Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008162.1 Hibiscus syriacus cultivar Beakdansim tig00110733_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3688897
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 16
Found at i:1178311 original size:2 final size:2
Alignment explanation
Indices: 1178304--1178334 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1178294 CTTACTCGTT
1178304 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1178335 GAGTTATCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1178579 original size:28 final size:28
Alignment explanation
Indices: 1178539--1178608 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
1178529 TCTGGTTTTA
1178539 TAATAATTGTTTTATATTAAATTATATG
1 TAATAATTGTTTTATATTAAATTATATG
1178567 TAATAATTGTTTTATATTAAATTATATG
1 TAATAATTGTTTTATATTAAATTATATG
*
1178595 -GATGAATTGTTTTA
1 TAAT-AATTGTTTTA
1178609 ATATGAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 2 0.05
28 38 0.95
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (28 bp):
TAATAATTGTTTTATATTAAATTATATG
Found at i:1178627 original size:28 final size:27
Alignment explanation
Indices: 1178543--1178627 Score: 75
Period size: 28 Copynumber: 3.0 Consensus size: 27
1178533 GTTTTATAAT
* *
1178543 AATTGTTTTATATTAAATTATATGTAAT-
1 AATTGTTTTATATGAAAATATATG--ATG
* *
1178571 AATTGTTTTATATTAAATTATATGGATG
1 AATTGTTTTATATGAAAATATAT-GATG
1178599 AATTGTTTTAATATGAAAATAGTAT-ATG
1 AATTGTTTT-ATATGAAAATA-TATGATG
1178627 A
1 A
1178628 TTTTTAATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
27 2 0.04
28 36 0.71
29 10 0.20
30 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (27 bp):
AATTGTTTTATATGAAAATATATGATG
Found at i:1179680 original size:2 final size:2
Alignment explanation
Indices: 1179669--1179697 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1179659 GTGCAACTTA
1179669 AT AT -T 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
1179698 GAGTTATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1186224 original size:16 final size:16
Alignment explanation
Indices: 1186203--1186234 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1186193 TTGACATCTG
*
1186203 ATTTTATTCATGTTTT
1 ATTTTATTAATGTTTT
1186219 ATTTTATTAATGTTTT
1 ATTTTATTAATGTTTT
1186235 TATACGATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.69
Consensus pattern (16 bp):
ATTTTATTAATGTTTT
Found at i:1192799 original size:27 final size:27
Alignment explanation
Indices: 1192769--1192823 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1192759 AAAATCAAAG
**
1192769 AAAATAAAAAAAATTGAAAATAAAATA
1 AAAATAAAAAAAACGGAAAATAAAATA
* *
1192796 AAAATTAAACAAACGGAAAATAAAATA
1 AAAATAAAAAAAACGGAAAATAAAATA
1192823 A
1 A
1192824 TAATGGGTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (27 bp):
AAAATAAAAAAAACGGAAAATAAAATA
Found at i:1196713 original size:63 final size:63
Alignment explanation
Indices: 1196635--1196759 Score: 214
Period size: 63 Copynumber: 2.0 Consensus size: 63
1196625 AGGGTGGGGC
* *
1196635 GTGATTTCATTAGGAGAAGGAGAAGGATGTGTGTTAGATATACCTTGTATTTCTGGAGGTGGA
1 GTGATTTCATGAGGAGAAGGAGAAGGATGTGTGTTAGATATACCTTGTATATCTGGAGGTGGA
* *
1196698 GTGATTTCATGAGGAGAATGAGAAGGATGTGTGTTAGATGTACCTTGTATATCTGGAGGTGG
1 GTGATTTCATGAGGAGAAGGAGAAGGATGTGTGTTAGATATACCTTGTATATCTGGAGGTGG
1196760 CGTTTCTTCT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.26, C:0.06, G:0.34, T:0.33
Consensus pattern (63 bp):
GTGATTTCATGAGGAGAAGGAGAAGGATGTGTGTTAGATATACCTTGTATATCTGGAGGTGGA
Found at i:1198542 original size:17 final size:17
Alignment explanation
Indices: 1198520--1198569 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
1198510 GGGGAGATAA
1198520 AAATTAAATAAAGAAAT
1 AAATTAAATAAAGAAAT
*
1198537 AAATTAATTAATA-AAAT
1 AAATTAAATAA-AGAAAT
*
1198554 AAATTGAGATAAAGAA
1 AAATT-AAATAAAGAA
1198570 GACTTATGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 20 0.74
18 7 0.26
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (17 bp):
AAATTAAATAAAGAAAT
Found at i:1199402 original size:71 final size:72
Alignment explanation
Indices: 1199324--1199461 Score: 224
Period size: 72 Copynumber: 1.9 Consensus size: 72
1199314 ATAAAGAAAA
* *
1199324 TAAATCCTAATTAAAATTCATAAAA-TATTTAAACTAAATTACCTAAAACAAAGATAAGATAAAA
1 TAAATCCTAATTAAAATACATAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAGATAAAA
1199388 TAATTCT
66 TAATTCT
* * *
1199395 TAAATCCTAATTAAAATACTTAAAACTATTTAAACTAAAATACCTAAACCAATGATAAGATAAAA
1 TAAATCCTAATTAAAATACATAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAGATAAAA
1199460 TA
66 TA
1199462 TAATATTTAA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
71 23 0.38
72 38 0.62
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (72 bp):
TAAATCCTAATTAAAATACATAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAGATAAAA
TAATTCT
Found at i:1201328 original size:23 final size:23
Alignment explanation
Indices: 1201298--1201349 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
1201288 AAAGTTGTAT
