Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008721.1 Hibiscus syriacus cultivar Beakdansim tig00111779_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: 2464137
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 12
Found at i:1181555 original size:163 final size:161
Alignment explanation
Indices: 1181354--1182473 Score: 1213
Period size: 163 Copynumber: 7.0 Consensus size: 161
1181344 GAGCGTCGAT
* *
1181354 AATTAAATCTTAAAAAGTTAGTACTAGTTCGGACATCGCAAACTCATAATCCCAAGTTCTAACTG
1 AATTAAATCTTAAAAAGTTAGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCTAACTG
*
1181419 CCTCTAAAGCCATTTCTTTCTTCTCCTAATCAGCTATCT-TGGAAATTCATAGTCGCATTTTAAA
66 CCTC-AAAGCCATTTCTTTCTTCTCCTAATCAGCTCTCTCT-GAAATTCATAGTCGCATTTTAAA
* *
1181483 CAGTAGAGCTAATTTTAGCAGAGGTAGCTTACG
129 CAGTAGAGCTAATTTTAGCAGAGGTAGCATACA
* * *
1181516 AATTAAATCTTAAAAATGTTTA-AACTAGTTTGGACATCGCAGAGTCATAATCCCACGTTCTAAC
1 AATTAAATCTTAAAAA-G-TTAGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCTAAC
* * * * * * *
1181580 TGCCTACAAAGCCCCTTTTTTTTCTTCTCCTAATCAGCTCTCTTTGAAA-TCTTAATCGTATCTT
64 TGCCT-CAAAG--CCATTTCTTTCTTCTCCTAATCAGCTCTCTCTGAAATTCATAGTCGCATTTT
* *
1181644 AAACAGTAGAGCTAATCTTAGCAGAGGTAGAATACA
126 AAACAGTAGAGCTAATTTTAGCAGAGGTAGCATACA
* * *
1181680 AATTAAGTCTTAAAAAAGTTTGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCTAATT
1 AATTAAATCTT-AAAAAGTTAGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCTAACT
* * * *
1181745 GCCAAT-AAAGCCTTTTTCTTTCTTCTCCTAATCAGCCCTCTATGAAATTCATAGTAGCATTTTA
65 GCC--TCAAAGCC-ATTTCTTTCTTCTCCTAATCAGCTCTCTCTGAAATTCATAGTCGCATTTTA
* * **
1181809 AACAATAGACCTAATTTTAGCAGAGGTAGCATATG
127 AACAGTAGAGCTAATTTTAGCAGAGGTAGCATACA
* * *
1181844 AATT-AATCTTAAAAAGTTAGAACTAGTTCAGACATTGCAGACTCATAATCCCAAGTTCTAAATG
1 AATTAAATCTTAAAAAGTTAGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCTAACTG
* * *
1181908 CCTACAAAGCCACGTCTCCTTCTTCTCCTAATCAGCTCTCTCTGAACTTCATAGTCGCATTTTAA
66 CCT-CAAAGCCA--TTTCTTTCTTCTCCTAATCAGCTCTCTCTGAAATTCATAGTCGCATTTTAA
* *
1181973 ACAGTAGAGCTAATTTTA--A-A--T--CTTAAA
128 ACAGTAGAGCTAATTTTAGCAGAGGTAGCATACA
* * * ** * * * *
1182000 AAGTTAGAA-C-T----AGTTCAGAAATCG--CAGAC-TCATA-ATCCCA-AGTTCTAA--T-TA
1 AA-TTA-AATCTTAAAAAGTT-AGAACTAGTTCGGACATCGCAGA-CTCATAATCCCAAGTTCTA
* * *
1182051 AC-GCCTGCAAAGCCCCGTTTCTTTCTCCTCCTAATCAGCTCTCTCTGAAATTCATAGTCTCATT
62 ACTGCCT-CAAAG--CCATTTCTTTCTTCTCCTAATCAGCTCTCTCTGAAATTCATAGTCGCATT
1182115 TTAAACAGTAGAGCTAATTTTAGCAGAGGTAGCATACA
124 TTAAACAGTAGAGCTAATTTTAGCAGAGGTAGCATACA
* * *
1182153 AATTAAATCTTAAAAAGTTAGAACTAGTTCGGGCATCACAGACTCATAATCCCAAGTTCTAAATG
1 AATTAAATCTTAAAAAGTTAGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCTAACTG
* *
1182218 CCTAAAAAGCCCCATTTCTTTCTTCT-CTAATCAGCTTTCTCTGAAATTCATAGTCGCATTTTAA
66 CCT-CAAAG--CCATTTCTTTCTTCTCCTAATCAGCTCTCTCTGAAATTCATAGTCGCATTTTAA
1182282 ACAGTAGAGCTAATTTTAGCAGAGGTAGCATACA
128 ACAGTAGAGCTAATTTTAGCAGAGGTAGCATACA
* * ** *
1182316 AATTAAATCTTAAAAAGTTAGAACTAGTTCGGACTTTGTTGACTCATAATCCCATGTTCTAA-TG
1 AATTAAATCTTAAAAAGTTAGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCTAACTG
* * *
1182380 CCTACAAAGCCCCGTTTCTTTCTTCTCCTAATCAGCTGTCT-TCGAAATTCTTAGTCGCA-TTTA
66 CCT-CAAAG--CCATTTCTTTCTTCTCCTAATCAGCTCTCTCT-GAAATTCATAGTCGCATTTTA
*
1182443 AACAGTAGAGCTAATTTTAGCAGATGTAGCA
127 AACAGTAGAGCTAATTTTAGCAGAGGTAGCA
1182474 CATGAATACA
Statistics
Matches: 811, Mismatches: 100, Indels: 94
0.81 0.10 0.09
Matches are distributed among these distances:
146 73 0.09
147 3 0.00
148 4 0.00
149 1 0.00
150 6 0.01
151 8 0.01
152 9 0.01
153 11 0.01
154 6 0.01
156 11 0.01
157 7 0.01
158 5 0.01
159 9 0.01
160 8 0.01
161 1 0.00
162 138 0.17
163 302 0.37
164 171 0.21
165 36 0.04
166 2 0.00
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.33
Consensus pattern (161 bp):
AATTAAATCTTAAAAAGTTAGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCTAACTG
CCTCAAAGCCATTTCTTTCTTCTCCTAATCAGCTCTCTCTGAAATTCATAGTCGCATTTTAAACA
GTAGAGCTAATTTTAGCAGAGGTAGCATACA
Found at i:1181708 original size:164 final size:162
Alignment explanation
Indices: 1181354--1181990 Score: 841
Period size: 164 Copynumber: 3.9 Consensus size: 162
1181344 GAGCGTCGAT
* *
1181354 AATTAAATCTTAAAAAGTTAGTACTAGTTCGGACATCGCAAACTCATAATCCCAAGTTCTAACTG
1 AATTAAATCTTAAAAAGTTAGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCTAACTG
* * *
1181419 CCT-CTAAAGCCATTTCTTTCTTCTCCTAATCAGCTATCTTGGAAATTCATAGTCGCATTTTAAA
66 CCTAC-AAAGCCTTTTCTTTCTTCTCCTAATCAGCTCTCTTTGAAATTCATAGTCGCATTTTAAA
*
1181483 CAGTAGAGCTAATTTTAGCAGAGGTAGCTTACG
130 CAGTAGAGCTAATTTTAGCAGAGGTAGCATACG
* * *
1181516 AATTAAATCTTAAAAATGTTTA-AACTAGTTTGGACATCGCAGAGTCATAATCCCACGTTCTAAC
1 AATTAAATCTTAAAAA-G-TTAGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCTAAC
* * * * *
1181580 TGCCTACAAAGCCCCTTTTTTTTCTTCTCCTAATCAGCTCTCTTTGAAA-TCTTAATCGTATCTT
64 TGCCTACAAAG--CCTTTTCTTTCTTCTCCTAATCAGCTCTCTTTGAAATTCATAGTCGCATTTT
* * *
1181644 AAACAGTAGAGCTAATCTTAGCAGAGGTAGAATACA
127 AAACAGTAGAGCTAATTTTAGCAGAGGTAGCATACG
* * *
1181680 AATTAAGTCTTAAAAAAGTTTGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCTAATT
1 AATTAAATCTT-AAAAAGTTAGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCTAACT
* * * * *
1181745 GCCAATAAAGCCTTTTTCTTTCTTCTCCTAATCAGCCCTCTATGAAATTCATAGTAGCATTTTAA
65 GCCTACAAAGCC-TTTTCTTTCTTCTCCTAATCAGCTCTCTTTGAAATTCATAGTCGCATTTTAA
* * *
1181810 ACAATAGACCTAATTTTAGCAGAGGTAGCATATG
129 ACAGTAGAGCTAATTTTAGCAGAGGTAGCATACG
* * *
1181844 AATT-AATCTTAAAAAGTTAGAACTAGTTCAGACATTGCAGACTCATAATCCCAAGTTCTAAATG
1 AATTAAATCTTAAAAAGTTAGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCTAACTG
* * * * *
1181908 CCTACAAAGCCACGTCTCCTTCTTCTCCTAATCAGCTCTCTCTGAACTTCATAGTCGCATTTTAA
66 CCTACAAAG-C-CTTTTCTTTCTTCTCCTAATCAGCTCTCTTTGAAATTCATAGTCGCATTTTAA
1181973 ACAGTAGAGCTAATTTTA
129 ACAGTAGAGCTAATTTTA
1181991 AATCTTAAAA
Statistics
Matches: 409, Mismatches: 55, Indels: 21
0.84 0.11 0.04
Matches are distributed among these distances:
162 75 0.18
163 147 0.36
164 150 0.37
165 37 0.09
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.33
Consensus pattern (162 bp):
AATTAAATCTTAAAAAGTTAGAACTAGTTCGGACATCGCAGACTCATAATCCCAAGTTCTAACTG
CCTACAAAGCCTTTTCTTTCTTCTCCTAATCAGCTCTCTTTGAAATTCATAGTCGCATTTTAAAC
AGTAGAGCTAATTTTAGCAGAGGTAGCATACG
Found at i:1182132 original size:146 final size:143
Alignment explanation
Indices: 1181848--1182136 Score: 461
Period size: 146 Copynumber: 2.0 Consensus size: 143
1181838 CATATGAATT
* * *
1181848 AATCTTAAAAAGTTAGAACTAGTTCAGACATTGCAGACTCATAATCCCAAGTTCTAAATGCCTAC
1 AATCTTAAAAAGTTAGAACTAGTTCAGAAATCGCAGACTCATAATCCCAAGTTCTAAACGCCTAC
* *
1181913 AAAGCCACGTCTCCTTCTTCTCCTAATCAGCTCTCTCTGAACTTCATAGTCGCATTTTAAACAGT
66 AAAGCCACGTCTCCTTCTCCTCCTAATCAGCTCTCTCTGAAATTCATAGTCGCATTTTAAACAGT
1181978 AGAGCTAATTTTA
131 AGAGCTAATTTTA
1181991 AATCTTAAAAAGTTAGAACTAGTTCAGAAATCGCAGACTCATAATCCCAAGTTCTAATTAACGCC
1 AATCTTAAAAAGTTAGAACTAGTTCAGAAATCGCAGACTCATAATCCCAAGTTCT-A--AACGCC
* * * * *
1182056 TGCAAAGCCCCGTTTCTTTCTCCTCCTAATCAGCTCTCTCTGAAATTCATAGTCTCATTTTAAAC
63 TACAAAGCCACGTCTCCTTCTCCTCCTAATCAGCTCTCTCTGAAATTCATAGTCGCATTTTAAAC
1182121 AGTAGAGCTAATTTTA
128 AGTAGAGCTAATTTTA
1182137 GCAGAGGTAG
Statistics
Matches: 133, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
143 53 0.40
144 1 0.01
146 79 0.59
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (143 bp):
AATCTTAAAAAGTTAGAACTAGTTCAGAAATCGCAGACTCATAATCCCAAGTTCTAAACGCCTAC
AAAGCCACGTCTCCTTCTCCTCCTAATCAGCTCTCTCTGAAATTCATAGTCGCATTTTAAACAGT
AGAGCTAATTTTA
Found at i:1186843 original size:36 final size:37
Alignment explanation
Indices: 1186796--1186865 Score: 124
Period size: 36 Copynumber: 1.9 Consensus size: 37
1186786 CTCGATTTGC
*
1186796 ACTTAAATAAACTTGGGTAC-AAGAAATTTACGTTTA
1 ACTTAAATAAACTTGGGTACAAAAAAATTTACGTTTA
1186832 ACTTAAATAAACTTGGGTACAAAAAAATTTACGT
1 ACTTAAATAAACTTGGGTACAAAAAAATTTACGT
1186866 ACGCCACTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 20 0.62
37 12 0.38
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (37 bp):
ACTTAAATAAACTTGGGTACAAAAAAATTTACGTTTA
Found at i:1197501 original size:24 final size:23
Alignment explanation
Indices: 1197445--1197504 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
1197435 CATGTTCATC
* * *
1197445 AAACAAACATATTGACGAACGCT
1 AAACGAACATGTTGACGAACGAT
*
1197468 GAACGAACATGTTGACGAACAGAT
1 AAACGAACATGTTGACGAAC-GAT
*
1197492 AAACGGACATGTT
1 AAACGAACATGTT
1197505 CTCGCAAACA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 17 0.57
24 13 0.43
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.18
Consensus pattern (23 bp):
AAACGAACATGTTGACGAACGAT
Found at i:1199946 original size:25 final size:25
Alignment explanation
Indices: 1199884--1199947 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
1199874 TATTGAATAT
*
1199884 GTTTTATTATTTATTATTTTTAAAA
1 GTTTCATTATTTATTATTTTTAAAA
* *
1199909 GTTTTATTATTTATTATTTTTTAAAC
1 GTTTCATTATTTATTA-TTTTTAAAA
*
1199935 G-TTCATTTTTTAT
1 GTTTCATTATTTAT
1199948 ATATAATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
25 26 0.74
26 9 0.26
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.66
Consensus pattern (25 bp):
GTTTCATTATTTATTATTTTTAAAA
Found at i:1201792 original size:21 final size:20
Alignment explanation
Indices: 1201768--1201807 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1201758 AGGCTCTCTA
*
1201768 TTTCTATTTTCCTAACTTAAT
1 TTTCAATTTTCCTAA-TTAAT
*
1201789 TTTCAATTTTTCTAATTAA
1 TTTCAATTTTCCTAATTAA
1201808 CTTATTGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTCAATTTTCCTAATTAAT
Found at i:1210155 original size:2 final size:2
Alignment explanation
Indices: 1210148--1210179 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1210138 AATATTTATT
1210148 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1210180 TATTTAGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1213654 original size:15 final size:15
Alignment explanation
Indices: 1213634--1213667 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1213624 TTTATTGTAT
1213634 TTTTAAAAATATGAG
1 TTTTAAAAATATGAG
1213649 TTTTAAAAATATGAG
1 TTTTAAAAATATGAG
