCACCACCACCATGTCCGCCGCCACCGCTTCCACC
1 CCTCCTCCACCACTTCCACCACCACCATGTCCGCCTCCACCACTACCACC
1182200 ACCTCCATAT
Statistics
Matches: 168, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
144 11 0.07
145 2 0.01
146 2 0.01
147 151 0.90
148 2 0.01
ACGTcount: A:0.15, C:0.54, G:0.08, T:0.22
Consensus pattern (146 bp):
CCTCCTCCACCACTTCCACCACCACCATGTCCGCCTCCACCACTACCACCGCTTCCTTTGCCTCC
TCCGCCACTTCCACCACGCTACCACCTCCACCACGTCCACTGCCACCACTTCCACCACCACCACT
ACCACCGCTACCTTTG
Found at i:1183936 original size:4 final size:4
Alignment explanation
Indices: 1183927--1183990 Score: 69
Period size: 4 Copynumber: 16.5 Consensus size: 4
1183917 TGATAAAATG
* * * *
1183927 ATGT ATGT ATGT ATGT ATGT GTGT GTGT ATGT GTGT ATGT GTGT ATG-
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
1183974 -TGT ATGT GTGT ATGT AT
1 ATGT ATGT ATGT ATGT AT
1183991 ACTAGGTTTG
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
2 2 0.04
4 48 0.96
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:1183944 original size:12 final size:12
Alignment explanation
Indices: 1183927--1183990 Score: 78
Period size: 12 Copynumber: 5.5 Consensus size: 12
1183917 TGATAAAATG
*
1183927 ATGTATGTATGT
1 ATGTATGTGTGT
1183939 ATGTATGTGTGT
1 ATGTATGTGTGT
*
1183951 GTGTATGTGTGT
1 ATGTATGTGTGT
*
1183963 ATG--TGTGTAT
1 ATGTATGTGTGT
*
1183973 GTGTATGTGTGT
1 ATGTATGTGTGT
1183985 ATGTAT
1 ATGTAT
1183991 ACTAGGTTTG
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
10 8 0.19
12 35 0.81
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (12 bp):
ATGTATGTGTGT
Found at i:1183967 original size:14 final size:14
Alignment explanation
Indices: 1183932--1183988 Score: 78
Period size: 14 Copynumber: 4.1 Consensus size: 14
1183922 AAATGATGTA
*
1183932 TGTATGTATGTATG
1 TGTATGTGTGTATG
* * *
1183946 TGTGTGTGTATGTG
1 TGTATGTGTGTATG
1183960 TGTATGTGTGTATG
1 TGTATGTGTGTATG
1183974 TGTATGTGTGTATG
1 TGTATGTGTGTATG
1183988 T
1 T
1183989 ATACTAGGTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.14, C:0.00, G:0.35, T:0.51
Consensus pattern (14 bp):
TGTATGTGTGTATG
Found at i:1184387 original size:24 final size:24
Alignment explanation
Indices: 1184314--1184387 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
1184304 TGCTCATTCA
*
1184314 TTTA-ATGTTCGCAAACATGTTCG
1 TTTATATGTTCACAAACATGTTCG
* * * * *
1184337 TTCATATGTTAACGAACGTGTTTG
1 TTTATATGTTCACAAACATGTTCG
*
1184361 TTTATATGTTCACAAATATGTTCG
1 TTTATATGTTCACAAACATGTTCG
1184385 TTT
1 TTT
1184388 GGCGTTTGTT
Statistics
Matches: 38, Mismatches: 12, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
23 3 0.08
24 35 0.92
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.45
Consensus pattern (24 bp):
TTTATATGTTCACAAACATGTTCG
Found at i:1184428 original size:21 final size:22
Alignment explanation
Indices: 1184389--1184431 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1184379 TGTTCGTTTG
1184389 GCGTTTGTTTGATGTCCATTTA
1 GCGTTTGTTTGATGTCCATTTA
1184411 GCGTTTGTTTGA-GTCCATTTA
1 GCGTTTGTTTGATGTCCATTTA
1184432 TATGTTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.49
Consensus pattern (22 bp):
GCGTTTGTTTGATGTCCATTTA
Found at i:1185598 original size:4 final size:4
Alignment explanation
Indices: 1185591--1185632 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
1185581 TCACACACAC
* *
1185591 ACAT ACAT ACAT ACAT AAAT ACAT ACAT ACAT AAAT ACAT AC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC
1185633 CTATATGATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:1185614 original size:16 final size:16
Alignment explanation
Indices: 1185593--1185632 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
1185583 ACACACACAC
1185593 ATACATACATACATAA
1 ATACATACATACATAA
1185609 ATACATACATACATAA
1 ATACATACATACATAA
1185625 ATACATAC
1 ATACATAC
1185633 CTATATGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25
Consensus pattern (16 bp):
ATACATACATACATAA
Found at i:1186836 original size:60 final size:60
Alignment explanation
Indices: 1186784--1186897 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
1186774 ATGGTCCCTT
*
1186784 GACTATAGGGTGATGCTTTGTTGAGT-CCCCAGACTATTAAAAGTTACAAAATGATCCTCC
1 GACTATAGAGTGATGCTTTGTTGAGTACCCC-GACTATTAAAAGTTACAAAATGATCCTCC
* * * *
1186844 GATTATAGAGTGTTGCTTTGTTGAGTATCTCGACTATTAAAAGTTACAAAATGA
1 GACTATAGAGTGATGCTTTGTTGAGTACCCCGACTATTAAAAGTTACAAAATGA
1186898 CATCTGAGTA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
60 46 0.96
61 2 0.04
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (60 bp):
GACTATAGAGTGATGCTTTGTTGAGTACCCCGACTATTAAAAGTTACAAAATGATCCTCC
Found at i:1188944 original size:3 final size:3
Alignment explanation
Indices: 1188936--1188973 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1188926 TTCGTCCCGC
*
1188936 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1188974 CAGGTCCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1198244 original size:60 final size:60
Alignment explanation
Indices: 1198117--1198244 Score: 132
Period size: 60 Copynumber: 2.1 Consensus size: 60
1198107 ATAGTCATGT
** ** * * *
1198117 GACCATTTTGTAACTTTTAATAGTTGAGGGACTCAACAATGCAACATCATATAATAGGGG
1 GACCATTTTGTAACTTTTAATAGTCAAAAGACTCAACAAAGCAACACCATATAATAGAGG
* * * * *
1198177 GATCATTTTGTAATTTTTACTAGTCAAAAGACTCAACAAAGCAACACCCTATAGA-CGAGG
1 GACCATTTTGTAACTTTTAATAGTCAAAAGACTCAACAAAGCAACACCATATA-ATAGAGG
1198237 GACCATTT
1 GACCATTT
1198245 GTTTACATCA
Statistics
Matches: 54, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
60 53 0.98
61 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTCAAAAGACTCAACAAAGCAACACCATATAATAGAGG
Found at i:1201465 original size:14 final size:14
Alignment explanation
Indices: 1201448--1201475 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1201438 TTCCTTTTTA
1201448 TTTTCTTTCTCTTT
1 TTTTCTTTCTCTTT
1201462 TTTTCTTTCTCTTT
1 TTTTCTTTCTCTTT
1201476 GCTCAAACCA
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:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTCTTTCTCTTT
Found at i:1213337 original size:29 final size:29
Alignment explanation
Indices: 1213295--1213352 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
1213285 CACAGCTTCG
* *
1213295 ATAAATGCAATGCAACCCAAAAGACAATT
1 ATAAACGCAATGCAACCCAAAACACAATT
1213324 ATAAACGCAATGCAACCCAAAACACAATT
1 ATAAACGCAATGCAACCCAAAACACAATT
1213353 TAAGCGTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.52, C:0.24, G:0.09, T:0.16
Consensus pattern (29 bp):
ATAAACGCAATGCAACCCAAAACACAATT
Found at i:1214379 original size:35 final size:35
Alignment explanation
Indices: 1214325--1214404 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
1214315 AATCATATCT
*
1214325 AAAATTTAGTTTTTATTTCATTTTAGTA-CCATGTC
1 AAAATTTAATTTTTATTTCATTTTAGTACCCAT-TC
* *