1201298 TTATAATTTGATGAGGGGAAGAG
1 TTATAATTTGATGAGGGGAAGAG
*
1201321 TTATAATTTGATGAGGGGCAGAG
1 TTATAATTTGATGAGGGGAAGAG
1201344 TTATAA
1 TTATAA
1201350 GTACATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.35, C:0.02, G:0.31, T:0.33
Consensus pattern (23 bp):
TTATAATTTGATGAGGGGAAGAG
Found at i:1203636 original size:75 final size:75
Alignment explanation
Indices: 1203547--1203705 Score: 178
Period size: 75 Copynumber: 2.1 Consensus size: 75
1203537 TTATTTAAGT
*** * *
1203547 ATTTATATTCGATTAAAATGTGAATATATTA-TTACGAATTTATATTCGATTGAAATAAAAATAT
1 ATTTATATTCGATT-AAATAAAAATATATTATTTACGAATTTATATTCAATTAAAATAAAAATAT
1203611 ATTGTTTATAA
65 ATTGTTTATAA
* * * **
1203622 ATTTTTATTTGATTAAATAAAAATATATTATTTATGAATTTATATTCAATTAAAATATGAATATA
1 ATTTATATTCGATTAAATAAAAATATATTATTTACGAATTTATATTCAATTAAAATAAAAATATA
* *
1203687 TT-ATTATGA
66 TTGTTTATAA
*
1203696 AGTTATATTC
1 ATTTATATTC
1203706 AATTGGAGTA
Statistics
Matches: 68, Mismatches: 15, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
74 25 0.37
75 43 0.63
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.47
Consensus pattern (75 bp):
ATTTATATTCGATTAAATAAAAATATATTATTTACGAATTTATATTCAATTAAAATAAAAATATA
TTGTTTATAA
Found at i:1203709 original size:37 final size:37
Alignment explanation
Indices: 1203547--1203705 Score: 176
Period size: 37 Copynumber: 4.3 Consensus size: 37
1203537 TTATTTAAGT
*** *
1203547 ATTTATATTCGATTAAAATGTGAATATATTATTACGA
1 ATTTATATTCGATTAAAATAAAAATATATTATTATGA
* * *
1203584 ATTTATATTCGATTGAAATAAAAATATATTGTTTATAA
1 ATTTATATTCGATTAAAATAAAAATATATT-ATTATGA
* *
1203622 ATTTTTATTTGATT-AAATAAAAATATATTATTTATGA
1 ATTTATATTCGATTAAAATAAAAATATATTA-TTATGA
* **
1203659 ATTTATATTCAATTAAAATATGAATATATTATTATGA
1 ATTTATATTCGATTAAAATAAAAATATATTATTATGA
*
1203696 AGTTATATTC
1 ATTTATATTC
1203706 AATTGGAGTA
Statistics
Matches: 102, Mismatches: 17, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
37 72 0.71
38 30 0.29
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.47
Consensus pattern (37 bp):
ATTTATATTCGATTAAAATAAAAATATATTATTATGA
Found at i:1206169 original size:29 final size:29
Alignment explanation
Indices: 1206129--1206204 Score: 134
Period size: 29 Copynumber: 2.6 Consensus size: 29
1206119 GCAGGAATCT
1206129 CTGCTCCATGCAGAGCTTCTGCAGCATTG
1 CTGCTCCATGCAGAGCTTCTGCAGCATTG
1206158 CTGCTCCATGCAGAGCTTCTGCAGCATTG
1 CTGCTCCATGCAGAGCTTCTGCAGCATTG
* *
1206187 CTGCTCCACGCAAAGCTT
1 CTGCTCCATGCAGAGCTT
1206205 TTGCTGCTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.18, C:0.33, G:0.22, T:0.26
Consensus pattern (29 bp):
CTGCTCCATGCAGAGCTTCTGCAGCATTG
Found at i:1206572 original size:27 final size:25
Alignment explanation
Indices: 1206481--1206570 Score: 94
Period size: 27 Copynumber: 3.5 Consensus size: 25
1206471 GGAGAAAAGG
1206481 TAATTTTATTATTTAAATTAATTT-A
1 TAATTTT-TTATTTAAATTAATTTAA
* *
1206506 T-ATTTTGTATTCAAATTAATTTAGA
1 TAATTTTTTATTTAAATTAATTTA-A
**
1206531 TTGTTTTTCTATTTAAATTAATTTAAA
1 TAATTTTT-TATTTAAATTAATTT-AA
1206558 TAATTTTTTATTT
1 TAATTTTTTATTT
1206571 TATCGAGTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
23 14 0.26
24 5 0.09
25 3 0.06
26 9 0.17
27 21 0.40
28 1 0.02
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.60
Consensus pattern (25 bp):
TAATTTTTTATTTAAATTAATTTAA
Found at i:1206791 original size:33 final size:31
Alignment explanation
Indices: 1206724--1206805 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 31
1206714 CATGTTCAAC
* *
1206724 ATTTCATTATTTATATTTTTTATTCAAATTA
1 ATTTAATTATTTTTATTTTTTATTCAAATTA
* *
1206755 ATTTAGATTATTTTTATTTTATTGTTTAAATTA
1 ATTTA-ATTATTTTTATTTT-TTATTCAAATTA
*
1206788 ATTTAAAT-TTTTTATTTT
1 ATTTAATTATTTTTATTTT
1206806 GTCTATTAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
31 14 0.32
32 15 0.34
33 15 0.34
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (31 bp):
ATTTAATTATTTTTATTTTTTATTCAAATTA
Found at i:1209212 original size:291 final size:291
Alignment explanation
Indices: 1208688--1209269 Score: 932
Period size: 291 Copynumber: 2.0 Consensus size: 291
1208678 ATACAACTAT
* * * * * *
1208688 TTGTCATCCACCAGAGGTGAGAGATCATAATGGTCGGCAATAATTTACAACACCGGAGAATATGC
1 TTGTCATCCACCAGAGATGAGAGAGCAGAATGGTCGGCAAGAATTTACAAAACCAGAGAATATGC
* * *
1208753 CCTCGCTGAATGAGCAGATTACCTATGATGATCAGACTCTCGAGAAACCACAATGACCACAACGA
66 CCTCGATGAATGAGCAGATTACCTATGATGATCAGACTCCCGAGAAACCACAACGACCACAACGA
* * * *
1208818 AATCGACGAGCCCGTTGACATTATTATTCAACAACACCCTATTATCGACAAGAATTATAAATGTT
131 AATCGACGAGCCCCTAGACATTATTATTCAACAACACCATATTATCAACAAGAATTATAAATGTT
* *
1208883 TTCTTGATCTTTGTATGAAAAATTACTATTAAATAAATGAGATTGGTATATGGCGATTGGGATAC
196 TTCTTGATATTTGTATGAAAAATTACTATTAAATAAATGAGATTGATATATGGCGATTGGGATAC
*
1208948 ATCATACAATGAGCTACCGTATATATATATA
261 ATCATACAATGAGCTACCGAATATATATATA
* *
1208979 TTGTCATCCACCGGAGATGGGAGAGCAGAATGGTCGGCAAGAATTTACAAAACCAGAGAATATGC
1 TTGTCATCCACCAGAGATGAGAGAGCAGAATGGTCGGCAAGAATTTACAAAACCAGAGAATATGC
* * *
1209044 CCTCGATGAATGAGCAGGTTACCTATGATGATCAGACTCCCGAGCAACCACAACGACCATAACGA