1213664 TTTT
1 TTTT
1213668 GTATTTACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (15 bp):
TTTTAAAAATATGAG
Found at i:1213902 original size:21 final size:20
Alignment explanation
Indices: 1213878--1213935 Score: 55
Period size: 22 Copynumber: 2.8 Consensus size: 20
1213868 TTCATATATT
1213878 TAAAATTCAATAAAAATACAA
1 TAAAATTCAATAAAAAT-CAA
* * *
1213899 TAAAAAAT-AATTAAAAGTGAA
1 T-AAAATTCAA-TAAAAATCAA
1213920 TAAAATTCAATAAAAA
1 TAAAATTCAATAAAAA
1213936 AAAGTAAAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
20 10 0.34
21 8 0.28
22 11 0.38
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.24
Consensus pattern (20 bp):
TAAAATTCAATAAAAATCAA
Found at i:1214132 original size:9 final size:10
Alignment explanation
Indices: 1214111--1214136 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1214101 TAAAAGTTTA
1214111 TTTTAATATT
1 TTTTAATATT
1214121 TTTTAATATT
1 TTTTAATATT
1214131 TTTTAA
1 TTTTAA
1214137 ATTATAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTAATATT
Found at i:1216481 original size:24 final size:24
Alignment explanation
Indices: 1216451--1216589 Score: 192
Period size: 24 Copynumber: 5.7 Consensus size: 24
1216441 TAATATAATA
1216451 TTAAAAAACTTAATATTTAATTTAT
1 TTAAAAAA-TTAATATTTAATTTAT
*
1216476 TTAAAAAATTAATATATATAATATAAT
1 TTAAAAAATTAATAT-T-TAAT-TTAT
*
1216503 ATTAAAAAAAT-ATA-TTAATTTAT
1 -TTAAAAAATTAATATTTAATTTAT
1216526 TTAAAAAATTAATATTTAATTTAT
1 TTAAAAAATTAATATTTAATTTAT
*
1216550 TTAAAAAATTAATATTTAGTTTAT
1 TTAAAAAATTAATATTTAATTTAT
1216574 TTAAAAAATTAATATT
1 TTAAAAAATTAATATT
1216590 AAAATTAAAA
Statistics
Matches: 103, Mismatches: 5, Indels: 13
0.85 0.04 0.11
Matches are distributed among these distances:
22 9 0.09
23 6 0.06
24 59 0.57
25 10 0.10
26 4 0.04
27 6 0.06
28 9 0.09
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.46
Consensus pattern (24 bp):
TTAAAAAATTAATATTTAATTTAT
Found at i:1216500 original size:74 final size:73
Alignment explanation
Indices: 1216407--1216564 Score: 205
Period size: 74 Copynumber: 2.2 Consensus size: 73
1216397 AATAATATAT
* * * **
1216407 AAAA-TAATTTATATGATATAAAATTAAATATCTATAATATAA-TA-TTAAAAAACTTAATATTT
1 AAAATTAATATATATAATATAAAATTAAAAAAATAT-AT-TAATTATTTAAAAAA-TTAATATTT
1216469 AATTTATTTAA
63 AATTTATTTAA
*
1216480 AAAATTAATATATATAATATAATATTAAAAAAATATATTAATTTATTTAAAAAATTAATATTTAA
1 AAAATTAATATATATAATATAAAATTAAAAAAATATATTAA-TTATTTAAAAAATTAATATTTAA
1216545 TTTATTTAA
65 TTTATTTAA
1216554 AAAATTAATAT
1 AAAATTAATAT
1216565 TTAGTTTATT
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
72 3 0.04
73 6 0.08
74 58 0.77
75 8 0.11
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (73 bp):
AAAATTAATATATATAATATAAAATTAAAAAAATATATTAATTATTTAAAAAATTAATATTTAAT
TTATTTAA
Found at i:1216595 original size:12 final size:11
Alignment explanation
Indices: 1216578--1216628 Score: 57
Period size: 12 Copynumber: 4.4 Consensus size: 11
1216568 GTTTATTTAA
1216578 AAAATTAATATT
1 AAAATTAATA-T
*
1216590 AAAATTAAAAT
1 AAAATTAATAT
*
1216601 CAAATATAATAT
1 AAAAT-TAATAT
1216613 AAAATTAAATAT
1 AAAATT-AATAT
1216625 AAAA
1 AAAA
1216629 CCTCTTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 6 0.18
12 27 0.82
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAATTAATAT
Found at i:1216611 original size:48 final size:47
Alignment explanation
Indices: 1216511--1216612 Score: 118
Period size: 48 Copynumber: 2.1 Consensus size: 47
1216501 ATATTAAAAA
* *
1216511 AATATATTAATTTATTTAAAAAATTAATATTTAATTTATTTAAA-AAAT-T
1 AATAT-TTAATTTATTTAAAAAATTAATA-TTAA--AATTAAAATAAATAT
*
1216560 AATATTTAGTTTATTTAAAAAATTAATATTAAAATTAAAATCAAATAT
1 AATATTTAATTTATTTAAAAAATTAATATTAAAATTAAAAT-AAATAT
1216608 AATAT
1 AATAT
1216613 AAAATTAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
45 6 0.13
47 8 0.17
48 28 0.60
49 5 0.11
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (47 bp):
AATATTTAATTTATTTAAAAAATTAATATTAAAATTAAAATAAATAT
Found at i:1218160 original size:12 final size:11
Alignment explanation
Indices: 1218144--1218181 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
1218134 GAAATTTTTA
1218144 AATTATTATTT
1 AATTATTATTT
1218155 ATATTATTATTT
1 A-ATTATTATTT
*
1218167 AATTAGT-TTT
1 AATTATTATTT
1218177 AATTA
1 AATTA
1218182 ACTAAAACGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 8 0.32
11 6 0.24
12 11 0.44
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (11 bp):
AATTATTATTT
Found at i:1218668 original size:24 final size:23
Alignment explanation
Indices: 1218625--1218675 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
1218615 AATCCATATA
*
1218625 ATTTTTAAAATAAAATAATATTT
1 ATTTTTAAAATAAAATAATAATT
*
1218648 ATTTTATAAAAT-ATATAAATAATT
1 ATTTT-TAAAATAAAAT-AATAATT
1218672 ATTT
1 ATTT
1218676 AATTATCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTTTAAAATAAAATAATAATT
Found at i:1220142 original size:21 final size:20
Alignment explanation
Indices: 1220118--1220180 Score: 81
Period size: 22 Copynumber: 3.0 Consensus size: 20
1220108 ATGTGAAATT
* *
1220118 TGTCCTGAATGACCTCATGTA
1 TGTCCCGAAGGACCT-ATGTA
1220139 TGTCCCGAAGGACCTATGTATA
1 TGTCCCGAAGGACCTATG--TA
1220161 TGTCCCGAAGGACCTATGTA
1 TGTCCCGAAGGACCTATGTA
1220181 ACCCTCGACT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
20 5 0.13
21 13 0.34
22 20 0.53
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (20 bp):
TGTCCCGAAGGACCTATGTA
Found at i:1220164 original size:22 final size:22
Alignment explanation
Indices: 1220137--1220180 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1220127 TGACCTCATG
1220137 TATGTCCCGAAGGACCTATGTA
1 TATGTCCCGAAGGACCTATGTA
1220159 TATGTCCCGAAGGACCTATGTA
1 TATGTCCCGAAGGACCTATGTA
1220181 ACCCTCGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (22 bp):
TATGTCCCGAAGGACCTATGTA
Found at i:1220331 original size:30 final size:31
Alignment explanation
Indices: 1220283--1220346 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
1220273 TATCACATAA
*
1220283 TCATATAAGCTTATGTCACATTCTCATATGG
1 TCATATAAGCTCATGTCACATTCTCATATGG
1220314 TCATAT-AGCTCATGTCACATTCTCATATGG
1 TCATATAAGCTCATGTCACATTCTCATATGG
1220344 TCA
1 TCA
1220347 CTTATCATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 26 0.81
31 6 0.19
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (31 bp):
TCATATAAGCTCATGTCACATTCTCATATGG
Found at i:1224814 original size:18 final size:19
Alignment explanation
Indices: 1224791--1224833 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1224781 CAGTAATCTT
1224791 ATTCCCA-GGTAATATTAC
1 ATTCCCACGGTAATATTAC
*
1224809 ATTCCCACCGGTAATCTTAC
1 ATTCCCA-CGGTAATATTAC
1224829 ATTCC
1 ATTCC
1224834 GTGGACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (19 bp):
ATTCCCACGGTAATATTAC
Found at i:1234247 original size:3 final size:3
Alignment explanation
Indices: 1234239--1234299 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
1234229 TAGGAAGGGA
1234239 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1234287 AAG AAG AAG AAG A
1 AAG AAG AAG AAG A
1234300 GAACTTTTTG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1234856 original size:112 final size:112
Alignment explanation
Indices: 1234713--1235242 Score: 825
Period size: 112 Copynumber: 4.8 Consensus size: 112
1234703 TTGTCGGTTT
* *
1234713 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAAGTTAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
1234778 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
1234825 GTGTCGATACTTTATAAAAATATATTAATCCATAACAATATAACAAGTAAAAAAATGATAAAACC
1 GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
* ** *
1234890 GGTCTATAAATGACAAAACAGGTAAATCGCTACTAGATATATTGAGA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
1234937 GTGTCGATACTTTATAAAAATGTATTTATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
*
1235002 GGTCTATAAATGACAAAACAGGTAAAGCGCTATCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
1235049 GTGTAGATACTTTATAAAAATGTATCGATCCATAACAAT-TAA-ATAGGTAAAAAAATGACAAAA
1 GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACA-A-GTAAAAAAATGACAAAA
* * *
1235112 CCGGTCTATAAATGACAAAACAGGTAAA--GTTACCGGATATGTTGATA
64 CCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
1235159 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
*
1235224 GGTCTATAAATAACAAAAC
66 GGTCTATAAATGACAAAAC
1235243 TATCGATCCA
Statistics
Matches: 386, Mismatches: 28, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
110 91 0.24
111 5 0.01
112 290 0.75
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.25
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:1235359 original size:175 final size:172
Alignment explanation
Indices: 1235071--1235417 Score: 568
Period size: 175 Copynumber: 2.0 Consensus size: 172
1235061 TATAAAAATG
* *
1235071 TATCGATCCATAACAATTAAATAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAAACAGG
1 TATCGATCCATAACAATAAAATAGGTAAAAAAATGACAAAACCGGTCTATAAATAACAAAACAGG
*
1235136 TAAAGTTACCGGATATGTTGATAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAA
66 TAAAGCTACCGGATATGTTGATAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAA
* *
1235201 ACAGGTAAAAAAATGACAAAACCGGTCTATAAATAACAAAAC
131 ACAGGTAAAAAAATGACAAAACCGATCTAGAAATAACAAAAC
* *
1235243 TATCGATCCATAACAATAAAATAGGTAAAAAAAATGACAAAACTGGTTTATAAATAACAAAACAG
1 TATCGATCCATAACAATAAAATAGGT-AAAAAAATGACAAAACCGGTCTATAAATAACAAAACAG
1235308 GTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAAT
65 GTAAA--GCTACCGGATATGTTGATAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAAT
* * * *
1235373 ATAACAGGTAAAAATATGACAAAACCGATCTCGAAATGACAAAAC
128 AAAACAGGTAAAAAAATGACAAAACCGATCTAGAAATAACAAAAC
1235418 CGGTAAAGAG
Statistics
Matches: 161, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
172 25 0.16
173 40 0.25
175 96 0.60
ACGTcount: A:0.48, C:0.15, G:0.14, T:0.23
Consensus pattern (172 bp):
TATCGATCCATAACAATAAAATAGGTAAAAAAATGACAAAACCGGTCTATAAATAACAAAACAGG
TAAAGCTACCGGATATGTTGATAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAA
ACAGGTAAAAAAATGACAAAACCGATCTAGAAATAACAAAAC
Found at i:1235441 original size:112 final size:113