1214360 AAACTTTAATTTTTGTTTCATTTTAGTACCCATTC
1 AAAATTTAATTTTTATTTCATTTTAGTACCCATTC
1214395 AAAATTTAAT
1 AAAATTTAAT
1214405 GTTAAGTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 36 0.90
36 4 0.10
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (35 bp):
AAAATTTAATTTTTATTTCATTTTAGTACCCATTC
Found at i:1215300 original size:12 final size:12
Alignment explanation
Indices: 1215285--1215314 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1215275 ATGGTGGTTA
1215285 TGGTGGTTGTGG
1 TGGTGGTTGTGG
1215297 TGGTGGTTGTGG
1 TGGTGGTTGTGG
1215309 TGGTGG
1 TGGTGG
1215315 CATTCCAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.60, T:0.40
Consensus pattern (12 bp):
TGGTGGTTGTGG
Found at i:1216463 original size:21 final size:21
Alignment explanation
Indices: 1216437--1216493 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
1216427 AAAAAGTTTG
*
1216437 AGATTGATCCTTTTTGTTGAG
1 AGATTGATCCTTTTTGTTGAC
* *
1216458 GGATTGATCCTTTTGGTTGAC
1 AGATTGATCCTTTTTGTTGAC
*
1216479 AGATTGATCTTTTTT
1 AGATTGATCCTTTTT
1216494 TTGGAATGAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.18, C:0.11, G:0.23, T:0.49
Consensus pattern (21 bp):
AGATTGATCCTTTTTGTTGAC
Found at i:1217076 original size:42 final size:41
Alignment explanation
Indices: 1216985--1217316 Score: 468
Period size: 42 Copynumber: 7.8 Consensus size: 41
1216975 CTATACACCA
* * *
1216985 GTAAGGCTTAACCTATGCACAAAGCAGA-GGAGCCTAGGAAAACT
1 GTAAGGCTT-ACCT-TGCACACAGCAAAGGGA-CCT-GGGAAACT
* *
1217029 GTAAGGTTTATTCTTGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
*
1217071 GTAAGGCTTACCCTTGCACACAGCAAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGC-AAAGGGACCTGGGAAACT
1217114 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAACT
*
1217156 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
1217198 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAACT
*
1217240 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
*
1217282 GTAAGGCTTACCTTCGCACACAACAAAGGGACCTG
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTG
1217317 ATAATACTTC
Statistics
Matches: 266, Mismatches: 14, Indels: 18
0.89 0.05 0.06
Matches are distributed among these distances:
41 8 0.03
42 186 0.70
43 59 0.22
44 13 0.05
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (41 bp):
GTAAGGCTTACCTTGCACACAGCAAAGGGACCTGGGAAACT
Found at i:1217233 original size:84 final size:84
Alignment explanation
Indices: 1216985--1217316 Score: 542
Period size: 84 Copynumber: 3.9 Consensus size: 84
1216975 CTATACACCA
* * * * * *
1216985 GTAAGGCTTAACCTATGCACAAAGCAGA-GGAGCCTAGGAAAACTGTAAGGTTTATTCTT-GCAC
1 GTAAGGCTTACCCT-TGCACACAGCAAAGGGA-CCT-GGTAAACTGTAAGGCTTA-CCTTCGCAC
1217048 ACAGCAAAGGGACCTGGGAAACT
62 ACAGCAAAGGGACCTGGGAAACT
1217071 GTAAGGCTTACCCTTGCACACAGCAAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACA
1 GTAAGGCTTACCCTTGCACACAGC-AAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACA
1217136 GCAAAGGGACCTGGGAAACT
65 GCAAAGGGACCTGGGAAACT
1217156 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1217221 CAAAGGGACCTGGGAAACT
66 CAAAGGGACCTGGGAAACT
*
1217240 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAA
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1217305 CAAAGGGACCTG
66 CAAAGGGACCTG
1217317 ATAATACTTC
Statistics
Matches: 236, Mismatches: 7, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
84 139 0.59
85 76 0.32
86 18 0.08
87 3 0.01
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (84 bp):
GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
CAAAGGGACCTGGGAAACT
Found at i:1218281 original size:29 final size:29
Alignment explanation
Indices: 1218244--1218316 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 29
1218234 CATTTTACAC
* *
1218244 AAATGGCACAATTTTTAAAATGATTACCA
1 AAATAGCACAATTTTTAAAATAATTACCA
** * * *
1218273 AAATAGCACCCTTTTTGAATTAATTCCCA
1 AAATAGCACAATTTTTAAAATAATTACCA
1218302 AAATAGCACCAATTT
1 AAATAGCA-CAATTT
1218317 AGAATTAATT
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
29 30 0.88
30 4 0.12
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (29 bp):
AAATAGCACAATTTTTAAAATAATTACCA
Found at i:1218321 original size:29 final size:29
Alignment explanation
Indices: 1218270--1218340 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
1218260 AAAATGATTA
** *
1218270 CCAAAATAGCACCCTTTTTGAATTAATTC
1 CCAAAATAGCACCAATTTAGAATTAATTC
1218299 CCAAAATAGCACCAATTTAGAATTAATTC
1 CCAAAATAGCACCAATTTAGAATTAATTC
* *
1218328 CCATAATATCACC
1 CCAAAATAGCACC
1218341 TTTTTTTTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.39, C:0.25, G:0.06, T:0.30
Consensus pattern (29 bp):
CCAAAATAGCACCAATTTAGAATTAATTC
Found at i:1224299 original size:42 final size:41
Alignment explanation
Indices: 1224208--1224539 Score: 459
Period size: 42 Copynumber: 7.8 Consensus size: 41
1224198 CTATACACTA
* * *
1224208 GTAAGGCTTAACCTATGCACAAAGCAGA-GGAGCCTAGGAAAACT
1 GTAAGGCTT-ACCT-TGCACACAGCAAAGGGA-CCT-GGTAAACT
* *
1224252 GTAAGGTTTATCCTTGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGTAAACT
1224294 GTAAGGCTTACCCTTGCACACAGCAAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGC-AAAGGGACCTGGTAAACT
*
1224337 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGAAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGTAAACT
* *
1224379 GTAAGGCTTACCCTTGTAGACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGTAAACT
*
1224421 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGTAAACT
1224463 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGTAAACT
*
1224505 GTAAGGCTTACCTTCGCACACAACAAAGGGACCTG
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTG
1224540 ATAATACTTC
Statistics
Matches: 264, Mismatches: 16, Indels: 18
0.89 0.05 0.06
Matches are distributed among these distances:
41 8 0.03
42 183 0.69
43 59 0.22
44 14 0.05
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.18
Consensus pattern (41 bp):
GTAAGGCTTACCTTGCACACAGCAAAGGGACCTGGTAAACT
Found at i:1224428 original size:84 final size:84
Alignment explanation
Indices: 1224208--1224539 Score: 524
Period size: 84 Copynumber: 3.9 Consensus size: 84
1224198 CTATACACTA
* * * * *
1224208 GTAAGGCTTAACCTATGCACAAAGCAGA-GGAGCCTAGGAAAACTGTAAGGTTTATCCTT-GCAC
1 GTAAGGCTTACCCT-TGCACACAGCAAAGGGA-CCT-GGTAAACTGTAAGGCTTA-CCTTCGCAC
1224271 ACAGCAAAGGGACCTGGGAAACT
62 ACAGCAAAGGGACCTGGGAAACT
1224294 GTAAGGCTTACCCTTGCACACAGCAAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACA
1 GTAAGGCTTACCCTTGCACACAGC-AAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACA
*
1224359 GCAAAGGGACCTGGAAAACT
65 GCAAAGGGACCTGGGAAACT
* *
1224379 GTAAGGCTTACCCTTGTAGACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1224444 CAAAGGGACCTGGGAAACT
66 CAAAGGGACCTGGGAAACT
*
