Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 4 of 356
Found at i:1199776 original size:72 final size:72
Alignment explanation
Indices: 1199659--1199914 Score: 503
Period size: 72 Copynumber: 3.6 Consensus size: 72
1199649 ACAACTTGAC
*
1199659 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1199724 ACTAACA
66 ACTAACA
1199731 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1199796 ACTAACA
66 ACTAACA
1199803 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1199868 ACTAACA
66 ACTAACA
1199875 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1199915 AATAATAATA
Statistics
Matches: 183, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 183 1.00
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.27
Consensus pattern (72 bp):
AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCACTTAAAATAAATCACCACCTACTAC
ACTAACA
Found at i:1199923 original size:3 final size:3
Alignment explanation
Indices: 1199915--1199955 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1199905 ATTACATCCA
1199915 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1199956 AACATGTGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1200048 original size:27 final size:27
Alignment explanation
Indices: 1200010--1200063 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
1200000 ATTGAGCATG
*
1200010 ACAGAGACATCATAACGATCATTTAAT
1 ACAGAAACATCATAACGATCATTTAAT
1200037 ACAGAAACATCATAACGATCATTTAAT
1 ACAGAAACATCATAACGATCATTTAAT
1200064 TTTGTTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.46, C:0.19, G:0.09, T:0.26
Consensus pattern (27 bp):
ACAGAAACATCATAACGATCATTTAAT
Found at i:1201339 original size:26 final size:26
Alignment explanation
Indices: 1201300--1201355 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
1201290 ACTATACTAA
*
1201300 TGAAAAGAATCAAATAAGGCCAAAAT
1 TGAAAAGAACCAAATAAGGCCAAAAT
*
1201326 TGAAAAGAACCAAATAAGGCCAAACT
1 TGAAAAGAACCAAATAAGGCCAAAAT
1201352 TGAA
1 TGAA
1201356 TAGATTTAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.55, C:0.14, G:0.16, T:0.14
Consensus pattern (26 bp):
TGAAAAGAACCAAATAAGGCCAAAAT
Found at i:1206111 original size:12 final size:12
Alignment explanation
Indices: 1206089--1206125 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1206079 GCACACACGC
1206089 ACATACATCCAT
1 ACATACATCCAT
* *
1206101 CCATCCATCCAT
1 ACATACATCCAT
1206113 ACATACATCCAT
1 ACATACATCCAT
1206125 A
1 A
1206126 TAGAGAGAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.24
Consensus pattern (12 bp):
ACATACATCCAT
Found at i:1211692 original size:17 final size:18
Alignment explanation
Indices: 1211670--1211707 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1211660 AAATTTATTT
*
1211670 TTAAAACTTA-AAAAACA
1 TTAAAACTTATAAAAAAA
*
1211687 TTAAAATTTATAAAAAAA
1 TTAAAACTTATAAAAAAA
1211705 TTA
1 TTA
1211708 TTTTTAATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
TTAAAACTTATAAAAAAA
Found at i:1211698 original size:39 final size:40
Alignment explanation
Indices: 1211622--1211701 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
1211612 ATCAGCATTT
* * *
1211622 ATTTAGTTTTTAAATTTAAAAACCTTTAAAAAATTATAAA
1 ATTTAGTTTTTAAACTTAAAAAACATTAAAAAATTATAAA
*
1211662 ATTTA-TTTTTAAAACTTAAAAAACATT-AAAATTTATAAA
1 ATTTAGTTTTT-AAACTTAAAAAACATTAAAAAATTATAAA
1211701 A
1 A
1211702 AAATTATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
39 17 0.49
40 18 0.51
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (40 bp):
ATTTAGTTTTTAAACTTAAAAAACATTAAAAAATTATAAA
Found at i:1216405 original size:22 final size:22
Alignment explanation
Indices: 1216361--1216405 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1216351 GTATTAAATT
*
1216361 ATTAAATATTAAGATAATATAA
1 ATTAAATATTAAGAAAATATAA
*
1216383 ATTAAATATTTAA-AAAATTTAA
1 ATTAAATA-TTAAGAAAATATAA
1216405 A
1 A
1216406 AATAATATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
ATTAAATATTAAGAAAATATAA
Found at i:1218231 original size:40 final size:40
Alignment explanation
Indices: 1218186--1218270 Score: 163
Period size: 40 Copynumber: 2.1 Consensus size: 40
1218176 AATGTATATA
1218186 TTAAAAATTTATATAAATAATAGATGAGACTTTGAAAAGG
1 TTAAAAATTTATATAAATAATAGATGAGACTTTGAAAAGG
1218226 TTAAAAATTTATATAAATAATAGATGAGACTTTGAAAAGG
1 TTAAAAATTTATATAAATAATAGATGAGACTTTGAAAAGG
1218266 -TAAAA
1 TTAAAA
1218271 TAATAATATT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 5 0.11
40 40 0.89
ACGTcount: A:0.52, C:0.02, G:0.14, T:0.32
Consensus pattern (40 bp):
TTAAAAATTTATATAAATAATAGATGAGACTTTGAAAAGG
Found at i:1233161 original size:28 final size:28
Alignment explanation
Indices: 1233124--1233184 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
1233114 TAATATATAG
1233124 TAAAATTGTACTTTGACCCCTAAAAATA
1 TAAAATTGTACTTTGACCCCTAAAAATA
1233152 TAAAATTGTACTTTGACCCCTAAAAATA
1 TAAAATTGTACTTTGACCCCTAAAAATA
*
1233180 AAAAA
1 TAAAA
1233185 AATCTATGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.30
Consensus pattern (28 bp):
TAAAATTGTACTTTGACCCCTAAAAATA
Found at i:1233339 original size:21 final size:22
Alignment explanation
Indices: 1233292--1233341 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1233282 CTGAATTCGT
*
1233292 CCATGGTCAATAAAGTACTTAA
1 CCATTGTCAATAAAGTACTTAA
1233314 CCATTGTCAATAAAGTACTT-A
1 CCATTGTCAATAAAGTACTTAA
1233335 CCATTGT
1 CCATTGT
1233342 TCTCTTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (22 bp):
CCATTGTCAATAAAGTACTTAA
Found at i:1242529 original size:16 final size:16
Alignment explanation
Indices: 1242508--1242538 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1242498 ATTATAAATG
1242508 ATAAAAAATAAAAAAA
1 ATAAAAAATAAAAAAA
*
1242524 ATAAAACATAAAAAA
1 ATAAAAAATAAAAAA
1242539 TTTGTTTCTA
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:0.84, C:0.03, G:0.00, T:0.13
Consensus pattern (16 bp):
ATAAAAAATAAAAAAA
Found at i:1243188 original size:22 final size:22
Alignment explanation
Indices: 1243136--1243188 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1243126 ATTATAATTG
1243136 AAACTTAA-T-TCAATTGGTAT
1 AAACTTAATTGTCAATTGGTAT
* *
1243156 AAATTTTATTGTCAATTGGTAT
1 AAACTTAATTGTCAATTGGTAT
1243178 AAACTTAATTG
1 AAACTTAATTG
1243189 AAACTTAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 6 0.22
21 1 0.04
22 20 0.74
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (22 bp):
AAACTTAATTGTCAATTGGTAT
Found at i:1244505 original size:16 final size:17
Alignment explanation
Indices: 1244475--1244506 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1244465 TTGTCATTGG
1244475 TTTCTTTTGCTTTTTCC
1 TTTCTTTTGCTTTTTCC
1244492 TTTCTTTT-CTTTTTC
1 TTTCTTTTGCTTTTTC
1244507 TAGTGTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.22, G:0.03, T:0.75
Consensus pattern (17 bp):
TTTCTTTTGCTTTTTCC
Found at i:1251182 original size:21 final size:21
Alignment explanation
Indices: 1251156--1251244 Score: 76
Period size: 21 Copynumber: 4.3 Consensus size: 21
1251146 GTGTTTTACT
*
1251156 TTCTGTTTAGCTCTT-TCGAGC
1 TTCTGTTCAGCTCTTAT-GAGC
* *
1251177 TTCTGTTCAACTCTTATGAGT
1 TTCTGTTCAGCTCTTATGAGC
* *
1251198 TTTTGTTTAGCTCTTATGAGC
1 TTCTGTTCAGCTCTTATGAGC
* * *
1251219 TTTTGCTCAGCT-TT-CGAGC
1 TTCTGTTCAGCTCTTATGAGC
1251238 TTCTGTT
1 TTCTGTT
1251245 GGCGTATTTG
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 9 0.16
20 2 0.04
21 43 0.78
22 1 0.02
ACGTcount: A:0.12, C:0.20, G:0.18, T:0.49
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTATGAGC
Found at i:1264139 original size:16 final size:17
Alignment explanation
Indices: 1264120--1264152 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1264110 AATTTGTTTT
*
1264120 TATATAAAAA-TAATAA
1 TATAAAAAAATTAATAA
1264136 TATAAAAAAATTAATAA
1 TATAAAAAAATTAATAA
1264153 GGCAGACTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TATAAAAAAATTAATAA
Found at i:1264311 original size:41 final size:41
Alignment explanation
Indices: 1264266--1264349 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
1264256 CAATCCAACC
**
1264266 CATGATCACTCTAGATCGAACCCTACCAAATGCATGATGCT