Alignment explanation
Indices: 1235243--1235460 Score: 312
Period size: 112 Copynumber: 1.9 Consensus size: 113
1235233 ATAACAAAAC
* * * * *
1235243 TATCGATCCATAACAATAAAATAGGTAAAAAAAATGACAAAACTGGTTTATAAATAACAAAACAG
1 TATCGATCCATAACAATAAAACAGGTAAAAAAAATGACAAAACCGATCTAGAAATAACAAAACAG
*
1235308 GTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATAAAAATG
66 GTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTATAAAAATG
* * * * *
1235356 TATCGATCCATAACAATATAACAGGT-AAAAATATGACAAAACCGATCTCGAAATGACAAAACCG
1 TATCGATCCATAACAATAAAACAGGTAAAAAAAATGACAAAACCGATCTAGAAATAACAAAACAG
**
1235420 GTAAAGAGCTACTTGATATGTTGATAGTGTCGATACTTTAT
66 GTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
1235461 TATAAGTATC
Statistics
Matches: 92, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
112 68 0.74
113 24 0.26
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (113 bp):
TATCGATCCATAACAATAAAACAGGTAAAAAAAATGACAAAACCGATCTAGAAATAACAAAACAG
GTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTATAAAAATG
Found at i:1235858 original size:23 final size:23
Alignment explanation
Indices: 1235829--1235876 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1235819 AAAATGGTCA
* *
1235829 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTAATAAATT
1235852 ATATAAGCGCTACCTAATAAATT
1 ATATAAGCGCTACCTAATAAATT
1235875 AT
1 AT
1235877 TGTACTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATAAATT
Found at i:1236235 original size:23 final size:23
Alignment explanation
Indices: 1236208--1236256 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1236198 TAATTTATTC
* *
1236208 TAATTCTAAAAAAATTAAATATA
1 TAATTATAAAAAAATAAAATATA
*
1236231 TAATTATAAAAAACTAAAATATA
1 TAATTATAAAAAAATAAAATATA
1236254 TAA
1 TAA
1236257 ATTTATAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (23 bp):
TAATTATAAAAAAATAAAATATA
Found at i:1250524 original size:19 final size:18
Alignment explanation
Indices: 1250482--1250524 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
1250472 ATTCTTTACA
*
1250482 AATT-TTTTCTTTATGTT
1 AATTCTTTTCTTTATGCT
1250499 AACTTCTTTTCCTTTATGCT
1 AA-TTCTTTT-CTTTATGCT
1250519 AATTCT
1 AATTCT
1250525 CATATATGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.09
18 2 0.09
19 8 0.36
20 10 0.45
ACGTcount: A:0.19, C:0.16, G:0.05, T:0.60
Consensus pattern (18 bp):
AATTCTTTTCTTTATGCT
Found at i:1251623 original size:3 final size:3
Alignment explanation
Indices: 1251615--1251649 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1251605 GATATTTTAC
1251615 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1251650 TTCTTTGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1251893 original size:20 final size:20
Alignment explanation
Indices: 1251868--1251950 Score: 76
Period size: 20 Copynumber: 3.9 Consensus size: 20
1251858 TCCATCTATA
1251868 TATTTTTTTAATTAAAATCT
1 TATTTTTTTAATTAAAATCT
* *
1251888 TATTTTATTAAATAAAAAAATCATT
1 TATTTT-TTTAAT--TAAAATC--T
1251913 TATGTTTTTTAATTAAAATCT
1 TAT-TTTTTTAATTAAAATCT
* *
1251934 TATTTTATTAAATAAAA
1 TATTTTTTTAATTAAAA
1251951 ATAAAAATCA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
20 18 0.35
21 9 0.18
23 12 0.24
25 9 0.18
26 3 0.06
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (20 bp):
TATTTTTTTAATTAAAATCT
Found at i:1258795 original size:2 final size:2
Alignment explanation
Indices: 1258790--1258824 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1258780 AAAAATAAAA
1258790 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1258825 AATCAGATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1261186 original size:30 final size:30
Alignment explanation
Indices: 1261132--1261223 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 30
1261122 CCCGAAGGAC
* *
1261132 CTATCCATATGTTCCG-AAGAACATATGTAA
1 CTATCCATATGTCCCGAAAG-ACATAGGTAA
*
1261162 CTGTCCATATGTCCCGAAAGACATAGGTAAA
1 CTATCCATATGTCCCGAAAGACATAGGT-AA
* * *
1261193 TTATCCATATATCTCGAAAGACATAGGTAA
1 CTATCCATATGTCCCGAAAGACATAGGTAA
1261223 C
1 C
1261224 CCTCAACTCT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
30 23 0.44
31 29 0.56
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (30 bp):
CTATCCATATGTCCCGAAAGACATAGGTAA
Found at i:1266921 original size:23 final size:23
Alignment explanation
Indices: 1266878--1266921 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1266868 GAAGACGGCC
*
1266878 GAAAATTCTTATCATTGATTTAT
1 GAAAATTCTTATCATTAATTTAT
*
1266901 GAAAATTTCTTAT-TTTAATTT
1 GAAAA-TTCTTATCATTAATTT
1266922 TATAATATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (23 bp):
GAAAATTCTTATCATTAATTTAT
Found at i:1267637 original size:16 final size:17
Alignment explanation
Indices: 1267607--1267640 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
1267597 AAATTAATTG
1267607 ATTATAATAATTAAATC
1 ATTATAATAATTAAATC
1267624 ATTATAAT-ATTAAATC
1 ATTATAATAATTAAATC
1267640 A
1 A
1267641 ACGTTATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTATAATAATTAAATC
Found at i:1267666 original size:19 final size:18
Alignment explanation
Indices: 1267644--1267717 Score: 65
Period size: 19 Copynumber: 4.4 Consensus size: 18
1267634 TAAATCAACG
1267644 TTATAATGTTGATTTAATA
1 TTATAATG-TGATTTAATA
1267663 TTATAA--TGATTT-A-A
1 TTATAATGTGATTTAATA
1267677 TTATAA--T-A-TTAATA
1 TTATAATGTGATTTAATA
*
1267691 TAATAATGTTGATTTAATA
1 TTATAATG-TGATTTAATA
1267710 TTATAATG
1 TTATAATG
1267718 ATTTATTATA
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
12 2 0.04
13 2 0.04
14 14 0.30
15 1 0.02
16 6 0.13
17 1 0.02
18 1 0.02
19 19 0.41
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (18 bp):
TTATAATGTGATTTAATA
Found at i:1267674 original size:16 final size:16
Alignment explanation
Indices: 1267653--1267722 Score: 76
Period size: 14 Copynumber: 4.4 Consensus size: 16
1267643 GTTATAATGT
1267653 TGATTTAATATTATAA
1 TGATTTAATATTATAA
1267669 TGATTT-A-ATTATAA
1 TGATTTAATATTATAA
*
1267683 T-A-TTAATATAATAA
1 TGATTTAATATTATAA
1267697 TGTTGATTTAATATTATAA
1 ---TGATTTAATATTATAA
1267716 TGATTTA
1 TGATTTA
1267723 TTATAATTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
12 2 0.04
13 2 0.04
14 14 0.31
15 1 0.02
16 13 0.29
17 1 0.02
18 1 0.02
19 11 0.24
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TGATTTAATATTATAA
Found at i:1267681 original size:14 final size:14
Alignment explanation
Indices: 1267662--1267729 Score: 52
Period size: 14 Copynumber: 4.6 Consensus size: 14
1267652 TTGATTTAAT
1267662 ATTATAATGATTTA
1 ATTATAATGATTTA
1267676 ATTATAAT-A-TTA
1 ATTATAATGATTTA
1267688 ATATAATAATGTTGATTTAA
1 AT-T-ATAA---TGATTT-A
1267708 TATTATAATGATTT-
1 -ATTATAATGATTTA
1267722 ATTATAAT
1 ATTATAAT
1267730 TAAATCAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 19
0.70 0.00 0.30
Matches are distributed among these distances:
12 5 0.11
13 10 0.22
14 12 0.27
16 6 0.13
17 1 0.02
18 1 0.02
19 6 0.13
20 2 0.04
21 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (14 bp):
ATTATAATGATTTA
Found at i:1267683 original size:52 final size:49
Alignment explanation
Indices: 1267624--1267744 Score: 171
Period size: 47 Copynumber: 2.5 Consensus size: 49
1267614 TAATTAAATC
1267624 ATTATAATATTAAATCAACGTTATAATGTTGATTTAATATTATAATGATTT
1 ATTATAATATTAAATCAA--TTATAATGTTGATTTAATATTATAATGATTT
*
1267675 AATTATAATATT-AAT--ATAATAATGTTGATTTAATATTATAATGATTT
1 -ATTATAATATTAAATCAATTATAATGTTGATTTAATATTATAATGATTT
1267722 ATTAT-A-ATTAAATCAATTATAAT
1 ATTATAATATTAAATCAATTATAAT
1267745 ATCAATCAAC
Statistics
Matches: 64, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
44 3 0.05
45 4 0.06
46 5 0.08
47 37 0.58
49 1 0.02
51 3 0.05
52 11 0.17
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (49 bp):
ATTATAATATTAAATCAATTATAATGTTGATTTAATATTATAATGATTT
Found at i:1267708 original size:25 final size:24
Alignment explanation
Indices: 1267646--1267714 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 24
1267636 AATCAACGTT
1267646 ATAATGTTGATTTAATA-T-TATA
1 ATAATGTTGATTTAATATTATATA
* *
1267668 ATGAT-TTAATTATAATATTAATATA
1 ATAATGTTGATT-TAATATT-ATATA
1267693 ATAATGTTGATTTAATATTATA
1 ATAATGTTGATTTAATATTATA
1267715 ATGATTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 5 0.13
22 9 0.24
23 1 0.03
24 3 0.08
25 15 0.39
26 5 0.13
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.49
Consensus pattern (24 bp):
ATAATGTTGATTTAATATTATATA
Found at i:1267732 original size:25 final size:25
Alignment explanation
Indices: 1267657--1267732 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
1267647 TAATGTTGAT
1267657 TTAATATTATAATGATTTAATTATAA
1 TTAATATTATAATGATTT-ATTATAA
* * * * *
1267683 -TATTAATATAATAATGT-TGAT--
1 TTAATATTATAATGATTTATTATAA
1267704 TTAATATTATAATGATTTATTATAA
1 TTAATATTATAATGATTTATTATAA
1267729 TTAA
1 TTAA
1267733 ATCAATTATA
Statistics
Matches: 36, Mismatches: 10, Indels: 9
0.65 0.18 0.16
Matches are distributed among these distances:
22 13 0.36
23 6 0.17
25 17 0.47
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (25 bp):
TTAATATTATAATGATTTATTATAA
Found at i:1270263 original size:130 final size:130
Alignment explanation
Indices: 1270122--1270369 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
1270112 TATTTATATA
* *
1270122 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATATGACATGTG
* * *
1270187 TTAGCACATGATCATGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
1270252 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATATGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATATGACATGTG
* * * *
1270317 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
1270370 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATATGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:1270400 original size:130 final size:129
Alignment explanation
Indices: 1270136--1270400 Score: 300
Period size: 130 Copynumber: 2.0 Consensus size: 129
1270126 ATTTGGTCCT
* * *
1270136 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATATGACATGTGTTAACACATGATCA
* * *** * * **** *
1270201 TGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