1224463 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAA
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1224528 CAAAGGGACCTG
66 CAAAGGGACCTG
1224540 ATAATACTTC
Statistics
Matches: 231, Mismatches: 12, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
84 137 0.59
85 73 0.32
86 18 0.08
87 3 0.01
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.18
Consensus pattern (84 bp):
GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
CAAAGGGACCTGGGAAACT
Found at i:1225534 original size:29 final size:29
Alignment explanation
Indices: 1225477--1225632 Score: 143
Period size: 29 Copynumber: 5.3 Consensus size: 29
1225467 CATTTTACAC
* * *
1225477 AAATAGCA-CCATTTTAAAATAATTGCCA
1 AAATAGCACCCATTTTGAATTAATTCCCA
*
1225505 AAATAGCACCCTTTTTGAATTAATTCCCA
1 AAATAGCACCCATTTTGAATTAATTCCCA
*
1225534 AAATAGCACCAATTTTGAATTAATTCCCA
1 AAATAGCACCCATTTTGAATTAATTCCCA
* * *** * ** *
1225563 GAATATCACATTTTTTCAAAAAAAATTACCA
1 AAATAGCACCCATTTT--GAATTAATTCCCA
* *
1225594 AAATAGCATCCATTTCGAATTAATTCCCA
1 AAATAGCACCCATTTTGAATTAATTCCCA
1225623 AAATAGCACC
1 AAATAGCACC
1225633 AAAATCGAAT
Statistics
Matches: 98, Mismatches: 27, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
28 8 0.08
29 72 0.73
31 18 0.18
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.30
Consensus pattern (29 bp):
AAATAGCACCCATTTTGAATTAATTCCCA
Found at i:1225640 original size:29 final size:29
Alignment explanation
Indices: 1225585--1225649 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
1225575 TTTTCAAAAA
* **
1225585 AAATTACCAAAATAGCATCCATTTCGAAT
1 AAATTCCCAAAATAGCATCCAAATCGAAT
*
1225614 TAATTCCCAAAATAGCA-CCAAAATCGAAT
1 AAATTCCCAAAATAGCATCC-AAATCGAAT
1225643 AAATTCC
1 AAATTCC
1225650 TAGAATAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 2 0.07
29 28 0.93
ACGTcount: A:0.46, C:0.23, G:0.06, T:0.25
Consensus pattern (29 bp):
AAATTCCCAAAATAGCATCCAAATCGAAT
Found at i:1225655 original size:89 final size:89
Alignment explanation
Indices: 1225492--1225661 Score: 241
Period size: 89 Copynumber: 1.9 Consensus size: 89
1225482 GCACCATTTT
* * * * ** * *
1225492 AAAATAATTGCCAAAATAGCACCCTTTTTGAATTAATTCCCAAAATAGCACCAATTTTGAATTAA
1 AAAAAAATTACCAAAATAGCACCCATTTCGAATTAATTCCCAAAATAGCACCAAAATCGAATAAA
*
1225557 TTCCCAGAATATCACATTTTTTCA
66 TTCCCAGAATAACACATTTTTTCA
*
1225581 AAAAAAATTACCAAAATAGCATCCATTTCGAATTAATTCCCAAAATAGCACCAAAATCGAATAAA
1 AAAAAAATTACCAAAATAGCACCCATTTCGAATTAATTCCCAAAATAGCACCAAAATCGAATAAA
*
1225646 TTCCTAGAATAACACA
66 TTCCCAGAATAACACA
1225662 GGTCAACGGT
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
89 70 1.00
ACGTcount: A:0.45, C:0.21, G:0.06, T:0.28
Consensus pattern (89 bp):
AAAAAAATTACCAAAATAGCACCCATTTCGAATTAATTCCCAAAATAGCACCAAAATCGAATAAA
TTCCCAGAATAACACATTTTTTCA
Found at i:1229013 original size:25 final size:25
Alignment explanation
Indices: 1228985--1229036 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1228975 ATCGCTAATG
1228985 ACGATGAGGTAATATTATAGAATAT
1 ACGATGAGGTAATATTATAGAATAT
1229010 ACGATGAGGTAATATTATAGAATAT
1 ACGATGAGGTAATATTATAGAATAT
1229035 AC
1 AC
1229037 TTAATCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (25 bp):
ACGATGAGGTAATATTATAGAATAT
Found at i:1235011 original size:21 final size:21
Alignment explanation
Indices: 1234958--1235009 Score: 97
Period size: 20 Copynumber: 2.5 Consensus size: 21
1234948 CACTTAGGGA
1234958 ACCGATTCCCCATGAGGGGGT
1 ACCGATTCCCCATGAGGGGGT
1234979 ACCGATTCCCCATGA-GGGGT
1 ACCGATTCCCCATGAGGGGGT
1234999 ACCGATTCCCC
1 ACCGATTCCCC
1235010 CACGCTCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.19, C:0.35, G:0.27, T:0.19
Consensus pattern (21 bp):
ACCGATTCCCCATGAGGGGGT
Found at i:1240741 original size:22 final size:22
Alignment explanation
Indices: 1240715--1240774 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
1240705 ATAGGGCAGA
*
1240715 GGGAATCGATACCCCCTTGA-AG
1 GGGAATCGATACCCCC-TCACAG
* *
1240737 GGGAACCGATTCCCCC-CACAG
1 GGGAATCGATACCCCCTCACAG
1240758 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
1240775 GAGGGTTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 1 0.03
21 16 0.52
22 14 0.45
ACGTcount: A:0.25, C:0.35, G:0.25, T:0.15
Consensus pattern (22 bp):
GGGAATCGATACCCCCTCACAG
Found at i:1242265 original size:18 final size:18
Alignment explanation
Indices: 1242244--1242283 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
1242234 GAACAGCACA
1242244 AGGAACAAGCACGAG-CAG
1 AGGAACAAGCAC-AGCCAG
1242262 AGGAACAAGCACAGCCAG
1 AGGAACAAGCACAGCCAG
1242280 AGGA
1 AGGA
1242284 TCAAATGCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.45, C:0.23, G:0.33, T:0.00
Consensus pattern (18 bp):
AGGAACAAGCACAGCCAG
Found at i:1242817 original size:2 final size:2
Alignment explanation
Indices: 1242810--1242847 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1242800 GCAGCTTAAG
1242810 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1242848 CAATTAACTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1243124 original size:13 final size:13
Alignment explanation
Indices: 1243106--1243140 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
1243096 AATGAATTTT
1243106 AAGATTTTCCAAA
1 AAGATTTTCCAAA
1243119 AAGATTTTCCAAA
1 AAGATTTTCCAAA
1243132 AAGATTTTC
1 AAGATTTTC
1243141 TAAGTATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (13 bp):
AAGATTTTCCAAA
Found at i:1246132 original size:29 final size:31
Alignment explanation
Indices: 1246083--1246141 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 31
1246073 TTTTACTTAT
1246083 TAATTATTTAACTATGTATTTAATTATTAAC
1 TAATTATTTAACTATGTATTTAATTATTAAC
1246114 TAATTA-TTAAC-ATGTATTTAATTATTAA
1 TAATTATTTAACTATGTATTTAATTATTAA
1246142 TTTTACCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 17 0.61
30 5 0.18
31 6 0.21
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (31 bp):
TAATTATTTAACTATGTATTTAATTATTAAC
Found at i:1246759 original size:32 final size:32
Alignment explanation
Indices: 1246718--1246779 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
1246708 CAACAACTTT
1246718 TTCAATTCAATTCAGTTTTCTTTAATCAGTCG
1 TTCAATTCAATTCAGTTTTCTTTAATCAGTCG
*
1246750 TTCAATTCAATTCATTTTTCTTTAATCAGT
1 TTCAATTCAATTCAGTTTTCTTTAATCAGT
1246780 AATTGGAGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (32 bp):
TTCAATTCAATTCAGTTTTCTTTAATCAGTCG
Found at i:1248513 original size:20 final size:20
Alignment explanation
Indices: 1248488--1248531 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1248478 TAATAATCAC
*
1248488 GGCCTTGCGACTAGCGTATT
1 GGCCTTGCGACCAGCGTATT
*
1248508 GGCCTTGCGACCGGCGTATT
1 GGCCTTGCGACCAGCGTATT
1248528 GGCC
1 GGCC
1248532 CTGGAGGACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.30, G:0.34, T:0.25
Consensus pattern (20 bp):
