Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 4 of 433
Found at i:1069187 original size:2 final size:2
Alignment explanation
Indices: 1069180--1069224 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1069170 GCTTTTATCT
1069180 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
1069222 TA T
1 TA T
1069225 CACTTGTTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1070961 original size:211 final size:209
Alignment explanation
Indices: 1070560--1070970 Score: 529
Period size: 211 Copynumber: 1.9 Consensus size: 209
1070550 ATTTTCTAAG
* * ** *
1070560 AAGCTTTATGTTGCTCGAGTTCTTCATTTTTCTTGAAGTACTCGTATCCAACACAGATATAAAAG
1 AAGCATTATATTGCTCGAACTCTTCATTTTTCTTGAAGTACCCGTATCCAACACAGATAT-AAAG
* * * *
1070625 GACATGACCTCCAAGGTTCTCTAAATACAGGAAAAAAAACTTTGAAAAGTCTAGCTATACCCATG
65 GACATAACCTCCAAGGATCTCTAAATACA-GAAAAAAAACTTAGAAAAGTCTAACTATACCCATG
* * * * *
1070690 TCAGATATAGAACTATGCCCGAAAAAAACGAATCCGAGTAACAGAGCCTAAAGTCTATAGTACAG
129 TCAGATATAGAACTACGCCCGAAAAAAACAAATCCGAATAACAGAGCCTAAAGCCTATAGTAAAG
1070755 GGACTAATTTGCTCCT
194 GGACTAATTTGCTCCT
* **
1070771 AAGCATTATATTGCTCGAACTCTTCATTTTTCTTGAAGTACCCGTTTCTGACACATGGATAT-AA
1 AAGCATTATATTGCTCGAACTCTTCATTTTTCTTGAAGTACCCGTATCCAACACA--GATATAAA
* * *
1070835 GGATATAACCTCCAAGGATCTCTAAATACA-AGAAAAAACTTAGAAAAGTCTAACTATACCCGTG
64 GGACATAACCTCCAAGGATCTCTAAATACAGAAAAAAAACTTAGAAAAGTCTAACTATACCCATG
** * * *
1070899 TCAGATATTTAACTACGCCCGGCAAAAAACAAATCCAGAATAACATAGCTTAAAGCCTATAGTAA
129 TCAGATATAGAACTACGCCC-GAAAAAAACAAATCC-GAATAACAGAGCCTAAAGCCTATAGTAA
1070964 AGGGACT
192 AGGGACT
1070971 GCCAGTAATT
Statistics
Matches: 171, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
209 47 0.27
210 13 0.08
211 106 0.62
213 5 0.03
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (209 bp):
AAGCATTATATTGCTCGAACTCTTCATTTTTCTTGAAGTACCCGTATCCAACACAGATATAAAGG
ACATAACCTCCAAGGATCTCTAAATACAGAAAAAAAACTTAGAAAAGTCTAACTATACCCATGTC
AGATATAGAACTACGCCCGAAAAAAACAAATCCGAATAACAGAGCCTAAAGCCTATAGTAAAGGG
ACTAATTTGCTCCT
Found at i:1072945 original size:123 final size:122
Alignment explanation
Indices: 1072662--1073026 Score: 414
Period size: 124 Copynumber: 3.0 Consensus size: 122
1072652 TACAAATATA
* * * ** *
1072662 TATAGTATTTACAGCATTTAGGTGCAAGCAATCTCATATTCTATCAATTGAAAGGCAAATCATAC
1 TATAGTATTTACAGCATTTAGATGCAA-AAAACTCATATTCTATCAATTCTAAGGCAAATCATAA
* * *
1072727 ATAAGCAACTATGGGTCAACTAATTATTCATTGACATAACTGCAGTGTATACAT-ATACG
65 ATAAGCAACTATGGGTCAACTTATCATTCATTGACATAACTGCA--ATATACATAATACG
* * *
1072786 TCTAGTATTTACAGCATGTAGATGCAAAAAACCTCATATTTTATCAATTCTAAGGCAAATCATAA
1 TATAGTATTTACAGCATTTAGATGCAAAAAA-CTCATATTCTATCAATTCTAAGGCAAATCATAA
* * * * *
1072851 ATCAGCAACTA-GGGTCAACTTGTCATTCATTGGCATAACAGCAACATACATACATACAG
65 ATAAGCAACTATGGGTCAACTTATCATTCATTGACATAACTGCAATATACATA-ATAC-G
* * * **
1072910 -ATAGTATTTGCAGTATTTAGATGCAATAAAACTCATATTCTATCAATTCTGAGGCAAAAAATAA
1 TATAGTATTTACAGCATTTAGATGCAA-AAAACTCATATTCTATCAATTCTAAGGCAAATCATAA
* *
1072974 ATAAGCATCTATGGGTCAA-TTAATCATTCAGTGACATAACTGCAATATACATA
65 ATAAGCAACTATGGGTCAACTT-ATCATTCATTGACATAACTGCAATATACATA
1073027 TACATGCATA
Statistics
Matches: 202, Mismatches: 32, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
121 6 0.03
123 95 0.47
124 101 0.50
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.30
Consensus pattern (122 bp):
TATAGTATTTACAGCATTTAGATGCAAAAAACTCATATTCTATCAATTCTAAGGCAAATCATAAA
TAAGCAACTATGGGTCAACTTATCATTCATTGACATAACTGCAATATACATAATACG
Found at i:1073097 original size:154 final size:151
Alignment explanation
Indices: 1072894--1073461 Score: 501
Period size: 154 Copynumber: 3.6 Consensus size: 151
1072884 CATAACAGCA
* * * *
1072894 ACATACATACATACAGATAGTATTTGCAGTATTTAGATGCAATAAAACTCATATTCTATCAATTC
1 ACATACATACATACATATAGTATTTACAGCATTTAGATGCAA-GAAACTCATATTCTATCAATTC
* * * * * * *
1072959 TGAGGCAAAAAATAAATAAGCATCTATGGGTCAATTAATCATTCAGTGACATAACTGCAATATAC
65 TAAGGCAAATAATAAAAAACCAACTATGGGTCAAATAATCATTCATTGACATAACTGCAATATAC
1073024 ATATACATGCATACATATCTACAT
130 ATATACAT-CATACATA-CTACAT
* * * * *
1073048 ATC-TACATCCATACATATAGTATTTACAGCATTTATATGCGAGAGAACTCATATTCTGTCAGTT
1 A-CATACATACATACATATAGTATTTACAGCATTTAGATGCAAGA-AACTCATATTCTATCAATT
* * ** * *
1073112 CTAAGGCAAATCATAAAAAACCAACTATGGGTCAACTGGTCATTCATTAACATAATTGCAATATA
64 CTAAGGCAAATAATAAAAAACCAACTATGGGTCAAATAATCATTCATTGACATAACTGCAATATA
*
1073177 CATATAC-T-ATAC--A-TGCAT
129 CATATACATCATACATACTACAT
1073195 ACATAC--ACAT--ATATAGTATTTACAGCATTTAGATGCAAGAAATCTCATATTCTATCAATTC
1 ACATACATACATACATATAGTATTTACAGCATTTAGATGCAAGAAA-CTCATATTCTATCAATTC
* * * * *
1073256 TAAGGCATATTATAAAGAAACCAACTATGGGTCAAATAATAATTGATTGACATAACCTACATACA
65 TAAGGCAAATAATAAA-AAACCAACTATGGGTCAAATAATCATTCATTGACATAA-CTGC--A-A
1073321 TACATACATACATACATACATACATACATACAT
125 T--ATACAT--ATACAT-CATACATAC-TACAT
* * *
1073354 ACATACATACATACATATA-TATATACGGTATCCAAAGTATTTAGATGCAATAAAACTCATATTT
1 ACATACATACATACATATAGTAT-T----TA--C--AGCATTTAGATGCAA-GAAACTCATATTC
* * *
1073418 TATCAATTCTAAGGCTAATTATTGAAAAACCAACTATGGGTCAA
56 TATCAATTCTAAGGC-AAATAATAAAAAACCAACTATGGGTCAA
1073462 GTAACCAGCA
Statistics
Matches: 333, Mismatches: 46, Indels: 53
0.77 0.11 0.12
Matches are distributed among these distances:
142 2 0.01
143 58 0.17
144 32 0.10
145 5 0.02
146 1 0.00
147 9 0.03
148 2 0.01
149 1 0.00
150 6 0.02
151 4 0.01
152 4 0.01
153 3 0.01
154 111 0.33
155 5 0.02
157 1 0.00
159 10 0.03
161 4 0.01
162 3 0.01
163 6 0.02
167 2 0.01
169 1 0.00
171 55 0.17
172 8 0.02
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.31
Consensus pattern (151 bp):
ACATACATACATACATATAGTATTTACAGCATTTAGATGCAAGAAACTCATATTCTATCAATTCT
AAGGCAAATAATAAAAAACCAACTATGGGTCAAATAATCATTCATTGACATAACTGCAATATACA
TATACATCATACATACTACAT
Found at i:1073320 original size:4 final size:4
Alignment explanation
Indices: 1073313--1073370 Score: 116
Period size: 4 Copynumber: 14.5 Consensus size: 4
1073303 TGACATAACC
1073313 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1073361 TACA TACA TA
1 TACA TACA TA
1073371 TATATATACG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:1073332 original size:143 final size:142
Alignment explanation
Indices: 1073062--1073344 Score: 356
Period size: 143 Copynumber: 2.0 Consensus size: 142
1073052 ACATCCATAC
* * * *
1073062 ATATAGTATTTACAGCATTTATATGCGAGAGAACTCATATTCTGTCAGTTCTAAGGCAAATCATA
1 ATATAGTATTTACAGCATTTAGATGCAAGAGAACTCATATTCTATCAATTCTAAGGCAAATCATA
* ** * * * * *
1073127 AAAAACCAACTATGGGTCAACTGGTCATTCATTAACATAATTGCAATATACATATACTATACATG
66 AAAAACCAACTATGGGTCAAATAATAATTCATTAACATAACTACAACATACA-ATACTATACATA
1073192 CATACATACACAT
130 CATACATACACAT
* *
1073205 ATATAGTATTTACAGCATTTAGATGCAAGA-AATCTCATATTCTATCAATTCTAAGGCATATTAT
1 ATATAGTATTTACAGCATTTAGATGCAAGAGAA-CTCATATTCTATCAATTCTAAGGCAAATCAT
* *
1073269 AAAGAAACCAACTATGGGTCAAATAATAATTGATTGACATAACCTACATACATAC-ATAC-ATAC
65 AAA-AAACCAACTATGGGTCAAATAATAATTCATTAACATAA-CTACA-ACATACAATACTATAC
1073332 ATACATACATACA
127 ATACATACATACA
1073345 TACATACATA
Statistics
Matches: 120, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
142 2 0.02
143 74 0.62
144 36 0.30
145 3 0.03
146 5 0.04
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (142 bp):
ATATAGTATTTACAGCATTTAGATGCAAGAGAACTCATATTCTATCAATTCTAAGGCAAATCATA
AAAAACCAACTATGGGTCAAATAATAATTCATTAACATAACTACAACATACAATACTATACATAC
ATACATACACAT
Found at i:1074507 original size:18 final size:20
Alignment explanation
Indices: 1074471--1074507 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1074461 TAAAATTTTA
*
1074471 TATATTATATACATTTATTG
1 TATATTATATACATATATTG
1074491 TATATTATA-A-ATATATT
1 TATATTATATACATATATT
1074508 TTAAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 6 0.38
19 1 0.06
20 9 0.56
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (20 bp):
TATATTATATACATATATTG
Found at i:1078128 original size:16 final size:16
Alignment explanation
Indices: 1078109--1078142 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1078099 AAAATACAAA
1078109 TTTTTAAAATTTTAAT
1 TTTTTAAAATTTTAAT
**
1078125 TTTTTTTAATTTTAAT
1 TTTTTAAAATTTTAAT
1078141 TT
1 TT
1078143 ACTCATTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTAAAATTTTAAT
Found at i:1078621 original size:10 final size:11
Alignment explanation
Indices: 1078591--1078647 Score: 53
Period size: 11 Copynumber: 4.9 Consensus size: 11
1078581 TTTCATGTTT
*
1078591 AATATTTTTTA
1 AATATATTTTA
1078602 AAT-TATTTTA
1 AATATATTTTA
1078612 AATATATTTATA
1 AATATATTT-TA
*
1078624 TATAATATGTATTA
1 AAT-ATAT-T-TTA
1078638 AATATATTTT
1 AATATATTTT
1078648 CATTTTCATT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
10 9 0.24
11 10 0.26
12 5 0.13
13 8 0.21
14 5 0.13
15 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (11 bp):
AATATATTTTA
Found at i:1081891 original size:18 final size:18
Alignment explanation
Indices: 1081857--1081892 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1081847 CAATTGAACC
**
1081857 GAAATTTTAATTTTTTAT
1 GAAATTTTAATAATTTAT
1081875 GAAATTTTAATAATTTAT
1 GAAATTTTAATAATTTAT
1081893 TTAATCGAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
GAAATTTTAATAATTTAT
Found at i:1084276 original size:20 final size:20
Alignment explanation
Indices: 1084251--1084292 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1084241 ATTTTTTAAA
*
1084251 TTTTC-TAGTATTTTATTTCT
1 TTTTCTTAGTAATTT-TTTCT
1084271 TTTTCTTAGTAATTTTTTCT
1 TTTTCTTAGTAATTTTTTCT
1084291 TT
1 TT
1084293 ATTTTTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.14, C:0.10, G:0.05, T:0.71
Consensus pattern (20 bp):
TTTTCTTAGTAATTTTTTCT
Found at i:1093742 original size:2 final size:2
Alignment explanation
Indices: 1093735--1093766 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1093725 TAGATTTTGT