1270266 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATATGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATATGACATGTGTTAACACATGATCA
* * * * *
1270331 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
1270395 -A
128 CA
1270396 AAATT
1 AAATT
1270401 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
130 99 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATATGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:1270728 original size:28 final size:27
Alignment explanation
Indices: 1270697--1270759 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
1270687 AGTTGATACA
*
1270697 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
1270725 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
1270753 ATATTTT
1 ATATTTT
1270760 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:1270860 original size:16 final size:18
Alignment explanation
Indices: 1270839--1270872 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1270829 ATTTCTTATT
1270839 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
1270855 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
1270873 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:1271019 original size:21 final size:21
Alignment explanation
Indices: 1270995--1271037 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1270985 TATTACCTTA
1270995 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
1271016 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
1271037 A
1 A
1271038 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:1271055 original size:35 final size:35
Alignment explanation
Indices: 1271006--1271091 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
1270996 ATTGAAGTAT
** * *
1271006 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
1271041 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
1271076 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
1271092 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:1273046 original size:13 final size:13
Alignment explanation
Indices: 1273028--1273054 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1273018 TTACAGATGC
1273028 GCATATGAAGACT
1 GCATATGAAGACT
1273041 GCATATGAAGACT
1 GCATATGAAGACT
1273054 G
1 G
1273055 TTCAACCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:1276557 original size:20 final size:20
Alignment explanation
Indices: 1276532--1276574 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1276522 TCTAAAAGCC
*
1276532 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
*
1276552 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
1276572 CAT
1 CAT
1276575 GTGGTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:1285124 original size:20 final size:20
Alignment explanation
Indices: 1285099--1285141 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1285089 TCTAAAAGCC
*
1285099 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
*
1285119 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
1285139 CAT
1 CAT
1285142 GTGGTGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:1300253 original size:16 final size:16
Alignment explanation
Indices: 1300234--1300286 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1300224 CCATAACCCC
1300234 TATCACACATATATCA
1 TATCACACATATATCA
** * *
1300250 TATCATGCACACATCA
1 TATCACACATATATCA
1300266 TATCACACATCATATACA
1 TATCACACAT-ATAT-CA
1300284 TAT
1 TAT
1300287 ATCACATAGC
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 19 0.70
17 3 0.11
18 5 0.19
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.30
Consensus pattern (16 bp):
TATCACACATATATCA
Found at i:1300487 original size:23 final size:23
Alignment explanation
Indices: 1300461--1300524 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
1300451 TAGCTCGTAT
1300461 AATTGCACCGAAGTGCCACATAG
1 AATTGCACCGAAGTGCCACATAG
* * *
1300484 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACATAG
*
1300507 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1300525 TATAATAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACATAG
Found at i:1300711 original size:103 final size:103
Alignment explanation
Indices: 1300540--1300860 Score: 579
Period size: 103 Copynumber: 3.1 Consensus size: 103
1300530 TAATGTCCAT
** * *
1300540 AAGGACCACATATCATTCCTTAAGAATCATATACATAAACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1300605 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1300643 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1300708 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1300746 AAGGACCCCATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
1300811 GACTTCACACATGTTCCAAAGAATATATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1300849 AAGGACCACATA
1 AAGGACCACATA
1300861 GACCCTCGAC
Statistics
Matches: 209, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 209 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1302367 original size:21 final size:21
Alignment explanation
Indices: 1302343--1302387 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1302333 TTTTGTTCGT
* *
1302343 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1302364 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1302385 TTG
1 TTG
1302388 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1307511 original size:145 final size:145
Alignment explanation
Indices: 1307190--1307498 Score: 600
Period size: 145 Copynumber: 2.1 Consensus size: 145
1307180 CTATATATTA
*
1307190 ATAATTAATAAAATTAATAATCAATTGATTTAGTGGAATTAGACACCAAATTCTTAAGTGAAACA
1 ATAATTAAT-CAATTAATAATCAATTGATTTAGTGGAATTAGACACCAAATTCTTAAGTGAAACA
1307255 AGAGATTCAAATTTTGATATCATAAATATAACAAATTCAATTAAGAAAATCATTCCATAATAAAA
65 AGAGATTCAAATTTTGATATCATAAATATAACAAATTCAATTAAGAAAATCATTCCATAATAAAA
1307320 TTCTATTATATTTAAT
130 TTCTATTATATTTAAT
1307336 ATAATTAATCAATTAATAATCAATTGATTTAGTGGAATTAGACACCAAATTCTTAAGTGAAACAA
1 ATAATTAATCAATTAATAATCAATTGATTTAGTGGAATTAGACACCAAATTCTTAAGTGAAACAA
1307401 GAGATTCAAATTTTGATATCATAAATATAACAAATTCAATTAAGAAAATCATTCCATAATAAAAT
66 GAGATTCAAATTTTGATATCATAAATATAACAAATTCAATTAAGAAAATCATTCCATAATAAAAT
1307466 TCTATTATATTTAAT
131 TCTATTATATTTAAT
1307481 ATAATTAATCAATTAATA
1 ATAATTAATCAATTAATA
1307499 GATTATATAT
Statistics
Matches: 162, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
145 153 0.94
146 9 0.06
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (145 bp):
ATAATTAATCAATTAATAATCAATTGATTTAGTGGAATTAGACACCAAATTCTTAAGTGAAACAA
GAGATTCAAATTTTGATATCATAAATATAACAAATTCAATTAAGAAAATCATTCCATAATAAAAT
TCTATTATATTTAAT
Found at i:1308445 original size:10 final size:10
Alignment explanation
Indices: 1308421--1308491 Score: 74
Period size: 10 Copynumber: 7.0 Consensus size: 10
1308411 GAGGTGAATG
1308421 AGATA-TTTT
1 AGATATTTTT
1308430 AGATATTTTT
1 AGATATTTTT
* **
1308440 AAATATTCAT
1 AGATATTTTT
1308450 AGATATTTTTTT
1 AGATA--TTTTT
1308462 AGATA-TTTT
1 AGATATTTTT
1308471 AGATATTTTT
1 AGATATTTTT
1308481 CAGATATTTTT
1 -AGATATTTTT
1308492 TATTGAAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
9 14 0.27
10 19 0.37
11 10 0.20
12 8 0.16
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.56
Consensus pattern (10 bp):
AGATATTTTT
Found at i:1308466 original size:32 final size:32
Alignment explanation
Indices: 1308426--1308492 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
1308416 GAATGAGATA
1308426 TTTTAGATATTTTTAAATATTCAT-AGATATTT
1 TTTTAGATA-TTTTAAATATTCATCAGATATTT
* **
1308458 TTTTAGATATTTTAGATATTTTTCAGATATTT
1 TTTTAGATATTTTAAATATTCATCAGATATTT
1308490 TTT
1 TTT
1308493 ATTGAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 11 0.35
32 20 0.65
ACGTcount: A:0.30, C:0.03, G:0.07, T:0.60
Consensus pattern (32 bp):
TTTTAGATATTTTAAATATTCATCAGATATTT
Found at i:1308485 original size:20 final size:19
Alignment explanation
Indices: 1308421--1308490 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 19
1308411 GAGGTGAATG
1308421 AGATATTTTAGATATTTTT
1 AGATATTTTAGATATTTTT
* *
1308440 AAATATTCATAGATATTTTTTT
1 AGATATT-TTAGATA--TTTTT
1308462 AGATATTTTAGATATTTTT
1 AGATATTTTAGATATTTTT
1308481 CAGATATTTT
1 -AGATATTTT
1308491 TTATTGAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 11 0.26
20 15 0.35
21 6 0.14
22 11 0.26
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.56
Consensus pattern (19 bp):
AGATATTTTAGATATTTTT
Found at i:1315639 original size:2 final size:2
Alignment explanation
Indices: 1315632--1315662 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1315622 CCATTATTGT
1315632 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1315663 GCTTTCGTTC
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:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1325205 original size:35 final size:35
Alignment explanation
Indices: 1325154--1325233 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
1325144 AACACAATCA
*
1325154 TCAATTACATTCTAAACCCCAAATTCCAAAATGCT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
* * *
1325189 TCAATTATATTTTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
1325224 TCAATTACAT
1 TCAATTACAT
1325234 GGTCAATCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.41, C:0.24, G:0.01, T:0.34
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAATACT
Found at i:1325247 original size:35 final size:34
Alignment explanation
Indices: 1325154--1325249 Score: 104
Period size: 35 Copynumber: 2.7 Consensus size: 34
1325144 AACACAATCA
*
1325154 TCAATTACAT-TCTAAACCCCAAATTCCAAAATGCT
1 TCAATTACATGTC-AAA-CCCAAATTCCAAAATACT
* * *
1325189 TCAATTATATTTTAAACCTCAAATTCCAAAATACT
1 TCAATTACATGTCAAACC-CAAATTCCAAAATACT
*
1325224 TCAATTACATGGTCAATCCCAAATTC
1 TCAATTACAT-GTCAAACCCAAATTC
1325250 ATAATCTATT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
34 2 0.04
35 43 0.84
36 6 0.12
ACGTcount: A:0.40, C:0.25, G:0.03, T:0.32
Consensus pattern (34 bp):
TCAATTACATGTCAAACCCAAATTCCAAAATACT
Found at i:1326259 original size:35 final size:35
Alignment explanation
Indices: 1326166--1326259 Score: 116
Period size: 35 Copynumber: 2.7 Consensus size: 35
1326156 AATGGATTAT
* * * *