GGCCTTGCGACCAGCGTATT
Found at i:1256444 original size:31 final size:31
Alignment explanation
Indices: 1256402--1256472 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
1256392 AACAAAATTT
1256402 CTTGTTCGTGTTCATTCGTGAAGGAATGCAG
1 CTTGTTCGTGTTCATTCGTGAAGGAATGCAG
* * * *
1256433 CTTGTTTGTGTTTATTCGTTAAGGAATGTAG
1 CTTGTTCGTGTTCATTCGTGAAGGAATGCAG
1256464 CTTGTTCGT
1 CTTGTTCGT
1256473 TCGTTAGAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.17, C:0.13, G:0.27, T:0.44
Consensus pattern (31 bp):
CTTGTTCGTGTTCATTCGTGAAGGAATGCAG
Found at i:1256475 original size:25 final size:25
Alignment explanation
Indices: 1256447--1256522 Score: 73
Period size: 28 Copynumber: 2.9 Consensus size: 25
1256437 TTTGTGTTTA
1256447 TTCGTTAAGGAATGTAGCTTGTTCG
1 TTCGTTAAGGAATGTAGCTTGTTCG
* *
1256472 TTCGTT-AGAGATTGTAGTTTGTTGTTCG
1 TTCGTTAAG-GAATGTAG---CTTGTTCG
* *
1256500 TTCGTTAAAGAATGTAACTTGTT
1 TTCGTTAAGGAATGTAGCTTGTT
1256523 TATGTTCTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
24 2 0.05
25 18 0.45
28 19 0.47
29 1 0.03
ACGTcount: A:0.21, C:0.09, G:0.25, T:0.45
Consensus pattern (25 bp):
TTCGTTAAGGAATGTAGCTTGTTCG
Found at i:1256521 original size:28 final size:28
Alignment explanation
Indices: 1256465--1256522 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
1256455 GGAATGTAGC
* * **
1256465 TTGTTCGTTCGTTAGAGATTGTAGTTTG
1 TTGTTCGTTCGTTAAAGAATGTAACTTG
1256493 TTGTTCGTTCGTTAAAGAATGTAACTTG
1 TTGTTCGTTCGTTAAAGAATGTAACTTG
1256521 TT
1 TT
1256523 TATGTTCTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.19, C:0.09, G:0.24, T:0.48
Consensus pattern (28 bp):
TTGTTCGTTCGTTAAAGAATGTAACTTG
Found at i:1256886 original size:28 final size:29
Alignment explanation
Indices: 1256835--1256893 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
1256825 AGGGGTGTAC
1256835 AAAAAATCCGAATATCCGATTTTGCGAAA
1 AAAAAATCCGAATATCCGATTTTGCGAAA
* *
1256864 AAAAATATCCGAA-ATCGGA-TTTGGGAAA
1 AAAAA-ATCCGAATATCCGATTTTGCGAAA
1256892 AA
1 AA
1256894 CCGGTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 10 0.37
29 10 0.37
30 7 0.26
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.22
Consensus pattern (29 bp):
AAAAAATCCGAATATCCGATTTTGCGAAA
Found at i:1256992 original size:12 final size:12
Alignment explanation
Indices: 1256977--1257022 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
1256967 CGGTTTTTTT
*
1256977 ACCGGATAAAAA
1 ACCGGTTAAAAA
1256989 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
1257004 ACCGGTTAAAAA
1 ACCGGTTAAAAA
1257016 ACCGGTT
1 ACCGGTT
1257023 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:1257004 original size:15 final size:13
Alignment explanation
Indices: 1256983--1257023 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
1256973 TTTTACCGGA
1256983 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1256996 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
1257010 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1257023 T
1 T
1257024 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:1259324 original size:21 final size:21
Alignment explanation
Indices: 1259300--1259339 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1259290 TTTATTTTAT
1259300 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
1259321 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
1259340 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:1259387 original size:33 final size:33
Alignment explanation
Indices: 1259334--1259432 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
1259324 TTTGTTTCAA
1259334 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1259366 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * * *
1259399 TTATCAAACTCGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1259432 T
1 T
1259433 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 11 0.18
33 51 0.82
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.44
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:1259461 original size:13 final size:13
Alignment explanation
Indices: 1259418--1259472 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1259408 TCGGAAGTAT
1259418 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
1259431 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
1259445 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
1259458 TTAAGTATTTGAA
1 TTAAGTATTTCAA
1259471 TT
1 TT
1259473 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:1259694 original size:21 final size:21
Alignment explanation
Indices: 1259668--1259716 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1259658 TGGAGCGTGG
1259668 GGGAATCAGTACCCTCTCATA
1 GGGAATCAGTACCCTCTCATA
* **
1259689 GGGAATCGGTTTCCTCTCATA
1 GGGAATCAGTACCCTCTCATA
1259710 GGGAATC
1 GGGAATC
1259717 GGTTCCCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (21 bp):
GGGAATCAGTACCCTCTCATA
Found at i:1259717 original size:21 final size:21
Alignment explanation
Indices: 1259680--1259720 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1259670 GAATCAGTAC
1259680 CCTCTCATAGGGAATCGGTTT
1 CCTCTCATAGGGAATCGGTTT
1259701 CCTCTCATAGGGAATCGGTT
1 CCTCTCATAGGGAATCGGTT
1259721 CCCTAAGTGT
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:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (21 bp):
CCTCTCATAGGGAATCGGTTT
Found at i:1259930 original size:17 final size:18
Alignment explanation
Indices: 1259910--1259943 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1259900 TTTTTTTTAT
1259910 AACC-GTTTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
1259927 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
1259944 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:1259943 original size:15 final size:15
Alignment explanation
Indices: 1259890--1259946 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
1259880 ATCTGGAATA
*
1259890 TTAAAATCGGTTTTTT
1 TTAAAACCGG-TTTTT
*
1259906 TTATAACC-GTTTTT
1 TTAAAACCGGTTTTT
1259920 TTAAAAAAACCGGTTTTT
1 TT---AAAACCGGTTTTT
1259938 TTAAAACCG
1 TTAAAACCG
1259947 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
14 7 0.21
15 8 0.24
16 6 0.18
17 5 0.15
18 8 0.24
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.46
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:1260079 original size:15 final size:16
Alignment explanation
Indices: 1260037--1260076 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
1260027 TTCTATGGGA
*
1260037 AAAAACCGGATCGGAT
1 AAAAACCGGATCGAAT
1260053 AAAAACCGGATCGAAT
1 AAAAACCGGATCGAAT
1260069 AAAAACCG
1 AAAAACCG
1260077 ATCCAGATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.50, C:0.20, G:0.20, T:0.10
Consensus pattern (16 bp):
AAAAACCGGATCGAAT
Found at i:1261340 original size:19 final size:19