1 CATGATCACTCTAGATCGAACCCTACCAAAAACATGATGCT
1264307 CATGATCACTCTAGATCGAACCCTACCAAAAACATGATGCT
1 CATGATCACTCTAGATCGAACCCTACCAAAAACATGATGCT
1264348 CA
1 CA
1264350 CATTCTCTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.23
Consensus pattern (41 bp):
CATGATCACTCTAGATCGAACCCTACCAAAAACATGATGCT
Found at i:1265145 original size:77 final size:77
Alignment explanation
Indices: 1265018--1265175 Score: 289
Period size: 77 Copynumber: 2.1 Consensus size: 77
1265008 GTGTCAACTT
*
1265018 ATTTAAAATTTAATCGATAAAAAAGTAATTGGTTAGATTGATAAGTTTATATAAAATTTGGAAAT
1 ATTTAAAATTTAATCGATAAAAAAATAATTGGTTAGATTGATAAGTTTATATAAAATTTGGAAAT
1265083 GTCTAAAATGAG
66 GTCTAAAATGAG
*
1265095 ATTTAAAATTTAATCGATAAAAAAATAATTGGTTAGATTGATAAGTTTATATATAATTTGGAAAT
1 ATTTAAAATTTAATCGATAAAAAAATAATTGGTTAGATTGATAAGTTTATATAAAATTTGGAAAT
*
1265160 GTCTAAAATGTG
66 GTCTAAAATGAG
1265172 ATTT
1 ATTT
1265176 TATTATAGTA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.44, C:0.03, G:0.15, T:0.39
Consensus pattern (77 bp):
ATTTAAAATTTAATCGATAAAAAAATAATTGGTTAGATTGATAAGTTTATATAAAATTTGGAAAT
GTCTAAAATGAG
Found at i:1273629 original size:20 final size:20
Alignment explanation
Indices: 1273601--1273647 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1273591 AAGCTTATAG
*
1273601 TATCAATACTTGCCCCAAGA
1 TATCGATACTTGCCCCAAGA
* * *
1273621 TATCGATACTTGTCCCAGGG
1 TATCGATACTTGCCCCAAGA
1273641 TATCGAT
1 TATCGAT
1273648 GCTCAGGCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (20 bp):
TATCGATACTTGCCCCAAGA
Found at i:1292139 original size:18 final size:18
Alignment explanation
Indices: 1292116--1292208 Score: 114
Period size: 18 Copynumber: 5.2 Consensus size: 18
1292106 CCCAACTACT
*
1292116 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
1292134 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
* * *
1292152 ATATACGTAAATAGTACT
1 GTATACGTGAATAGTACC
* *
1292170 GTATACGTAAATAGTGCC
1 GTATACGTGAATAGTACC
*
1292188 GTATACGTGAATAGTATC
1 GTATACGTGAATAGTACC
1292206 GTA
1 GTA
1292209 AACGGTCGTA
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:1292168 original size:36 final size:36
Alignment explanation
Indices: 1292117--1292208 Score: 130
Period size: 36 Copynumber: 2.6 Consensus size: 36
1292107 CCAACTACTG
* *
1292117 TATACGTGAACAGTACCGTATACGTGAATAGTGCCA
1 TATACGTGAATAGTACCGTATACGTAAATAGTGCCA
* * *
1292153 TATACGTAAATAGTACTGTATACGTAAATAGTGCCG
1 TATACGTGAATAGTACCGTATACGTAAATAGTGCCA
*
1292189 TATACGTGAATAGTATCGTA
1 TATACGTGAATAGTACCGTA
1292209 AACGGTCGTA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (36 bp):
TATACGTGAATAGTACCGTATACGTAAATAGTGCCA
Found at i:1295206 original size:19 final size:20
Alignment explanation
Indices: 1295182--1295221 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1295172 ATTTAACATG
1295182 CTTAA-TTTTTTATTTTTAT
1 CTTAATTTTTTTATTTTTAT
1295201 CTTAATTTTTTTATTTTTAT
1 CTTAATTTTTTTATTTTTAT
1295221 C
1 C
1295222 AATTTTCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.72
Consensus pattern (20 bp):
CTTAATTTTTTTATTTTTAT
Found at i:1302183 original size:30 final size:30
Alignment explanation
Indices: 1302147--1302207 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
1302137 CCCCAACAGG
1302147 ATATAAAGGAAACCAAGTAATGGATCATGA
1 ATATAAAGGAAACCAAGTAATGGATCATGA
*
1302177 ATATAAAGGAAACCAAGTCATGGATCATGA
1 ATATAAAGGAAACCAAGTAATGGATCATGA
1302207 A
1 A
1302208 AGCCGGTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.49, C:0.11, G:0.20, T:0.20
Consensus pattern (30 bp):
ATATAAAGGAAACCAAGTAATGGATCATGA
Found at i:1316141 original size:18 final size:18
Alignment explanation
Indices: 1316115--1316157 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1316105 TTTAATCATT
*
1316115 TAAAATATTATAAA-AATA
1 TAAATTATTA-AAATAATA
1316133 TAAATTATTAAAATAATA
1 TAAATTATTAAAATAATA
1316151 -AAATTAT
1 TAAATTAT
1316158 ATTTTAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAATTATTAAAATAATA
Found at i:1316145 original size:15 final size:17
Alignment explanation
Indices: 1316121--1316158 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
1316111 CATTTAAAAT
1316121 ATTATAAAAAT-AT-AA
1 ATTATAAAAATAATAAA
*
1316136 ATTATTAAAATAATAAA
1 ATTATAAAAATAATAAA
1316153 ATTATA
1 ATTATA
1316159 TTTTAACTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 10 0.53
16 2 0.11
17 7 0.37
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTATAAAAATAATAAA
Found at i:1317567 original size:22 final size:23
Alignment explanation
Indices: 1317535--1317590 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
1317525 GCTATTCAAT
*
1317535 TTTAAAAAATTATAAAATAAA-TA
1 TTTAAATAATTATAAAA-AAATTA
1317558 -TTAAATAATT-TAAAAAAATTA
1 TTTAAATAATTATAAAAAAATTA
*
1317579 TTTAAATTATTA
1 TTTAAATAATTA
1317591 GATTATTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 3 0.11
21 7 0.25
22 18 0.64
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TTTAAATAATTATAAAAAAATTA
Found at i:1317761 original size:14 final size:15
Alignment explanation
Indices: 1317737--1317765 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1317727 AATATCAAAA
1317737 AAAATTATTTAAATT
1 AAAATTATTTAAATT
1317752 AAAA-TATTTAAATT
1 AAAATTATTTAAATT
1317766 TTGATTCGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATTATTTAAATT
Found at i:1322358 original size:31 final size:31
Alignment explanation
Indices: 1322323--1322382 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
1322313 CAAAATGGTT
1322323 ATTGAACTATTCGAAAG-TTTTCATTTAAGTC
1 ATTGAACTATTCGAAAGTTTTTC-TTTAAGTC
* *
1322354 ATTGAATTATTTGAAAGTTTTTCTTTAAG
1 ATTGAACTATTCGAAAGTTTTTCTTTAAG
1322383 CAATTGGGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.47
Consensus pattern (31 bp):
ATTGAACTATTCGAAAGTTTTTCTTTAAGTC
Found at i:1324224 original size:16 final size:16
Alignment explanation
Indices: 1324203--1324256 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
1324193 TTTGGTTCAG
*
1324203 TGTAATGGAATAGGGT
1 TGTAATGGAATAGAGT
**
1324219 TGTAATGGAATAGAAC
1 TGTAATGGAATAGAGT
*
1324235 TGTAACGGAATAGAGT
1 TGTAATGGAATAGAGT
1324251 TGTAAT
1 TGTAAT
1324257 AGCAATTCAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.37, C:0.04, G:0.30, T:0.30
Consensus pattern (16 bp):
TGTAATGGAATAGAGT
Found at i:1324493 original size:61 final size:60
Alignment explanation
Indices: 1324428--1324580 Score: 150
Period size: 58 Copynumber: 2.5 Consensus size: 60
1324418 TTTAATAGGA
** *
1324428 TTATTATTAGATATAATTTAATAAAAATAATAATACATAATTTAACCCTATT-TTAATAAAT
1 TTATTATTA-ATATAA-TTAATAAAAATAATAATACATAATTTAACAATATTCTTAATAAAG
* * * *
1324489 TTATTATTAATTATAATT--TAACAATAATAATATATAATTTAATAATATTCTTAATATAG
1 TTATTATTAA-TATAATTAATAAAAATAATAATACATAATTTAACAATATTCTTAATAAAG
**
1324548 CAATTATTAAAATATAAATTAATAAAAATAATA
1 TTATTATT--AATAT-AATTAATAAAAATAATA
1324581 TATAATATTA
Statistics
Matches: 75, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
58 26 0.35
59 13 0.17
60 6 0.08
61 20 0.27
63 10 0.13
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (60 bp):
TTATTATTAATATAATTAATAAAAATAATAATACATAATTTAACAATATTCTTAATAAAG
Found at i:1324524 original size:21 final size:20
Alignment explanation
Indices: 1324496--1324535 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1324486 AATTTATTAT
1324496 TAATTATAATTTAACAATAA
1 TAATTATAATTTAACAATAA
*
1324516 TAATATATAATTTAATAATA
1 TAAT-TATAATTTAACAATA
1324536 TTCTTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TAATTATAATTTAACAATAA
Found at i:1324596 original size:22 final size:21
Alignment explanation
Indices: 1324559--1324604 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 21
1324549 AATTATTAAA
1324559 ATATAAATTAATAAAAATAAT
1 ATATAAATTAATAAAAATAAT
1324580 ATATAATATTACA-AAAAATAAT
1 ATATAA-ATTA-ATAAAAATAAT
1324602 ATA
1 ATA
1324605 CAACCTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.26
22 16 0.70
23 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
ATATAAATTAATAAAAATAAT
Found at i:1324737 original size:12 final size:12
Alignment explanation