1326166 GAATTTGGGATTGAGCATGTAATTGAAGTATTTTG
1 GAATTTGGGGTTTAGAATGTAATTGAAGCATTTTG
* ** *
1326201 GAATTTGAGGTTTATTATATAATTGAAGCATTTTG
1 GAATTTGGGGTTTAGAATGTAATTGAAGCATTTTG
1326236 GAATTTGGGGTTTAGAATGTAATT
1 GAATTTGGGGTTTAGAATGTAATT
1326260 AATGACTGTG
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.43
Consensus pattern (35 bp):
GAATTTGGGGTTTAGAATGTAATTGAAGCATTTTG
Found at i:1327357 original size:21 final size:21
Alignment explanation
Indices: 1327331--1327379 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
1327321 ATATTTAGAT
1327331 TATTGATT-TAATTATAAGTTA
1 TATTGATTATAATTATAA-TTA
**
1327352 TATTGATTATTTTTATAATTA
1 TATTGATTATAATTATAATTA
1327373 TATTGAT
1 TATTGAT
1327380 AGCACTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (21 bp):
TATTGATTATAATTATAATTA
Found at i:1328323 original size:193 final size:185
Alignment explanation
Indices: 1327958--1328323 Score: 448
Period size: 193 Copynumber: 1.9 Consensus size: 185
1327948 AAATATCACA
* * * * *
1327958 TCAAA-AAATTGAATAAAAAAATTAATGATATTAACAATTAGATTTGAATTTCTAAATTTAAAAA
1 TCAAATAAATTTAAT-AAAAAATTAACGATATTAACAATTAGACTTAAATTTCTAAATTAAAAAA
* * * * * *
1328022 GTAGAGGACTAAGTTTTTAAAAATAAAATAGGGGGACCAATTCCAAATGAGTATAGGGACTCAAA
65 ATAGAGGACTAAATTTTTAAAAATAAAATAAGAGGACAAATTCCAAAAGAGTATAGGGACTCAAA
* * *
1328087 GCATATTTTAGCCGTAAAAGAATCAAATCATTGAAAGGAAAAAATAATTATTAATT
130 GCATATTTTAGCCATAAAAGAATCAAATAATTGAAAAGAAAAAATAATTATTAATT
* *
1328143 TCAAATAAATTTAATAAAAAATTAACGTTATTAAACAATTAGACTTAAATTTGTAAATCTAAAAA
1 TCAAATAAATTTAATAAAAAATTAACGATATT-AACAATTAGACTTAAATTTCTAAAT-TAAAAA
*
1328208 CAATAGAGGACTAAATTTTTAAGAATAAAAATAAGAGGACAAAATTCCAAACAAAGAGTATAGGG
64 -AATAGAGGACTAAATTTTTAAAAAT-AAAATAAGAGGAC-AAATTCC--A-AAAGAGTATAGGG
** *
1328273 ACTCAAAGCATATTTTTTCCATAAATGAATCAAATAAATT-AAAAGAAAAAA
123 ACTCAAAGCATATTTTAGCCATAAAAGAATCAAAT-AATTGAAAAGAAAAAA
1328324 AGTAAATCAA
Statistics
Matches: 151, Mismatches: 20, Indels: 12
0.83 0.11 0.07
Matches are distributed among these distances:
185 20 0.13
186 30 0.20
187 5 0.03
188 22 0.15
189 11 0.07
190 6 0.04
192 1 0.01
193 53 0.35
194 3 0.02
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.28
Consensus pattern (185 bp):
TCAAATAAATTTAATAAAAAATTAACGATATTAACAATTAGACTTAAATTTCTAAATTAAAAAAA
TAGAGGACTAAATTTTTAAAAATAAAATAAGAGGACAAATTCCAAAAGAGTATAGGGACTCAAAG
CATATTTTAGCCATAAAAGAATCAAATAATTGAAAAGAAAAAATAATTATTAATT
Found at i:1329228 original size:2 final size:2
Alignment explanation
Indices: 1329221--1329267 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1329211 ATCTCTAAAT
1329221 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1329263 TA TA T
1 TA TA T
1329268 CATGTTTCTT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1334389 original size:250 final size:252
Alignment explanation
Indices: 1333765--1334509 Score: 937
Period size: 254 Copynumber: 2.9 Consensus size: 252
1333755 TTTAGGAAAT
*
1333765 ACCCGACCCGAAAATGTATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTC
1 ACCCGACCC-AAAA-ATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTC
* **
1333830 TATATATAATTCTTTTCCAATTAAGTCACTGCTTTTATTGAAT-AAATAA-TTTTT-TTA-TT--
64 TATATATAATT-TTTTTCAATTAAGTCACTATTTTTATTGAATAAAATAATTTTTTATTATTTCG
* * * *
1333889 --TCGGATCGGATTTCTAATTCATATATTTGGGTCGGGTC-GGTGAAACTTTATTTTGGTCAGGT
128 GGTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGT
* * ** * ** * *
1333951 CGGGTC-GGGTTTTTTAAGTGT--GATATTCGGGTCGGGTCGGATTCGGGTTTAGAGTGAAAAAT
193 CGGGTCTCGG--ATGGAGGT-TCCCTTGTTC---TCGGGTCGG-GTCGGG-TTAGA--GAAAAAT
*
1334013 ACCCG
248 ACCCA
*
1334018 ACCCGTCCCAAAAATATATAATTTTACCTTATATA-TTAGGAATAATTACAATAATACCCCTCTA
1 ACCCGACCCAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTC--
*
1334082 TATATATATATATTTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATATTTTTTTATTATT
64 --TATATATA-ATTTTTTTCAATTAAGTCACTATTTTTATTGAAT-AAAATAATTTTTTATTATT
1334147 TCGGGTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCG
125 TCGGGTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCG
**
1334212 GGTCGGGTCTCGGATGGAGGTTCCCTTGTTCTCGGGTCGGGTCGGG-TAGA-CCAAA-ACCCA
190 GGTCGGGTCTCGGATGGAGGTTCCCTTGTTCTCGGGTCGGGTCGGGTTAGAGAAAAATACCCA
*
1334272 ACCCGACCCAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTG
1 ACCCGACCCAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTA
1334337 TATATAATTTTTTTCAATTAAGTCACTATTTTTATTGAATAAAATAATTTTTTATTATTTCGGGT
66 TATATAATTTTTTTCAATTAAGTCACTATTTTTATTGAATAAAATAATTTTTTATTATTTCGGGT
*
1334402 CGGGTCAGGTCAGGTTTCTAATTCATATATTCAGGTCGGGTCGGGTGAAACTTTATTTTGGTCGG
131 CGGGTC--G---GGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGG
*
1334467 GTCGGGTCTCGGATGGAGGTTCCCTTGTTCTCAGGTCGGGTCG
191 GTCGGGTCTCGGATGGAGGTTCCCTTGTTCTCGGGTCGGGTCG
1334510 AGAATACTAA
Statistics
Matches: 441, Mismatches: 27, Indels: 47
0.86 0.05 0.09
Matches are distributed among these distances:
249 30 0.07
250 61 0.14
251 29 0.07
252 4 0.01
253 8 0.02
254 168 0.38
255 33 0.07
256 5 0.01
257 5 0.01
258 7 0.02
259 2 0.00
260 5 0.01
261 9 0.02
262 1 0.00
263 39 0.09
264 33 0.07
265 2 0.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (252 bp):
ACCCGACCCAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTA
TATATAATTTTTTTCAATTAAGTCACTATTTTTATTGAATAAAATAATTTTTTATTATTTCGGGT
CGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGG
GTCTCGGATGGAGGTTCCCTTGTTCTCGGGTCGGGTCGGGTTAGAGAAAAATACCCA
Found at i:1334898 original size:44 final size:44
Alignment explanation
Indices: 1334773--1334886 Score: 201
Period size: 44 Copynumber: 2.6 Consensus size: 44
1334763 TCTAACATGT
* *
1334773 CTGCGAACCAAACAGAATATGGAATTGGATTCCAATTCAATTTG
1 CTGCCAACCAAACAGAATATGGAATTGGATTCCAATTCAATTTC
*
1334817 CTGTCAACCAAACAGAATATGGAATTGGATTCCAATTCAATTTC
1 CTGCCAACCAAACAGAATATGGAATTGGATTCCAATTCAATTTC
1334861 CTGCCAACCAAACAGAATATGGAATT
1 CTGCCAACCAAACAGAATATGGAATT
1334887 TAATTTCAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 66 1.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (44 bp):
CTGCCAACCAAACAGAATATGGAATTGGATTCCAATTCAATTTC
Found at i:1337920 original size:2 final size:2
Alignment explanation
Indices: 1337913--1337952 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1337903 TGCTTAACTT
1337913 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1337953 AAAGAAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1338103 original size:22 final size:20
Alignment explanation
Indices: 1338053--1338103 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1338043 CAACACGAAA
*
1338053 TCCAAATTCGCAACATAGTT
1 TCCAAATTCGCAACAGAGTT
*
1338073 TTCAAATTCGCAACAAGAGTT
1 TCCAAATTCGCAAC-AGAGTT
1338094 TGCCAAATTC
1 T-CCAAATTC
1338104 AGTTTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 13 0.50
21 6 0.23
22 7 0.27
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (20 bp):
TCCAAATTCGCAACAGAGTT
Found at i:1338243 original size:39 final size:40
Alignment explanation
Indices: 1338176--1338283 Score: 130
Period size: 39 Copynumber: 2.7 Consensus size: 40
1338166 GAATATAGAT
* *
1338176 TTCGCAACTTGAAAATCGAATTCGCAACTCGA-AATTCAAA
1 TTCGCAACTCGAAAATCGAATTCACAACTCGAGAA-TCAAA
* *
1338216 TTCGCAACTCGAAACTC-AATTCACAACTCGAGAATCGAA
1 TTCGCAACTCGAAAATCGAATTCACAACTCGAGAATCAAA
** *
1338255 TTCGCAACTCGAATTTCGAATTCGCAACT
1 TTCGCAACTCGAAAATCGAATTCACAACT
1338284 TAAATTTCAT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 32 0.54
40 27 0.46
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (40 bp):
TTCGCAACTCGAAAATCGAATTCACAACTCGAGAATCAAA
Found at i:1338289 original size:20 final size:20
Alignment explanation
Indices: 1338112--1338291 Score: 102
Period size: 20 Copynumber: 8.9 Consensus size: 20
1338102 TCAGTTTTTA
* *
1338112 AATTCGCAACTCGAATTTGCC
1 AATTCGCAACTCAAATTT-CG
*
1338133 AATTTCGCAACTCAATTTTCG
1 AA-TTCGCAACTCAAATTTCG
* * ** * *
1338154 AATTCGTAATTTGAATATAG
1 AATTCGCAACTCAAATTTCG
* * *
1338174 ATTTCGCAACTTGAAA-ATCG
1 AATTCGCAAC-TCAAATTTCG
*
1338194 AATTCGCAACTCGAAA-TTCA
1 AATTCGCAACTC-AAATTTCG
*
1338214 AATTCGCAACTCGAAA-CTC-
1 AATTCGCAACTC-AAATTTCG
*
1338233 AATTCACAACTCGAGAA--TCG
1 AATTCGCAACTC-A-AATTTCG
*
1338253 AATTCGCAACTCGAATTTCG
1 AATTCGCAACTCAAATTTCG
*
1338273 AATTCGCAACTTAAATTTC
1 AATTCGCAACTCAAATTTC
1338292 ATTTTCGAGT
Statistics
Matches: 126, Mismatches: 26, Indels: 15
0.75 0.16 0.09
Matches are distributed among these distances:
18 2 0.02
19 16 0.13
20 86 0.68
21 8 0.06
22 14 0.11
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (20 bp):
AATTCGCAACTCAAATTTCG
Found at i:1338311 original size:20 final size:20
Alignment explanation
Indices: 1338288--1338329 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1338278 GCAACTTAAA
1338288 TTTCATTTTCGAGTTGCGAT
1 TTTCATTTTCGAGTTGCGAT
1338308 TTTCATTTTCGAGTTGCGAT
1 TTTCATTTTCGAGTTGCGAT
1338328 TT
1 TT
1338330 CCGTGTTGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.19, T:0.52
Consensus pattern (20 bp):
TTTCATTTTCGAGTTGCGAT
Found at i:1338446 original size:39 final size:40
Alignment explanation
Indices: 1338369--1338446 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 40
1338359 GAATTCCAAA
*
1338369 TTCGAGTTGCGAATTCGGAAACTTTGTTGCGAAATTGGCT
1 TTCGAGTTGCGAATTCGGAAACTTAGTTGCGAAATTGGCT
* *
1338409 TTCGTGTTGCGAATTC-GAAA-TTGAGTTGCGAATTTGGC
1 TTCGAGTTGCGAATTCGGAAACTT-AGTTGCGAAATTGGC
1338447 ACTCCACCTC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 2 0.06
39 17 0.50
40 15 0.44
ACGTcount: A:0.22, C:0.14, G:0.28, T:0.36
Consensus pattern (40 bp):
TTCGAGTTGCGAATTCGGAAACTTAGTTGCGAAATTGGCT
Found at i:1342942 original size:2 final size:2
Alignment explanation
Indices: 1342935--1342960 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1342925 AACTTATTTA
1342935 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
1342961 GAAAAACTAA
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:1347509 original size:28 final size:29
Alignment explanation
Indices: 1347461--1347520 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
1347451 TTTTATATAA
1347461 ATAAATATAATATGAATATTAT-TTAAAT
1 ATAAATATAATATGAATATTATATTAAAT
* * *
1347489 ATAAATTTAATAT-ACTAATTATATTAATT