Alignment explanation
Indices: 1261316--1261388 Score: 76
Period size: 19 Copynumber: 3.7 Consensus size: 19
1261306 ATTGATCTTA
1261316 CAGTATCGATACCCCTCCT
1 CAGTATCGATACCCCTCCT
**
1261335 CAGTATCGATACCCAACC-
1 CAGTATCGATACCCCTCCT
*
1261353 CAAGGTTTCGATATCCCCTCCT
1 C-A-GTATCGATA-CCCCTCCT
*
1261375 TAGTATCGATACCC
1 CAGTATCGATACCC
1261389 AACCCAAGGT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
18 1 0.02
19 20 0.47
20 16 0.37
21 6 0.14
ACGTcount: A:0.25, C:0.37, G:0.12, T:0.26
Consensus pattern (19 bp):
CAGTATCGATACCCCTCCT
Found at i:1261365 original size:20 final size:20
Alignment explanation
Indices: 1261337--1261408 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
1261327 CCCCTCCTCA
1261337 GTATCGATACCCAACCCAAG
1 GTATCGATACCCAACCCAAG
* ** **
1261357 GTTTCGATATCCCCTCCTTA-
1 GTATCGATA-CCCAACCCAAG
1261377 GTATCGATACCCAACCCAAG
1 GTATCGATACCCAACCCAAG
1261397 GTATCGATACCC
1 GTATCGATACCC
1261409 CAACTGAAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 6 0.15
20 28 0.70
21 6 0.15
ACGTcount: A:0.28, C:0.35, G:0.14, T:0.24
Consensus pattern (20 bp):
GTATCGATACCCAACCCAAG
Found at i:1261382 original size:40 final size:39
Alignment explanation
Indices: 1261318--1261409 Score: 157
Period size: 40 Copynumber: 2.3 Consensus size: 39
1261308 TGATCTTACA
1261318 GTATCGATACCCCTCCTCAGTATCGATACCCAACCCAAG
1 GTATCGATACCCCTCCTCAGTATCGATACCCAACCCAAG
* *
1261357 GTTTCGATATCCCCTCCTTAGTATCGATACCCAACCCAAG
1 GTATCGATA-CCCCTCCTCAGTATCGATACCCAACCCAAG
1261397 GTATCGATACCCC
1 GTATCGATACCCC
1261410 AACTGAAATG
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
39 12 0.24
40 37 0.76
ACGTcount: A:0.26, C:0.37, G:0.13, T:0.24
Consensus pattern (39 bp):
GTATCGATACCCCTCCTCAGTATCGATACCCAACCCAAG
Found at i:1262330 original size:96 final size:94
Alignment explanation
Indices: 1262223--1262408 Score: 282
Period size: 96 Copynumber: 2.0 Consensus size: 94
1262213 TACCTTAGTC
* *
1262223 GCTTCAACTAAACTTGGAAATCTTAAAAAACTTCTACTTTTAGTTGGCTCTTGGAGAGAAAAAGA
1 GCTTCAACTAAACTTGGAAATCTCAAAAAACTTATACTTTTAGTTGGCTCTTGGAGAG--AAAGA
*
1262288 AGGAAGAAGAGAAGAGGAAATGAAGAGAGTT
64 AGGAAGAAGAGAAGAGGAAACGAAGAGAGTT
* * *
1262319 GCTTTAACTAAACTTGGAAATCTCAAAAAGCTTATACTTTTGGTTGGCTCTTGGAGAGAAAGAAG
1 GCTTCAACTAAACTTGGAAATCTCAAAAAACTTATACTTTTAGTTGGCTCTTGGAGAGAAAGAAG
* *
1262384 GAAGAAGATAATAGGAAACGAAGAG
66 GAAGAAGAGAAGAGGAAACGAAGAG
1262409 TGCTTGGGAA
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
94 29 0.35
96 53 0.65
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (94 bp):
GCTTCAACTAAACTTGGAAATCTCAAAAAACTTATACTTTTAGTTGGCTCTTGGAGAGAAAGAAG
GAAGAAGAGAAGAGGAAACGAAGAGAGTT
Found at i:1272165 original size:6 final size:6
Alignment explanation
Indices: 1272154--1272186 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1272144 TTTGAATCAT
1272154 ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG ATT
1 ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG ATT
1272187 GGGTCGGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.00, G:0.30, T:0.52
Consensus pattern (6 bp):
ATTTGG
Found at i:1274945 original size:13 final size:13
Alignment explanation
Indices: 1274927--1274951 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1274917 TTGAAAAAAT
1274927 AAATAAATTATCA
1 AAATAAATTATCA
1274940 AAATAAATTATC
1 AAATAAATTATC
1274952 TGTTCACCTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATAAATTATCA
Found at i:1279983 original size:120 final size:119
Alignment explanation
Indices: 1279762--1279997 Score: 368
Period size: 120 Copynumber: 2.0 Consensus size: 119
1279752 AAAATTAACC
**
1279762 CAAAGGTCTAGTTTGGTTCCTAATCATGTGCTAAAGCTTTAGGAAGTTACATAGGGTCATAAATT
1 CAAAGGTCTAGTTTGGTTCCTAATCATACGCTAAAGCTTTAGGAAGTTACATAGGGTCATAAATT
* *
1279827 GATATAAAAACACATTATTTACTCTAAATTCATCATCAAATCATGAAATCATCT
66 GACATAAAAACACATTATTTACTCTAAATACATCATCAAATCATGAAATCATCT
* *
1279881 CAAAGGTCATAGTTTGGTTCCTAATCATACGCTAAAGCTTTAGGAAGTTGA-TTAGGGTCATACA
1 CAAAGGTC-TAGTTTGGTTCCTAATCATACGCTAAAGCTTTAGGAAGTT-ACATAGGGTCATAAA
*
1279945 TTGACATAAAAACACATGT-TTTACTCTAAATACGTCATCAAATCATGAAATCA
64 TTGACATAAAAACACAT-TATTTACTCTAAATACATCATCAAATCATGAAATCA
1279998 AGTATAAAGG
Statistics
Matches: 107, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
119 8 0.07
120 97 0.91
121 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (119 bp):
CAAAGGTCTAGTTTGGTTCCTAATCATACGCTAAAGCTTTAGGAAGTTACATAGGGTCATAAATT
GACATAAAAACACATTATTTACTCTAAATACATCATCAAATCATGAAATCATCT
Found at i:1285613 original size:30 final size:30
Alignment explanation
Indices: 1285577--1285681 Score: 88
Period size: 30 Copynumber: 3.5 Consensus size: 30
1285567 TTATTTTCAA
1285577 GTTCAGCGTCATTAATTTCAGGTTCAAGTC
1 GTTCAGCGTCATTAATTTCAGGTTCAAGTC
* ** * *
1285607 GTTCAGCTTGGTGT-ATTTCAGGTTCAACTG
1 GTTCAGCGTCAT-TAATTTCAGGTTCAAGTC
* * *
1285637 GTTCACCGTCATTAATTT-TGAGTTCAAGTT
1 GTTCAGCGTCATTAATTTCAG-GTTCAAGTC
* *
1285667 GGTCAGCATCATTAA
1 GTTCAGCGTCATTAA
1285682 ATTTAGTTTC
Statistics
Matches: 57, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
29 2 0.04
30 54 0.95
31 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (30 bp):
GTTCAGCGTCATTAATTTCAGGTTCAAGTC
Found at i:1286954 original size:37 final size:37
Alignment explanation
Indices: 1286881--1286955 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
1286871 GTTGAAAATT
* *
1286881 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
1286918 ATTTATATAATTTTTTTTACAAAAA-TGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAAATTGAAAATCATAAA
1286955 A
1 A
1286956 AGCTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 14 0.42
39 5 0.15
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:1291515 original size:5 final size:5
Alignment explanation
Indices: 1291505--1291529 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1291495 ACATGTTACA
1291505 ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT
1291530 GATATGTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:1294989 original size:69 final size:69
Alignment explanation
Indices: 1294907--1295045 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
1294897 TCTTCATTTG
*
1294907 AGTCCCTAATAATTGTTTAAATGGCCTCATAGGTACTCATATTTTCATACTTTTCACCCAACATG
1 AGTCCCTAATAATTGTTTAAATGGCCTCATAGGTACTCACATTTTCATACTTTTCACCCAACATG
1294972 TTAA
66 TTAA
1294976 AGTCCCTAATAATTGTTTAAATGGCCTCATAGGTACTCACATTTTCATACTTTTCACCCAACATG
1 AGTCCCTAATAATTGTTTAAATGGCCTCATAGGTACTCACATTTTCATACTTTTCACCCAACATG
1295041 TTAA
66 TTAA
1295045 A
1 A
1295046 CCTGGACTGA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (69 bp):
AGTCCCTAATAATTGTTTAAATGGCCTCATAGGTACTCACATTTTCATACTTTTCACCCAACATG
TTAA
Found at i:1296342 original size:17 final size:17
Alignment explanation