1093735 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
1093767 AAGAATTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1095544 original size:2 final size:2
Alignment explanation
Indices: 1095537--1095568 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1095527 TTCCCTTCCC
1095537 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1095569 GGTAAATTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1098671 original size:16 final size:16
Alignment explanation
Indices: 1098637--1098671 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1098627 AAATTTCTCG
*
1098637 AATCCAAAATTATTCA
1 AATCCAAAATGATTCA
*
1098653 AATCCAAAATGATTTA
1 AATCCAAAATGATTCA
1098669 AAT
1 AAT
1098672 TTATCTATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.31
Consensus pattern (16 bp):
AATCCAAAATGATTCA
Found at i:1103072 original size:83 final size:84
Alignment explanation
Indices: 1102902--1103107 Score: 270
Period size: 83 Copynumber: 2.5 Consensus size: 84
1102892 TGTAACAGTT
* * * * * *
1102902 AAATTAGCTGTCTTTAAGATGTTTGATAAAATGTTTGTGTTGGGCCAAATCGAGTTGTAGAAGAA
1 AAATTAGTTGTCTTTCAGATGTTTGATAATATGTTTGTGTTAGACCAAATCAAGTTGTAGAAGAA
* * *
1102967 ATATTAGTGACCCAAAGTC
66 AAATTAATGACCCAAAGAC
* * * * *
1102986 AAATTAGTTGCCTTTCAGATGTTTGATAATATG-TTGTGTTAGACTAATTCAAGTTTTAGCAGAA
1 AAATTAGTTGTCTTTCAGATGTTTGATAATATGTTTGTGTTAGACCAAATCAAGTTGTAGAAGAA
1103050 AAATTAATGACCCAAAGAC
66 AAATTAATGACCCAAAGAC
*
1103069 AAATTAGTTGTCTTTCAGATGTTTGATAATATCTTTGTG
1 AAATTAGTTGTCTTTCAGATGTTTGATAATATGTTTGTG
1103108 CGGATAAATA
Statistics
Matches: 105, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
83 71 0.68
84 34 0.32
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (84 bp):
AAATTAGTTGTCTTTCAGATGTTTGATAATATGTTTGTGTTAGACCAAATCAAGTTGTAGAAGAA
AAATTAATGACCCAAAGAC
Found at i:1113652 original size:31 final size:31
Alignment explanation
Indices: 1113614--1113731 Score: 191
Period size: 31 Copynumber: 3.8 Consensus size: 31
1113604 ACAAATGACA
* *
1113614 AGTGAAAAGTGGAAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1113645 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
1113676 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
1113707 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
1113732 AAGTGACAAG
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 80 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:1113874 original size:46 final size:46
Alignment explanation
Indices: 1113756--1113878 Score: 165
Period size: 47 Copynumber: 2.7 Consensus size: 46
1113746 AAGTGATTTC
* * *
1113756 CGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTA
1 CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* * *
1113802 CTATATAAGACCATATCTGGGATATGGCATCAGTGAGATATGTGATT
1 C-GTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* *
1113849 CGTATAAGACCATAGCTGGGCTATGGCATC
1 CGTATAAGACCATATCTGGGATATGGCATC
1113879 GATATATGAA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
46 27 0.40
47 40 0.60
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (46 bp):
CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
Found at i:1113958 original size:42 final size:42
Alignment explanation
Indices: 1113853--1113947 Score: 138
Period size: 42 Copynumber: 2.3 Consensus size: 42
1113843 GTGATTCGTA
*
1113853 TAAGACCATAGCTGGGCTATGGCATCGATATATGAATATGTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATATGAAGATGTG
* * *
1113895 TAAGACCATAGCCGGGCTATGGTATC-ATTATGTGAAGATGTG
1 TAAGACCATAGCTGGGCTATGGCATCGA-TATATGAAGATGTG
1113937 TAAGACCATAG
1 TAAGACCATAG
1113948 TTGAACTATG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 1 0.02
42 47 0.98
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (42 bp):
TAAGACCATAGCTGGGCTATGGCATCGATATATGAAGATGTG
Found at i:1121000 original size:20 final size:20
Alignment explanation
Indices: 1120975--1121014 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1120965 AAGAATTACA
1120975 TTGCACTTTCCTTGCAATTC
1 TTGCACTTTCCTTGCAATTC
*
1120995 TTGCACTTTTCTTGCAATTC
1 TTGCACTTTCCTTGCAATTC
1121015 CAAGGAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.28, G:0.10, T:0.47
Consensus pattern (20 bp):
TTGCACTTTCCTTGCAATTC
Found at i:1122490 original size:20 final size:20
Alignment explanation
Indices: 1122458--1122495 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1122448 TGTTTCACAT
1122458 TCATATAACTAATATTTATG
1 TCATATAACTAATATTTATG
*
1122478 TCAT-TAACATAATTTTTA
1 TCATATAAC-TAATATTTA
1122496 ACTTAATAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (20 bp):
TCATATAACTAATATTTATG
Found at i:1123061 original size:18 final size:18
Alignment explanation
Indices: 1123038--1123078 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1123028 TACTTTTCTC
1123038 TTTCTA-TCACAATTCCAA
1 TTTCTATTCACAATT-CAA
*
1123056 TTTCTATTCATAATTCAA
1 TTTCTATTCACAATTCAA
1123074 TTTCT
1 TTTCT
1123079 TTTTCTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTCTATTCACAATTCAA
Found at i:1124604 original size:15 final size:14
Alignment explanation
Indices: 1124586--1124674 Score: 55
Period size: 13 Copynumber: 6.5 Consensus size: 14
1124576 TTAATTTATT
1124586 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
1124601 TAATAATAATCTAA
1 TAATAATAATCTAA
*
1124615 T-ATAA-AACCATAA
1 TAATAATAATC-TAA
*
1124628 TATTAATTAA--TAA
1 TAATAA-TAATCTAA
* *
1124641 TTATAATAATTTAA
1 TAATAATAATCTAA
*
1124655 T-ATAA-AACCATAA
1 TAATAATAATC-TAA
1124668 TAATAAT
1 TAATAAT
1124675 CATTATAATA
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
12 8 0.14
13 23 0.39
14 16 0.27
15 10 0.17
16 2 0.03
ACGTcount: A:0.56, C:0.07, G:0.01, T:0.36
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:1124627 original size:21 final size:20
Alignment explanation
Indices: 1124603--1124671 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 20
1124593 AATGCTAATA
1124603 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
**
1124624 ATAAT-ATTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
1124643 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
1124664 ATAATAAT
1 ATAATAAT
1124672 AATCATTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.28
20 4 0.10
21 19 0.47
22 3 0.08
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:1124656 original size:40 final size:40
Alignment explanation
Indices: 1124598--1124674 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
1124588 ATAATAATGC
*
1124598 TAATAATAATAATCTAATATAAAACCATAATATTAATTAA
1 TAATAATAATAATCTAATATAAAACCATAATAATAATTAA
* *
1124638 TAATTATAATAATTTAATATAAAACCATAATAATAAT
1 TAATAATAATAATCTAATATAAAACCATAATAATAAT
1124675 CATTATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (40 bp):
TAATAATAATAATCTAATATAAAACCATAATAATAATTAA
Found at i:1134089 original size:13 final size:13
Alignment explanation
Indices: 1134071--1134099 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1134061 CATGCCAGTC
1134071 CCCCTGACTACGT
1 CCCCTGACTACGT
1134084 CCCCTGACTACGT
1 CCCCTGACTACGT
1134097 CCC
1 CCC
1134100 TGGTACTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.52, G:0.14, T:0.21
Consensus pattern (13 bp):
CCCCTGACTACGT
Found at i:1139476 original size:36 final size:36
Alignment explanation
Indices: 1139429--1139505 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 36
1139419 AGAAAGCATT
*
1139429 GAAAATAATGCATATGCTTGTAGGACCAAGTGTCAA
1 GAAAATAATGCATATGCGTGTAGGACCAAGTGTCAA
1139465 GAAAATAATGCATATGCGTGTAGGACCAAGTGTCAA
1 GAAAATAATGCATATGCGTGTAGGACCAAGTGTCAA
*
1139501 TAAAA
1 GAAAA
1139506 ACTTTTTAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.23
Consensus pattern (36 bp):
GAAAATAATGCATATGCGTGTAGGACCAAGTGTCAA
Found at i:1146124 original size:4 final size:4
Alignment explanation
Indices: 1146115--1146151 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
1146105 CAAAGTAGGC
1146115 TGTA TGTA TGTA TGTA TGTA TGTA TGTA --TA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
1146152 CAGTGAATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
4 29 0.94
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:1153755 original size:46 final size:46
Alignment explanation
Indices: 1153688--1153955 Score: 264
Period size: 46 Copynumber: 5.8 Consensus size: 46
1153678 TGTAACCCGC
*
1153688 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
1153734 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * * *
1153784 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* *
1153827 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * ** *
1153877 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
1153920 CCATAAGTGAACTCGGACTCAACTCAAGGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1153956 ATGCTCAACC
Statistics
Matches: 180, Mismatches: 24, Indels: 36
0.75 0.10 0.15
Matches are distributed among these distances:
42 4 0.02
43 6 0.03
44 4 0.02
45 4 0.02
46 88 0.49
47 54 0.30
48 5 0.03
49 4 0.02
50 6 0.03
51 5 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:1153808 original size:93 final size:93
Alignment explanation
Indices: 1153696--1153959 Score: 465
Period size: 93 Copynumber: 2.8 Consensus size: 93
1153686 GCCCATAAGT
* *
1153696 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1153761 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
1153789 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
1153854 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
1153882 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
1153947 GGAGTTCGGATGC
66 CGAGTTCGGATGC
1153960 TCAACCATCC
Statistics
Matches: 162, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 162 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:1153810 original size:47 final size:47