1 ATAAATATAATATGAAT-ATTATATTAAAT
1347518 ATA
1 ATA
1347521 TATTAAATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 2 0.07
28 17 0.63
29 8 0.30
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (29 bp):
ATAAATATAATATGAATATTATATTAAAT
Found at i:1348173 original size:20 final size:20
Alignment explanation
Indices: 1348148--1348192 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
1348138 GTCATCTAAT
1348148 TTTTTAAA-CCTCAGACCGGA
1 TTTTTAAACCCT-AGACCGGA
1348168 TTTTTAAACCCTAGACCGGA
1 TTTTTAAACCCTAGACCGGA
1348188 TTTTT
1 TTTTT
1348193 TTCCGGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (20 bp):
TTTTTAAACCCTAGACCGGA
Found at i:1354804 original size:16 final size:16
Alignment explanation
Indices: 1354783--1354813 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1354773 AATGATAATG
*
1354783 ATATTAATTTAATTAC
1 ATATTAATTGAATTAC
1354799 ATATTAATTGAATTA
1 ATATTAATTGAATTA
1354814 TTCTTTGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (16 bp):
ATATTAATTGAATTAC
Found at i:1356642 original size:48 final size:48
Alignment explanation
Indices: 1356590--1356699 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 48
1356580 ATAGGTTTTT
* * * * ** * *
1356590 CTGATGTTGCAGTCGTTGCACCAAGAGATGTTTTTCGTATTGGTGTGC
1 CTGATGTTGCAGCCATTACACCAAGAGATGGTGCTCGTATTAGCGTGC
*
1356638 CTGATGTTGCAGCCATTACACCAGGAGATGGTGCTCGTATTAGCGTGC
1 CTGATGTTGCAGCCATTACACCAAGAGATGGTGCTCGTATTAGCGTGC
*
1356686 CTGATGTTGTAGCC
1 CTGATGTTGCAGCC
1356700 GATGCACTGG
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.33
Consensus pattern (48 bp):
CTGATGTTGCAGCCATTACACCAAGAGATGGTGCTCGTATTAGCGTGC
Found at i:1356713 original size:48 final size:48
Alignment explanation
Indices: 1356590--1356721 Score: 122
Period size: 48 Copynumber: 2.8 Consensus size: 48
1356580 ATAGGTTTTT
* * * * * ** * *
1356590 CTGATGTTGCAGTCGTTGCACCAAGAGATGTTTTTCGTATTGGTGTGC
1 CTGATGTTGCAGCCATTACACCAGGAGATGATGCTCGTATTAGCGTGC
*
1356638 CTGATGTTGCAGCCATTACACCAGGAGATGGTGCTCGTATTAGCGTGC
1 CTGATGTTGCAGCCATTACACCAGGAGATGATGCTCGTATTAGCGTGC
* * **
1356686 CTGATGTTGTAGCCGA-TGCACTGGGAGATGATGCTC
1 CTGATGTTGCAGCC-ATTACACCAGGAGATGATGCTC
1356722 CAATAGGCAT
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
48 68 0.99
49 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.31
Consensus pattern (48 bp):
CTGATGTTGCAGCCATTACACCAGGAGATGATGCTCGTATTAGCGTGC
Found at i:1356928 original size:48 final size:48
Alignment explanation
Indices: 1356835--1356935 Score: 130
Period size: 48 Copynumber: 2.1 Consensus size: 48
1356825 ACCGATAGGC
* *
1356835 GGTGCTCCTATTGGATTGCATGATGTAATATCCAGTGCATAGGGAGGT
1 GGTGCTCCTATTGGATTGCATGATATAACATCCAGTGCATAGGGAGGT
* * * * * *
1356883 GGTGCTCCTATTGGCTTGCTTGATATAGCATCTAGTGTATCGGGAGGT
1 GGTGCTCCTATTGGATTGCATGATATAACATCCAGTGCATAGGGAGGT
1356931 GGTGC
1 GGTGC
1356936 ACTAGTTTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.19, C:0.16, G:0.33, T:0.33
Consensus pattern (48 bp):
GGTGCTCCTATTGGATTGCATGATATAACATCCAGTGCATAGGGAGGT
Found at i:1362074 original size:24 final size:24
Alignment explanation
Indices: 1361975--1362074 Score: 80
Period size: 24 Copynumber: 4.2 Consensus size: 24
1361965 ATATTTTATC
* *
1361975 TGATTTCTGATTTGAATTCTGTTT
1 TGATATCTGATCTGAATTCTGTTT
*
1361999 TG-TCATCTGATCTGAAATCTGTTCT
1 TGAT-ATCTGATCTGAATTCTGTT-T
* * * *
1362024 T-AT-TCCTAACCTGGATTCTGTTA
1 TGATAT-CTGATCTGAATTCTGTTT
*
1362047 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTCTGTTT
1362071 TGAT
1 TGAT
1362075 TTTTGATATC
Statistics
Matches: 57, Mismatches: 13, Indels: 12
0.70 0.16 0.15
Matches are distributed among these distances:
23 3 0.05
24 50 0.88
25 4 0.07
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.49
Consensus pattern (24 bp):
TGATATCTGATCTGAATTCTGTTT
Found at i:1374940 original size:24 final size:23
Alignment explanation
Indices: 1374908--1374965 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
1374898 ATCTGAAATC
* * *
1374908 TGTTCTGATTCCTAACCTGGATTT
1 TGTTTTGATT-CTAACCTGAATTA
*
1374932 TGTTTTGATATCTAATCTGAATTA
1 TGTTTTGAT-TCTAACCTGAATTA
1374956 TGTTTTGATT
1 TGTTTTGATT
1374966 TTTGATATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 1 0.03
24 27 0.93
25 1 0.03
ACGTcount: A:0.21, C:0.12, G:0.16, T:0.52
Consensus pattern (23 bp):
TGTTTTGATTCTAACCTGAATTA
Found at i:1375132 original size:2 final size:2
Alignment explanation
Indices: 1375125--1375154 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1375115 ATGTGAACGG
1375125 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
1375155 GTTTTAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1379950 original size:2 final size:2
Alignment explanation
Indices: 1379943--1379973 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1379933 CGGATGAGGG
1379943 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1379974 GTTTTAAAAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1384615 original size:24 final size:24
Alignment explanation
Indices: 1384507--1384615 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
1384497 GAATATTTTA
*
1384507 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* * *
1384531 TTTGACATT-TGATCTGAAATCTGT
1 TCTGA-TTTCTGATCTGAATTCTGT
* * * *
1384555 TCTGATTCCTAACCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* *
1384579 TCTGATATCTGATCTGAATTATGT
1 TCTGATTTCTGATCTGAATTCTGT
* *
1384603 TTTGATTTTTGAT
1 TCTGATTTCTGAT
1384616 ATCTCCGTTT
Statistics
Matches: 63, Mismatches: 20, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 1 0.02
24 60 0.95
25 2 0.03
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:1403742 original size:22 final size:22
Alignment explanation
Indices: 1403712--1403763 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
1403702 AAAAATTCAA
* * *
1403712 TTCGACCACACGTTGTTTGGTG
1 TTCGGCCACACGTCGTTTAGTG
*
1403734 TTCGGCCACATGTCGTTTAGTG
1 TTCGGCCACACGTCGTTTAGTG
*
1403756 TTCAGCCA
1 TTCGGCCA
1403764 ATTAATGGCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (22 bp):
TTCGGCCACACGTCGTTTAGTG
Found at i:1404069 original size:18 final size:19
Alignment explanation
Indices: 1404034--1404071 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1404024 GATACATAAT
1404034 TTAAACACTTATTCTTATA
1 TTAAACACTTATTCTTATA
1404053 TTAAAC-CTTAATT-TTATA
1 TTAAACACTT-ATTCTTATA
1404071 T
1 T
1404072 CAAGAATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAAACACTTATTCTTATA
Found at i:1404525 original size:34 final size:33
Alignment explanation
Indices: 1404471--1404537 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 33
1404461 AATTAAAATA
*
1404471 CAATTTAAAAATATATTAATATAATTTTCATAT
1 CAATTAAAAAATATATTAATATAATTTTCATAT
1404504 CAATTAAAAAACTATATTAATATAATTTTCATAT
1 CAATTAAAAAA-TATATTAATATAATTTTCATAT
1404538 GAATATGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 10 0.31
34 22 0.69
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.43
Consensus pattern (33 bp):
CAATTAAAAAATATATTAATATAATTTTCATAT
Found at i:1404537 original size:17 final size:17
Alignment explanation
Indices: 1404483--1404543 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
1404473 ATTTAAAAAT
1404483 ATATTAATATAATTTTC
1 ATATTAATATAATTTTC
* ****
1404500 ATATCAAT-TAAAAAAC
1 ATATTAATATAATTTTC
1404516 TATATTAATATAATTTTC
1 -ATATTAATATAATTTTC
*
1404534 ATATGAATAT
1 ATATTAATAT
1404544 GTTAAAATTT
Statistics
Matches: 31, Mismatches: 11, Indels: 4
0.67 0.24 0.09
Matches are distributed among these distances:
16 4 0.13
17 23 0.74
18 4 0.13
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.44
Consensus pattern (17 bp):
ATATTAATATAATTTTC
Found at i:1417848 original size:20 final size:20
Alignment explanation
Indices: 1417800--1418040 Score: 302
Period size: 20 Copynumber: 11.8 Consensus size: 20
1417790 TTCTCTTCTA
* *
1417800 AATCGCGTTGCGATTCTCTTC
1 AATCGCATTGCGATTCT-ATC
* * *
1417821 TAAATCGCGTTGCGAATCTCTC
1 --AATCGCATTGCGATTCTATC
* * *
1417843 AATCGCGTTGCGATTCTCTT
1 AATCGCATTGCGATTCTATC
* *
1417863 AATCGCGTTGCGATTCTATA
1 AATCGCATTGCGATTCTATC
1417883 AATCGCATTGCGATTCTATC
1 AATCGCATTGCGATTCTATC
1417903 AATCGCATTGCGATTCTATC
1 AATCGCATTGCGATTCTATC
*
1417923 AATCGCATTGCGATTCTCTTC
1 AATCGCATTGCGATTCT-ATC
* * *
1417944 TAAATCGCGTTGCGAATCTCTC
1 --AATCGCATTGCGATTCTATC
1417966 AATCGCATTGCGATTCTATC
1 AATCGCATTGCGATTCTATC
1417986 AATCGCATTGCGATTCTATC
1 AATCGCATTGCGATTCTATC
1418006 AATCGCATTGCGATTCTATC
1 AATCGCATTGCGATTCTATC
1418026 AATCGCATTGCGATT
1 AATCGCATTGCGATT
1418041 TTCTTCTAAA
Statistics
Matches: 200, Mismatches: 15, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
20 163 0.81
21 2 0.01
22 4 0.02
23 31 0.16
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.35
Consensus pattern (20 bp):
AATCGCATTGCGATTCTATC
Found at i:1417944 original size:123 final size:123
Alignment explanation
Indices: 1417800--1418040 Score: 428
Period size: 123 Copynumber: 2.0 Consensus size: 123
1417790 TTCTCTTCTA
* * * *
1417800 AATCGCGTTGCGATTCTCTTCTAAATCGCGTTGCGAATCTCTCAATCGCGTTGCGATTCTCTTAA
1 AATCGCATTGCGATTCTCTTCTAAATCGCGTTGCGAATCTCTCAATCGCATTGCGATTCTATCAA
*
1417865 TCGCGTTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTATC
66 TCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTATC
1417923 AATCGCATTGCGATTCTCTTCTAAATCGCGTTGCGAATCTCTCAATCGCATTGCGATTCTATCAA
1 AATCGCATTGCGATTCTCTTCTAAATCGCGTTGCGAATCTCTCAATCGCATTGCGATTCTATCAA
*
1417988 TCGCATTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCATTGCGATT
66 TCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCGATT
1418041 TTCTTCTAAA
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
123 112 1.00
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.35
Consensus pattern (123 bp):
AATCGCATTGCGATTCTCTTCTAAATCGCGTTGCGAATCTCTCAATCGCATTGCGATTCTATCAA
TCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTATC
Found at i:1417950 original size:103 final size:103
Alignment explanation
Indices: 1417800--1418062 Score: 397
Period size: 103 Copynumber: 2.6 Consensus size: 103
1417790 TTCTCTTCTA
* * * * *
1417800 AATCGCGTTGCGATTCTCTTCTAAATCGCGTTGCGAATCTC-TC--AATCGCGTTGCGATTCTCT