66 CCTCGATGAATGAGCAGATTACCTATGATGATCAGACTCCCGAGAAACCACAACGACCACAACGA
* * *
1209109 AATCGACGAGCCCCTAGACATTATTATTCAATAATACCAT-TTCATCAATAAGAATTATAAATGT
131 AATCGACGAGCCCCTAGACATTATTATTCAACAACACCATATT-ATCAACAAGAATTATAAATGT
1209173 TTTCTTGATATTTGTATGAAAAATTACTATTAAATAAATGAGATTGATATATGGCGATTGGGATA
195 TTTCTTGATATTTGTATGAAAAATTACTATTAAATAAATGAGATTGATATATGGCGATTGGGATA
1209238 CATCATACAATGAGCTACCGAATATATATATA
260 CATCATACAATGAGCTACCGAATATATATATA
1209270 ATATATCAAC
Statistics
Matches: 266, Mismatches: 24, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
290 2 0.01
291 264 0.99
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (291 bp):
TTGTCATCCACCAGAGATGAGAGAGCAGAATGGTCGGCAAGAATTTACAAAACCAGAGAATATGC
CCTCGATGAATGAGCAGATTACCTATGATGATCAGACTCCCGAGAAACCACAACGACCACAACGA
AATCGACGAGCCCCTAGACATTATTATTCAACAACACCATATTATCAACAAGAATTATAAATGTT
TTCTTGATATTTGTATGAAAAATTACTATTAAATAAATGAGATTGATATATGGCGATTGGGATAC
ATCATACAATGAGCTACCGAATATATATATA
Found at i:1210711 original size:81 final size:81
Alignment explanation
Indices: 1210595--1211064 Score: 529
Period size: 81 Copynumber: 5.8 Consensus size: 81
1210585 ATTTCTTTAT
* * * * * * * *
1210595 TCTTTTACCCAAAGGTATTTAGCCTTTCATCTAACTTGCATATTTGACACTTTTCTATCAAATAC
1 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTTGCATACTTGACACATTTCTACCAAATGC
*
1210660 ACAACTAGTCCATT-A
66 ACAGCTAGTCCATTCA
* * * * *
1210675 TTCTTTTAATCAATGGTATTTAACCATTCATTTAACTTGCATATTTGACACCTTTC-AGCCAAAT
1 -TCTTTTACTCAACGGTATTTAACCATTCATCTAACTTGCATACTTGACACATTTCTA-CCAAAT
*
1210739 GTACAGCTAGGT-CATTCA
64 GCACAGCTA-GTCCATTCA
* * *
1210757 TCTTTTACTCAACGGTATTTAACCCTTCATCTAACTGGCATACTTGACACATTTCTTCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTTGCATACTTGACACATTTCTACCAAATGC
*
1210822 ACAGCTAGACCATTCA
66 ACAGCTAGTCCATTCA
* * * * * *
1210838 TCTTTTACTCAACGTTATTTAACCGTTCTTCTAACTTACATACTTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTTGCATACTTGACACATTTCTACCAAATGC
1210903 ACAGCTA-TGCCATTCA
66 ACAGCTAGT-CCATTCA
* * *
1210919 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATACTTGACACATTTCTGCCAAAAGC
1 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTTGCATACTTGACACATTTCTACCAAATGC
* * * *
1210984 ACAACTAG-GCGTTCT
66 ACAGCTAGTCCATTCA
* * * *
1210999 TCTTTTACTCAACGGTATTTAACCGTTCATCTAAC-TGACATACTTGACACTTTTTTGCCAAATG
1 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTTG-CATACTTGACACATTTCTACCAAATG
1211063 CA
65 CA
1211065 TAGTTTGGCC
Statistics
Matches: 336, Mismatches: 45, Indels: 17
0.84 0.11 0.04
Matches are distributed among these distances:
79 1 0.00
80 65 0.19
81 267 0.79
82 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.36
Consensus pattern (81 bp):
TCTTTTACTCAACGGTATTTAACCATTCATCTAACTTGCATACTTGACACATTTCTACCAAATGC
ACAGCTAGTCCATTCA
Found at i:1210887 original size:162 final size:161
Alignment explanation
Indices: 1210595--1211064 Score: 613
Period size: 162 Copynumber: 2.9 Consensus size: 161
1210585 ATTTCTTTAT
* * * * * * * *
1210595 TCTTTTACCCAAAGGTATTTAGCCTTTCATCTAACTTGCATATTTGACACTTTTCTAT-CAAATA
1 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATACTTGACACATTTCT-TCCAAATG
* * * * *
1210659 CACAACTAGTCCATT-ATTCTTTTAATCAATGGTATTTAACCATTCATT-TAACTTGCATATTTG
65 CACAACTAG-CCATTCA-TCTTTTACTCAACGGTATTTAACCGTTC-TTCTAACTTACATACTTG
* * *
1210722 ACACCTTTCAGCCAAATGTACAGCTAGGTCATTCA
127 ACACCTTTCTGCCAAATGCACAGCTAGGCCATTCA
*
1210757 TCTTTTACTCAACGGTATTTAACCCTTCATCTAACTGGCATACTTGACACATTTCTTCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATACTTGACACATTTCTTCCAAATGC
* *
1210822 ACAGCTAGACCATTCATCTTTTACTCAACGTTATTTAACCGTTCTTCTAACTTACATACTTGACA
66 ACAACTAG-CCATTCATCTTTTACTCAACGGTATTTAACCGTTCTTCTAACTTACATACTTGACA
*
1210887 CCTTTCTGCCAAATGCACAGCTATGCCATTCA
130 CCTTTCTGCCAAATGCACAGCTAGGCCATTCA
* *
1210919 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATACTTGACACATTTCTGCCAAAAGC
1 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATACTTGACACATTTCTTCCAAATGC
* * * * *
1210984 ACAACTAGGCGTTCTTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGACATACTTGACAC
66 ACAACTAGCCATTCATCTTTTACTCAACGGTATTTAACCGTTCTTCTAACTTACATACTTGACAC
* *
1211049 TTTTTTGCCAAATGCA
131 CTTTCTGCCAAATGCA
1211065 TAGTTTGGCC
Statistics
Matches: 273, Mismatches: 32, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
161 68 0.25
162 204 0.75
163 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.36
Consensus pattern (161 bp):
TCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATACTTGACACATTTCTTCCAAATGC
ACAACTAGCCATTCATCTTTTACTCAACGGTATTTAACCGTTCTTCTAACTTACATACTTGACAC
CTTTCTGCCAAATGCACAGCTAGGCCATTCA
Found at i:1211115 original size:68 final size:68
Alignment explanation
Indices: 1211024--1211483 Score: 627
Period size: 68 Copynumber: 6.8 Consensus size: 68
1211014 TATTTAACCG
* * * * * * * *
1211024 TTCATCTAACTGACATACTTGACACTTTTTTGCCAAATGCATAGTTTGGCCTCAAAGGCACATAA
1 TTCATCTAACTGGCATAATTGACACTTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1211089 CCT