Indices: 1296315--1296353 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1296305 AAAATACAAT
1296315 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
1296331 TAATTATAAATAATATC
1 TAATTATAAATAATATC
1296348 TAATTA
1 TAATTA
1296354 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:1296353 original size:37 final size:33
Alignment explanation
Indices: 1296283--1296357 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 33
1296273 AGAATTTTAG
* *
1296283 AATTTAATAATTTTTAATTAAAAAAATACAATT
1 AATTTAATAATATCTAATTAAAAAAATACAATT
*
1296316 AATTTAAATAATATCTAATTATAAATAATATCTAATT
1 AATTT-AATAATATCTAATTA-AAAAAATA-C-AATT
1296353 AATTT
1 AATTT
1296358 GATTCAAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 5 0.14
34 13 0.37
35 7 0.20
36 1 0.03
37 9 0.26
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (33 bp):
AATTTAATAATATCTAATTAAAAAAATACAATT
Found at i:1300533 original size:394 final size:393
Alignment explanation
Indices: 1299775--1300845 Score: 1660
Period size: 394 Copynumber: 2.7 Consensus size: 393
1299765 CTGTAAATGA
1299775 TTTAGTGGTA-TACAGTAAG-TTTGATTA---GGGGAGAGTTTAATTCATTCATTAGTTGAATCT
1 TTTAGTGGTATTACAGTAAGTTTTGATTAGCCGGGGAGAGTTTAATTCATTCATTAGTTGAATCT
1299835 TCTATAAGAAAGGTATTGTTGAATCTCCTATATTTCATTCTAGTTTTGCATCTGTTAACTCTAGA
66 TCTATAAGAAAGGTATTGTTGAATCTCCTATATTTCATTCTAGTTTTGCATCTGTTAACTCTAGA
1299900 AGTAACTGCAGAGCAACCGTTTTCGGGCATTGAATCAGA-TTTCTTTTGTCGAAACAGTCGACTT
131 AGTAACTGCAGAGCAACCGTTTTCGGGCATTGAATCAGATTTTCTTTTGTCGAAACAGTCGACTT
* *
1299964 TTTGTCTTATAGATCTTAATTTGCGAACCGAAGTGGTACATTTTGCATGTAAGAGTTCATAGAAG
196 TTTGTCTTATAGATCTTAAATTGCGAACCAAAGTGGTACATTTTGCATGTAAGAGTTCATAGAAG
* * * *
1300029 GCGCCTGTTAGCTTATTTAGTCAAGAATTTCGATGGCTAAACATGACGAAAGGACCTTTTATAAT
261 GTGCCTGTTAGCTTATTTAGTCAAGGATTTCAATGGCTAAACATGACGAAAAGACCTTTTATAAT
* *
1300094 GCGAGACTCATATTTTACCGGTTAACCTTATCTGGAACGTTTCAGATGGTCCGTGAGAACACAAT
326 GCGAGACTCACATTTTACCGGTTAACCTTATCTGGAACATTTCAGATGGTCCGTGAGAACACAAT
1300159 TAC
391 TAC
1300162 TTTAGTGGTATTACAGTAAGTTTTGATTAGCCGGGGAGAGTTTAATTCATTCATTAGTTGAATCT
1 TTTAGTGGTATTACAGTAAGTTTTGATTAGCCGGGGAGAGTTTAATTCATTCATTAGTTGAATCT
1300227 TCTATAAGAAAGGTATTGTTGAATCTCCTATATTTCATTCTAGTTTTGCATCTGTTAACTCTAGA
66 TCTATAAGAAAGGTATTGTTGAATCTCCTATATTTCATTCTAGTTTTGCATCTGTTAACTCTAGA
*
1300292 AGTAACTGCAGAGCAACCGTTTTCGGGCATTGAATCAGATTTCTCTTTTGTCGAAACAGTTGACT
131 AGTAACTGCAGAGCAACCGTTTTCGGGCATTGAATCAGATTT-TCTTTTGTCGAAACAGTCGACT
* * *
1300357 TTTTGTCTTATAGATATTAAATTGTGAACCAAAGTGGTACATTTTGCTTGTAAGAGTTCATAGAA
195 TTTTGTCTTATAGATCTTAAATTGCGAACCAAAGTGGTACATTTTGCATGTAAGAGTTCATAGAA
* * *
1300422 GGTTCCTGTTAGCTTATTTAGTCAAGGATTTTAATGGCTAAACATGGCGAAAAGACCTTTTATAA
260 GGTGCCTGTTAGCTTATTTAGTCAAGGATTTCAATGGCTAAACATGACGAAAAGACCTTTTATAA
* * * * *
1300487 TGTGAGACTCACCTTTTACTGGTTAACCTTATCTGGAGCATTTCAGATGGTCCGTGAGAACACGA
325 TGCGAGACTCACATTTTACCGGTTAACCTTATCTGGAACATTTCAGATGGTCCGTGAGAACACAA
1300552 TTAC
390 TTAC
**
1300556 TTGTAGTGGTATTACAGTAAGTTTTGATTAGCCAAGGAGAGTTTAATTCATTCATTAGTTGAATC
1 TT-TAGTGGTATTACAGTAAGTTTTGATTAGCCGGGGAGAGTTTAATTCATTCATTAGTTGAATC
* * *
1300621 TTCTATAAG-AAGGTGTTGTTGAATCTCCTATATTTCATTTTAGTTTTGCATCGGTTAACAT-TA
65 TTCTATAAGAAAGGTATTGTTGAATCTCCTATATTTCATTCTAGTTTTGCATCTGTTAAC-TCTA
* * * * ** * * * *
1300684 GTAGTAGCTACTGAAG-AATCATTTTTC-GTCATTTAATCAGTTTTTCTTTTGTCGAAACAGTCA
129 GAAGTAACTGCAG-AGCAA-CCGTTTTCGGGCATTGAATCAGATTTTCTTTTGTCGAAACAGTCG
* * * *
1300747 ACTTTTTGTCTAATGGATCTTAAATTGCAAACCAAAGTGGTACATTTTGCATGTTAGAGTTCATA
192 ACTTTTTGTCTTATAGATCTTAAATTGCGAACCAAAGTGGTACATTTTGCATGTAAGAGTTCATA
*
1300812 GAA-GTGCCGGTTAGCTTATTTAGTCAAGGATTTC
257 GAAGGTGCCTGTTAGCTTATTTAGTCAAGGATTTC
1300846 GACGGCTGTA
Statistics
Matches: 627, Mismatches: 46, Indels: 17
0.91 0.07 0.02
Matches are distributed among these distances:
387 10 0.02
388 9 0.01
389 8 0.01
392 165 0.26
393 80 0.13
394 277 0.44
395 78 0.12
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.38
Consensus pattern (393 bp):
TTTAGTGGTATTACAGTAAGTTTTGATTAGCCGGGGAGAGTTTAATTCATTCATTAGTTGAATCT
TCTATAAGAAAGGTATTGTTGAATCTCCTATATTTCATTCTAGTTTTGCATCTGTTAACTCTAGA
AGTAACTGCAGAGCAACCGTTTTCGGGCATTGAATCAGATTTTCTTTTGTCGAAACAGTCGACTT
TTTGTCTTATAGATCTTAAATTGCGAACCAAAGTGGTACATTTTGCATGTAAGAGTTCATAGAAG
GTGCCTGTTAGCTTATTTAGTCAAGGATTTCAATGGCTAAACATGACGAAAAGACCTTTTATAAT
GCGAGACTCACATTTTACCGGTTAACCTTATCTGGAACATTTCAGATGGTCCGTGAGAACACAAT
TAC
Found at i:1301213 original size:275 final size:274
Alignment explanation
Indices: 1300658--1301219 Score: 743
Period size: 274 Copynumber: 2.0 Consensus size: 274
1300648 CTATATTTCA
* * * *
1300658 TTTTAGTTTTGCATCGGTTAACATTAGTAGTAGCTACTGAAGAATCATTTTTCGTCATTTAATCA
1 TTTTAGTTTTGCATAGGTTAACATTAGAAGTAGCTACTGAACAATCATTTTTCGGCATTTAATCA
* * *
1300723 GTTTTTCTTTTGTCGAAACAGTCAACTTTTTGTCTAATGGATCTTAAATTGCAAACCAAAGTGGT
66 GTTTTTCATTTGTCCAAACAGTCAACTTTTTGTCTAATAGATCTTAAATTGCAAACCAAAGTGGT
* * *
1300788 ACATTTTGCATGTTAGAGTTCATAGAAGTGCCGGTTAGCTTATTTAGTCAAGGATTTCGACGGCT
131 ACATTTTGCATGTAAGAGTTCATAGAAGAGCCGGTTAGCTTATATAGTCAAGGATTTCGACGGCT
* * *
1300853 GTATCAGGAAAATGCCTATCACCTTTTACCGGTTAAGCTTATCTGGAATGTTTCAGTTGGTCTGT
196 GTATCAGGAAAATGCCTATCACCATTTACCGGTTAACCTTATCTGGAATGTTTCAGATGGTCTGT
*
1300918 GCAGATACGATTAC
261 GCAGACACGATTAC
** * *
1300932 TTTTAGTTTTGCATATTTTAACATTAGAAGTGGCT-TTAGAACAATCATTTTTCGGCATTTAATC
1 TTTTAGTTTTGCATAGGTTAACATTAGAAGTAGCTACT-GAACAATCATTTTTCGGCATTTAATC
* * * * ** *
1300996 GGTTTTTCATTTGTCCAAACTGTCGACTTTTTGTCCT-ATAGATCTTAATTTGTGAACCGAAGTG
65 AGTTTTTCATTTGTCCAAACAGTCAACTTTTTGT-CTAATAGATCTTAAATTGCAAACCAAAGTG
* * * * * *
1301060 TTGCATTTTGCTTGTAAGAGTTCATAGAAAGAGTCGGTTAGCTTATATAGTCAAGGATTTTGATG
129 GTACATTTTGCATGTAAGAGTTCATAG-AAGAGCCGGTTAGCTTATATAGTCAAGGATTTCGACG
* * **
1301125 GCTGTATCATGAAAGTGCCGT-TGGCCATTTACCGGTTAACCTTATCTGGAATGTTTCAGATGGT
193 GCTGTATCAGGAAAATGCC-TATCACCATTTACCGGTTAACCTTATCTGGAATGTTTCAGATGGT
*
1301189 CTGTGCGGACACGATTAC
257 CTGTGCAGACACGATTAC
1301207 TTTTAGTTTTGCA
1 TTTTAGTTTTGCA
1301220 CCTATCCATT
Statistics
Matches: 248, Mismatches: 36, Indels: 7
0.85 0.12 0.02
Matches are distributed among these distances:
273 1 0.00
274 128 0.52
275 118 0.48
276 1 0.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.39
Consensus pattern (274 bp):
TTTTAGTTTTGCATAGGTTAACATTAGAAGTAGCTACTGAACAATCATTTTTCGGCATTTAATCA
GTTTTTCATTTGTCCAAACAGTCAACTTTTTGTCTAATAGATCTTAAATTGCAAACCAAAGTGGT
ACATTTTGCATGTAAGAGTTCATAGAAGAGCCGGTTAGCTTATATAGTCAAGGATTTCGACGGCT
GTATCAGGAAAATGCCTATCACCATTTACCGGTTAACCTTATCTGGAATGTTTCAGATGGTCTGT
GCAGACACGATTAC
Found at i:1304358 original size:2 final size:2
Alignment explanation
Indices: 1304351--1304376 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1304341 ACAGAAAACG
1304351 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