Indices: 1324707--1324741 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
1324697 TCTATGTTAC
1324707 TTAAAGAATAAT
1 TTAAAGAATAAT
1324719 TTAAAAGAATAAT
1 TT-AAAGAATAAT
1324732 TTAAAGAATA
1 TTAAAGAATA
1324742 TATTGTCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (12 bp):
TTAAAGAATAAT
Found at i:1325514 original size:5 final size:5
Alignment explanation
Indices: 1325506--1325532 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1325496 ATACAAATCA
1325506 AAAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AA
1325533 CATATATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1328602 original size:18 final size:20
Alignment explanation
Indices: 1328560--1328596 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1328550 ATATTTTATG
*
1328560 ATTA-TTTAATTAGATATAT
1 ATTATTTTAATGAGATATAT
1328579 ATTATTTTAATGAGATAT
1 ATTATTTTAATGAGATAT
1328597 TTTATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
ATTATTTTAATGAGATATAT
Found at i:1330809 original size:46 final size:46
Alignment explanation
Indices: 1330757--1331030 Score: 352
Period size: 46 Copynumber: 6.0 Consensus size: 46
1330747 AGTGTGCTCT
* *
1330757 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
1330803 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
1330849 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ** * * *
1330895 ATGACGGGAAATAAATAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
1330941 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
1330987 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGACATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
1331031 TCATGTCAAA
Statistics
Matches: 205, Mismatches: 22, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
45 1 0.00
46 204 1.00
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:1330914 original size:92 final size:92
Alignment explanation
Indices: 1330757--1331030 Score: 404
Period size: 92 Copynumber: 3.0 Consensus size: 92
1330747 AGTGTGCTCT
* * * *
1330757 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAGTAAG
1330822 ACCATGGTTGAAAGATACCATGGCAGC
66 ACCATGGTTGAAAGATACCATGGCAGC
* * * *
1330849 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACGGGAAATAAATAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAGTAAG
1330914 ACCATGGTTGAAAGATACCATGGCAGC
66 ACCATGGTTGAAAGATACCATGGCAGC
* * ** *
1330941 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAGTAAG
* * *
1331006 ACCATAGTTGAAAGACACTATGGCA
66 ACCATGGTTGAAAGATACCATGGCA
1331031 TCATGTCAAA
Statistics
Matches: 162, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
92 162 1.00
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.21
Consensus pattern (92 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAGTAAG
ACCATGGTTGAAAGATACCATGGCAGC
Found at i:1332282 original size:9 final size:9
Alignment explanation
Indices: 1332268--1332292 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1332258 TGATTATTAG
1332268 CACATTCAA
1 CACATTCAA
1332277 CACATTCAA
1 CACATTCAA
1332286 CACATTC
1 CACATTC
1332293 GTACTCTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.40, C:0.36, G:0.00, T:0.24
Consensus pattern (9 bp):
CACATTCAA
Found at i:1333920 original size:18 final size:20
Alignment explanation
Indices: 1333878--1333914 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1333868 ATATTTTATG
*
1333878 ATTA-TTTAATTAGATATAT
1 ATTATTTTAATGAGATATAT
1333897 ATTATTTTAATGAGATAT
1 ATTATTTTAATGAGATAT
1333915 TTTATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
ATTATTTTAATGAGATATAT
Found at i:1336129 original size:46 final size:46
Alignment explanation
Indices: 1336073--1336392 Score: 426
Period size: 46 Copynumber: 7.0 Consensus size: 46
1336063 AGTGTGCTCT
*
1336073 CTGATTTGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1336119 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
1336165 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
1336211 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** *** * *
1336257 ATGACGGGAAATAAATAAGACCGTGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * **
1336303 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
1336349 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
1336393 TCATGTCAAA
Statistics
Matches: 248, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 1 0.00
46 247 1.00
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:1337149 original size:25 final size:25
Alignment explanation
Indices: 1337121--1337171 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
1337111 GCAACAACAC
1337121 ACCTTAGTTAAATCTTCGATGGAGG
1 ACCTTAGTTAAATCTTCGATGGAGG
*
1337146 ACCTTAGTTAAATCTTGGATGGAGG
1 ACCTTAGTTAAATCTTCGATGGAGG
1337171 A
1 A
1337172 GAGCCATTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.31
Consensus pattern (25 bp):
ACCTTAGTTAAATCTTCGATGGAGG
Found at i:1337946 original size:31 final size:30
Alignment explanation
Indices: 1337908--1337976 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 30
1337898 GGACACTAAT
1337908 TTTAAAAAGTTACA-AAACGGTCATTAAACTA
1 TTTAAAAAGTTACATAAA--GTCATTAAACTA
* * *
1337939 TTTAAAAATTTTCATTTAAGTCATTAAACTA
1 TTTAAAAAGTTACA-TAAAGTCATTAAACTA
1337970 TTTAAAA
1 TTTAAAA
1337977 GTTTTTATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 31 0.94
33 2 0.06
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (30 bp):
TTTAAAAAGTTACATAAAGTCATTAAACTA
Found at i:1341997 original size:18 final size:18
Alignment explanation
Indices: 1341976--1342016 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1341966 TGAGCGTGAT
1341976 CGTGACCATGATAGAGAC
1 CGTGACCATGATAGAGAC
* *
1341994 CGTGATCGTGATAGAGAC
1 CGTGACCATGATAGAGAC
1342012 CGTGA
1 CGTGA
1342017 GCGTTATAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.32, T:0.20
Consensus pattern (18 bp):
CGTGACCATGATAGAGAC
Found at i:1342025 original size:18 final size:18
Alignment explanation
Indices: 1341984--1342025 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1341974 ATCGTGACCA
*
1341984 TGATAGAGACCGTGATCG
1 TGATAGAGACCGTGAGCG
1342002 TGATAGAGACCGTGAGCG
1 TGATAGAGACCGTGAGCG
*
1342020 TTATAG
1 TGATAG
1342026 GGAGAGGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.24
Consensus pattern (18 bp):
TGATAGAGACCGTGAGCG
Found at i:1349979 original size:16 final size:17
Alignment explanation
Indices: 1349960--1349991 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1349950 TTATTAAATC
1349960 ATATATTTAA-ATTAAA
1 ATATATTTAATATTAAA
1349976 ATATATTTAATATTAA
1 ATATATTTAATATTAA
1349992 TTATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATTTAATATTAAA
Found at i:1350055 original size:66 final size:63
Alignment explanation
Indices: 1349984--1350196 Score: 194
Period size: 61 Copynumber: 3.4 Consensus size: 63
1349974 AAATATATTT
1349984 AATATTAATTATTTAA-AATTTTATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTA-TTAAGAATTTTA--TTA-AGTATCATATATTATGATTTGAGTAAATTCATATA
1350048 AG
62 AG
* * * * * * *
1350050 AATATTAATTATTAAGAATTTTATTAA--ATTATATATTTTAATTAT-ATTATATTTA-ATAAT
1 AATATTAATTATTAAGAATTTTATTAAGTATCATATATTATGATT-TGAGTAAATTCATATAAG
* * * *
1350110 AATTATGTTATT-TT-A-TATTTTA--CAGTATCATATATTATGGTTTGAGTAAATTCATATAAG
1 AA-TAT-TAATTATTAAGAATTTTATTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
1350170 AATATTAATTATTAAGAATTTTATTAA
1 AATATTAATTATTAAGAATTTTATTAA
1350197 ATTATATATT
Statistics
Matches: 113, Mismatches: 21, Indels: 29
0.69 0.13 0.18
Matches are distributed among these distances:
57 1 0.01
58 5 0.04
59 30 0.27
60 14 0.12
61 31 0.27
62 5 0.04
63 2 0.02
64 3 0.03
65 4 0.04
66 18 0.16
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (63 bp):
AATATTAATTATTAAGAATTTTATTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:1350070 original size:120 final size:120
Alignment explanation
Indices: 1349946--1350238 Score: 482
Period size: 120 Copynumber: 2.4 Consensus size: 120
1349936 AATTATTTTA
* * *
1349946 AATTTTATTAAATCATATATTTAAATTAAAATATATTTAATATTAATTAT-TTAAAATTT-TATT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT--AATTTATATT