Alignment explanation
Indices: 1153742--1153908 Score: 234
Period size: 47 Copynumber: 3.6 Consensus size: 47
1153732 ATCCATAAGT
1153742 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
* * * *
1153789 GAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-TCA-C
*
1153835 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
1153882 GAACTCGGACTCAACTCAACGAGTTCG
1 GAACTCGGACTCAACTCAACGAGTTCG
1153909 AACATTCGCA
Statistics
Matches: 103, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 32 0.31
47 59 0.57
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.21
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:1157751 original size:29 final size:28
Alignment explanation
Indices: 1157696--1157767 Score: 87
Period size: 30 Copynumber: 2.6 Consensus size: 28
1157686 TTCTTGGATA
*
1157696 AATAT-CAAATATATACATGAAATTTAG
1 AATATACAATTATATACATGAAATTTAG
1157723 TCAATATACAATTATATACATGAAA-TTAG
1 --AATATACAATTATATACATGAAATTTAG
1157752 AAT-TACAATTTATATA
1 AATATACAA-TTATATA
1157768 ATTTTGATTC
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
26 5 0.12
27 10 0.25
29 9 0.22
30 16 0.40
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.36
Consensus pattern (28 bp):
AATATACAATTATATACATGAAATTTAG
Found at i:1171375 original size:13 final size:13
Alignment explanation
Indices: 1171354--1171383 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1171344 TAAAATGGTG
1171354 TTATATTAATAAT
1 TTATATTAATAAT
*
1171367 TTATTTTAATAAT
1 TTATATTAATAAT
1171380 TTAT
1 TTAT
1171384 GAAAATTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATATTAATAAT
Found at i:1173351 original size:23 final size:22
Alignment explanation
Indices: 1173304--1173351 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
1173294 CTAAGTATAT
* *
1173304 AAATTATAATTGTTTAAGTAAA
1 AAATTATAATTGTATAAATAAA
1173326 AAATATATAATT-TATAAATAAGA
1 AAAT-TATAATTGTATAAATAA-A
1173349 AAA
1 AAA
1173352 GTATTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (22 bp):
AAATTATAATTGTATAAATAAA
Found at i:1175103 original size:23 final size:23
Alignment explanation
Indices: 1175077--1175125 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1175067 ACAAAAGAGG
*
1175077 AAAATATAATAACAATAATAGTA
1 AAAATACAATAACAATAATAGTA
* **
1175100 AAAATACACTAGTAATAATAGTA
1 AAAATACAATAACAATAATAGTA
1175123 AAA
1 AAA
1175126 GGTGTAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.24
Consensus pattern (23 bp):
AAAATACAATAACAATAATAGTA
Found at i:1175174 original size:3 final size:3
Alignment explanation
Indices: 1175152--1175216 Score: 51
Period size: 3 Copynumber: 20.7 Consensus size: 3
1175142 AATATGATGG
* * *
1175152 TAA TAA AAA TACA GTAA TAA TAA T-A TAT TAAA TAA CAAA TAA TAA TAA
1 TAA TAA TAA TA-A -TAA TAA TAA TAA TAA T-AA TAA -TAA TAA TAA TAA
*
1175200 TAA TAA TGA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
1175217 TAGAAATATG
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
2 2 0.04
3 39 0.80
4 6 0.12
5 2 0.04
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1175213 original size:28 final size:28
Alignment explanation
Indices: 1175130--1175214 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
1175120 GTAAAAGGTG
* *
1175130 TAAC-AAT-ATAATAAT-ATGATGGTAA
1 TAACAAATAATAATAATAATAATGATAA
*
1175155 TAA-AAATACAGTAATAATAATATATTA-AA
1 TAACAAATA-A-TAATAATAATA-ATGATAA
1175184 TAACAAATAATAATAATAATAATGATAA
1 TAACAAATAATAATAATAATAATGATAA
1175212 TAA
1 TAA
1175215 TATAGAAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
25 6 0.12
27 4 0.08
28 23 0.48
29 8 0.17
30 7 0.15
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.31
Consensus pattern (28 bp):
TAACAAATAATAATAATAATAATGATAA
Found at i:1178009 original size:44 final size:45
Alignment explanation
Indices: 1177919--1178047 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
1177909 GACAGAACGA
*
1177919 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
1177965 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
1178009 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
1178048 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:1184131 original size:44 final size:45
Alignment explanation
Indices: 1184041--1184169 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
1184031 GACAGAACGA
*
1184041 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
1184087 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
1184131 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
1184170 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:1188542 original size:19 final size:20
Alignment explanation
Indices: 1188497--1188544 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1188487 AGTCCAAACA
1188497 AATTTCAATTAAAATTGAATT
1 AATTT-AATTAAAATTGAATT
* *
1188518 AA-TTAATTAAATTTGTA-T
1 AATTTAATTAAAATTGAATT
1188536 AATTTAATT
1 AATTTAATT
1188545 GACTTAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 3 0.12
19 17 0.71
20 2 0.08
21 2 0.08
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (20 bp):
AATTTAATTAAAATTGAATT
Found at i:1191660 original size:24 final size:24
Alignment explanation
Indices: 1191611--1191662 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1191601 AAAGTTCCGG
*
1191611 ATAGACCAAAATCAACATCCTTTT
1 ATAGACCAAAATCAACATCCTATT
1191635 ATAGACCAAAAT--ACAATCCGTATT
1 ATAGACCAAAATCAAC-ATCC-TATT
1191659 ATAG
1 ATAG
1191663 TATAAAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 2 0.08
23 4 0.16
24 19 0.76
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.27
Consensus pattern (24 bp):
ATAGACCAAAATCAACATCCTATT
Found at i:1202162 original size:19 final size:20
Alignment explanation
Indices: 1202120--1202166 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1202110 AATAAAAAAT
*
1202120 AATTAAAAATAAATTTCAAA
1 AATTCAAAATAAATTTCAAA
*
1202140 AATTCAAAATAAATTT-TAA
1 AATTCAAAATAAATTTCAAA
1202159 AATTCAAA
1 AATTCAAA
1202167 GTATTTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (20 bp):
AATTCAAAATAAATTTCAAA
Found at i:1203677 original size:34 final size:34
Alignment explanation
Indices: 1203634--1203701 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
1203624 TTTACCAAGT
1203634 GTATTTGGGTGAGGATGCAATTATTCAAGAGTTA
1 GTATTTGGGTGAGGATGCAATTATTCAAGAGTTA
1203668 GTATTTGGGTGAGGATGCAATTATTCAAGAGTTA
1 GTATTTGGGTGAGGATGCAATTATTCAAGAGTTA
1203702 AGATAGATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.35
Consensus pattern (34 bp):
GTATTTGGGTGAGGATGCAATTATTCAAGAGTTA
Found at i:1207259 original size:31 final size:31
Alignment explanation
Indices: 1207221--1207289 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
1207211 CTTAACTACC
* *
1207221 CAGTGATTTAAACAAAAACTTTTGAATAGTT
1 CAGTGATTTAAACAAAAACTTTTAAATAATT
**
1207252 CAGTGATTTAAATGAAAACTTTTAAATAATT
1 CAGTGATTTAAACAAAAACTTTTAAATAATT
1207283 CAGTGAT
1 CAGTGAT
1207290 CAAATTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (31 bp):
CAGTGATTTAAACAAAAACTTTTAAATAATT
Found at i:1207681 original size:31 final size:31
Alignment explanation
Indices: 1207643--1207711 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
1207633 CTTAACTACC
* *
1207643 CAGTGATTTAAATAAAAACTTTTGAATAGTT
1 CAGTGATTTAAATAAAAACTTTTAAATAATT
*
1207674 CAGTGATTTAAATGAAAACTTTTAAATAATT
1 CAGTGATTTAAATAAAAACTTTTAAATAATT
1207705 CAGTGAT
1 CAGTGAT
1207712 CAAATTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (31 bp):
CAGTGATTTAAATAAAAACTTTTAAATAATT
Found at i:1207848 original size:422 final size:423
Alignment explanation
Indices: 1207063--1207911 Score: 1630
Period size: 422 Copynumber: 2.0 Consensus size: 423
1207053 CTAAAATTCA
1207063 AACAATTTTTTCTCCAATATCCAAAATTGATTGTCAGATCAACTTAGATATAATGTATGTTATTC
1 AACAATTTTTTCTCCAATATCCAAAATTGATTGTCAGATCAACTTAGATATAATGTATGTTATTC
1207128 TATTCTTCGATGTGTACTGATCTACCATATCAATCATTGAATCATCACATGAAGCTCGCTGGTAG
66 TATTCTTCGATGTGTACTGATCTACCATATCAATCATTGAATCATCACATGAAGCTCGCTGGTAG
1207193 AACTTTTTTTGAAAAAAACTTAACTACCCAGTGATTTAAACAAAAACTTTTGAATAGTTCAGTGA
131 AACTTTTTTTGAAAAAAACTTAACTACCCAGTGATTTAAACAAAAACTTTTGAATAGTTCAGTGA
*
1207258 TTTAAATGAAAACTTTTAAATAATTCAGTGATCAAATTTTAATTTATTTTAGTTAAGTGGCTAAA
196 TTTAAATGAAAACTTTTAAATAATTCAGTGATCAAATTTTAATTTATTTTAGTTAAGTGACTAAA
1207323 ACAAAAACTTACTCATAGTTTAGGAACTAATAATGTAGTTTACCCTTTTTTTGGGTATCATTCGT
261 ACAAAAACTTACTCATAGTTTAGGAACTAATAATGTAGTTTACCCTTTTTTTGGGTATCATTCGT
1207388 TTTAGTTTTTTGGTTCATATTCACTCAATCTTCGTTTTATAATTATTGTTTGTGATTTGTGATTG
326 TTTAGTTTTTTGGTTCATATTCACTCAATCTTCGTTTTATAATTATTGTTTGTGATTTGTGATTG
1207453 TTGTATTATATCTTTAAGGGTGCAATGTGTCTT
391 TTGTATTATATCTTTAAGGGTGCAATGTGTCTT
1207486 AACAATTTTTTCTCCAATATCCAAAATTGATTGTCAGATCAACTTAGATATAATGTATGTTATTC
1 AACAATTTTTTCTCCAATATCCAAAATTGATTGTCAGATCAACTTAGATATAATGTATGTTATTC
1207551 TATTCTTCGATGTGTACTGATCTACCATATCAATCATTGAATCATCACATGAAGCTCGCTGGTAG
66 TATTCTTCGATGTGTACTGATCTACCATATCAATCATTGAATCATCACATGAAGCTCGCTGGTAG
*
1207616 AAC-TTTTTTGAAAAAAACTTAACTACCCAGTGATTTAAATAAAAACTTTTGAATAGTTCAGTGA
131 AACTTTTTTTGAAAAAAACTTAACTACCCAGTGATTTAAACAAAAACTTTTGAATAGTTCAGTGA
*
1207680 TTTAAATGAAAACTTTTAAATAATTCAGTGATCAAATTTTAATTTTTTTTAGTTAAGTGACTAAA
196 TTTAAATGAAAACTTTTAAATAATTCAGTGATCAAATTTTAATTTATTTTAGTTAAGTGACTAAA
1207745 A-AAAAACTTACTCATAGTTTAGGAACTAATAATGTAGTTTACCCTTTTTTTTGGGTATCATTCG
261 ACAAAAACTTACTCATAGTTTAGGAACTAATAATGTAGTTTACCC-TTTTTTTGGGTATCATTCG
*
1207809 TTTTAGTTTTTTGGTTCATATTCACTCAATCTTCGTTTTATAATTATTTTTTGTGATTTGTGATT
325 TTTTAGTTTTTTGGTTCATATTCACTCAATCTTCGTTTTATAATTATTGTTTGTGATTTGTGATT
*
1207874 GTTGTATTATATCTTTAAGGGTGTAATGTGTCTT
390 GTTGTATTATATCTTTAAGGGTGCAATGTGTCTT
1207908 AACA
1 AACA
1207912 TTACTTCTAA
Statistics
Matches: 420, Mismatches: 5, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