66 CCT
* * *
1211092 TTCATCTAACTGGCATAATTGACACCTTTATGTTAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACTTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1211157 CCT
66 CCT
* * *
1211160 TTAATCTAACTGGCATAATTGACA-TCTTTCTGTCAAATGCACAGTTAGGCCTTAAAGGTACTTA
1 TTCATCTAACTGGCATAATTGACACT-TTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
1211224 GCCT
65 GCCT
*
1211228 TTCATGTAACTGGCATAATTGACACTTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACTTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1211293 CCT
66 CCT
* * *
1211296 TTCATCTAACTGGTATAATTGACA-TCATTCTGTCAAATGCACAGTTAGGCCTCAAAGTCACTTA
1 TTCATCTAACTGGCATAATTGACACT-TTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
1211360 GCCT
65 GCCT
** * * * * *
1211364 TTCATCTAACTAACATAATTGACACCTTTATGACAAATGCACAATTAGGCCTCAAAAGCACTTAG
1 TTCATCTAACTGGCATAATTGACACTTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1211429 CCT
66 CCT
* * * *
1211432 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAGTGTACAATTAGGCCT
1 TTCATCTAACTGGCATAATTGACACTTTTCTGTCAAATGCACAGTTAGGCCT
1211484 ATTAATTTTT
Statistics
Matches: 348, Mismatches: 40, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
67 1 0.00
68 346 0.99
69 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (68 bp):
TTCATCTAACTGGCATAATTGACACTTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:1212439 original size:154 final size:154
Alignment explanation
Indices: 1212158--1212469 Score: 547
Period size: 154 Copynumber: 2.0 Consensus size: 154
1212148 GTATCGATAT
* *
1212158 TACTATACTAGGGTATCGATCCTCTATTATGGTACCGATACCATTTTTGTATTATGTGATCAAAT
1 TACTATACTAGGGTATCGATACTCTATTATGGTACCAATACCATTTTTGTATTATGTGATCAAAT
* *
1212223 GGTATCGCTAACATCCTCATGTTATCGATACTCCCTCTTGGTATCGATATTACTCTGCAGATTCT
66 GGTATCGCTAACATCCTCATGTTATCGATACTCCCTCTTGGTATCGATACTACTCTACAGATTCT
*
1212288 ACTGATTTTAAGCCTATAGTATTGG
131 ACTGA-TTTAAGCCTATAGTATCGG
1212313 TACTATACTAGGGTATCGATACTCTATTATGGT-CTCAATACCA-TTTTGTATTATGTGATCAAA
1 TACTATACTAGGGTATCGATACTCTATTATGGTAC-CAATACCATTTTTGTATTATGTGATCAAA
1212376 TGGTATCGCTAACATCCTCATGTTATCGATACTCCCTCTTGGTATCGATACTACTCTACAGATTC
65 TGGTATCGCTAACATCCTCATGTTATCGATACTCCCTCTTGGTATCGATACTACTCTACAGATTC
1212441 TACTGATTTAAGCCTATAGTATCGG
130 TACTGATTTAAGCCTATAGTATCGG
1212466 TACT
1 TACT
1212470 GTTCTATCAG
Statistics
Matches: 151, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
153 22 0.15
154 90 0.60
155 39 0.26
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (154 bp):
TACTATACTAGGGTATCGATACTCTATTATGGTACCAATACCATTTTTGTATTATGTGATCAAAT
GGTATCGCTAACATCCTCATGTTATCGATACTCCCTCTTGGTATCGATACTACTCTACAGATTCT
ACTGATTTAAGCCTATAGTATCGG
Found at i:1213860 original size:3 final size:3
Alignment explanation
Indices: 1213852--1213889 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
1213842 CATATGATAT
1213852 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1213890 TTCTAACAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1218363 original size:2 final size:2
Alignment explanation
Indices: 1218358--1218396 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1218348 TAGTACACTA
* *
1218358 AT AT AT AT AT GT AT AT AT AT GT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1218397 AAAATTATAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1218374 original size:10 final size:10
Alignment explanation
Indices: 1218359--1218396 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
1218349 AGTACACTAA
1218359 TATATATATG
1 TATATATATG
1218369 TATATATATG
1 TATATATATG
*
1218379 TATATATATA
1 TATATATATG
1218389 TATATATA
1 TATATATA
1218397 AAAATTATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (10 bp):
TATATATATG
Found at i:1223938 original size:511 final size:510
Alignment explanation
Indices: 1222907--1224429 Score: 2772
Period size: 511 Copynumber: 3.0 Consensus size: 510
1222897 CCACGCTAAG
* * *
1222907 AGAAGCATAACCAATGGTGAATCAGACGATCTGAGAATTAACCGCAACTCCCAGCATTCAGTAGC
1 AGAAGCATAACCAATGGTGATTCAGACGATCAGAGAATTAACCGCAACTCCCGGCATTCAGTAGC
*
1222972 CATTTTGCATCACATTTCCTCACGGTGAGACTCCATTTCAACTCAAGATGAGACTAATCCACCAC
66 CATTTTGCATCACATTTCCTCACGGTGAGACTCCATTTCAACTCAAGATGAGACTAATCCACCTC
1223037 TTTCCTCCTATCACGTTCTACCCAGTAAAAGTTCGCACAAACATCTCACAAAATTTCACATTGTA
131 TTTCCTCCTATCACGTTCTACCCAGTAAAAGTTCG-ACAAACATCTCACAAAATTTCACATTGTA
*
1223102 TACTCTAGTATAAAGCCCCAGGGAGTATTGGAAGATTAGATTAAACTCAGAGCATCTCTTTTTTC
195 TACTCTAGTATAAAGCCCCAGGGAGTATCGGAAGATTAGATTAAACTCAGAGCATCTCTTTTTTC
* *
1223167 CTTAG-GTATTGGCTAAGGAATGTTTATTTTATTTACCACCCAACTACATTACAACTTGGAATAA
260 CTTAGCGTAATGGCTAAGGAATGTTTATTTTATTTACCACCCAACTCCATTACAACTTGGAATAA
* * *
1223231 TTTAACGCATGTTTTTCCTGTTATGTTTTTCCCAT-GG-G--AGAAAGCGAATTGAGGTGAAGTA
325 TTTAACGCATGTTTTTCTTGATATGTTTTTCCCATGGGCGAAAGCAAGCGAATTGAGGTGAAGTA
1223292 TCCTGGGAATTCGACAAAATAAAGGAGAATCACTTTACGACTATTTAGAGTGGTTTAAAAAAATA
390 TCCTGGGAATTCGACAAAATAAAGGAGAATCACTTTACGACTATTTAGAGTGGTTTAAAAAAATA
1223357 TGTGCCAGTTCTCTGTAATATGGCTCATTCAAACAAACACTCTTTTAGTATTTTTA