1304377 TAGGGTAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1307105 original size:28 final size:29
Alignment explanation
Indices: 1307072--1307129 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
1307062 CTCTATTTAT
1307072 ATTATGTCATCGAACCAGTGCTT-AAAAC
1 ATTATGTCATCGAACCAGTGCTTGAAAAC
* * *
1307100 ATTATGTCGTCGAGCCAGTGTTTGAAAAC
1 ATTATGTCATCGAACCAGTGCTTGAAAAC
1307129 A
1 A
1307130 ACGATGATGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (29 bp):
ATTATGTCATCGAACCAGTGCTTGAAAAC
Found at i:1311091 original size:17 final size:17
Alignment explanation
Indices: 1311065--1311098 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1311055 GTTGATGAGT
1311065 TTTATATTATATCTTAG
1 TTTATATTATATCTTAG
* *
1311082 TTTATCTTATATTTTAG
1 TTTATATTATATCTTAG
1311099 GTAGTTTATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (17 bp):
TTTATATTATATCTTAG
Found at i:1311431 original size:60 final size:59
Alignment explanation
Indices: 1311366--1311480 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 59
1311356 ATAGTCGAGT
** * * * *
1311366 GACCATTTTGTAACTTTTAATAGTCGAATGACTTAACAAAATAACATTCTATAATCGGAG
1 GACCATTTTACAACTTTTAATAATAG-ATGACTTAACAAAACAACAATCTATAATCGGAG
* *
1311426 GACCATTTTACAACTTTTAATAATAGATGACTTAATAAAACAATAATCTATAATC
1 GACCATTTTACAACTTTTAATAATAGATGACTTAACAAAACAACAATCTATAATC
1311481 AGTGAATCAT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
59 25 0.53
60 22 0.47
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.34
Consensus pattern (59 bp):
GACCATTTTACAACTTTTAATAATAGATGACTTAACAAAACAACAATCTATAATCGGAG
Found at i:1313104 original size:63 final size:63
Alignment explanation
Indices: 1313028--1313291 Score: 519
Period size: 63 Copynumber: 4.2 Consensus size: 63
1313018 TAACCTAATT
1313028 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1313091 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
*
1313154 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGTTAGTTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1313217 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1313280 TTAGCATTATCA
1 TTAGCATTATCA
1313292 AGAAATGACA
Statistics
Matches: 199, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 199 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (63 bp):
TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
Found at i:1313298 original size:41 final size:41
Alignment explanation
Indices: 1313236--1313369 Score: 250
Period size: 41 Copynumber: 3.2 Consensus size: 41
1313226 TCATTATCAA
1313236 AATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1 AATT-AGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1313278 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1313319 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
*
1313360 AATGAGCATT
1 AATTAGCATT
1313370 GTACAATACT
Statistics
Matches: 91, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
41 87 0.96
42 4 0.04
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (41 bp):
AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
Found at i:1314752 original size:17 final size:17
Alignment explanation
Indices: 1314726--1314759 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1314716 GTTGATGAGT
1314726 TTTATATTATATCTTAG
1 TTTATATTATATCTTAG
* *
1314743 TTTATCTTATATTTTAG
1 TTTATATTATATCTTAG
1314760 GTAGTTTATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (17 bp):
TTTATATTATATCTTAG
Found at i:1316788 original size:63 final size:63
Alignment explanation
Indices: 1316689--1316826 Score: 267
Period size: 63 Copynumber: 2.2 Consensus size: 63
1316679 TAACCTAATT
1316689 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGATGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGATGAA
*
1316752 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGATGAA
1316815 TTAGCATTATCA
1 TTAGCATTATCA
1316827 AGAAATGACA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 74 1.00
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.33
Consensus pattern (63 bp):
TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGATGAA
Found at i:1316833 original size:41 final size:41
Alignment explanation
Indices: 1316771--1316865 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
1316761 TCATTATCAA
1316771 AATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1 AATT-AGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1316813 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
*
1316854 AATGAGCATTAT
1 AATTAGCATTAT
1316866 ACAATACTCA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 48 0.92
42 4 0.08
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.32
Consensus pattern (41 bp):
AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
Found at i:1321502 original size:9 final size:9
Alignment explanation
Indices: 1321488--1321514 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1321478 TTTTGTTGTC
1321488 TTTCTCGTA
1 TTTCTCGTA
1321497 TTTCTCGTA
1 TTTCTCGTA
1321506 TTTCTCGTA
1 TTTCTCGTA
1321515 GGTAGCGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.11, T:0.56
Consensus pattern (9 bp):
TTTCTCGTA
Found at i:1322237 original size:63 final size:63
Alignment explanation
Indices: 1322161--1322484 Score: 336
Period size: 63 Copynumber: 5.2 Consensus size: 63
1322151 TAACCTAATT
1322161 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1322224 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
** * * * * * *
1322287 TTAGCATTATCAAGAAATGACAATTTA-CA--ATGCTAGTTGAATGAGC-ATTATA-AA-G--AA
1 TTAGCATTATC-A-TTATCAAAATTGAGCATTAT-CAAG--AAATGA-CAATT-TACAATGCTAG
*
1322344 ATGACAA
59 TTG--AA
**
1322351 TTTA-CA--ATGC--TAGT-TGAATT-AGCATTATCAAGAAATGACAATTTACAATGCTAGTTGA
1 -TTAGCATTAT-CATTA-TCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGA
1322409 A
63 A
1322410 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1322473 TTAGCATTATCA
1 TTAGCATTATCA
1322485 AGAAATGACA
Statistics
Matches: 216, Mismatches: 18, Indels: 54
0.75 0.06 0.19
Matches are distributed among these distances:
57 3 0.01
58 14 0.06
59 12 0.06
60 5 0.02
61 8 0.04
62 13 0.06
63 129 0.60
64 8 0.04
65 21 0.10
66 3 0.01
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (63 bp):
TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
Found at i:1322305 original size:41 final size:41
Alignment explanation
Indices: 1322243--1322421 Score: 331
Period size: 41 Copynumber: 4.3 Consensus size: 41
1322233 TCATTATCAA
1322243 AATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1 AATT-AGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1322285 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
* *
1322326 AATGAGCATTATAAAGAAATGACAATTTACAATGCTAGTTG