421 43 0.10
422 244 0.58
423 133 0.32
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (423 bp):
AACAATTTTTTCTCCAATATCCAAAATTGATTGTCAGATCAACTTAGATATAATGTATGTTATTC
TATTCTTCGATGTGTACTGATCTACCATATCAATCATTGAATCATCACATGAAGCTCGCTGGTAG
AACTTTTTTTGAAAAAAACTTAACTACCCAGTGATTTAAACAAAAACTTTTGAATAGTTCAGTGA
TTTAAATGAAAACTTTTAAATAATTCAGTGATCAAATTTTAATTTATTTTAGTTAAGTGACTAAA
ACAAAAACTTACTCATAGTTTAGGAACTAATAATGTAGTTTACCCTTTTTTTGGGTATCATTCGT
TTTAGTTTTTTGGTTCATATTCACTCAATCTTCGTTTTATAATTATTGTTTGTGATTTGTGATTG
TTGTATTATATCTTTAAGGGTGCAATGTGTCTT
Found at i:1209336 original size:17 final size:17
Alignment explanation
Indices: 1209314--1209367 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
1209304 CATTATGATT
1209314 ATTACATGGACTATCAC
1 ATTACATGGACTATCAC
* *
1209331 ATTACAT----TATGATT
1 ATTACATGGACTATCA-C
1209345 ATTACATGGACTATCAC
1 ATTACATGGACTATCAC
1209362 ATTACA
1 ATTACA
1209368 AGTATTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 10
0.67 0.10 0.24
Matches are distributed among these distances:
13 4 0.14
14 7 0.25
17 13 0.46
18 4 0.14
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (17 bp):
ATTACATGGACTATCAC
Found at i:1209338 original size:31 final size:31
Alignment explanation
Indices: 1209302--1209367 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
1209292 TTTTATCAAG
1209302 TACATTATGATTATTACATGGACTATCACAT
1 TACATTATGATTATTACATGGACTATCACAT
1209333 TACATTATGATTATTACATGGACTATCACAT
1 TACATTATGATTATTACATGGACTATCACAT
1209364 TACA
1 TACA
1209368 AGTATTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (31 bp):
TACATTATGATTATTACATGGACTATCACAT
Found at i:1210285 original size:39 final size:39
Alignment explanation
Indices: 1210209--1210287 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
1210199 TTTTCGTGCA
* * * * * *
1210209 ATTATAAAGCGTAGAATTAAACTATTATAGCACAAATAG
1 ATTAAAAAACGTAGAATCAAACAATTACAACACAAATAG
*
1210248 ATTAAAAAACGTAGAATCAAACAATTACAACATAAATAG
1 ATTAAAAAACGTAGAATCAAACAATTACAACACAAATAG
1210287 A
1 A
1210288 CTAAGAATAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.54, C:0.11, G:0.10, T:0.24
Consensus pattern (39 bp):
ATTAAAAAACGTAGAATCAAACAATTACAACACAAATAG
Found at i:1217135 original size:12 final size:12
Alignment explanation
Indices: 1217118--1217142 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1217108 AACAGATCGA
1217118 TCGGTTGGCTAT
1 TCGGTTGGCTAT
1217130 TCGGTTGGCTAT
1 TCGGTTGGCTAT
1217142 T
1 T
1217143 TGATCTAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.32, T:0.44
Consensus pattern (12 bp):
TCGGTTGGCTAT
Found at i:1219741 original size:18 final size:19
Alignment explanation
Indices: 1219711--1219751 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
1219701 ATGCCTCTAA
1219711 AATAATAACAAAATTA-AT
1 AATAATAACAAAATTATAT
1219729 AATAA-AACAAAAATTATAT
1 AATAATAAC-AAAATTATAT
1219748 AATA
1 AATA
1219752 TCCAAACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 12 0.57
19 6 0.29
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (19 bp):
AATAATAACAAAATTATAT
Found at i:1219791 original size:22 final size:22
Alignment explanation
Indices: 1219766--1219808 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1219756 AACAAAAACA
1219766 ATAACAATAAAATAATAGTAAT
1 ATAACAATAAAATAATAGTAAT
* *
1219788 ATAACAATGAAATGATAGTAA
1 ATAACAATAAAATAATAGTAA
1219809 AACAGTGAGA
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:0.60, C:0.05, G:0.09, T:0.26
Consensus pattern (22 bp):
ATAACAATAAAATAATAGTAAT
Found at i:1219832 original size:22 final size:22
Alignment explanation
Indices: 1219807--1219853 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1219797 AAATGATAGT
** *
1219807 AAAACAGTGAGAAAACAACAAG
1 AAAACAGCAAGAAAACAAAAAG
*
1219829 AAAATAGCAAGAAAACAAAAAG
1 AAAACAGCAAGAAAACAAAAAG
1219851 AAA
1 AAA
1219854 CTATCAGATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.70, C:0.11, G:0.15, T:0.04
Consensus pattern (22 bp):
AAAACAGCAAGAAAACAAAAAG
Found at i:1224706 original size:129 final size:131
Alignment explanation
Indices: 1224555--1224813 Score: 504
Period size: 131 Copynumber: 2.0 Consensus size: 131
1224545 GTTGACATTC
1224555 ATGTTTCATTTATGTAAATTATGAATGTTAAATTTAGCATAATTT-ATTTATAATTTTTGTG-AA
1 ATGTTTCATTTATGTAAATTATGAATGTTAAATTTAGCATAATTTAATTTATAATTTTTGTGAAA
1224618 AAAATTTAATCATTAAATATATATTAATATAGTAATATTTTAGATTAATATGATGAAAATATCAA
66 AAAATTTAATCATTAAATATATATTAATATAGTAATATTTTAGATTAATATGATGAAAATATCAA
1224683 T
131 T
1224684 ATGTTTCATTTATGTAAATTATGAATGTTAAATTTAGCATAATTTAATTTATAATTTTTGTGAAA
1 ATGTTTCATTTATGTAAATTATGAATGTTAAATTTAGCATAATTTAATTTATAATTTTTGTGAAA
1224749 AAAATTTAATCATTAAATATATATTAATATAGTAATATTTTAGATTAATATGATGAAAATATCAA
66 AAAATTTAATCATTAAATATATATTAATATAGTAATATTTTAGATTAATATGATGAAAATATCAA
1224814 ATCGATTTAA
Statistics
Matches: 128, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
129 45 0.35
130 16 0.12
131 67 0.52
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (131 bp):
ATGTTTCATTTATGTAAATTATGAATGTTAAATTTAGCATAATTTAATTTATAATTTTTGTGAAA
AAAATTTAATCATTAAATATATATTAATATAGTAATATTTTAGATTAATATGATGAAAATATCAA
T
Found at i:1227971 original size:19 final size:19
Alignment explanation
Indices: 1227921--1227973 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1227911 AAAAAAAATC
* *
1227921 TGTTATTTTTTTTATTGTTT
1 TGTTGTTTTTTTT-TTATTT
* *
1227941 TATTGCTTTTTTTTTATTT
1 TGTTGTTTTTTTTTTATTT
1227960 TGTTGTTTTTTTTT
1 TGTTGTTTTTTTTT
1227974 CACTATTTTG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.08, C:0.02, G:0.09, T:0.81
Consensus pattern (19 bp):
TGTTGTTTTTTTTTTATTT
Found at i:1228590 original size:2 final size:2
Alignment explanation
Indices: 1228583--1228624 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1228573 GGTTAAGCGC
1228583 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1228625 TCAAGTTCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1231964 original size:16 final size:17
Alignment explanation
Indices: 1231943--1231975 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1231933 TCACTGATAT
1231943 CATA-TTTTGTTGTGAA
1 CATATTTTTGTTGTGAA
1231959 CATATTTTTGTTGTGAA
1 CATATTTTTGTTGTGAA
1231976 GAAAGATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.52
Consensus pattern (17 bp):
CATATTTTTGTTGTGAA
Found at i:1233587 original size:93 final size:93
Alignment explanation
Indices: 1233428--1233600 Score: 292
Period size: 93 Copynumber: 1.9 Consensus size: 93
1233418 CGCCCATAAG
* * * *
1233428 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAGGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
1233493 ACAAGTTCGGATGCCTTGTTACATTTCA
66 ACAAGTTCGGATGCCTTGTTACATTTCA
*
1233521 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
*
1233586 ACGAGTTCGGATGCC
66 ACAAGTTCGGATGCC
1233601 CAAATACCCC
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
ACAAGTTCGGATGCCTTGTTACATTTCA
Found at i:1233596 original size:46 final size:46
Alignment explanation
Indices: 1233421--1233596 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
1233411 TGTAACCCGC
* * *
1233421 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* * * * *
1233467 CCATAGGTGAACTCGGACTCAACTCAACAAGTTCGGATGCCTT-G-TT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA--CATTCGCAT
* *
1233513 ACATTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCA--TAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
1233560 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
1233597 TGCCCAAATA
Statistics
Matches: 105, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
45 5 0.05
46 64 0.61
47 32 0.30
48 4 0.04
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:1235944 original size:22 final size:22
Alignment explanation
Indices: 1235907--1235965 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
1235897 AAATGATAGT
**
1235907 AAAACAGTGAGAAAACAAAAAG
1 AAAACAGAAAGAAAACAAAAAG
* * * *
1235929 ATAATAGCAAGAAAACAACAAG
1 AAAACAGAAAGAAAACAAAAAG
1235951 AAAACAGAAAGAAAA
1 AAAACAGAAAGAAAA
1235966 TATCTGATTT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.69, C:0.10, G:0.15, T:0.05
Consensus pattern (22 bp):
AAAACAGAAAGAAAACAAAAAG
Found at i:1237652 original size:2 final size:2
Alignment explanation
Indices: 1237645--1237672 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1237635 AATCAAAAAG
1237645 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
1237673 GAAACAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1242614 original size:19 final size:19
Alignment explanation
Indices: 1242590--1242626 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1242580 AAACTCATGA
1242590 TAATCTCCTAAGAAATCAT
1 TAATCTCCTAAGAAATCAT
1242609 TAATCTCCTAAGAAATCA
1 TAATCTCCTAAGAAATCA
1242627 ATTGGGAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.22, G:0.05, T:0.30
Consensus pattern (19 bp):
TAATCTCCTAAGAAATCAT
Found at i:1244163 original size:30 final size:30
Alignment explanation
Indices: 1244129--1244190 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1244119 TATGTATGTA
1244129 TCACTTTAAGTATTTGATTAAAAAATTATG
1 TCACTTTAAGTATTTGATTAAAAAATTATG
1244159 TCACTTTAAGTATTTGATTAAAAAATTATG
1 TCACTTTAAGTATTTGATTAAAAAATTATG
1244189 TC
1 TC
1244191 TTTTCATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.44
Consensus pattern (30 bp):
TCACTTTAAGTATTTGATTAAAAAATTATG
Found at i:1246049 original size:13 final size:13
Alignment explanation
Indices: 1246033--1246060 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1246023 AGAATTCGTG
1246033 CACCAAATTCTTC
1 CACCAAATTCTTC
1246046 CACCAAATTCTTC
1 CACCAAATTCTTC
1246059 CA
1 CA
1246061 TTCCACGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.39, G:0.00, T:0.29