1 AATCGCATTGCGATTCT-ATC--AATCGCATTGCGATTCTCTTCTAAATCGCGTTGCGAATCTCT
* *
1417862 TAATCGCGTTGCGATTCTATAAATCGCATTGCGATTCTATC
63 CAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
1417903 AATCGCATTGCGATTCTATCAATCGCATTGCGATTCTCTTCTAAATCGCGTTGCGAATCTCTCAA
1 AATCGCATTGCGATTCTATCAATCGCATTGCGATTCTCTTCTAAATCGCGTTGCGAATCTCTCAA
*
1417968 TCGCATTGCGATTCTATCAATCGCATTGCGATTCTATC
66 TCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
*
1418006 AATCGCATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGAA
1 AATCGCATTGCGATTCTATCAATCGCATTGCGATTCTCTTCTAAATCGCGTTGCGAA
1418063 CTTGGAAGCT
Statistics
Matches: 148, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
100 16 0.11
101 2 0.01
102 2 0.01
103 128 0.86
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.35
Consensus pattern (103 bp):
AATCGCATTGCGATTCTATCAATCGCATTGCGATTCTCTTCTAAATCGCGTTGCGAATCTCTCAA
TCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
Found at i:1417957 original size:83 final size:80
Alignment explanation
Indices: 1417798--1418038 Score: 320
Period size: 83 Copynumber: 2.9 Consensus size: 80
1417788 GATTCTCTTC
* * * * * *
1417798 TAAATCGCGTTGCGATTCTCTTCTAAATCGCGTTGCGAATCTCTCAATCGCGTTGCGATTCTCTT
1 TAAATCGCATTGCGATTCT-ATC--AATCGCATTGCGATTCTATCAATCGCATTGCGATTCTCTT
*
1417863 AATCGCGTTGCGATTCTA
63 AATCGCGTTGCGAATCTA
1417881 TAAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTCTTCTA
1 TAAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTC-T-T-
*
1417946 AATCGCGTTGCGAATCTC
63 AATCGCGTTGCGAATCTA
* * *
1417964 TCAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTATCAAT
1 TAAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTCTTAAT
*
1418029 CGCATTGCGA
66 CGCGTTGCGA
1418039 TTTTCTTCTA
Statistics
Matches: 143, Mismatches: 12, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
80 46 0.32
81 1 0.01
82 4 0.03
83 92 0.64
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (80 bp):
TAAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTATCAATCGCATTGCGATTCTCTTAAT
CGCGTTGCGAATCTA
Found at i:1418100 original size:20 final size:19
Alignment explanation
Indices: 1418075--1418128 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 19
1418065 TGGAAGCTCG
1418075 CGTTGCGATTTTCTTTTGA
1 CGTTGCGATTTTCTTTTGA
*
1418094 CCGTTGCGATTTTCTTTTTTA
1 -CGTTGCGATTTTC-TTTTGA
1418115 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
1418129 AAATCGCAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 1 0.03
20 26 0.81
21 5 0.16
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.54
Consensus pattern (19 bp):
CGTTGCGATTTTCTTTTGA
Found at i:1419167 original size:2 final size:2
Alignment explanation
Indices: 1419160--1419207 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1419150 TATTTTCGAG
*
1419160 TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1419202 TA TA TA
1 TA TA TA
1419208 CATAATTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1423507 original size:32 final size:32
Alignment explanation
Indices: 1423471--1423666 Score: 123
Period size: 32 Copynumber: 6.2 Consensus size: 32
1423461 ACGTGCTATG
* *
1423471 TCATCATTTACATACATGTGGCATGTGATACA
1 TCATCATTTACATACACGTGGCATGTGACACA
* * *
1423503 TCATCGCTTT-GA-ACACGTGGCATGTGATACA
1 TCATC-ATTTACATACACGTGGCATGTGACACA
* ** *
1423534 TCATCACTTTA-A-ACACATGATATGTGTCACA
1 TCATCA-TTTACATACACGTGGCATGTGACACA
* * * *
1423565 TCATCTTTTACGTACACGTGGTACGTGACACA
1 TCATCATTTACATACACGTGGCATGTGACACA
* ** * *
1423597 ACATCATTTATGTACACATGGCACGTGACACA
1 TCATCATTTACATACACGTGGCATGTGACACA
** * * *
1423629 TCATC-TCTTATGTACATGTAGCATGTGACACG
1 TCATCAT-TTACATACACGTGGCATGTGACACA
1423661 TCATCA
1 TCATCA
1423667 CTCATTTACG
Statistics
Matches: 131, Mismatches: 26, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
30 4 0.03
31 47 0.36
32 77 0.59
33 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (32 bp):
TCATCATTTACATACACGTGGCATGTGACACA
Found at i:1423524 original size:31 final size:31
Alignment explanation
Indices: 1423471--1423549 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
1423461 ACGTGCTATG
*
1423471 TCATCA-TTTACATACATGTGGCATGTGATACA
1 TCATCACTTTA-A-ACACGTGGCATGTGATACA
* *
1423503 TCATCGCTTTGAACACGTGGCATGTGATACA
1 TCATCACTTTAAACACGTGGCATGTGATACA
1423534 TCATCACTTTAAACAC
1 TCATCACTTTAAACAC
1423550 ATGATATGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
31 32 0.78
32 6 0.15
33 3 0.07
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (31 bp):
TCATCACTTTAAACACGTGGCATGTGATACA
Found at i:1423559 original size:31 final size:31
Alignment explanation
Indices: 1423492--1423569 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
1423482 ATACATGTGG
* * * *
1423492 CATGTGATACATCATCGCTTTGAACACGTGG
1 CATGTGATACATCATCACTTTAAACACATGA
1423523 CATGTGATACATCATCACTTTAAACACATGA
1 CATGTGATACATCATCACTTTAAACACATGA
*
1423554 TATGTG-TCACATCATC
1 CATGTGAT-ACATCATC
1423570 TTTTACGTAC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
30 1 0.02
31 40 0.98
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (31 bp):
CATGTGATACATCATCACTTTAAACACATGA
Found at i:1424426 original size:32 final size:32
Alignment explanation
Indices: 1424390--1424497 Score: 83
Period size: 32 Copynumber: 3.2 Consensus size: 32
1424380 GCACAAGGGC
1424390 TTCTACTCTCTTTATACTGGAACAATACCAGT
1 TTCTACTCTCTTTATACTGGAACAATACCAGT
** * * * * * *
1424422 TTCTACTCATGATAAAATTAGTG-CCAGAAAGCAGGT
1 TTCTACTC-TCTTTATACT-G-GAACA-ATACCA-GT
*
1424458 ATCTACTCTCTTTATACTGGAACAATACCAGT
1 TTCTACTCTCTTTATACTGGAACAATACCAGT
1424490 TTCTACTC
1 TTCTACTC
1424498 ATGATAAAAT
Statistics
Matches: 52, Mismatches: 18, Indels: 12
0.63 0.22 0.15
Matches are distributed among these distances:
32 17 0.33
33 10 0.19
34 6 0.12
35 10 0.19
36 9 0.17
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (32 bp):
TTCTACTCTCTTTATACTGGAACAATACCAGT
Found at i:1424500 original size:68 final size:68
Alignment explanation
Indices: 1424391--1424529 Score: 278
Period size: 68 Copynumber: 2.0 Consensus size: 68
1424381 CACAAGGGCT
1424391 TCTACTCTCTTTATACTGGAACAATACCAGTTTCTACTCATGATAAAATTAGTGCCAGAAAGCAG
1 TCTACTCTCTTTATACTGGAACAATACCAGTTTCTACTCATGATAAAATTAGTGCCAGAAAGCAG
1424456 GTA
66 GTA
1424459 TCTACTCTCTTTATACTGGAACAATACCAGTTTCTACTCATGATAAAATTAGTGCCAGAAAGCAG
1 TCTACTCTCTTTATACTGGAACAATACCAGTTTCTACTCATGATAAAATTAGTGCCAGAAAGCAG
1424524 GTA
66 GTA
1424527 TCT
1 TCT
1424530 TCTTGTATAC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 71 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (68 bp):
TCTACTCTCTTTATACTGGAACAATACCAGTTTCTACTCATGATAAAATTAGTGCCAGAAAGCAG
GTA
Found at i:1424579 original size:19 final size:19
Alignment explanation
Indices: 1424555--1424592 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1424545 TACCTCTTTT
*
1424555 GAATCTCTTGTACTCCCCA
1 GAATCTCTTCTACTCCCCA
1424574 GAATCTCTTCTACTCCCCA
1 GAATCTCTTCTACTCCCCA
1424593 TATCAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.39, G:0.08, T:0.32
Consensus pattern (19 bp):
GAATCTCTTCTACTCCCCA
Found at i:1426811 original size:249 final size:250
Alignment explanation
Indices: 1426373--1426974 Score: 940
Period size: 249 Copynumber: 2.4 Consensus size: 250
1426363 TTCTTGATTC
* *
1426373 GTAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGCATGATGCTTAAATCTTTCGGGTCATCTGTA
1 GTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
* * * *
1426438 AGCCTTTCGAGCCAGATGATAAGTCCTTTGGGCCACCCGTCAAACCTTTGGGTAGGATGTTTACC
66 AGCCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTCAAACCTTTGGGTAGGATGTTTACA
*
1426503 TATGATTTTCACATGAAAATGAGAAAACAATTTTCAAAGTTTCTCATTTAATGTTCAAGAAAATG
131 TATGATTTTCACATGAAAATGAGAAAACAATTTTCAAAGCTTCTCATTTAATGTTCAAGAAAATG
*
1426568 AAAATTTTGAAAAGTAAGAAG-TTTCTTACCTAGTAAATTATTTCGCACAAATTT
196 AAAATTTTGAAAAGTAAGAAGTTTTCTTACCTAGTAAATTATTTCCCACAAATTT
** * *
1426622 GTAAATCCTTCGGGTCATCAATAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGATCATCTGTA
1 GTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
*
1426687 AGCCTTTCGAGCTAGATGATAAGTCCTTAGGGCCATCCGTCAAACCTTTGGGTAGGATGTTTACA
66 AGCCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTCAAACCTTTGGGTAGGATGTTTACA
*
1426752 TATGATTTTCGCATGAAAATGAGAAAGAC-ATTTTCAAAGCTTCTCATTTAATGTTCAAGAAAAT
131 TATGATTTTCACATGAAAATGAGAAA-ACAATTTTCAAAGCTTCTCATTTAATGTTCAAGAAAAT
* * *
1426816 GAAATTTTTGAAAAGTAATAAGTTTTTTTTACCTAGTAAATTATTTCCCACAAATTT
195 GAAAATTTTGAAAAGTAAGAAG-TTTTCTTACCTAGTAAATTATTTCCCACAAATTT
* * * *
1426873 GTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCCA-GATGTTTAAATCCTTAGGGTCATCTAT
1 GTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAG-CATGATGCTTAAATCCTTCGGGTCATCTGT
* *
1426937 TAGTCTTTCGAGCAAGATGAATAAGTCCTTAGGGCCAT
65 AAGCCTTTCGAGCAAGATG-ATAAGTCCTTAGGGCCAT
1426975 TTGTAAGACC
Statistics
Matches: 321, Mismatches: 27, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
249 199 0.62
250 2 0.01
251 100 0.31
252 20 0.06
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (250 bp):
GTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
AGCCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTCAAACCTTTGGGTAGGATGTTTACA
TATGATTTTCACATGAAAATGAGAAAACAATTTTCAAAGCTTCTCATTTAATGTTCAAGAAAATG
AAAATTTTGAAAAGTAAGAAGTTTTCTTACCTAGTAAATTATTTCCCACAAATTT
Found at i:1426933 original size:42 final size:42
Alignment explanation
Indices: 1426874--1426970 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 42
1426864 CACAAATTTG
* * * **
1426874 TAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCCAGATGTT
1 TAAATCCTTAGGGTCATCTATCAGTCTTTCGAGCAAGATGAA
*
1426916 TAAATCCTTAGGGTCATCTATTAGTCTTTCGAGCAAGATGAA
1 TAAATCCTTAGGGTCATCTATCAGTCTTTCGAGCAAGATGAA
*
1426958 TAAGTCCTTAGGG
1 TAAATCCTTAGGG
1426971 CCATTTGTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.34
Consensus pattern (42 bp):
TAAATCCTTAGGGTCATCTATCAGTCTTTCGAGCAAGATGAA
Found at i:1427152 original size:3 final size:3
Alignment explanation
Indices: 1427144--1427190 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
1427134 CTAATTATAT
* * * *