455 TGTGCCAGTTCTCTGTAATATGGCTCATTCAAACAAACACTCTTTTAGTATTTTTA
1223413 AGAAGCATAACCAATGGTGATTCAGACGATCAGAGAATTAACCGCAACTCCCGGCATTCAGTAGC
1 AGAAGCATAACCAATGGTGATTCAGACGATCAGAGAATTAACCGCAACTCCCGGCATTCAGTAGC
*
1223478 TATTTTGCATCACATTTCCTCACGGTGAGACTCCATTTCAACTCAAGATGAGACTAATCCACCTC
66 CATTTTGCATCACATTTCCTCACGGTGAGACTCCATTTCAACTCAAGATGAGACTAATCCACCTC
1223543 TTTCCTCCTATCACGTTCTACCCAGTAAAAGTTCGACAAACATCTCACAAAATTTCACATTGTAT
131 TTTCCTCCTATCACGTTCTACCCAGTAAAAGTTCGACAAACATCTCACAAAATTTCACATTGTAT
1223608 ACTCTAGTATAAAGCCCCAGGGAGTATCGGAAGATTAGATTAAACTCAGAGCATCTCTTTTTTCC
196 ACTCTAGTATAAAGCCCCAGGGAGTATCGGAAGATTAGATTAAACTCAGAGCATCTCTTTTTTCC
1223673 TTAGCCGTAATGGCTAAGGAATGTTTATTTTATTTACCACCCAACTCCATTACAACTTGGAATAA
261 TTAG-CGTAATGGCTAAGGAATGTTTATTTTATTTACCACCCAACTCCATTACAACTTGGAATAA
1223738 TTTAACGCATGTTTTTCTTGATATGTTTTTCCCATGGGCGAAAGCAAGCGAATTGAGGTGAAGTA
325 TTTAACGCATGTTTTTCTTGATATGTTTTTCCCATGGGCGAAAGCAAGCGAATTGAGGTGAAGTA
1223803 TCCTGGGAATTCGACAAAATAAAGGAGAATCACTTTACGACTATTTAGAGTGGTTTAAAAAAATA
390 TCCTGGGAATTCGACAAAATAAAGGAGAATCACTTTACGACTATTTAGAGTGGTTTAAAAAAATA
1223868 TGTGCCAGTTCTCTGTAATATGGCTCATTCAAACAAACACTCTTTTAGTATTTTTA
455 TGTGCCAGTTCTCTGTAATATGGCTCATTCAAACAAACACTCTTTTAGTATTTTTA
1223924 AGAAGCATAACCAATGGTGATTCAGACGATCAGAGAATTAACCGCAACTCCCGGCATTCAGTAGC
1 AGAAGCATAACCAATGGTGATTCAGACGATCAGAGAATTAACCGCAACTCCCGGCATTCAGTAGC
*
1223989 CA-TTTGCATCACATTTCCTCACGGTGAGACT-CATTTAAACTCAAGATGAGGACTAATCCACCT
66 CATTTTGCATCACATTTCCTCACGGTGAGACTCCATTTCAACTCAAGATGA-GACTAATCCACCT
*
1224052 C-TTCCTCCTATCACGTTCTACCCAGT-AAAGTTCAACAAACAT-TCACAAAAATTTCACATTGT
130 CTTTCCTCCTATCACGTTCTACCCAGTAAAAGTTCGACAAACATCTCAC-AAAATTTCACATTGT
1224114 ATACTCTAGTATAAAGCCCCAGGGAGTATCGGAAGATTAGATTAAACTCAGAGCA--TCTTTTTT
194 ATACTCTAGTATAAAGCCCCAGGGAGTATCGGAAGATTAGATTAAACTCAGAGCATCTCTTTTTT
1224177 CCTTAGCGT-ATGGCTAAGGAATGTTTATTTTATTTACCACCCAA-TCCATTACAAC-TGGAATA
259 CCTTAGCGTAATGGCTAAGGAATGTTTATTTTATTTACCACCCAACTCCATTACAACTTGGAATA
1224239 ATTTAACGCATGTTTTTCTTGATATGTTTTT-CCATGGGCGAAAGCAAGCGAATTGAGGTGAAGT
324 ATTTAACGCATGTTTTTCTTGATATGTTTTTCCCATGGGCGAAAGCAAGCGAATTGAGGTGAAGT
1224303 ATCCTGGGAATTCGACAAAATAAAGGAGAATCACTTTACGACTATTTAGAGTGGTTTAAAAAAAT
389 ATCCTGGGAATTCGACAAAATAAAGGAGAATCACTTTACGACTATTTAGAGTGGTTTAAAAAAAT
1224368 ATGTGCCAGTTCTCTGTAATATGGCTCATTCAAACAAACACTCTTTTAGTATTTTTA
454 ATGTGCCAGTTCTCTGTAATATGGCTCATTCAAACAAACACTCTTTTAGTATTTTTA
*
1224425 TGAAG
1 AGAAG
1224430 TGATGTTCCA
Statistics
Matches: 994, Mismatches: 15, Indels: 21
0.97 0.01 0.02
Matches are distributed among these distances:
501 159 0.16
502 38 0.04
503 11 0.01
504 35 0.04
505 101 0.10
506 174 0.18
507 94 0.09
508 87 0.09
509 43 0.04
510 43 0.04
511 209 0.21
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (510 bp):
AGAAGCATAACCAATGGTGATTCAGACGATCAGAGAATTAACCGCAACTCCCGGCATTCAGTAGC
CATTTTGCATCACATTTCCTCACGGTGAGACTCCATTTCAACTCAAGATGAGACTAATCCACCTC
TTTCCTCCTATCACGTTCTACCCAGTAAAAGTTCGACAAACATCTCACAAAATTTCACATTGTAT
ACTCTAGTATAAAGCCCCAGGGAGTATCGGAAGATTAGATTAAACTCAGAGCATCTCTTTTTTCC
TTAGCGTAATGGCTAAGGAATGTTTATTTTATTTACCACCCAACTCCATTACAACTTGGAATAAT
TTAACGCATGTTTTTCTTGATATGTTTTTCCCATGGGCGAAAGCAAGCGAATTGAGGTGAAGTAT
CCTGGGAATTCGACAAAATAAAGGAGAATCACTTTACGACTATTTAGAGTGGTTTAAAAAAATAT
GTGCCAGTTCTCTGTAATATGGCTCATTCAAACAAACACTCTTTTAGTATTTTTA
Found at i:1227707 original size:24 final size:24
Alignment explanation
Indices: 1227679--1227750 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
1227669 GTAGACAGAG
*
1227679 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
1227703 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
1227727 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
1227750 A
1 A
1227751 GGTAACTTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 15 0.36
24 27 0.64
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.19
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:1227710 original size:12 final size:12
Alignment explanation
Indices: 1227683--1227751 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
1227673 ACAGAGATAT
* *
1227683 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
1227695 CAGAATTCATAT
1 CAGAATTCAGAA
1227707 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
1227719 CAGAATCCAGAT
1 CAGAATTCAGAA
1227731 CAGAA-TCAGAA
1 CAGAATTCAGAA
1227742 CAGAATTCAG
1 CAGAATTCAG
1227752 GTAACTTATC
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
11 11 0.24
12 32 0.71
13 2 0.04
ACGTcount: A:0.49, C:0.19, G:0.14, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1230215 original size:18 final size:18
Alignment explanation
Indices: 1230188--1230228 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1230178 CAACGGTCAA
*
1230188 CGGGTCAACGAGTCGGGT
1 CGGGTAAACGAGTCGGGT
*
1230206 CGGGTAAACGGGTCGGGT
1 CGGGTAAACGAGTCGGGT
1230224 CGGGT
1 CGGGT
1230229 TATGACCGGT
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:0.15, C:0.20, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTAAACGAGTCGGGT
Found at i:1234920 original size:42 final size:42
Alignment explanation
Indices: 1234825--1234927 Score: 102
Period size: 42 Copynumber: 2.5 Consensus size: 42
1234815 CATATAGAAC
* * *
1234825 ATATGTCCCGAA-TGACCACATACATATTCTAATGGATCAAAT
1 ATATGTCCTGAAGT-ACCACATACATATTCCAAAGGATCAAAT
* * * *
1234867 A-AGTGTACTGAAGTACCACATATATATTCCAAAGGATTATAT
1 ATA-TGTCCTGAAGTACCACATACATATTCCAAAGGATCAAAT
*
1234909 ATATGTCCTGAAGGACCAC
1 ATATGTCCTGAAGTACCAC
1234928 GTAGAACCCT
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
41 1 0.02
42 46 0.94
43 2 0.04
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (42 bp):
ATATGTCCTGAAGTACCACATACATATTCCAAAGGATCAAAT
Found at i:1235784 original size:22 final size:21
Alignment explanation
Indices: 1235735--1235791 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
1235725 TAATGTTCTC
1235735 TGGTATCGATACCCTCCTAAT
1 TGGTATCGATACCCTCCTAAT
* *
1235756 TGGTATCGATATTCCTTCCTTA-
1 TGGTATCGATA--CCCTCCTAAT
1235778 TGGTATCGATACCC
1 TGGTATCGATACCC
1235792 CATATATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 2 0.06
21 11 0.35
22 11 0.35
23 7 0.23
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (21 bp):
TGGTATCGATACCCTCCTAAT
Found at i:1238500 original size:2 final size:2
Alignment explanation
Indices: 1238493--1238535 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
1238483 ATAATGCTTT
* * *
1238493 TA TA TA TA TA TA -A TA AA TA AA TA AA 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
1238534 TA
1 TA
1238536 CATGTACATA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (2 bp):
TA
Found at i:1239171 original size:18 final size:18
Alignment explanation
Indices: 1239128--1239168 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1239118 AATAAGTGTT
*
1239128 CTTGAATGAAAAATGAGT
1 CTTGAATGAAAAATGAGG
*
1239146 ATTGAATGAAAAAT-AGG
1 CTTGAATGAAAAATGAGG
1239163 CTTGAA
1 CTTGAA
1239169 ATGCTCAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.46, C:0.05, G:0.22, T:0.27
Consensus pattern (18 bp):
CTTGAATGAAAAATGAGG
Found at i:1239455 original size:19 final size:17
Alignment explanation
Indices: 1239431--1239481 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
1239421 TTGGACCCTT
*
1239431 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TAA
*
1239449 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATAA
1239467 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
1239482 GGCTGGTGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 15 0.50
18 2 0.07
19 13 0.43
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATAA
Found at i:1239492 original size:19 final size:17
Alignment explanation
Indices: 1239431--1239515 Score: 80
Period size: 19 Copynumber: 4.7 Consensus size: 17
1239421 TTGGACCCTT
* *
1239431 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
1239449 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
*
1239467 AGTGCATCGATGCATGGCT
1 AGTGCATCGATGCAT--CA
*
1239486 GGTGCATCGATGCATCA
1 AGTGCATCGATGCATCA
*
1239503 AATGCATTCGATG
1 AGTGCA-TCGATG
1239516 TTTTCATAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
17 20 0.36
18 8 0.14
19 28 0.50
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:1248244 original size:65 final size:63
Alignment explanation
Indices: 1248046--1248255 Score: 192
Period size: 65 Copynumber: 3.3 Consensus size: 63
1248036 AGCACTAAGA
* ** * * * *
1248046 GTGCACCGATGCATCAAGCGCATTCGATGTTTCA-AAATAGCTAGAGTGCATTGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCT-CAGTGCATCGATGCATGGTTG
* * **
1248110 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGTATCGGTGCATGGTAA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGTTG
* **
1248175 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-T
1248238 TG
62 TG
*
1248240 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
1248256 CTTTGAAAAT
Statistics
Matches: 119, Mismatches: 20, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 45 0.38
65 63 0.53
66 5 0.04
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:1248642 original size:21 final size:21
Alignment explanation
Indices: 1248616--1248655 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1248606 ACATAGAATT
* *
1248616 TGTCCCTAATGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
1248637 TGTCCCGAAGGACCACATA
1 TGTCCCGAAGGACCACATA
1248656 TAACACATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATAGA
Found at i:1249616 original size:22 final size:22
Alignment explanation
Indices: 1249567--1249622 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
1249557 CGATATTCCC
1249567 TGGTATCGATAC-CCTACACAT
1 TGGTATCGATACTCCTACACAT
* *
1249588 TGGTATCGATACTCCTTC-CTT
1 TGGTATCGATACTCCTACACAT
1249609 ATGGTATCGATACT
1 -TGGTATCGATACT
1249623 GTTCATACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 14 0.45
22 17 0.55
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (22 bp):
TGGTATCGATACTCCTACACAT
Found at i:1263358 original size:20 final size:21
Alignment explanation