Consensus pattern (13 bp):
CACCAAATTCTTC
Found at i:1250142 original size:33 final size:33
Alignment explanation
Indices: 1250103--1250172 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
1250093 ACAAACATAC
*
1250103 AAAGTAATAATTAAATAATGCATGATATACAAA
1 AAAGTAATAATTAAATAATGCATGACATACAAA
1250136 AAAGTAATAATTAAATAATGCATGACATACAAA
1 AAAGTAATAATTAAATAATGCATGACATACAAA
1250169 AAAG
1 AAAG
1250173 AGTAATACGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.59, C:0.07, G:0.10, T:0.24
Consensus pattern (33 bp):
AAAGTAATAATTAAATAATGCATGACATACAAA
Found at i:1250900 original size:13 final size:13
Alignment explanation
Indices: 1250821--1250900 Score: 55
Period size: 13 Copynumber: 6.5 Consensus size: 13
1250811 CAAGTAAAAT
1250821 ATAAT-AATAAT-
1 ATAATAAATAATG
1250832 ATAA-AAATAATG
1 ATAATAAATAATG
*
1250844 AT-GTAAAATAATG
1 ATAAT-AAATAATG
* **
1250857 ATAATAATTTGTG
1 ATAATAAATAATG
*
1250870 A-AA-AAATAATAT
1 ATAATAAATAAT-G
1250882 ATAATAAATAATG
1 ATAATAAATAATG
1250895 ATAATA
1 ATAATA
1250901 TATATAATAA
Statistics
Matches: 51, Mismatches: 10, Indels: 14
0.68 0.13 0.19
Matches are distributed among these distances:
11 14 0.27
12 5 0.10
13 24 0.47
14 8 0.16
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (13 bp):
ATAATAAATAATG
Found at i:1250900 original size:20 final size:18
Alignment explanation
Indices: 1250872--1250924 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
1250862 AATTTGTGAA
1250872 AAAATAATATATAATAAAT
1 AAAATAATATATAAT-AAT
*
1250891 AATGATAATATAT-ATAAT
1 AA-AATAATATATAATAAT
1250909 AAAATAATATTATAAT
1 AAAATAATA-TATAAT
1250925 GTATAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 6 0.21
18 8 0.28
19 6 0.21
20 9 0.31
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
AAAATAATATATAATAAT
Found at i:1250923 original size:38 final size:38
Alignment explanation
Indices: 1250821--1250924 Score: 103
Period size: 37 Copynumber: 2.8 Consensus size: 38
1250811 CAAGTAAAAT
*
1250821 ATAATAATA-AT-ATAAAAATAATGATGT-A-AAATAATG
1 ATAATAATATATGA-AAAAATAAT-ATATAATAAATAATG
* *
1250857 ATAATAATTTGTGAAAAAATAATATATAATAAATAATG
1 ATAATAATATATGAAAAAATAATATATAATAAATAATG
1250895 ATAAT-ATATAT-AATAAAATAATATTATAAT
1 ATAATAATATATGAA-AAAATAATA-TATAAT
1250925 GTATAATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
36 13 0.23
37 24 0.42
38 20 0.35
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.35
Consensus pattern (38 bp):
ATAATAATATATGAAAAAATAATATATAATAAATAATG
Found at i:1250929 original size:23 final size:24
Alignment explanation
Indices: 1250874--1250932 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 24
1250864 TTTGTGAAAA
1250874 AATAATATATAAT-AAATAATGAT
1 AATAATATATAATAAAATAATGAT
1250897 AAT-ATATATAATAAAATAAT-AT
1 AATAATATATAATAAAATAATGAT
* *
1250919 TATAATGTATAATA
1 AATAATATATAATA
1250933 TAAAAGTAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 13 0.41
23 19 0.59
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (24 bp):
AATAATATATAATAAAATAATGAT
Found at i:1250935 original size:25 final size:27
Alignment explanation
Indices: 1250875--1250937 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 27
1250865 TTGTGAAAAA
*
1250875 ATAATATATAATAAATAATGATAATAT
1 ATAATATAAAATAAATAATGATAATAT
* *
1250902 AT-ATAATAAAAT-AAT-ATTATAATGT
1 ATAAT-ATAAAATAAATAATGATAATAT
1250927 ATAATATAAAA
1 ATAATATAAAA
1250938 GTAAGGTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 16 0.52
26 7 0.23
27 8 0.26
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (27 bp):
ATAATATAAAATAAATAATGATAATAT
Found at i:1253372 original size:70 final size:70
Alignment explanation
Indices: 1253291--1253431 Score: 237
Period size: 70 Copynumber: 2.0 Consensus size: 70
1253281 ATTGTATATA
*
1253291 ATAATTATATTTTATTGTATAAAGGATAATTTTTATATGATGTAGAAATTTGCATACAACCAAAC
1 ATAATTATATTTTATTGTATAAAGGATAATTTTTATATGACGTAGAAATTTGCATACAACCAAAC
1253356 TAGGT
66 TAGGT
* * * *
1253361 ATAATTATATTTTATTGTATAAAGGGTAGTTTTTATATGACGTAGAAATTTGGATACAACCAAAT
1 ATAATTATATTTTATTGTATAAAGGATAATTTTTATATGACGTAGAAATTTGCATACAACCAAAC
1253426 TAGGT
66 TAGGT
1253431 A
1 A
1253432 GTGGAATTAT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.40
Consensus pattern (70 bp):
ATAATTATATTTTATTGTATAAAGGATAATTTTTATATGACGTAGAAATTTGCATACAACCAAAC
TAGGT
Found at i:1255993 original size:14 final size:14
Alignment explanation
Indices: 1255974--1256020 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1255964 GAACTGCATC
1255974 ACTAAAAAAATAAA
1 ACTAAAAAAATAAA
*
1255988 ACTAAAAAATTAAA
1 ACTAAAAAAATAAA
* *
1256002 A-TATAAATATAAA
1 ACTAAAAAAATAAA
*
1256015 ATTAAA
1 ACTAAA
1256021 TTCATCAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.23
Consensus pattern (14 bp):
ACTAAAAAAATAAA
Found at i:1256004 original size:19 final size:19
Alignment explanation
Indices: 1255980--1256020 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1255970 CATCACTAAA
1255980 AAAATA-AAACTAAAAAATT
1 AAAATATAAA-TAAAAAATT
*
1255999 AAAATATAAATATAAAATT
1 AAAATATAAATAAAAAATT
1256018 AAA
1 AAA
1256021 TTCATCAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAATATAAATAAAAAATT
Found at i:1258341 original size:20 final size:20
Alignment explanation
Indices: 1258316--1258371 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
1258306 AGCTACGTTG
1258316 AAAATCATAGAAAATTA-TTA
1 AAAATCATA-AAAATTATTTA
**
1258336 AAAATCATATTAATTATTTA
1 AAAATCATAAAAATTATTTA
*
1258356 AAACTCATAAAAATTA
1 AAAATCATAAAAATTA
1258372 ATTTTTTGGC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 5 0.17
20 25 0.83
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (20 bp):
AAAATCATAAAAATTATTTA
Found at i:1260811 original size:131 final size:130
Alignment explanation
Indices: 1260635--1261106 Score: 393
Period size: 130 Copynumber: 3.6 Consensus size: 130
1260625 AATAAAGACC
* * * * ** * * * *
1260635 TAAAGGAATACTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAAGGCATGATTC
1 TAAAGGGATATTCGATTATTTTGAACAATCGAGAAATTGCAACCCAACACGTTAGGGCACGATTC
* * * **
1260700 C-CGAATTGTCAAACACC-GAAAATTGCCCTCATTTTAAAGGGTTTTTAGGAAAG-C-CGAGTGA
66 CACGAATTGCCAAACACCAG-AAATCGCCCTCATTTT--AGGGATTTTA--AAAGACACGAGCAA
1260761 AATTT
126 AATTT
* * * * * *
1260766 TGAAGGGATATTTGATTATTTTAAACAATCGAGAAATTGCTACCCAACATGTTAGGGCACGATCC
1 TAAAGGGATATTCGATTATTTTGAACAATCGAGAAATTGCAACCCAACACGTTAGGGCACGATTC
* * *
1260831 CACGAATTGCCAAATACCAGATATCGCCTTCATTTTAGGGATTTTAAAAGACACGAGCAAAATTT
66 CACGAATTGCCAAACACCAGAAATCGCCCTCATTTTAGGGATTTTAAAAGACACGAGCAAAATTT
* * *
1260896 TAAAGTGATATTCGATTATTTTGAGCAAAT-GCGAAATTGCAACCCAACACGTTAGGGCACGATT
1 TAAAGGGATATTCGATTATTTTGAAC-AATCGAGAAATTGCAACCCAACACGTTAGGGCACGATT
* * * * * * * * ****
1260960 CCACGAATTGCCAAACATC--AAATCTCATCTTCGTTTAAGGGATGTTAAAAGATATGAATGGAA
65 CCACGAATTGCCAAACACCAGAAATCGC--CCTCATTTTAGGGATTTTAAAAGACACGAGCAAAA
1261023 TTT
128 TTT
** * * *
1261026 CGAAGGGAAATTCGATTATTTTGAGCAAAT-GCGAAATTGCAACCCAACACGTTAGGGCACGATT
1 TAAAGGGATATTCGATTATTTTGAAC-AATCGAGAAATTGCAACCCAACACGTTAGGGCACGATT
* *
1261090 CCGCGAATTGCCGAACA
65 CCACGAATTGCCAAACA
1261107 TCAAATTTCG
Statistics
Matches: 282, Mismatches: 52, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
128 9 0.03
129 1 0.00
130 191 0.68
131 53 0.19
132 27 0.10
133 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (130 bp):
TAAAGGGATATTCGATTATTTTGAACAATCGAGAAATTGCAACCCAACACGTTAGGGCACGATTC
CACGAATTGCCAAACACCAGAAATCGCCCTCATTTTAGGGATTTTAAAAGACACGAGCAAAATTT
Found at i:1261121 original size:130 final size:130
Alignment explanation
Indices: 1260760--1261125 Score: 455
Period size: 130 Copynumber: 2.8 Consensus size: 130
1260750 AAGCCGAGTG
* * * * * *
1260760 AAATTTTGAAGGGATATTTGATTATTTTAAAC-AATCGAGAAATTGCTACCCAACATGTTAGGGC
1 AAATTTTGAAGGGATATTCGATTATTTTGAGCAAAT-GCGAAATTGCAACCCAACACGTTAGGGC
* * * * * * * * *
1260824 ACGATCCCACGAATTGCCAAATACCAGATATCGCCTTCATTTTAGGGATTTTAAAAGACACGAGC
65 ACGATTCCACGAATTGCCAAACATCAAATATCGTCTTCGTTTAAGGGATGTTAAAAGACACGAAC
1260889 A
130 A
* *
1260890 AAATTTTAAAGTGATATTCGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCA
1 AAATTTTGAAGGGATATTCGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCA
* * * * **
1260955 CGATTCCACGAATTGCCAAACATCAAATCTCATCTTCGTTTAAGGGATGTTAAAAGATATGAATG
66 CGATTCCACGAATTGCCAAACATCAAATATCGTCTTCGTTTAAGGGATGTTAAAAGACACGAACA
* * *
1261020 GAATTTCGAAGGGAAATTCGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCA
1 AAATTTTGAAGGGATATTCGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCA
* * *
1261085 CGATTCCGCGAATTGCCGAACATCAAATTTCGTCTTCGTTT
66 CGATTCCACGAATTGCCAAACATCAAATATCGTCTTCGTTT
1261126 TGAAGAATTT
Statistics
Matches: 203, Mismatches: 32, Indels: 2
0.86 0.14 0.01
Matches are distributed among these distances:
130 200 0.99
131 3 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (130 bp):
AAATTTTGAAGGGATATTCGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCA
CGATTCCACGAATTGCCAAACATCAAATATCGTCTTCGTTTAAGGGATGTTAAAAGACACGAACA
Found at i:1261848 original size:2 final size:2
Alignment explanation
Indices: 1261841--1261871 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1261831 ATGCTTATGA
1261841 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1261872 AAAGAGTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1264391 original size:132 final size:132
Alignment explanation
Indices: 1264198--1264728 Score: 776
Period size: 132 Copynumber: 4.0 Consensus size: 132
1264188 TCCACTGGAG
** * ** * * *
1264198 ACGAGATCTGCAATTGTCAGCCTACTCCACTACAACTTTAAAGATCTAGGGT-GATGGCTTAAAT
1 ACGAGATCTAAAATT-TCAACCTACTCCACTACAACTTTAGGGAGCTAGGTTAG-TGACTTAAAT
* * * * * *
1264262 CTGCTTCACTGCAACTTCAGGAAGTCAAGATTCATCATATTCGATCTGCTCCACTGCAACTTCGG