*
1350009 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
64 TTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* * *
1350066 AATTTTATTAAATTATATATTTTAATTATATTATATTTAATAATAATTATGTTATTTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
*
1350131 ACAGTATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
1350186 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1350239 TAAATATGAT
Statistics
Matches: 161, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
119 4 0.02
120 155 0.96
121 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:1350098 original size:18 final size:17
Alignment explanation
Indices: 1350067--1350101 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1350057 ATTATTAAGA
1350067 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
1350084 ATTTTAATTATATTATAT
1 ATTTT-ATTAAATTATAT
1350102 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:1350215 original size:18 final size:17
Alignment explanation
Indices: 1350187--1350221 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1350177 ATTATTAAGA
*
1350187 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
1350204 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
1350222 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:1350335 original size:147 final size:149
Alignment explanation
Indices: 1350175--1350449 Score: 482
Period size: 147 Copynumber: 1.9 Consensus size: 149
1350165 ATAAGAATAT
*
1350175 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
* *
1350240 AAATATGATTAAATTATTTATTATTGAT-ATTAATAATTTTATTAAAATTTAAATAA-AATAATT
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
1350303 TACCAAAACAAATTTCTGC
131 TACCAAAACAAATTTCTGC
*
1350322 TAATTATTAAGAATTTTATTAAATTTTATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
* *
1350387 AAATATGGTTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
1350450 CAATAATCAT
Statistics
Matches: 120, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
147 89 0.74
148 26 0.22
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (149 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
TACCAAAACAAATTTCTGC
Found at i:1350579 original size:44 final size:45
Alignment explanation
Indices: 1350530--1350624 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
1350520 TTACACCTCT
* *
1350530 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
1350574 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
1350619 ATTACA
1 ATTACA
1350625 CTTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:1350624 original size:16 final size:16
Alignment explanation
Indices: 1350605--1350656 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
1350595 GATTTGCTAT
* *
1350605 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
*
1350621 TACACTTCTAATCCAA
1 TACACCTCTAATCCAA
1350637 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1350653 TACA
1 TACA
1350657 GCGAACCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:1363806 original size:14 final size:14
Alignment explanation
Indices: 1363787--1363814 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1363777 CTCAATCAAC
1363787 TTTTTTAAAAAATA
1 TTTTTTAAAAAATA
1363801 TTTTTTAAAAAATA
1 TTTTTTAAAAAATA
1363815 AATAAGAAAG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTTTTAAAAAATA
Found at i:1365966 original size:20 final size:20
Alignment explanation
Indices: 1365943--1365980 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1365933 TTACATTTGA
1365943 TTTTTTTT-AATGTACTATT
1 TTTTTTTTCAATGTACTATT
*
1365962 TTTTTTTTCAATGTGCTAT
1 TTTTTTTTCAATGTACTAT
1365981 ATATATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.18, C:0.08, G:0.08, T:0.66
Consensus pattern (20 bp):
TTTTTTTTCAATGTACTATT
Found at i:1369258 original size:13 final size:14
Alignment explanation
Indices: 1369242--1369270 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1369232 AGGGTTCTGA
1369242 GTTCAG-GTTTAAG
1 GTTCAGAGTTTAAG
1369255 GTTCAGAGTTTAAG
1 GTTCAGAGTTTAAG
1369269 GT
1 GT
1369271 AAAAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.24, C:0.07, G:0.31, T:0.38
Consensus pattern (14 bp):
GTTCAGAGTTTAAG
Found at i:1369991 original size:22 final size:22
Alignment explanation
Indices: 1369966--1370009 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1369956 TCACGTCAAC
* *
1369966 AAATAACTAAAAATTATAAAAA
1 AAATAACCAAAAATCATAAAAA
**
1369988 AAATCCCCAAAAATCATAAAAA
1 AAATAACCAAAAATCATAAAAA
1370010 CTTAAAAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.68, C:0.14, G:0.00, T:0.18
Consensus pattern (22 bp):
AAATAACCAAAAATCATAAAAA
Found at i:1382995 original size:21 final size:20
Alignment explanation
Indices: 1382954--1383018 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
1382944 CAGAATCTAT
* *
1382954 ATTTCAAAAAAGATTATAAA
1 ATTTCAAAAAAAATTAAAAA
1382974 ATTTCAAAAAAAATCTAAAAA
1 ATTTCAAAAAAAAT-TAAAAA
* *
1382995 ATATAT-AAAGAAAGTTAAAAA
1 AT-T-TCAAAAAAAATTAAAAA
1383016 ATT
1 ATT
1383019 AAATTTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
20 14 0.37
21 15 0.39
22 8 0.21
23 1 0.03
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.28
Consensus pattern (20 bp):
ATTTCAAAAAAAATTAAAAA
Found at i:1384764 original size:23 final size:20
Alignment explanation
Indices: 1384726--1384773 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 20
1384716 AAAAATATTT
1384726 ATTTTATTTTAATATT-AATA
1 ATTTTATTTTAATATTGAA-A
1384746 ATTTTATTTTCTAATTATTGAAA
1 ATTTTA-TTT-TAA-TATTGAAA
1384769 ATTTT
1 ATTTT
1384774 TATATAGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 6 0.25
21 3 0.12
22 3 0.12
23 10 0.42
24 2 0.08
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
ATTTTATTTTAATATTGAAA
Found at i:1384868 original size:18 final size:17
Alignment explanation
Indices: 1384842--1384880 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1384832 AATGTATTAT
*
1384842 AAATTACATAACATATAA
1 AAATAACATAACATA-AA
*
1384860 AAATAACATAATATAAA
1 AAATAACATAACATAAA
1384877 AAAT
1 AAAT
1384881 TATGAACTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATAACATAACATAAA
Found at i:1385191 original size:6 final size:6
Alignment explanation
Indices: 1385180--1385212 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1385170 AAAAGAGTAA
*
1385180 AAAAAG AAAAAG AAAAAG AGAAAG -AAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1385213 CCCCACAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1396289 original size:10 final size:10
Alignment explanation
Indices: 1396274--1396327 Score: 53
Period size: 9 Copynumber: 5.8 Consensus size: 10
1396264 TTTTTAGAAC
1396274 TTTATAATAT
1 TTTATAATAT
1396284 TTTAT-A-AT
1 TTTATAATAT
1396292 TTTAT-ATAT
1 TTTATAATAT
*
1396301 TTTATGAT-T
1 TTTATAATAT
* *
1396310 TTTATAAAAA
1 TTTATAATAT
1396320 TTTATAAT
1 TTTATAAT
1396328 TTATAATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
8 8 0.22
9 15 0.41
10 14 0.38
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (10 bp):
TTTATAATAT
Found at i:1396293 original size:8 final size:8
Alignment explanation
Indices: 1396282--1396337 Score: 51
Period size: 8 Copynumber: 6.6 Consensus size: 8
1396272 ACTTTATAAT
1396282 ATTTTATA
1 ATTTTATA
1396290 ATTTTATA
1 ATTTTATA
1396298 TATTTTATGA
1 -ATTTTAT-A
*
1396308 TTTTTATAAA
1 ATTTTAT--A
*
1396318 AATTTATA
1 ATTTTATA
1396326 A-TTTATA
1 ATTTTATA
1396333 ATTTT
1 ATTTT
1396338 TTACTATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
7 7 0.17
8 13 0.32
9 13 0.32
10 7 0.17
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (8 bp):
ATTTTATA
Found at i:1396340 original size:36 final size:37
Alignment explanation
Indices: 1396257--1396340 Score: 93
Period size: 36 Copynumber: 2.3 Consensus size: 37
1396247 TTACATTTTG
* *
1396257 TATAATTTTTT-TAGAACTTTATAATATTTTATAATT
1 TATAATTTTTTATAGAACTTTATAAAAATTTATAATT
* **
1396293 T-TATATATTTTAT-GATTTTTATAAAAATTTATAATT
1 TATA-ATTTTTTATAGAACTTTATAAAAATTTATAATT
1396329 TATAATTTTTTA
1 TATAATTTTTTA
1396341 CTATTTTATT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