1427144 TTA TTA TTA TTA TTA CTA CTA TTA TTA TAA TAA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1427191 CAAATAATAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:1431058 original size:2 final size:2
Alignment explanation
Indices: 1431051--1431091 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1431041 CCATCCCTAA
1431051 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1431092 CTTTGGATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1434709 original size:20 final size:19
Alignment explanation
Indices: 1434676--1434756 Score: 90
Period size: 20 Copynumber: 4.1 Consensus size: 19
1434666 TTTTCCAAAT
*
1434676 TCGCTACGTGAATATGTAAA
1 TCGCAACGT-AATATGTAAA
1434696 TCGCAACGATAATATGTAAA
1 TCGCAACG-TAATATGTAAA
* *
1434716 TCGCAACGTGAAGAGGTAAA
1 TCGCAACGT-AATATGTAAA
*
1434736 TCGCAACGCGAATATGTAAA
1 TCGCAACG-TAATATGTAAA
1434756 T
1 T
1434757 TAGCAACGCG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
19 1 0.02
20 50 0.96
21 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (19 bp):
TCGCAACGTAATATGTAAA
Found at i:1434735 original size:40 final size:40
Alignment explanation
Indices: 1434676--1434756 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
1434666 TTTTCCAAAT
* * * *
1434676 TCGCTACGTGAATATGTAAATCGCAACGATAATATGTAAA
1 TCGCAACGTGAAGAGGTAAATCGCAACGAGAATATGTAAA
*
1434716 TCGCAACGTGAAGAGGTAAATCGCAACGCGAATATGTAAA
1 TCGCAACGTGAAGAGGTAAATCGCAACGAGAATATGTAAA
1434756 T
1 T
1434757 TAGCAACGCG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (40 bp):
TCGCAACGTGAAGAGGTAAATCGCAACGAGAATATGTAAA
Found at i:1434884 original size:57 final size:57
Alignment explanation
Indices: 1434759--1434904 Score: 175
Period size: 57 Copynumber: 2.6 Consensus size: 57
1434749 ATGTAAATTA
* * **
1434759 GCAACGCGATTTTCAAATCCGCAACGCCAACTACCGATATAGGTAAACAGTACTATC
1 GCAACGCGATTTTCAAATTCGCAACGCCAATTACCGATATAGGTAAACACAACTATC
* * * *
1434816 GTAACACGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACACAATTATC
1 GCAACGCGATTTTCAAATTCGCAACGCCAATTACCGATATAGGTAAACACAACTATC
* *** *
1434873 GCAACGTGATTTTCGTTTTCGCAACGCGAATT
1 GCAACGCGATTTTCAAATTCGCAACGCCAATT
1434905 TCGCAAATCG
Statistics
Matches: 74, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
57 74 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.27
Consensus pattern (57 bp):
GCAACGCGATTTTCAAATTCGCAACGCCAATTACCGATATAGGTAAACACAACTATC
Found at i:1435281 original size:20 final size:20
Alignment explanation
Indices: 1435256--1435304 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1435246 TCGGTAATTA
1435256 GCGTTGCGAATTTGAAAATC
1 GCGTTGCGAATTTGAAAATC
*
1435276 GCGTTGCGAATTTGAAAATT
1 GCGTTGCGAATTTGAAAATC
1435296 GCGTTGCGA
1 GCGTTGCGA
1435305 TAGTACTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (20 bp):
GCGTTGCGAATTTGAAAATC
Found at i:1435318 original size:77 final size:77
Alignment explanation
Indices: 1435201--1435361 Score: 286
Period size: 77 Copynumber: 2.1 Consensus size: 77
1435191 TGAAAATAAA
* *
1435201 GTTGCGAATTTGAAAATCACGTTGCGATAGTAGTGTTTACCTATGTCGGTAATTAGCGTTGCGAA
1 GTTGCGAATTTGAAAATCACGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAA
1435266 TTTGAAAATCGC
66 TTTGAAAATCGC
**
1435278 GTTGCGAATTTGAAAATTGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAA
1 GTTGCGAATTTGAAAATCACGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAA
1435343 TTTGAAAATCGC
66 TTTGAAAATCGC
1435355 GTTGCGA
1 GTTGCGA
1435362 TAGTACTGTT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 80 1.00
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (77 bp):
GTTGCGAATTTGAAAATCACGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAA
TTTGAAAATCGC
Found at i:1435364 original size:57 final size:57
Alignment explanation
Indices: 1435276--1435418 Score: 268
Period size: 57 Copynumber: 2.5 Consensus size: 57
1435266 TTTGAAAATC
*
1435276 GCGTTGCGAATTTGAAAATTGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTA
1 GCGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTA
1435333 GCGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTA
1 GCGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTA
*
1435390 GCGTTGCGGATTTGAAAATCGCGTTGCGA
1 GCGTTGCGAATTTGAAAATCGCGTTGCGA
1435419 ATTTACATAT
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 84 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (57 bp):
GCGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTA
Found at i:1435444 original size:20 final size:20
Alignment explanation
Indices: 1435408--1435502 Score: 109
Period size: 20 Copynumber: 4.7 Consensus size: 20
1435398 GATTTGAAAA
1435408 TCGCGTTGCGAATTTACATAT
1 TCGCGTTGCG-ATTTACATAT
*
1435429 TTGCGTTGCGATTTACATAT
1 TCGCGTTGCGATTTACATAT
**
1435449 TCGTATTGCGATTTACATAT
1 TCGCGTTGCGATTTACATAT
** * * *
1435469 TATCTTTTCGATTTACTTAT
1 TCGCGTTGCGATTTACATAT
1435489 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
1435503 TGGAACCTGT
Statistics
Matches: 60, Mismatches: 14, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
20 51 0.85
21 9 0.15
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.46
Consensus pattern (20 bp):
TCGCGTTGCGATTTACATAT
Found at i:1436712 original size:20 final size:20
Alignment explanation
Indices: 1436687--1436728 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1436677 ACTGAACTAT
1436687 TTTACGGTACGAGTTAAATA
1 TTTACGGTACGAGTTAAATA
1436707 TTTACGGTACGAGTTAAATA
1 TTTACGGTACGAGTTAAATA
1436727 TT
1 TT
1436729 AAAATTAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (20 bp):
TTTACGGTACGAGTTAAATA
Found at i:1440167 original size:3 final size:3
Alignment explanation
Indices: 1440159--1440190 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1440149 ATTCACCTCT
*
1440159 AAC AAC AAC AAC AAC AAT AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1440191 AACCCTATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.28, G:0.00, T:0.03
Consensus pattern (3 bp):
AAC
Found at i:1442830 original size:23 final size:23
Alignment explanation
Indices: 1442804--1442854 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
1442794 ATCTTATATA
*
1442804 GCACTATAGTGCAATTCTACGCG
1 GCACTACAGTGCAATTCTACGCG
* *
1442827 GCACTACGGTGCAATTCTACGTG
1 GCACTACAGTGCAATTCTACGCG
1442850 GCACT
1 GCACT
1442855 TTGGTGCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (23 bp):
GCACTACAGTGCAATTCTACGCG
Found at i:1444351 original size:32 final size:32
Alignment explanation
Indices: 1444227--1444414 Score: 170
Period size: 32 Copynumber: 5.9 Consensus size: 32
1444217 TACATACATG
*
1444227 TGGCATGTGACACATCATCACTT-TGAACACA
1 TGGCATGTGACACATCATCACTTATGTACACA
* * **
1444258 TGGCATGTGATACACCATCACTT-TAAACACA
1 TGGCATGTGACACATCATCACTTATGTACACA
* * ** **
1444289 TGGTATGTGCCACATCATCTTTTACATACACA
1 TGGCATGTGACACATCATCACTTATGTACACA
* *
1444321 TGGCATGAGACACGTCATCACTTATGTACAC-
1 TGGCATGTGACACATCATCACTTATGTACACA
*
1444352 --GCAATACGTGACACAACATCACTTATGTACACA
1 TGGC-AT--GTGACACATCATCACTTATGTACACA
* *
1444385 TGGCACGTGACACATCATCTCTTATGTACA
1 TGGCATGTGACACATCATCACTTATGTACA
1444415 TGTAGCATTC
Statistics
Matches: 125, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
29 2 0.02
30 2 0.02
31 45 0.36
32 73 0.58
34 1 0.01
35 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (32 bp):
TGGCATGTGACACATCATCACTTATGTACACA
Found at i:1447028 original size:23 final size:22
Alignment explanation
Indices: 1447002--1447045 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
1446992 GTCTTTTGGA
*
1447002 TTAGAAGTAAATTATTAATTTTC
1 TTAGAAGTAAAATA-TAATTTTC
* *
1447025 TTAGGATTAAAATATAATTTT
1 TTAGAAGTAAAATATAATTTT
1447046 ATCATTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (22 bp):
TTAGAAGTAAAATATAATTTTC
Found at i:1450402 original size:30 final size:30
Alignment explanation
Indices: 1450360--1450437 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
1450350 AAATTTCTAT
* *
1450360 TTTTTTCCATTTTAGTCCCCTAGGTTCCTA
1 TTTTTACCATTTTAGTCCCCTAAGTTCCTA
* * **
1450390 TTTTTACTATTTTAGT-CTCTAAGTTTTTA
1 TTTTTACCATTTTAGTCCCCTAAGTTCCTA
*
1450419 TTTTTGCCATTTTAGTCCC
1 TTTTTACCATTTTAGTCCC
1450438 TTTAGTTTCT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 23 0.61
30 15 0.39
ACGTcount: A:0.15, C:0.21, G:0.09, T:0.55
Consensus pattern (30 bp):
TTTTTACCATTTTAGTCCCCTAAGTTCCTA
Found at i:1450451 original size:29 final size:29
Alignment explanation
Indices: 1450353--1450453 Score: 94
Period size: 30 Copynumber: 3.4 Consensus size: 29
1450343 GCCATGTAAA
* *
1450353 TTTCTATTTTTTTCCATTTTAGTCCCCTAGG
1 TTTCTA-TTTTTACCATTTTAGTCCCTTA-G
* * * *
1450384 TTCCTATTTTTACTATTTTAGTCTCTAAG
1 TTTCTATTTTTACCATTTTAGTCCCTTAG
* *
1450413 TTTTTATTTTTGCCATTTTAGTCCCTTTAG
1 TTTCTATTTTTACCATTTTAGTCCC-TTAG
*
1450443 TTTCTTTTTTT
1 TTTCTATTTTT
1450454 TATTAATTTA
Statistics
Matches: 55, Mismatches: 14, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
29 21 0.38
30 29 0.53
31 5 0.09
ACGTcount: A:0.14, C:0.18, G:0.08, T:0.60
Consensus pattern (29 bp):
TTTCTATTTTTACCATTTTAGTCCCTTAG
Found at i:1469438 original size:17 final size:17
Alignment explanation
Indices: 1469426--1469489 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
1469416 CGAAGAGAAT
1469426 AGAAAAAGAAAGAAAAA
1 AGAAAAAGAAAGAAAAA
1469443 AGAAAAAG--A-AAAAA
1 AGAAAAAGAAAGAAAAA
*
1469457 AG-AAAAGAAAAGCAAAA
1 AGAAAAAG-AAAGAAAAA
*
1469474 AGAAAAACAAAGAAAA
1 AGAAAAAGAAAGAAAA
1469490 TAGCAAAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
13 5 0.13
14 7 0.18
15 1 0.03
16 1 0.03
17 21 0.54
18 4 0.10
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (17 bp):
AGAAAAAGAAAGAAAAA
Found at i:1469457 original size:14 final size:13
Alignment explanation
Indices: 1469428--1469480 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1469418 AAGAGAATAG
1469428 AAAAAG-AAAG-A
1 AAAAAGAAAAGAA
1469439 AAAAAGAAAAAGAA
1 AAAAAG-AAAAGAA
1469453 AAAAAGAAAAGAA
1 AAAAAGAAAAGAA
**
1469466 AAGCA-AAAAGAA
1 AAAAAGAAAAGAA
1469478 AAA
1 AAA
1469481 CAAAGAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 6 0.17
12 9 0.25
13 14 0.39
14 7 0.19
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAGAA
Done.