64 CTGCTTCACTGCAACCTCAAGAAGTCGAGATTCATCGTCTTCGATCTGCTCCACTGCAACTTCAG
1264327 GGAA
129 GGAA
*
1264331 ACGAGATCTAAAATTTCAACCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATAT
1 ACGAGATCTAAAATTTCAACCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCT
* * * *
1264396 GCTTCACTACAACCTCAGGAAGTCGAGATTCGTTGTCTTCGATCTGCTCCACTGCAACTTCAGGG
66 GCTTCACTGCAACCTCAAGAAGTCGAGATTCATCGTCTTCGATCTGCTCCACTGCAACTTCAGGG
1264461 AA
131 AA
*
1264463 ACGGGATCTAAAATTTCAACCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCT
1 ACGAGATCTAAAATTTCAACCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCT
* *
1264528 GCTTCACTGCAACCTCAAGAAGTCGAGATTCGTCGTCTTCGATCTGCTCCGCTGCAACTTCAGGG
66 GCTTCACTGCAACCTCAAGAAGTCGAGATTCATCGTCTTCGATCTGCTCCACTGCAACTTCAGGG
1264593 AA
131 AA
* *
1264595 ACAAGGTCTAAAATTTCAACCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCT
1 ACGAGATCTAAAATTTCAACCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCT
* * * * *
1264660 GCTTCACTGCAACTTTAAGAAGTCGAGATTCATCGTCTTTGATCTGTTCCACTGTAACTTCAGGG
66 GCTTCACTGCAACCTCAAGAAGTCGAGATTCATCGTCTTCGATCTGCTCCACTGCAACTTCAGGG
1264725 AA
131 AA
1264727 AC
1 AC
1264729 AGGATCTGTG
Statistics
Matches: 364, Mismatches: 33, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
132 350 0.96
133 14 0.04
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (132 bp):
ACGAGATCTAAAATTTCAACCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCT
GCTTCACTGCAACCTCAAGAAGTCGAGATTCATCGTCTTCGATCTGCTCCACTGCAACTTCAGGG
AA
Found at i:1276773 original size:130 final size:129
Alignment explanation
Indices: 1276554--1276899 Score: 412
Period size: 130 Copynumber: 2.7 Consensus size: 129
1276544 CTAGAAAAGC
* * * * *
1276554 CGAGTGAAATTTTGAAGGGATATTTGATTATTTTAAAC-AATCGAGAAATTGCTA-CCAACACGT
1 CGAGTGAAATTTTGAAGGGATATTCGATTATTTTGAGCAAAT-GCGAAATTGCAACCCAACACGT
* * * * * *
1276617 TAGGGCATGATCCCACGAATTACCAAATACCAGATAT-TGCA-TTCATTTTAGGGATTTTAAAAG
65 TAGGGCATGATTCCGCGAATTGCCAAACACCA-A-ATCT-CACTTCATTTAAGGGATGTTAAAAG
1276680 ACA
127 ACA
* * *
1276683 CGAGCGAAATTTTAAAGTGATATTCGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTT
1 CGAGTGAAATTTTGAAGGGATATTCGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTT
* * * *
1276748 AGGGCACGATTCCGCGAATTGCCAAACATCAAATCTCATCTTCGTTTAAGGGATGTTAAAAGATA
66 AGGGCATGATTCCGCGAATTGCCAAACACCAAATCTCA-CTTCATTTAAGGGATGTTAAAAGACA
* * * * *
1276813 TGAATGGAATTTCGAAGGGAAATTCGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTT
1 CGAGTGAAATTTTGAAGGGATATTCGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTT
1276878 AGGGCATGATTCCGCGAATTGC
66 AGGGCATGATTCCGCGAATTGC
1276900 GGAACATCAA
Statistics
Matches: 185, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
128 4 0.02
129 44 0.24
130 137 0.74
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (129 bp):
CGAGTGAAATTTTGAAGGGATATTCGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTT
AGGGCATGATTCCGCGAATTGCCAAACACCAAATCTCACTTCATTTAAGGGATGTTAAAAGACA
Found at i:1278420 original size:2 final size:2
Alignment explanation
Indices: 1278413--1278450 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1278403 ACATGCGTAA
1278413 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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 A
1278451 ATCATATTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1287606 original size:20 final size:20
Alignment explanation
Indices: 1287581--1287618 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1287571 AGATAGGGGC
1287581 ACATGCCCGTGTGGCCTGGG
1 ACATGCCCGTGTGGCCTGGG
1287601 ACATGCCCGTGTGGCCTG
1 ACATGCCCGTGTGGCCTG
1287619 CCCATGTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.32, G:0.37, T:0.21
Consensus pattern (20 bp):
ACATGCCCGTGTGGCCTGGG
Found at i:1288484 original size:53 final size:52
Alignment explanation
Indices: 1288414--1288552 Score: 136
Period size: 52 Copynumber: 2.7 Consensus size: 52
1288404 CACATAACAT
* * * *
1288414 ACCGATG-CTATATCCTAGATATGGTTTTATACGGGATCACATTATCACATCAC
1 ACCGATGTC-ATAGCCTAGATATGGTCTTATACGGGAACACA-AATCACATCAC
* * * ***
1288467 ACCGATGTCATAGCCTAGTTATGGTCTTATATGGGAACGCAAATCACATTGT
1 ACCGATGTCATAGCCTAGATATGGTCTTATACGGGAACACAAATCACATCAC
** *
1288519 ACCGATGTCATAGCCCGGCTATGGTCTTATACGG
1 ACCGATGTCATAGCCTAGATATGGTCTTATACGG
1288553 AAGTATATAT
Statistics
Matches: 71, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
52 37 0.52
53 33 0.46
54 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (52 bp):
ACCGATGTCATAGCCTAGATATGGTCTTATACGGGAACACAAATCACATCAC
Found at i:1298830 original size:42 final size:44
Alignment explanation
Indices: 1298764--1298867 Score: 104
Period size: 47 Copynumber: 2.3 Consensus size: 44
1298754 TATAGTTCAA
** *
1298764 CTATGGTCTTACACATTTTTACATA-A-TGATGCCATAGCCCAG
1 CTATGGTCTTACACATAATCACATACACTGATGCCATAGCCCAG
* * *
1298806 CTATGGTCTTACACGTAATCACATATCTCACTGATGTCATATCCCAG
1 CTATGGTCTTACACATAATCACATA---CACTGATGCCATAGCCCAG
*
1298853 ATATGGTCTTACACA
1 CTATGGTCTTACACA
1298868 GTAGCATATA
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
42 21 0.43
46 1 0.02
47 27 0.55
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (44 bp):
CTATGGTCTTACACATAATCACATACACTGATGCCATAGCCCAG
Found at i:1298852 original size:47 final size:47
Alignment explanation
Indices: 1298790--1298915 Score: 139
Period size: 47 Copynumber: 2.7 Consensus size: 47
1298780 TTTTACATAA
* * *
1298790 TGATGCCATAGCCCAGCTATGGTCTTACAC-GTAATCACATATCTCAC
1 TGATGCCATATCCCAGCTATGGTCTTACACAGT-AGCACATATCACAC
* * *
1298837 TGATGTCATATCCCAGATATGGTCTTACACAGTAGCATATATCACAC
1 TGATGCCATATCCCAGCTATGGTCTTACACAGTAGCACATATCACAC
* * *
1298884 CGATACCATATCCCAGAC-ATGGTCTTATACAG
1 TGATGCCATATCCCAG-CTATGGTCTTACACAG
1298916 AAATCGCTTG
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
47 64 0.97
48 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (47 bp):
TGATGCCATATCCCAGCTATGGTCTTACACAGTAGCACATATCACAC
Found at i:1298976 original size:31 final size:31
Alignment explanation
Indices: 1298939--1299109 Score: 254
Period size: 31 Copynumber: 5.5 Consensus size: 31
1298929 CTTGTAGCCA
*
1298939 AAGCTACCACTATTCACTGATCAGGTAGCTG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
** *
1298970 GTGCTACCA-TTTCTCACTGATCAGGTAGCCG
1 AAGCTACCACTTT-TCACTGATCAGGTAGCTG
* * * *
1299001 GAGCTACTACTTTTCACTGATCAGGCAGCCG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
1299032 AAGCTACCACTTTTCACTGATCAGGTAGCTG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
1299063 AAGCTACCACTTTTCACTGATCAGGTAGCTG
1 AAGCTACCACTTTTCACTGATCAGGTAGCTG
1299094 AAGCTACCACTTTTCA
1 AAGCTACCACTTTTCA
1299110 GTTGTCACTT
Statistics
Matches: 127, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
30 2 0.02
31 122 0.96
32 3 0.02
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.28
Consensus pattern (31 bp):
AAGCTACCACTTTTCACTGATCAGGTAGCTG
Found at i:1299186 original size:50 final size:50
Alignment explanation
Indices: 1299087--1299263 Score: 237
Period size: 50 Copynumber: 3.5 Consensus size: 50
1299077 CACTGATCAG
* * * * *
1299087 GTAGCTGAAGCTACCACTTTTCAGTTGTCACTTGCCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCACTTGTCATTGATCAGATAAGT
* *
1299138 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCTTTAATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCATTGATCAGATAAGT
* * * * *
1299188 GTAGCCGAAGTTATTACTTATCACTTTCATTTATCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCATTGATCAGATAAGT
1299238 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
1299264 GTTTCCATGG
Statistics
Matches: 111, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 89 0.80
51 22 0.20
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCATTGATCAGATAAGT
Found at i:1304051 original size:21 final size:21
Alignment explanation
Indices: 1304013--1304053 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1304003 AGACGAGCAA
* *
1304013 TACTCCACAGCAGATGGAGTG
1 TACTCCAAAACAGATGGAGTG
*
1304034 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGATGGAGT
1304054 TTGAGCAGAT
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:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGATGGAGTG
Found at i:1312044 original size:2 final size:2
Alignment explanation
Indices: 1312031--1312070 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1312021 CTCTATACCT
*
1312031 TA TA TT 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
1312071 ATCTTTTCCG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1315370 original size:43 final size:43
Alignment explanation
Indices: 1315317--1315398 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
1315307 TAAATAAAAT
1315317 TCTGAAATATTCAAGATGAGTTTTCAATTAAATTTTTATAGAC
1 TCTGAAATATTCAAGATGAGTTTTCAATTAAATTTTTATAGAC
* * *
1315360 TCTGTAATATTGAAGATGAGTTTTTAATTAAATTTTTAT
1 TCTGAAATATTCAAGATGAGTTTTCAATTAAATTTTTAT
1315399 GGACAAAGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.46
Consensus pattern (43 bp):
TCTGAAATATTCAAGATGAGTTTTCAATTAAATTTTTATAGAC
Found at i:1320621 original size:61 final size:61
Alignment explanation
Indices: 1320526--1320647 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
1320516 AAGAAACCCG
1320526 ACCATATGGATGGCGTGGGTAACAGATTTCATTAATTTCTTCAAAACCAAATCTGTCATGA
1 ACCATATGGATGGCGTGGGTAACAGATTTCATTAATTTCTTCAAAACCAAATCTGTCATGA
*
1320587 ACCATATGGATGGTGTGGGTAACAGATTTCATTAATTTCTTCAAAACCAAATCTGTCATGA
1 ACCATATGGATGGCGTGGGTAACAGATTTCATTAATTTCTTCAAAACCAAATCTGTCATGA
1320648 CGTGTGAATA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (61 bp):
ACCATATGGATGGCGTGGGTAACAGATTTCATTAATTTCTTCAAAACCAAATCTGTCATGA
Found at i:1324847 original size:26 final size:24
Alignment explanation
Indices: 1324816--1324889 Score: 82
Period size: 26 Copynumber: 3.1 Consensus size: 24