1 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1322367 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1322408 AATTAGCATTATCA
1 AATTAGCATTATCA
1322422 TTATCAAAAT
Statistics
Matches: 133, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
41 129 0.97
42 4 0.03
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (41 bp):
AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
Found at i:1322446 original size:145 final size:146
Alignment explanation
Indices: 1322285--1322590 Score: 537
Period size: 145 Copynumber: 2.1 Consensus size: 146
1322275 ATGCTAGTTG
1322285 AATT-AGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAATGAGCATTATAAAGAAATGAC
1 AATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAATGAGCATTATAAAGAAATGAC
*
1322349 AATTTACAATGCTAGTTGAATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAATTAG
66 AATTTACAATGCTAGTTGAATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAATGAG
*
1322414 CATTAT-CATTATCA-A
131 CATTATACAATA-CACA
* *
1322429 AATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAATTAGCATTATCAAGAAATGAC
1 AATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAATGAGCATTATAAAGAAATGAC
1322494 AATTTACAATGCTAGTTGAATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAATGAG
66 AATTTACAATGCTAGTTGAATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAATGAG
1322559 CATTATACAATACACA
131 CATTATACAATACACA
*
1322575 ATTTGAGCATTATCAA
1 AATTGAGCATTATCAA
1322591 CATTCGTCAT
Statistics
Matches: 154, Mismatches: 5, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
144 4 0.03
145 130 0.84
146 20 0.13
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (146 bp):
AATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAATGAGCATTATAAAGAAATGAC
AATTTACAATGCTAGTTGAATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAATGAG
CATTATACAATACACA
Found at i:1322491 original size:41 final size:41
Alignment explanation
Indices: 1322429--1322564 Score: 254
Period size: 41 Copynumber: 3.3 Consensus size: 41
1322419 TCATTATCAA
1322429 AATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1 AATT-AGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1322471 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1322512 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
*
1322553 AATGAGCATTAT
1 AATTAGCATTAT
1322565 ACAATACACA
Statistics
Matches: 93, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
41 89 0.96
42 4 0.04
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (41 bp):
AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
Found at i:1322499 original size:186 final size:186
Alignment explanation
Indices: 1322180--1322564 Score: 734
Period size: 186 Copynumber: 2.1 Consensus size: 186
1322170 TCATTATCAA
1322180 AATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAATTAGCATTATCATTATCAAAA
1 AATT-AGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAATTAGCATTATCATTATCAAAA
1322245 TTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAATTAGCATTATCAAGAAATGACAA
65 TTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAATTAGCATTATCAAGAAATGACAA
1322310 TTTACAATGCTAGTTGAATGAGCATTATAAAGAAATGACAATTTACAATGCTAGTTG
130 TTTACAATGCTAGTTGAATGAGCATTATAAAGAAATGACAATTTACAATGCTAGTTG
1322367 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAATTAGCATTATCATTATCAAAAT
1 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAATTAGCATTATCATTATCAAAAT
1322432 TGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAATTAGCATTATCAAGAAATGACAAT
66 TGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAATTAGCATTATCAAGAAATGACAAT
* *
1322497 TTACAATGCTAGTTGAATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
131 TTACAATGCTAGTTGAATGAGCATTATAAAGAAATGACAATTTACAATGCTAGTTG
*
1322553 AATGAGCATTAT
1 AATTAGCATTAT
1322565 ACAATACACA
Statistics
Matches: 195, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
186 191 0.98
187 4 0.02
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.32
Consensus pattern (186 bp):
AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAATTAGCATTATCATTATCAAAAT
TGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAATTAGCATTATCAAGAAATGACAAT
TTACAATGCTAGTTGAATGAGCATTATAAAGAAATGACAATTTACAATGCTAGTTG
Found at i:1322508 original size:104 final size:104
Alignment explanation
Indices: 1322328--1322525 Score: 387
Period size: 104 Copynumber: 1.9 Consensus size: 104
1322318 GCTAGTTGAA
1322328 TGAGCATTATAAAGAAATGACAATTTACAATGCTAGTTGAATTAGCATTATCAAGAAATGACAAT
1 TGAGCATTATAAAGAAATGACAATTTACAATGCTAGTTGAATTAGCATTATCAAGAAATGACAAT
1322393 TTACAATGCTAGTTGAATTAGCATTATCATTATCAAAAT
66 TTACAATGCTAGTTGAATTAGCATTATCATTATCAAAAT
*
1322432 TGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAATTAGCATTATCAAGAAATGACAAT
1 TGAGCATTATAAAGAAATGACAATTTACAATGCTAGTTGAATTAGCATTATCAAGAAATGACAAT
1322497 TTACAATGCTAGTTGAATTAGCATTATCA
66 TTACAATGCTAGTTGAATTAGCATTATCA
1322526 AGAAATGACA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 93 1.00
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.32
Consensus pattern (104 bp):
TGAGCATTATAAAGAAATGACAATTTACAATGCTAGTTGAATTAGCATTATCAAGAAATGACAAT
TTACAATGCTAGTTGAATTAGCATTATCATTATCAAAAT
Found at i:1323106 original size:2 final size:2
Alignment explanation
Indices: 1323099--1323169 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
1323089 AAGACATTCA
1323099 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1323141 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
1323170 ATAAAAATCC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1326147 original size:20 final size:21
Alignment explanation
Indices: 1326119--1326158 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1326109 ATATTGGGTT
1326119 TTTTATTAAAAAATATTTTTA
1 TTTTATTAAAAAATATTTTTA
* *
1326140 TTTT-TTAAATATTATTTTT
1 TTTTATTAAAAAATATTTTT
1326159 TTGAAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTATTAAAAAATATTTTTA
Found at i:1326159 original size:16 final size:17
Alignment explanation
Indices: 1326129--1326170 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1326119 TTTTATTAAA
* *
1326129 AAATATTTTTATTTTTT
1 AAATATTATTATTTTTG
1326146 AAATATTATT-TTTTTG
1 AAATATTATTATTTTTG
*
1326162 AAATTTTAT
1 AAATATTAT
1326171 ATGGTTAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
AAATATTATTATTTTTG
Found at i:1328646 original size:15 final size:15
Alignment explanation
Indices: 1328606--1328647 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 15
1328596 TAATCCTAAT
1328606 TAATAAATATTAA--
1 TAATAAATATTAACC
1328619 TAATAAATATTAACC
1 TAATAAATATTAACC
1328634 TAATGAAAT-TTAAC
1 TAAT-AAATATTAAC
1328648 ATTAGTGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 13 0.50
15 9 0.35
16 4 0.15
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (15 bp):
TAATAAATATTAACC
Done.