35 2 0.05
36 34 0.87
37 3 0.08
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (37 bp):
TATAATTTTTTATAGAACTTTATAAAAATTTATAATT
Found at i:1396340 original size:53 final size:53
Alignment explanation
Indices: 1396274--1396381 Score: 130
Period size: 53 Copynumber: 2.0 Consensus size: 53
1396264 TTTTTAGAAC
*
1396274 TTTATAATATTTTA-TAATTTTATATATTTTATGATTTTTATAAAAATTT-ATAA
1 TTTATAATATTTTACT-ATTTTAT-TATTTTATAATTTTTATAAAAATTTAATAA
* * * * *
1396327 TTTATAATTTTTTACTATTTTATTTTTTTCTAATTTTTTTAAAATTTTAATAA
1 TTTATAATATTTTACTATTTTATTATTTTATAATTTTTATAAAAATTTAATAA
1396380 TT
1 TT
1396382 GAATTTTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
52 20 0.43
53 26 0.55
54 1 0.02
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (53 bp):
TTTATAATATTTTACTATTTTATTATTTTATAATTTTTATAAAAATTTAATAA
Found at i:1396635 original size:88 final size:89
Alignment explanation
Indices: 1396464--1396639 Score: 198
Period size: 88 Copynumber: 2.0 Consensus size: 89
1396454 AATAAAAACA
*
1396464 AGGGCTTAATTTCTTTTTTTTGAAAAAGTTTGAGAGTATTTTTAATGTATTTTAAAAGTTCAAGT
1 AGGGCTTAATTACTTTTTTTTGAAAAAGTTTGAGAGTATTTTTAATGTATTTTAAAAGTTCAAGT
* * **
1396529 ACTCAATTTAATGCAAAAAAAAGT
66 ACTCAAATGAATAAAAAAAAAAGT
* * * *
1396553 AGGGACTTAATTAC-TTTTTTTGAAAAGGTTTGAG-GCTCTTTTT-CTGTATTTTGAAAGTTCAA
1 AGGG-CTTAATTACTTTTTTTTGAAAAAGTTTGAGAG-TATTTTTAATGTATTTTAAAAGTTCAA
* *
1396615 GT-GTCCAAATGAGTAAAAAAAAAAG
64 GTACT-CAAATGAATAAAAAAAAAAG
1396640 CTTAATTGCT
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
87 1 0.01
88 35 0.48
89 29 0.40
90 8 0.11
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (89 bp):
AGGGCTTAATTACTTTTTTTTGAAAAAGTTTGAGAGTATTTTTAATGTATTTTAAAAGTTCAAGT
ACTCAAATGAATAAAAAAAAAAGT
Found at i:1425652 original size:20 final size:21
Alignment explanation
Indices: 1425602--1425652 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
1425592 TTTTATGGAA
1425602 ATTTT-TATGAATTTTCTAAT
1 ATTTTATATGAATTTTCTAAT
* *
1425622 ATTTTAAATGAATTTT-TATT
1 ATTTTATATGAATTTTCTAAT
*
1425642 TTTTTATATGA
1 ATTTTATATGA
1425653 GGCAGCATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (21 bp):
ATTTTATATGAATTTTCTAAT
Found at i:1435808 original size:18 final size:18
Alignment explanation
Indices: 1435777--1435826 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
1435767 ATTACATGCC
*
1435777 ATAATTTGATTTAAAATAT
1 ATAATTT-ATTTAAAATAA
*
1435796 TTAATTTATTTAAAATAA
1 ATAATTTATTTAAAATAA
*
1435814 ATATTTTATTTAA
1 ATAATTTATTTAA
1435827 TTAAAAATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 21 0.78
19 6 0.22
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
ATAATTTATTTAAAATAA
Found at i:1435818 original size:22 final size:22
Alignment explanation
Indices: 1435790--1435832 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1435780 ATTTGATTTA
*
1435790 AAATATTTAATTTATTTAAAAT
1 AAATATTTAATTTAATTAAAAT
*
1435812 AAATATTTTATTTAATTAAAA
1 AAATATTTAATTTAATTAAAA
1435833 ATGACACATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AAATATTTAATTTAATTAAAAT
Found at i:1439885 original size:22 final size:22
Alignment explanation
Indices: 1439846--1439887 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1439836 TAGGCTTTCT
**
1439846 TGAAACAATTCTACAACACACA
1 TGAAACAAAACTACAACACACA
*
1439868 TGAAACAAAACTAGAACACA
1 TGAAACAAAACTACAACACA
1439888 GGGACTGAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.24, G:0.07, T:0.14
Consensus pattern (22 bp):
TGAAACAAAACTACAACACACA
Found at i:1441975 original size:12 final size:12
Alignment explanation
Indices: 1441958--1441987 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
1441948 TGTTAATATC
1441958 TTTAACTTTATT
1 TTTAACTTTATT
1441970 TTTAACTTTATT
1 TTTAACTTTATT
1441982 TGTTAA
1 T-TTAA
1441988 ATTAGTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.27, C:0.07, G:0.03, T:0.63
Consensus pattern (12 bp):
TTTAACTTTATT
Found at i:1445850 original size:19 final size:19
Alignment explanation
Indices: 1445823--1445865 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1445813 ATATTTTCCG
1445823 TTTTCTCATTTATT-TAATAA
1 TTTTCTCATTT-TTCTAAT-A
1445843 TTTT-TCATTTTTCTAATA
1 TTTTCTCATTTTTCTAATA
1445861 TTTTC
1 TTTTC
1445866 AAAAAATATC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 7 0.33
19 10 0.48
20 4 0.19
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTCTCATTTTTCTAATA
Found at i:1451895 original size:25 final size:25
Alignment explanation
Indices: 1451861--1451913 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
1451851 GTGTATTGGT
1451861 AAATGACTTGCGATATATGAGGTTG
1 AAATGACTTGCGATATATGAGGTTG
1451886 AAATGACTTGCGATATATGAGGTTG
1 AAATGACTTGCGATATATGAGGTTG
1451911 AAA
1 AAA
1451914 CTAGATGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (25 bp):
AAATGACTTGCGATATATGAGGTTG
Found at i:1452583 original size:13 final size:13
Alignment explanation
Indices: 1452565--1452590 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1452555 CTATAAAAAT
1452565 GTGGACCGTTAAA
1 GTGGACCGTTAAA
1452578 GTGGACCGTTAAA
1 GTGGACCGTTAAA
1452591 ACAAATTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (13 bp):
GTGGACCGTTAAA
Found at i:1452852 original size:21 final size:21
Alignment explanation
Indices: 1452825--1452872 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1452815 AATTTTGAAC
* *
1452825 TTTAAATTTTG-AATCTCGAA
1 TTTAAAATTTGAAATCTCAAA
1452845 TTTAAAATTTGAAATCTCAAA
1 TTTAAAATTTGAAATCTCAAA
1452866 TTTAAAA
1 TTTAAAA
1452873 CTCTAAATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (21 bp):
TTTAAAATTTGAAATCTCAAA
Found at i:1452880 original size:21 final size:21
Alignment explanation
Indices: 1452836--1452880 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1452826 TTAAATTTTG
* *
1452836 AATCTCGAATTTAAAATTTGA
1 AATCTCAAATTTAAAATCTGA
1452857 AATCTCAAATTTAAAACTCT-A
1 AATCTCAAATTTAAAA-TCTGA
1452878 AAT
1 AAT
1452881 GATATTGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (21 bp):
AATCTCAAATTTAAAATCTGA
Found at i:1453035 original size:21 final size:21
Alignment explanation
Indices: 1453001--1453041 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1452991 AATAATTAAA
* *
1453001 AAAATTATAGATAATATAATG
1 AAAATTATACATAAAATAATG
*
1453022 AAAATTATCCATAAAATAAT
1 AAAATTATACATAAAATAAT
1453042 TTCTCATGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (21 bp):
AAAATTATACATAAAATAATG
Found at i:1468857 original size:19 final size:19
Alignment explanation
Indices: 1468833--1468870 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1468823 TTTTCATGTC
*
1468833 TGATTCTTTAACTAAGTTT
1 TGATTCCTTAACTAAGTTT
1468852 TGATTCCTTAACTAAGTTT
1 TGATTCCTTAACTAAGTTT
1468871 CAACCCGGAA
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:0.26, C:0.13, G:0.11, T:0.50
Consensus pattern (19 bp):
TGATTCCTTAACTAAGTTT
Found at i:1475616 original size:16 final size:16
Alignment explanation
Indices: 1475590--1475658 Score: 111
Period size: 16 Copynumber: 4.2 Consensus size: 16
1475580 TTTGGTTCGC
1475590 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
1475606 CGTATTAGATTAGAGG
1 TGTATTGGATTAGAGG
1475622 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
1475639 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
1475655 TGTA
1 TGTA
1475659 ATAGCTAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
16 33 0.69
17 15 0.31
ACGTcount: A:0.26, C:0.01, G:0.36, T:0.36
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:1475636 original size:33 final size:32
Alignment explanation
Indices: 1475590--1475658 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
1475580 TTTGGTTCGC
1475590 TGTATTGGATTAGAGGCGTATTAGATTAGAGG
1 TGTATTGGATTAGAGGCGTATTAGATTAGAGG
* *
1475622 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGCGTATTAGATTAGAGG
1475655 TGTA
1 TGTA
1475659 ATAGCTAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.26, C:0.01, G:0.36, T:0.36
Consensus pattern (32 bp):
TGTATTGGATTAGAGGCGTATTAGATTAGAGG
Found at i:1475723 original size:44 final size:45