Indices: 1263312--1263372 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
1263302 TTCCCCTGTG
1263312 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
1263335 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
1263355 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
1263373 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:1271416 original size:12 final size:12
Alignment explanation
Indices: 1271388--1271420 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1271378 TGTTCCACGA
1271388 AAAAAAGAGATTT
1 AAAAAA-AGATTT
1271401 -AAAAAAGATTT
1 AAAAAAAGATTT
1271412 AAAAAAAGA
1 AAAAAAAGA
1271421 AAAGGAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.18
Consensus pattern (12 bp):
AAAAAAAGATTT
Found at i:1280999 original size:20 final size:20
Alignment explanation
Indices: 1280970--1281007 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1280960 CAGAACCCCA
*
1280970 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
1280990 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
1281008 TACATCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.34, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:1284851 original size:22 final size:21
Alignment explanation
Indices: 1284809--1284848 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1284799 GAGTTTATTT
*
1284809 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1284830 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1284849 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1286769 original size:20 final size:20
Alignment explanation
Indices: 1286744--1286783 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1286734 CGTTGAACAG
1286744 TGGGGGGAATCGGTACCCTC
1 TGGGGGGAATCGGTACCCTC
*
1286764 TGGGGGGAATCGGTTCCCTC
1 TGGGGGGAATCGGTACCCTC
1286784 CGAGCGTACT
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:0.12, C:0.25, G:0.40, T:0.23
Consensus pattern (20 bp):
TGGGGGGAATCGGTACCCTC
Found at i:1287961 original size:37 final size:36
Alignment explanation
Indices: 1287853--1287962 Score: 150
Period size: 37 Copynumber: 3.0 Consensus size: 36
1287843 AAACCAATTC
* * *
1287853 TTCCAGCCCTAAAATAAAACAAA-ATTTTAAACCAGA
1 TTCCAGCCCT-AAACAAAACAAAGATTTTAAACAATA
*
1287889 TTGCAGTCCCTAAACAAAACAAAGATTTTAAACAATA
1 TTCCAG-CCCTAAACAAAACAAAGATTTTAAACAATA
1287926 TTCCAGCCCCTAAACAAAACAAAGATTTTAAACAATA
1 TTCCAG-CCCTAAACAAAACAAAGATTTTAAACAATA
1287963 GCCCCTAAGC
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
36 16 0.24
37 50 0.76
ACGTcount: A:0.49, C:0.22, G:0.06, T:0.23
Consensus pattern (36 bp):
TTCCAGCCCTAAACAAAACAAAGATTTTAAACAATA
Found at i:1288573 original size:32 final size:32
Alignment explanation
Indices: 1288536--1288608 Score: 76
Period size: 33 Copynumber: 2.3 Consensus size: 32
1288526 AAATTGTCTC
*
1288536 TATTTAAAAT-TTAAAAATTCAAAAATATATT
1 TATTTAAAATCCTAAAAATTCAAAAATATATT
* ** * *
1288567 TAATTTATAATCCTATTATTTCAAAATTATATT
1 T-ATTTAAAATCCTAAAAATTCAAAAATATATT
1288600 TATTTAAAA
1 TATTTAAAA
1288609 ATATCCGAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
31 1 0.03
32 15 0.45
33 17 0.52
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (32 bp):
TATTTAAAATCCTAAAAATTCAAAAATATATT
Found at i:1288795 original size:23 final size:24
Alignment explanation
Indices: 1288758--1288803 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
1288748 TTCGATATTG
1288758 AAAAAATATTAAAATAATTTATTTT
1 AAAAAATATTAAAATAA-TTATTTT
*
1288783 AAAAAATA-T-AAATTATTATTT
1 AAAAAATATTAAAATAATTATTT
1288804 ATCATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 5 0.25
24 1 0.05
25 8 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAAAATATTAAAATAATTATTTT
Found at i:1291801 original size:18 final size:18
Alignment explanation
Indices: 1291763--1291801 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1291753 GGATAATGGT
* *
1291763 AACTGGGCTGAGGATGGC
1 AACTGGGCTGAAGAAGGC
*
1291781 AACTGGGCTGAAGAAGTC
1 AACTGGGCTGAAGAAGGC
1291799 AAC
1 AAC
1291802 AATAGGATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.31, C:0.18, G:0.36, T:0.15
Consensus pattern (18 bp):
AACTGGGCTGAAGAAGGC
Found at i:1295072 original size:10 final size:11
Alignment explanation
Indices: 1295047--1295073 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1295037 TGTTTTCCAT
1295047 TTTTTCTTCTC
1 TTTTTCTTCTC
1295058 TTTTTCTTCTC
1 TTTTTCTTCTC
1295069 TTTTT
1 TTTTT
1295074 TTCGAACAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTCTTCTC
Found at i:1295121 original size:29 final size:29
Alignment explanation
Indices: 1295058--1295124 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
1295048 TTTTCTTCTC
* *
1295058 TTTTTCTTCTCTTTTTTTCGAACAGTTCT
1 TTTTTTTTCTCTTTTTTTCGAACAGCTCT
* * *
1295087 TCTTTTTTC-CTTTTTTTCCGAACTGCTGT
1 TTTTTTTTCTCTTTTTTT-CGAACAGCTCT
1295116 TTTTTTTTC
1 TTTTTTTTC
1295125 AACATTTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
28 8 0.26
29 23 0.74
ACGTcount: A:0.07, C:0.21, G:0.07, T:0.64