1324806 TAAGTTGTAT
1324816 AAGACAATTTTAAATAAATATACATA
1 AAGACAATTTTAAATAAATAT--ATA
1324842 AAGACAAGTTTTAAAT-AATATATA
1 AAGACAA-TTTTAAATAAATATATA
* *
1324866 AAGA-AATCTAAAATAAATAT-TA
1 AAGACAATTTTAAATAAATATATA
1324888 AA
1 AA
1324890 AGGCTCAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
22 10 0.23
23 7 0.16
24 7 0.16
26 12 0.27
27 8 0.18
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.30
Consensus pattern (24 bp):
AAGACAATTTTAAATAAATATATA
Found at i:1326092 original size:18 final size:16
Alignment explanation
Indices: 1326063--1326100 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 16
1326053 ATTTAAGAAA
1326063 AAAAGAATAAAAAAAT
1 AAAAGAATAAAAAAAT
1326079 AAAAGATATAAAAAAAAT
1 AAAAGA-AT-AAAAAAAT
1326097 AAAA
1 AAAA
1326101 AAACGGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.30
17 2 0.10
18 12 0.60
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (16 bp):
AAAAGAATAAAAAAAT
Found at i:1326098 original size:9 final size:9
Alignment explanation
Indices: 1326061--1326103 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
1326051 TGATTTAAGA
1326061 AAAAAAGAAT
1 AAAAAA-AAT
1326071 -AAAAAAAT
1 AAAAAAAAT
* *
1326079 AAAAGATAT
1 AAAAAAAAT
1326088 AAAAAAAAT
1 AAAAAAAAT
1326097 AAAAAAA
1 AAAAAAA
1326104 CGGAAATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
8 3 0.11
9 25 0.89
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.12
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:1326902 original size:44 final size:44
Alignment explanation
Indices: 1326840--1327274 Score: 277
Period size: 44 Copynumber: 9.7 Consensus size: 44
1326830 CTATCTTTAG
** * *
1326840 TCTGCTCCGTTGCAACTTCAAGGAGATAAGACTTGTGACTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGACTTCAA
* * * * ***
1326884 CCTGCTCCACTACAACTTCAGGGAGATAAG-GTTG-G-TTTTGT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGACTTCAA
* * *
1326925 TCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTTTATTTATAGCTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG------T-GA-CTTCAA
* * * * * * **
1326977 TCTGTTCCATTGCATCTTCAAGGAAATAAGATTTGCT-ATCCTCTG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TGA-CTTCAA
* * *
1327022 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGTGATTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGACTTCAA
* * * * *
1327066 CCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTTTGGCTTCGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGACTTCAA
* * * ** *
1327110 TCTGC-CTCACTGCGACTTCAGGAAGATGAGATTTGCCATCTTCAG
1 TCTGCTC-CACTGCAACTTCAGGGAGATAAGATTTGTGA-CTTCAA
* ** * *
1327155 TCTTCTCCACTATAACTTCAGGGAGATAAGACTTGTAACTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGACTTCAA
* * * * *
1327199 CCTACTCCACTGCATCTTCAGGGAGATAAGGTTAGTGACTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGACTTCAA
* * **
1327243 TCTACTTCACTGCAACTTCAGAAAGATAAGAT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT
1327275 CTGCCATCTT
Statistics
Matches: 289, Mismatches: 87, Indels: 30
0.71 0.21 0.07
Matches are distributed among these distances:
41 28 0.10
42 4 0.01
43 4 0.01
44 157 0.54
45 64 0.22
46 1 0.00
47 1 0.00
52 30 0.10
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGACTTCAA
Found at i:1327163 original size:133 final size:133
Alignment explanation
Indices: 1326987--1327285 Score: 384
Period size: 133 Copynumber: 2.2 Consensus size: 133
1326977 TCTGTTCCAT
* * * * *
1326987 TGCATCTTCAAGGAA-ATAAGATTTGCTATCCTCTGTCTGCTCCACTGCAACTTCAGGGAGATAA
1 TGCAACTTC-AGGAAGATAAGATTTGCCATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAA
* * * ** * * *
1327051 GACTAGTGATTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTTTGGCTTCGATCTGCC
65 GACTAGTAACTTCAACCTACTCCACTGCAACTTCAGGGAGATAAGGTTAGTGACTTCAATCTACC
1327116 TCAC
130 TCAC
* * * *
1327120 TGCGACTTCAGGAAGATGAGATTTGCCATCTTCAGTCTTCTCCACTATAACTTCAGGGAGATAAG
1 TGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAG
* * *
1327185 ACTTGTAACTTCAACCTACTCCACTGCATCTTCAGGGAGATAAGGTTAGTGACTTCAATCTACTT
66 ACTAGTAACTTCAACCTACTCCACTGCAACTTCAGGGAGATAAGGTTAGTGACTTCAATCTACCT
1327250 CAC
131 CAC
* *
1327253 TGCAACTTCAGAAAGATAAGATCTGCCATCTTC
1 TGCAACTTCAGGAAGATAAGATTTGCCATCTTC
1327286 GTAGCTTCAA
Statistics
Matches: 141, Mismatches: 24, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
132 5 0.04
133 136 0.96
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (133 bp):
TGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAG
ACTAGTAACTTCAACCTACTCCACTGCAACTTCAGGGAGATAAGGTTAGTGACTTCAATCTACCT
CAC
Found at i:1341251 original size:14 final size:14
Alignment explanation
Indices: 1341232--1341258 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1341222 CTAATTCAAT
1341232 TTTATTAGAAGAAC
1 TTTATTAGAAGAAC
1341246 TTTATTAGAAGAA
1 TTTATTAGAAGAA
1341259 AAATTTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.15, T:0.37
Consensus pattern (14 bp):
TTTATTAGAAGAAC
Found at i:1345040 original size:28 final size:26
Alignment explanation
Indices: 1345008--1345066 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
1344998 AAAATCAACC
* *
1345008 ATATACAAAACAATTTAAAATAGATGAT
1 ATATACAAAA-AA-ATAAAATAAATGAT
* *
1345036 ATATATAAAAAAATAAATTAAATGAT
1 ATATACAAAAAAATAAAATAAATGAT
1345062 ATATA
1 ATATA
1345067 TAATAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 16 0.59
27 2 0.07
28 9 0.33
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (26 bp):
ATATACAAAAAAATAAAATAAATGAT
Found at i:1345052 original size:26 final size:28
Alignment explanation
Indices: 1345023--1345078 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 28
1345013 CAAAACAATT
*
1345023 TAAAATAGATGATATATATAA-AAA-AA
1 TAAAATAAATGATATATATAATAAATAA
*
1345049 TAAATTAAATGATATATATAATAAATAA
1 TAAAATAAATGATATATATAATAAATAA
1345077 TA
1 TA
1345079 TATGGAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 19 0.73
27 3 0.12
28 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (28 bp):
TAAAATAAATGATATATATAATAAATAA
Found at i:1345183 original size:26 final size:25
Alignment explanation
Indices: 1345152--1345218 Score: 77
Period size: 24 Copynumber: 2.7 Consensus size: 25
1345142 TAAGTTGTAT
1345152 AAGACAATTTTAAATAAACATACATA
1 AAGACAATTTTAAATAAA-ATACATA
*
1345178 AAGACAAGTTTTAAAT--AATATATA
1 AAGACAA-TTTTAAATAAAATACATA
*
1345202 AAGA-AATTTAAAATAAA
1 AAGACAATTTTAAATAAA
1345219 TATTAAGAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
22 7 0.19
23 2 0.06
24 11 0.31
25 1 0.03
26 7 0.19
27 8 0.22
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (25 bp):
AAGACAATTTTAAATAAAATACATA
Found at i:1345213 original size:21 final size:21
Alignment explanation
Indices: 1345175--1345226 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
1345165 ATAAACATAC
*
1345175 ATAAAGACAAGTTTTAAATAATAT
1 ATAAAGA-AA-TTTAAAATAA-AT
1345199 ATAAAGAAATTTAAAATAAAT
1 ATAAAGAAATTTAAAATAAAT
*
1345220 ATTAAGA
1 ATAAAGA
1345227 GGCTCAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 8 0.31
22 9 0.35
23 2 0.08
24 7 0.27
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.31
Consensus pattern (21 bp):
ATAAAGAAATTTAAAATAAAT
Found at i:1347481 original size:17 final size:18
Alignment explanation
Indices: 1347459--1347496 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1347449 ATTTCATAAC
1347459 CCATTACA-GACCCAAAA
1 CCATTACAGGACCCAAAA
*
1347476 CCATTATAGTGACCCAAAA
1 CCATTACAG-GACCCAAAA
1347495 CC
1 CC
1347497 CAAATACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
19 11 0.61
ACGTcount: A:0.42, C:0.34, G:0.08, T:0.16
Consensus pattern (18 bp):
CCATTACAGGACCCAAAA
Found at i:1357036 original size:24 final size:23
Alignment explanation
Indices: 1356999--1357044 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1356989 GATAAATTAG
1356999 TTTTTCTAGTAAAAACTAAGGTAT
1 TTTTTCTAGTAAAAACT-AGGTAT
*
1357023 TTTTTCTA-TGAAAACCTAGGTA
1 TTTTTCTAGT-AAAAACTAGGTA
1357045 ATTCCCTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (23 bp):
TTTTTCTAGTAAAAACTAGGTAT
Found at i:1358335 original size:21 final size:18
Alignment explanation
Indices: 1358318--1358363 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
1358308 TTATATTGAG
1358318 TTAATTTTGATAATTATTAA
1 TTAATTTT-AT-ATTATTAA
* *
1358338 TTAAATTTATATTATTAT
1 TTAATTTTATATTATTAA
1358356 TTAATTTT
1 TTAATTTT
1358364 TTTTGAGTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 14 0.61
19 2 0.09
20 7 0.30
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
TTAATTTTATATTATTAA
Found at i:1358681 original size:21 final size:21
Alignment explanation
Indices: 1358657--1358698 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1358647 ATTTTGAGCA
1358657 ATTTAAT-TTTTCTTTTACATT
1 ATTTAATCTTTT-TTTTACATT
* *
1358678 ATTTTATCTTTTTTTTTCATT
1 ATTTAATCTTTTTTTTACATT
1358699 CTCTTTTGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (21 bp):
ATTTAATCTTTTTTTTACATT
Found at i:1363321 original size:2 final size:2
Alignment explanation
Indices: 1363314--1363338 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1363304 GTACAATAAA
1363314 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 A
1363339 GTAATAGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1363763 original size:3 final size:3
Alignment explanation
Indices: 1363739--1363799 Score: 70
Period size: 3 Copynumber: 19.7 Consensus size: 3
1363729 AAGTACCTAT
*
1363739 TAA TAA TAT TATA TAA -ATA TAA TAAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TA-A TAA T-AA TAA TAA TAA TAA TAA TAA TAA
*
1363786 TAA TAA CAA TAA TA
1 TAA TAA TAA TAA TA
1363800 GCGATAATAG
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 1 0.02
3 43 0.86
4 6 0.12