Alignment explanation
Indices: 1475639--1475729 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
1475629 GGATTAGAGG
* * *
1475639 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
1475684 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
1475728 TG
1 TG
1475730 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:1475915 original size:18 final size:17
Alignment explanation
Indices: 1475894--1475928 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1475884 TTATTATTAA
*
1475894 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
1475912 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
1475929 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:1475995 original size:38 final size:38
Alignment explanation
Indices: 1475953--1476237 Score: 118
Period size: 38 Copynumber: 7.2 Consensus size: 38
1475943 ATTCTTATAT
1475953 TAAATTACTGAAATCATAATATATGATACTGTAAAATA
1 TAAATTACTGAAATCATAATATATGATACTGTAAAATA
* ** *
1475991 TAAATTAACAT-AATTATTATTAAATATATTTTAAT-TAAAATA
1 TAAATT-AC-TGAA--ATCA-T-AATATATGATACTGTAAAATA
* * * * * * *
1476033 TATAATTTAATGAAATTCTTAATA-ATTAATATTCTTATAT-
1 TA-AA-TTACTGAAA-TCATAATATA-TGATACTGTAAAATA
*
1476073 TAATTTACTGAAATCATAATATATGATACTGTAAAATA
1 TAAATTACTGAAATCATAATATATGATACTGTAAAATA
* ** *
1476111 TAAATTAACAT-AATTATTATTAAATATATTTTAAT-TAAAATA
1 TAAATT-AC-TGAA--ATCA-T-AATATATGATACTGTAAAATA
* * * * * * *
1476153 TATAATTTAATGAAATTCTTAATA-ATTAATATTCTTATAT-
1 TA-AA-TTACTGAAA-TCATAATATA-TGATACTGTAAAATA
*
1476193 TAATTTACTGAAATCATAATATATGATACTGTAAAATA
1 TAAATTACTGAAATCATAATATATGATACTGTAAAATA
1476231 TAAATTA
1 TAAATTA
1476238 ACATAATTAT
Statistics
Matches: 177, Mismatches: 42, Indels: 56
0.64 0.15 0.20
Matches are distributed among these distances:
37 32 0.18
38 35 0.20
39 12 0.07
40 22 0.12
41 18 0.10
42 24 0.14
43 30 0.17
44 4 0.02
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (38 bp):
TAAATTACTGAAATCATAATATATGATACTGTAAAATA
Found at i:1476090 original size:120 final size:120
Alignment explanation
Indices: 1475877--1476620 Score: 1353
Period size: 120 Copynumber: 6.2 Consensus size: 120
1475867 ATCATATTTA
*
1475877 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAAAAAAATTCTTAATAATTAA
* *
1475942 TATTCTTATATTAAATTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
**
1475997 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAAAAAAATTCTTAATAATTAA
*
1476062 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
**
1476117 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAAAAAAATTCTTAATAATTAA
*
1476182 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
1476237 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAAAAAAATTCTTAATAATTAA
1476302 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
1476357 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAAATTCTTAATAATTA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTT-AAAAAAATTCTTAATAATTA
*
1476422 ATGTTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
65 ATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* *
1476478 AACATAATTATTATTAAATGTATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAAAAAAATTCTTAATAATTAA
1476543 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
1476598 AACATAATTATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
1476621 AACTTGAAAA
Statistics
Matches: 613, Mismatches: 10, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
120 495 0.81
121 118 0.19
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAAAAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:1476479 original size:57 final size:57
Alignment explanation
Indices: 1475936--1476599 Score: 291
Period size: 59 Copynumber: 11.1 Consensus size: 57
1475926 AATTCTTAAT
*
1475936 AATTAATATTCTTATATTAAATTACTGAAATCATAATATATGATACTGTAAAATATA
1 AATTAATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATA
* ** * * ** * * * * * *
1475993 AATTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATG-AAATTCTTAA
1 AATTAATATTCTTA-TATT-AATTTACTGAAATCATAATATATGA--TACTGTAAAAT-AT-A
1476055 TAATTAATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATA
1 -AATTAATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATA
* ** * * ** * * * * * *
1476113 AATTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATG-AAATTCTTAA
1 AATTAATATTCTTA-TATT-AATTTACTGAAATCATAATATATGA--TACTGTAAAAT-AT-A
1476175 TAATTAATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATA
1 -AATTAATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATA
* ** * * ** * * * ** *
1476233 AATTAACATAATTATTATTAAATATATTTTAATTA-AACTATATAAT-TTAAAAAAATTCTTAA
1 AATTAATATTCTTA-TATT-AATTTACTGAAATCATAA-TATATGATACT-GTAAAA-T-AT-A
*
1476295 TAATTAATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATA
1 -AATTAATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATA
* ** * * ** * * *** *
1476353 AATTAACATAATTATTATTAAATATATTTTAATTA-AACTATATAATTTA-AAAAAAATTCTTAA
1 AATTAATATTCTTA-TATT-AATTTACTGAAATCATAA-TATATGA--TACTGTAAAA-T-AT-A
* *
1476416 TAATTAATGTTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATA
1 -AATTAATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATA
* ** * * ** * * * ** *
1476474 AATTAACATAATTATTATTAAATGTATTTTAATTA-AACTATATAAT-TTAAAAAAATTCTTAA
1 AATTAATATTCTTA-TATT-AATTTACTGAAATCATAA-TATATGATACT-GTAAAA-T-AT-A
*
1476536 TAATTAATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATA
1 -AATTAATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATA
1476594 AATTAA
1 AATTAA
1476600 CATAATTATT
Statistics
Matches: 427, Mismatches: 133, Indels: 94
0.65 0.20 0.14
Matches are distributed among these distances:
57 60 0.14
58 33 0.08
59 106 0.25
60 27 0.06
61 97 0.23
62 43 0.10
63 51 0.12
64 10 0.02
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (57 bp):
AATTAATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATA
Found at i:1479678 original size:33 final size:33
Alignment explanation
Indices: 1479639--1479714 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
1479629 ATTATAAAGC
*
1479639 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
1479672 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
1479705 ATGTATAATT
1 ATGTATAATT
1479715 CAAGTTTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTAT
Found at i:1479826 original size:37 final size:37
Alignment explanation
Indices: 1479749--1479830 Score: 119
Period size: 37 Copynumber: 2.2 Consensus size: 37
1479739 TTTGTTAAGT
* ***
1479749 ATTGATTAGTTCATTAAAGCATGTTCAAAGTTTTCGC
1 ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
*
1479786 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
1 ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
1479823 ATTGATTA
1 ATTGATTA
1479831 ATAAATATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (37 bp):
ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
Found at i:1488127 original size:31 final size:29
Alignment explanation
Indices: 1488054--1488141 Score: 72
Period size: 31 Copynumber: 3.0 Consensus size: 29
1488044 GCACTCTAAT
1488054 CTATTA-AAAAATGATAAAAATTTTATTTA
1 CTATTATAAAAATGAT-AAAATTTTATTTA
* * * *
1488083 CATCTTTTTAAAATGATAAAATTATATTTTTA
1 C-TATTATAAAAATGATAAAATT-T-TATTTA
* *
1488115 CTATTATAAAAAT-ATACAATTTAATTT
1 CTATTATAAAAATGATAAAATTTTATTT
1488142 CTACATTCAA
Statistics
Matches: 45, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
28 3 0.07
29 2 0.04
30 16 0.36
31 18 0.40
32 6 0.13
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (29 bp):
CTATTATAAAAATGATAAAATTTTATTTA
Found at i:1491950 original size:44 final size:45
Alignment explanation
Indices: 1491901--1491996 Score: 167
Period size: 44 Copynumber: 2.2 Consensus size: 45
1491891 ACCATCTATT
1491901 TTTTAAATATTTTCAAAGAAATAAGTTTAAAATTTATGATTTAG-
1 TTTTAAATATTTTCAAAGAAATAAGTTTAAAATTTATGATTTAGA
* *
1491945 TTTTAAATTTTTTCAAAGAAATAAGTTTAAAATTTATGGTTTAGA
1 TTTTAAATATTTTCAAAGAAATAAGTTTAAAATTTATGATTTAGA
1491990 TTTTAAA
1 TTTTAAA
1491997 ATGTAGAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 42 0.86
45 7 0.14
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (45 bp):
TTTTAAATATTTTCAAAGAAATAAGTTTAAAATTTATGATTTAGA
Found at i:1498644 original size:56 final size:58
Alignment explanation
Indices: 1498538--1498650 Score: 144
Period size: 56 Copynumber: 2.0 Consensus size: 58
1498528 ATTAAATATT
*
1498538 AAAATTTTATTAAAAATTAGAAAAAAATATAAAAATCTTAAAAAATATAAAATTTTAC
1 AAAATTTTATTAAAAATTAGAAAAAAATATAAAAATCATAAAAAATATAAAATTTTAC
* * *
1498596 AAAATTTTA-TAAAAA-TAGTAAAAAAATGT-AAAAT-ATATAGAAATATAAACTTTTA
1 AAAATTTTATTAAAAATTAG-AAAAAAATATAAAAATCATA-AAAAATATAAAATTTTA
1498651 TAAAGTCGTA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
55 2 0.04
56 23 0.47
57 15 0.31
58 9 0.18
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.33
Consensus pattern (58 bp):
AAAATTTTATTAAAAATTAGAAAAAAATATAAAAATCATAAAAAATATAAAATTTTAC
Found at i:1498709 original size:44 final size:43
Alignment explanation
Indices: 1498597--1498710 Score: 129
Period size: 44 Copynumber: 2.6 Consensus size: 43
1498587 AAATTTTACA
* *
1498597 AAATTTTATAAAAATAGTAAAAAAATGTAAAATATATAGAAATAT
1 AAATTTTATAAAAA-AGT-AAAAAATATAAAATATAAAGAAATAT
*** *
1498642 AAACTTTTATAAAGTCGTAAAAAATATAAAATGTAAAGAAATAT
1 AAA-TTTTATAAAAAAGTAAAAAATATAAAATATAAAGAAATAT
*
1498686 AAATTTTATAAAAAATTATAAAAAT
1 AAATTTTATAAAAAAGTA-AAAAAT
1498711 TATTGTATCA
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
43 11 0.19
44 32 0.56
45 5 0.09
46 9 0.16
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.32
Consensus pattern (43 bp):
AAATTTTATAAAAAAGTAAAAAATATAAAATATAAAGAAATAT
Found at i:1499285 original size:3 final size:3
Alignment explanation
Indices: 1499277--1499305 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1499267 TAATTGCTTT
1499277 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1499306 TTAAGTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:1516334 original size:1 final size:1
Alignment explanation
Indices: 1516328--1516354 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1516318 CCACAAAAGC
1516328 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1516355 GAGTTGAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1522659 original size:17 final size:18
Alignment explanation
Indices: 1522625--1522670 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
1522615 CCGTTATGTC
1522625 CGCGACCGCGA-C--AAA
1 CGCGACCGCGACCGAAAA
1522640 CGCGA-CGCGACCGAAAA
1 CGCGACCGCGACCGAAAA
1522657 CGCGACCGCGACCG
1 CGCGACCGCGACCG
1522671 CAATTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
17 8 0.30
18 8 0.30
ACGTcount: A:0.28, C:0.41, G:0.30, T:0.00
Consensus pattern (18 bp):
CGCGACCGCGACCGAAAA
Found at i:1540347 original size:23 final size:22
Alignment explanation
Indices: 1540317--1540359 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1540307 TTAAAAAAAA
*
1540317 AAAGGAAAAAAAAAGCGAAATT
1 AAAGGAAAAAAAAAGAGAAATT
*
1540339 AAAGAGAAAAAAGAAGAGAAA
1 AAAG-GAAAAAAAAAGAGAAA
1540360 AATTCATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.72, C:0.02, G:0.21, T:0.05
Consensus pattern (22 bp):
AAAGGAAAAAAAAAGAGAAATT
Found at i:1543522 original size:5 final size:5
Alignment explanation
Indices: 1543512--1543539 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1543502 TTATACACTC
1543512 TCAAA TCAAA TCAAA TCAAA TCAAA TCA
1 TCAAA TCAAA TCAAA TCAAA TCAAA TCA
1543540 TACACTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.21, G:0.00, T:0.21
Consensus pattern (5 bp):
TCAAA
Found at i:1547942 original size:11 final size:11
Alignment explanation
Indices: 1547926--1547951 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1547916 CTCTGTAAAC
1547926 AAAAAAAACAA
1 AAAAAAAACAA
1547937 AAAAAAAACAA
1 AAAAAAAACAA
1547948 AAAA
1 AAAA
1547952 TGTCAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:1553714 original size:31 final size:31
Alignment explanation
Indices: 1553676--1553734 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
1553666 AGGAAACCAA
*
1553676 TTTCCAGTAAGGTTACAACTAAATGTATATT
1 TTTCCAGTAAGCTTACAACTAAATGTATATT
1553707 TTTCCAGTAAGCTTACAACTAAATGTAT
1 TTTCCAGTAAGCTTACAACTAAATGTAT
1553735 GTTTGGAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (31 bp):
TTTCCAGTAAGCTTACAACTAAATGTATATT
Found at i:1556737 original size:6 final size:6
Alignment explanation
Indices: 1556704--1556739 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
1556694 CAAATTTATC
* *
1556704 CGCCGA CGCAGA CGCAGA CGCCGA CGCCGA CGCCGA
1 CGCCGA CGCCGA CGCCGA CGCCGA CGCCGA CGCCGA
1556740 TTCATTCGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.22, C:0.44, G:0.33, T:0.00
Consensus pattern (6 bp):
CGCCGA
Found at i:1560867 original size:47 final size:47
Alignment explanation
Indices: 1560798--1560894 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
1560788 AAAGATTGCA
1560798 TTTAAATGAAGAGAGGCGTTTTCGTTGTTCAATTGGAAAACGTAACC
1 TTTAAATGAAGAGAGGCGTTTTCGTTGTTCAATTGGAAAACGTAACC
1560845 TTTAAATGAAGAGAGGCGTTTTCGTTGTTCAATTGGAAAACGTAACC
1 TTTAAATGAAGAGAGGCGTTTTCGTTGTTCAATTGGAAAACGTAACC
1560892 TTT
1 TTT
1560895 TAGGAAAGGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.34
Consensus pattern (47 bp):
TTTAAATGAAGAGAGGCGTTTTCGTTGTTCAATTGGAAAACGTAACC
Found at i:1561203 original size:17 final size:17
Alignment explanation
Indices: 1561174--1561222 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
1561164 TCACTATAAA
*
1561174 ATATAATAAATAAAATT
1 ATATAAAAAATAAAATT
* *
1561191 AT-TCTAAAAATAATATT
1 ATAT-AAAAAATAAAATT
1561208 ATATAAAAAATAAAA
1 ATATAAAAAATAAAA
1561223 ATACTTTCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
16 1 0.04
17 23 0.92
18 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAAAAAATAAAATT
Found at i:1561219 original size:34 final size:34
Alignment explanation
Indices: 1561174--1561239 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
1561164 TCACTATAAA
* *
1561174 ATATAATAAATAAAATTA-TTCTAAAAATAATATT
1 ATATAAAAAATAAAAATACTT-TAAAAATAATATT
*
1561208 ATATAAAAAATAAAAATACTTTCAAAATAATA
1 ATATAAAAAATAAAAATACTTTAAAAATAATA
1561240 CTTTTCGTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (34 bp):
ATATAAAAAATAAAAATACTTTAAAAATAATATT
Found at i:1563572 original size:13 final size:14
Alignment explanation
Indices: 1563556--1563597 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
1563546 TTTTAATTTT
1563556 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
1563569 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
1563584 ATTTTAAATAATAT
1 ATTTT-AATAATAT
1563598 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:1563582 original size:16 final size:16
Alignment explanation
Indices: 1563560--1563596 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1563550 AATTTTATTT
1563560 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
1563577 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
1563592 TAATA
1 TAATA
1563597 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:1564158 original size:14 final size:14
Alignment explanation
Indices: 1564136--1564174 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1564126 CCAGAAAAGT
*
1564136 AAATAATTTTCCAA
1 AAATCATTTTCCAA
* *
1564150 AAATCATTTTTCGA
1 AAATCATTTTCCAA
1564164 AAATCATTTTC
1 AAATCATTTTC
1564175 GGTGAAACAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (14 bp):
AAATCATTTTCCAA
Found at i:1567917 original size:16 final size:15
Alignment explanation
Indices: 1567883--1567919 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 15
1567873 AATTGGTTTA
1567883 AATATATTATAAAATT
1 AATA-ATTATAAAATT
1567899 AATAATTATAAAATAT
1 AATAATTATAAAAT-T
1567915 AATAA
1 AATAA
1567920 ATTGAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATAATTATAAAATT
Found at i:1569781 original size:18 final size:18
Alignment explanation
Indices: 1569758--1569793 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1569748 TACTAAATCA
*
1569758 TCCACTACCTCCATCACC
1 TCCACTAACTCCATCACC
1569776 TCCACTAACTCCATCACC
1 TCCACTAACTCCATCACC
1569794 ATACTTGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.53, G:0.00, T:0.22