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1363992 original size:3 final size:3
Alignment explanation
Indices: 1363986--1364275 Score: 129
Period size: 3 Copynumber: 95.7 Consensus size: 3
1363976 ATAGTAAATG
* * *
1363986 TAA TAA TAA TAA TAA TAA TAT TAA GT-A TAG T-A TAAA TAA TATG TACA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA T-AA TAA TA-A TA-A
* *
1364033 TAA CAG TAA TAA TAA TAA GTAA TAA TAA TAA TAA TAA T-A TAGA -AA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA-A TAA
* * * * * * * * *
1364078 T-T TAA AAA AAA AAA GAG TAA -ACA CAA T-A TAA TAA TAT TGA -AA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
* * *
1364120 TAA -AA T-A TACA CTAA TAT TTA TGAA TAA TAA TAG TAA -ATA TAA TAA
1 TAA TAA TAA TA-A -TAA TAA TAA T-AA TAA TAA TAA TAA TA-A TAA TAA
* * *
1364166 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAT TAA GT-A TAG T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA
* * * *
1364210 TAAA TAA TATG TACA TAA CAG TAA TAA TAA TAA GTAA CAA TAA TAA TAA
1 T-AA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
1364259 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
1364276 TAGAAATTCG
Statistics
Matches: 216, Mismatches: 44, Indels: 54
0.69 0.14 0.17
Matches are distributed among these distances:
2 17 0.08
3 170 0.79
4 27 0.12
5 2 0.01
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1364040 original size:23 final size:22
Alignment explanation
Indices: 1364020--1364071 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
1364010 GTATAGTATA
*
1364020 AATAATATGTACATAACAGTAAT
1 AATAATAAGTA-ATAACAGTAAT
* *
1364043 AATAATAAGTAATAATAATAAT
1 AATAATAAGTAATAACAGTAAT
1364065 AATAATA
1 AATAATA
1364072 TAGAAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.31
Consensus pattern (22 bp):
AATAATAAGTAATAACAGTAAT
Found at i:1364324 original size:16 final size:15
Alignment explanation
Indices: 1364300--1364334 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
1364290 AACTAAACAT
*
1364300 AATATAATAATATTAA
1 AATAAAATAATA-TAA
1364316 AATAAAATAATATAA
1 AATAAAATAATATAA
1364331 AATA
1 AATA
1364335 CTATGTAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATAAAATAATATAA
Found at i:1364351 original size:24 final size:24
Alignment explanation
Indices: 1364324--1364376 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
1364314 AAAATAAAAT
*
1364324 AATATAAAATAC-TATGTAGATATA
1 AATATAAAATACGTATGTAAATA-A
* *
1364348 AATA-CATATACGTATGTAAATAA
1 AATATAAAATACGTATGTAAATAA
1364371 AATATA
1 AATATA
1364377 TACTAATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.55, C:0.06, G:0.08, T:0.32
Consensus pattern (24 bp):
AATATAAAATACGTATGTAAATAA
Found at i:1365233 original size:15 final size:16
Alignment explanation
Indices: 1365202--1365238 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
1365192 TTTTTGGATT
1365202 TTTTTTTGCTGGAAAA
1 TTTTTTTGCTGGAAAA
1365218 TTTTTTTGCTGG-AAA
1 TTTTTTTGCTGGAAAA
1365233 TTTTTT
1 TTTTTT
1365239 GCTCTCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.19, C:0.05, G:0.16, T:0.59
Consensus pattern (16 bp):
TTTTTTTGCTGGAAAA
Found at i:1366943 original size:28 final size:28
Alignment explanation
Indices: 1366903--1366958 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1366893 CCAATATGAA
1366903 CGTTTAGCTCCTGCTGTACTTTACTCAT
1 CGTTTAGCTCCTGCTGTACTTTACTCAT
1366931 CGTTTAGCTCCTGCTGTACTTTACTCAT
1 CGTTTAGCTCCTGCTGTACTTTACTCAT
1366959 TGCATCACGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.14, C:0.29, G:0.14, T:0.43
Consensus pattern (28 bp):
CGTTTAGCTCCTGCTGTACTTTACTCAT
Found at i:1377239 original size:43 final size:43
Alignment explanation
Indices: 1377191--1377375 Score: 291
Period size: 43 Copynumber: 4.3 Consensus size: 43
1377181 TTAAAAAAAT
1377191 GCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTCCCACAAAC
* *
1377234 GCCGCTAAAGGTCATGACCTTTAGCAGCGCTTTTCCGACAAAC
1 GCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTCCCACAAAC
*
1377277 GCCGCTAAATG-CATGACCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTCCCACAAAC
* * * **
1377319 GTCGCTAATGGTCATGACCTTTAGCGGGGCTGATCCCACAAAC
1 GCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTCCCACAAAC
1377362 GCCGCTAAAGGTCA
1 GCCGCTAAAGGTCA
1377376 CAAAATTTAA
Statistics
Matches: 128, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
42 37 0.29
43 91 0.71
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.23
Consensus pattern (43 bp):
GCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTCCCACAAAC
Found at i:1377360 original size:85 final size:86
Alignment explanation
Indices: 1377191--1377375 Score: 291
Period size: 85 Copynumber: 2.2 Consensus size: 86
1377181 TTAAAAAAAT
1377191 GCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGGTCATGACCTTT
1 GCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGGTCATGACCTTT
** *
1377256 AGCAGCGCTTTTCCGACAAAC
66 AGCAGCGCTGATCCCACAAAC
* * *
1377277 GCCGCTAAATG-CATGACCTTTAGCGGCGCTTTTCCCACAAACGTCGCTAATGGTCATGACCTTT
1 GCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGGTCATGACCTTT
* *
1377341 AGCGGGGCTGATCCCACAAAC
66 AGCAGCGCTGATCCCACAAAC
1377362 GCCGCTAAAGGTCA
1 GCCGCTAAAGGTCA
1377376 CAAAATTTAA
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
85 77 0.87
86 12 0.13
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.23
Consensus pattern (86 bp):
GCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGGTCATGACCTTT
AGCAGCGCTGATCCCACAAAC
Found at i:1377684 original size:19 final size:19
Alignment explanation
Indices: 1377639--1377685 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
1377629 TAAATATTAA
*
1377639 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
1377658 AATCAAAACT-AAAATAAAT
1 AAT-AAAAATAAAAATAAAG
1377677 AATAAAAAT
1 AATAAAAAT
1377686 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:1377960 original size:23 final size:23
Alignment explanation
Indices: 1377924--1378149 Score: 219
Period size: 23 Copynumber: 9.9 Consensus size: 23
1377914 AAACAGATGC
* *
1377924 CAATTTACAACATTTAAGCACTT
1 CAATTTACAGCATTTAAACACTT
*
1377947 CAATTTATAGCATTTAAACACTT
1 CAATTTACAGCATTTAAACACTT
* *
1377970 CAATTTGCAGCACTTT-ATCA-TCT
1 CAATTTACAGCA-TTTAAACACT-T
* * *
1377993 CAATTAACAACATTTATACAAC-T
1 CAATTTACAGCATTTAAAC-ACTT
* *
1378016 CAA-TTACAGCAATAAAACA-TCT
1 CAATTTACAGCATTTAAACACT-T
* **
1378038 CAATTTCCAGCAACTAAACACTT
1 CAATTTACAGCATTTAAACACTT
* *
1378061 CAATTTACAACATTTAAACACTG
1 CAATTTACAGCATTTAAACACTT
*
1378084 CAATTTACAACATTTAAACACTT
1 CAATTTACAGCATTTAAACACTT
1378107 CAATTTACAGCATTTAAACACTT
1 CAATTTACAGCATTTAAACACTT
* *
1378130 TAATTTGCAGCATTTAAACA
1 CAATTTACAGCATTTAAACA
1378150 ACAGCATCCA
Statistics
Matches: 166, Mismatches: 28, Indels: 18
0.78 0.13 0.08
Matches are distributed among these distances:
21 1 0.01
22 18 0.11
23 142 0.86
24 5 0.03
ACGTcount: A:0.41, C:0.22, G:0.04, T:0.33
Consensus pattern (23 bp):
CAATTTACAGCATTTAAACACTT
Found at i:1381813 original size:41 final size:40
Alignment explanation
Indices: 1381731--1381834 Score: 118
Period size: 41 Copynumber: 2.5 Consensus size: 40
1381721 TTTAAAAAAC
* * * *
1381731 AACGCCACTATAGTTTAGTTTTTTGTGGCGTTTTTGATAAA
1 AACG-CACTATAGCTTAATTTTTTGTGGCATTTTTCATAAA
* *
1381772 AATGTCACTATAGCTTAATTTTTTGTGGCATTTTTCCTAAA
1 AACG-CACTATAGCTTAATTTTTTGTGGCATTTTTCATAAA
*
1381813 AACGCTACTATTGCTTAATTTT
1 AACGC-ACTATAGCTTAATTTT
1381835 AATTTTTTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 1 0.02
41 52 0.98
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.45
Consensus pattern (40 bp):
AACGCACTATAGCTTAATTTTTTGTGGCATTTTTCATAAA
Found at i:1381982 original size:7 final size:7
Alignment explanation
Indices: 1381980--1382026 Score: 85
Period size: 7 Copynumber: 6.7 Consensus size: 7
1381970 GTTTTTTAGT
1381980 TTTTTAA
1 TTTTTAA
1381987 TTTTTAA
1 TTTTTAA
1381994 TTTTTAA
1 TTTTTAA
1382001 TTTTTAA
1 TTTTTAA
*
1382008 ATTTTAA
1 TTTTTAA
1382015 TTTTTAA
1 TTTTTAA
1382022 TTTTT
1 TTTTT
1382027 TTGAGCATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTTAA
Found at i:1381997 original size:21 final size:21
Alignment explanation
Indices: 1381972--1382027 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
1381962 AAATATTAGT
*
1381972 TTTTTAGTTTTTTAATTTTTAA
1 TTTTTA-TTTTTTAAATTTTAA
*
1381994 TTTTTAATTTTTAAATTTTAA
1 TTTTTATTTTTTAAATTTTAA
1382015 TTTTTAATTTTTT
1 TTTTT-ATTTTTT
1382028 TGAGCATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTTATTTTTTAAATTTTAA
Found at i:1382045 original size:9 final size:8
Alignment explanation
Indices: 1381979--1382052 Score: 57
Period size: 7 Copynumber: 9.2 Consensus size: 8
1381969 AGTTTTTTAG
*
1381979 TTTTTTAA
1 TTTTTAAA
1381987 TTTTT-AA
1 TTTTTAAA
1381994 TTTTT-AA
1 TTTTTAAA
1382001 TTTTTAAA
1 TTTTTAAA
1382009 -TTTT-AA
1 TTTTTAAA
*
1382015 TTTTTAATT
1 TTTTTAA-A
*
1382024 TTTTTGAGCA
1 TTTTT-A-AA
1382034 TTTTTATAA
1 TTTTTA-AA
1382043 TTTTTAAA
1 TTTTTAAA
1382051 TT
1 TT
1382053 ATCATATAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
6 2 0.04
7 22 0.40
8 12 0.22
9 13 0.24
10 6 0.11
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.68
Consensus pattern (8 bp):
TTTTTAAA
Found at i:1382613 original size:21 final size:21
Alignment explanation
Indices: 1382582--1382647 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1382572 TATAACACTT
*
1382582 AACCCCAAACCCATAAGCCTTA
1 AACCCC-AACCCATAAACCTTA
* *
1382604 AACCCCAACCCTTAAACCATA
1 AACCCCAACCCATAAACCTTA
** *
1382625 AACCATAATCCATAAACCTTA
1 AACCCCAACCCATAAACCTTA
1382646 AA
1 AA
1382648 ATAGTAACTC
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
21 30 0.83
22 6 0.17
ACGTcount: A:0.45, C:0.36, G:0.02, T:0.17
Consensus pattern (21 bp):
AACCCCAACCCATAAACCTTA
Done.