Consensus pattern (18 bp):
TCCACTAACTCCATCACC
Found at i:1570196 original size:11 final size:11
Alignment explanation
Indices: 1570171--1570209 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
1570161 GAGTTATGTT
1570171 TTATATTATTATA
1 TTAT-TTATT-TA
1570184 TTATTTATTTA
1 TTATTTATTTA
*
1570195 TTATATATTTA
1 TTATTTATTTA
1570206 TTAT
1 TTAT
1570210 GTAAATAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 16 0.64
12 5 0.20
13 4 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:1570548 original size:13 final size:12
Alignment explanation
Indices: 1570527--1570576 Score: 57
Period size: 13 Copynumber: 4.1 Consensus size: 12
1570517 ATTACTGTTG
1570527 TTTTATTAATTA
1 TTTTATTAATTA
1570539 TTTCTATTAATTA
1 TTT-TATTAATTA
*
1570552 CTATTATT-ATTA
1 -TTTTATTAATTA
*
1570564 TTTTATTATTTA
1 TTTTATTAATTA
1570576 T
1 T
1570577 ATATGGTTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
11 6 0.19
12 11 0.34
13 13 0.41
14 2 0.06
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTTATTAATTA
Found at i:1570911 original size:126 final size:126
Alignment explanation
Indices: 1570676--1570919 Score: 452
Period size: 126 Copynumber: 1.9 Consensus size: 126
1570666 CATTGATCTT
* *
1570676 CTCTCAAAATTTTTCAAAATAAAGGCAATGTTCGGTATTTAAAGAATTCGAAGAATCGTGCCCTA
1 CTCTAAAAAATTTTCAAAATAAAGGCAATGTTCGGTATTTAAAGAATTCGAAGAATCGTGCCCTA
*
1570741 ACGTACTGGGTTTCGCTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTACCAGTTCA
66 ACGTACTGGGTTTCACTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTACCAGTTCA
1570802 CTCTAAAAAATTTTCAAAATAAAGGCAATGTTCGGTATTTAAAGAATTCGAAGAATCGTGCCCTA
1 CTCTAAAAAATTTTCAAAATAAAGGCAATGTTCGGTATTTAAAGAATTCGAAGAATCGTGCCCTA
*
1570867 ACGTACTGGGTTTCACTTTCTTTGTTTGTTTTGAATATTCGAATATCCTCTTA
66 ACGTACTGGGTTTCACTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTA
1570920 AGGCTAAAAC
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 114 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (126 bp):
CTCTAAAAAATTTTCAAAATAAAGGCAATGTTCGGTATTTAAAGAATTCGAAGAATCGTGCCCTA
ACGTACTGGGTTTCACTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTACCAGTTCA
Found at i:1572751 original size:21 final size:22
Alignment explanation
Indices: 1572716--1572756 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
1572706 TTAACAATTT
1572716 AATAATTTAAATAATTTTTTTG
1 AATAATTTAAATAATTTTTTTG
1572738 AATAATTT-AATAATTTTTT
1 AATAATTTAAATAATTTTTT
1572757 AAAATTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
AATAATTTAAATAATTTTTTTG
Found at i:1572762 original size:18 final size:20
Alignment explanation
Indices: 1572713--1572766 Score: 76
Period size: 18 Copynumber: 2.7 Consensus size: 20
1572703 GTTTTAACAA
1572713 TTTAATAATTTAAATAATTTT
1 TTTAATAATTT-AATAATTTT
1572734 TTTGAATAATTTAATAA-TTT
1 TTT-AATAATTTAATAATTTT
1572754 TTTAA-AATTTAAT
1 TTTAATAATTTAAT
1572767 GATTAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.25
19 2 0.06
20 6 0.19
21 8 0.25
22 8 0.25
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTAATAATTTAATAATTTT
Found at i:1578625 original size:20 final size:20
Alignment explanation
Indices: 1578600--1578659 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
1578590 ACAAACGAAC
1578600 TTGAATGAATAACCTGAATT
1 TTGAATGAATAACCTGAATT
* *
1578620 TTGAATGGAT-A--T--A-C
1 TTGAATGAATAACCTGAATT
1578634 TTGAATGAATAACCTGAATT
1 TTGAATGAATAACCTGAATT
1578654 TTGAAT
1 TTGAAT
1578660 AGATATACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
14 9 0.30
15 2 0.07
17 2 0.07
19 2 0.07
20 15 0.50
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (20 bp):
TTGAATGAATAACCTGAATT
Found at i:1578636 original size:34 final size:34
Alignment explanation
Indices: 1578598--1578669 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
1578588 GAACAAACGA
*
1578598 ACTTGAATGAATAACCTGAATTTTGAATGGATAT
1 ACTTGAATGAATAACCTGAATTTTGAATAGATAT
1578632 ACTTGAATGAATAACCTGAATTTTGAATAGATAT
1 ACTTGAATGAATAACCTGAATTTTGAATAGATAT
1578666 ACTT
1 ACTT
1578670 TTTATCCGTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (34 bp):
ACTTGAATGAATAACCTGAATTTTGAATAGATAT
Found at i:1581236 original size:17 final size:17
Alignment explanation
Indices: 1581202--1581235 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1581192 AACAAGTTTG
1581202 ATTAAAAAATCATTAAA
1 ATTAAAAAATCATTAAA
1581219 ATTAAAAAAT-ATTAAA
1 ATTAAAAAATCATTAAA
1581235 A
1 A
1581236 AACCCAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
ATTAAAAAATCATTAAA
Found at i:1588423 original size:24 final size:24
Alignment explanation
Indices: 1588366--1588424 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
1588356 AGGAGTAGAA
1588366 GATGCTCCAAAAGCAGGACTGCTT
1 GATGCTCCAAAAGCAGGACTGCTT
* **
1588390 GAAG-TGCCAAAAGCAGGTGTGCTT
1 GATGCT-CCAAAAGCAGGACTGCTT
1588414 GATGCTCCAAA
1 GATGCTCCAAA
1588425 TGTGCCTCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 1 0.03
24 27 0.93
25 1 0.03
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (24 bp):
GATGCTCCAAAAGCAGGACTGCTT
Found at i:1588538 original size:24 final size:24
Alignment explanation
Indices: 1588504--1588597 Score: 134
Period size: 24 Copynumber: 3.9 Consensus size: 24
1588494 ACTTCCAGTT
* *
1588504 GAACCAAAGGCCGGAGTGCTGGTA
1 GAACCAAAGGCAGGAGTGCTTGTA
* * *
1588528 GCACCAAAGGCAGGGGTGCTTGTG
1 GAACCAAAGGCAGGAGTGCTTGTA
*
1588552 GAACCAAAGGCAGGAGTGCTTGTG
1 GAACCAAAGGCAGGAGTGCTTGTA
1588576 GAACCAAAGGCAGGAGTGCTTG
1 GAACCAAAGGCAGGAGTGCTTG
1588598 AGGCACCAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.28, C:0.19, G:0.38, T:0.15
Consensus pattern (24 bp):
GAACCAAAGGCAGGAGTGCTTGTA
Found at i:1588582 original size:48 final size:48
Alignment explanation
Indices: 1588504--1588608 Score: 147
Period size: 48 Copynumber: 2.2 Consensus size: 48
1588494 ACTTCCAGTT
* * * *
1588504 GAACCAAAGGCCGGAGTGCTGGTAGCACCAAAGGCAGGGGTGCTTGTG
1 GAACCAAAGGCAGGAGTGCTGGTAGAACCAAAGGCAGGAGTGCTTGAG
* *
1588552 GAACCAAAGGCAGGAGTGCTTGTGGAACCAAAGGCAGGAGTGCTTGAG
1 GAACCAAAGGCAGGAGTGCTGGTAGAACCAAAGGCAGGAGTGCTTGAG
*
1588600 GCACCAAAG
1 GAACCAAAG
1588609 CTACCAAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.30, C:0.20, G:0.37, T:0.13
Consensus pattern (48 bp):
GAACCAAAGGCAGGAGTGCTGGTAGAACCAAAGGCAGGAGTGCTTGAG
Found at i:1588605 original size:24 final size:24
Alignment explanation
Indices: 1588504--1588608 Score: 131
Period size: 24 Copynumber: 4.4 Consensus size: 24
1588494 ACTTCCAGTT
* *
1588504 GAACCAAAGGCCGGAGTGCTGGTA-
1 GAACCAAAGGCAGGAGTGCTTG-AG
* * *
1588528 GCACCAAAGGCAGGGGTGCTTGTG
1 GAACCAAAGGCAGGAGTGCTTGAG
*
1588552 GAACCAAAGGCAGGAGTGCTTGTG
1 GAACCAAAGGCAGGAGTGCTTGAG
1588576 GAACCAAAGGCAGGAGTGCTTGAG
1 GAACCAAAGGCAGGAGTGCTTGAG
*
1588600 GCACCAAAG
1 GAACCAAAG
1588609 CTACCAAATG
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
24 71 1.00
ACGTcount: A:0.30, C:0.20, G:0.37, T:0.13
Consensus pattern (24 bp):
GAACCAAAGGCAGGAGTGCTTGAG
Found at i:1588708 original size:24 final size:24
Alignment explanation
Indices: 1588675--1588739 Score: 112
Period size: 24 Copynumber: 2.7 Consensus size: 24
1588665 TGAAGATGCT
*
1588675 CCAAAAGCAGGAGTGCTCGAACCC
1 CCAAATGCAGGAGTGCTCGAACCC
*
1588699 CCAAATGCAGGAGTGCTTGAACCC
1 CCAAATGCAGGAGTGCTCGAACCC
1588723 CCAAATGCAGGAGTGCT
1 CCAAATGCAGGAGTGCT
1588740 GGAAGTGCCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.31, C:0.29, G:0.26, T:0.14
Consensus pattern (24 bp):
CCAAATGCAGGAGTGCTCGAACCC
Found at i:1588750 original size:24 final size:24
Alignment explanation
Indices: 1588675--1588763 Score: 106
Period size: 24 Copynumber: 3.7 Consensus size: 24
1588665 TGAAGATGCT
1588675 CCAAAAGCAGGAGTGCTCGAACCC
1 CCAAAAGCAGGAGTGCTCGAACCC
* *
1588699 CCAAATGCAGGAGTGCTTGAACCC
1 CCAAAAGCAGGAGTGCTCGAACCC
* * ***
1588723 CCAAATGCAGGAGTGCTGGAAGTG
1 CCAAAAGCAGGAGTGCTCGAACCC
*
1588747 CCAAAAGCAGGTGTGCT
1 CCAAAAGCAGGAGTGCT
1588764 TGATGCTCCA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.30, C:0.26, G:0.29, T:0.15
Consensus pattern (24 bp):
CCAAAAGCAGGAGTGCTCGAACCC
Done.