Consensus pattern (29 bp):
TTTTTTTTCTCTTTTTTTCGAACAGCTCT
Found at i:1296019 original size:21 final size:17
Alignment explanation
Indices: 1295977--1296012 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1295967 GATGTCTGAA
1295977 TTGGAAATAAATGGGGT
1 TTGGAAATAAATGGGGT
1295994 TTGGAAATAAATGGGGT
1 TTGGAAATAAATGGGGT
1296011 TT
1 TT
1296013 TTGTGGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (17 bp):
TTGGAAATAAATGGGGT
Found at i:1296414 original size:11 final size:11
Alignment explanation
Indices: 1296395--1296429 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1296385 TGCTCGATCG
1296395 AATAAAAATAA
1 AATAAAAATAA
*
1296406 AATAGAAATAA
1 AATAAAAATAA
1296417 AAGTAAAAATAA
1 AA-TAAAAATAA
1296429 A
1 A
1296430 TGTACGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:1303469 original size:21 final size:22
Alignment explanation
Indices: 1303422--1303482 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
1303412 CCCCCCCTGA
*
1303422 GGGAACCGATTCCCCCTTTAAAG
1 GGGAACCGATTCCCCC-TCAAAG
*
1303445 GGGAACCGATTCCCCC-CACAG
1 GGGAACCGATTCCCCCTCAAAG
* *
1303466 GGGAATCGATACCCCCT
1 GGGAACCGATTCCCCCT
1303483 GGGGTTCTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 17 0.52
23 16 0.48
ACGTcount: A:0.25, C:0.36, G:0.23, T:0.16
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTCAAAG
Found at i:1314153 original size:19 final size:19
Alignment explanation
Indices: 1314131--1314172 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
1314121 TAAAATATGA
1314131 ATAATTTTATAAAAGTTTT
1 ATAATTTTATAAAAGTTTT
*
1314150 ATAATTTTATTAAAGTTTT
1 ATAATTTTATAAAAGTTTT
1314169 ATAA
1 ATAA
1314173 CTAGTATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (19 bp):
ATAATTTTATAAAAGTTTT
Found at i:1314180 original size:20 final size:19
Alignment explanation
Indices: 1314142--1314180 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1314132 TAATTTTATA
**
1314142 AAAGTTTTATAATTTTATT
1 AAAGTTTTATAATAGTATT
1314161 AAAGTTTTATAACTAGTATT
1 AAAGTTTTATAA-TAGTATT
1314181 TCTTTTACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (19 bp):
AAAGTTTTATAATAGTATT
Found at i:1324212 original size:32 final size:32
Alignment explanation
Indices: 1324176--1324243 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
1324166 TTAACCACAC
1324176 TTAACAAGCATAAGAGAGTTTAATTTAAGCAA
1 TTAACAAGCATAAGAGAGTTTAATTTAAGCAA
1324208 TTAACAAGCATAAGAGAGTTTAATTTAAGCAA
1 TTAACAAGCATAAGAGAGTTTAATTTAAGCAA
1324240 TTAA
1 TTAA
1324244 GTTCATTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.29
Consensus pattern (32 bp):
TTAACAAGCATAAGAGAGTTTAATTTAAGCAA
Found at i:1327044 original size:29 final size:30
Alignment explanation
Indices: 1327000--1327058 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
1326990 CCCATTTTGA
*
1327000 GTAACGGAATAAAACGTTAGGCACCAAACT
1 GTAACGGAAAAAAACGTTAGGCACCAAACT
*
1327030 GTAAC-GAAAAAAACGTTAGGCACTAAACT
1 GTAACGGAAAAAAACGTTAGGCACCAAACT
1327059 AGAAAAACGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.46, C:0.19, G:0.19, T:0.17
Consensus pattern (30 bp):
GTAACGGAAAAAAACGTTAGGCACCAAACT
Found at i:1330285 original size:10 final size:11
Alignment explanation
Indices: 1330259--1330284 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1330249 CGATAGTTGC
1330259 AAAAATTAGAA
1 AAAAATTAGAA
1330270 AAAAATTAGAA
1 AAAAATTAGAA
1330281 AAAA
1 AAAA
1330285 TCAAATTTGT
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:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (11 bp):
AAAAATTAGAA
Found at i:1331330 original size:16 final size:13
Alignment explanation
Indices: 1331297--1331321 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1331287 AGATTTACAA
1331297 ATTAACAATTAAC
1 ATTAACAATTAAC
1331310 ATTAACAATTAA
1 ATTAACAATTAA
1331322 ACACATTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAACAATTAAC
Found at i:1333135 original size:18 final size:18
Alignment explanation
Indices: 1333112--1333151 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1333102 GGAAAGCCAT
1333112 ATGAATTAATAA-ATTGCA
1 ATGAATTAATAACA-TGCA
*
1333130 ATGAATTACTAACATGCA
1 ATGAATTAATAACATGCA
1333148 ATGA
1 ATGA
1333152 CATACAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.30
Consensus pattern (18 bp):
ATGAATTAATAACATGCA
Found at i:1333997 original size:132 final size:130
Alignment explanation
Indices: 1333618--1333997 Score: 426
Period size: 132 Copynumber: 2.9 Consensus size: 130
1333608 TTTCAACACC
* *
1333618 GATCTACCTCATTCTGTGATAGAATC-AAACAAAATAAGGTTACGCTGATTCAACTCCTTCTATG
1 GATCTACCTCATTCTGTGATAGAATCGAGA-AAAATAAGGTTATGCTGATTCAACTCCTTCTATG
* * * *
1333682 AAGAATCGAACAAAATGACACTATCAATCCAACTCATTT-TGTGAAGAATCAAATAGAATGTCGA
65 AAGAATCGAGCAAAA-GATACGAT-GATCCAACTC-TTTCTGTGAAGAATCAAATAGAATGTCGA
1333746 TGTT
127 TGTT
* * *
1333750 GATCTACCTCATTATGTGATAGAATCGAGAAAAATAAGCTTATGCTGATTTAACTCCTTCTATGA
1 GATCTACCTCATTCTGTGATAGAATCGAGAAAAATAAGGTTATGCTGATTCAACTCCTTCTATGA
* * ** * * *
1333815 AGAATCGAG-AGGAATA-AGACTGTTGATTTAAATCCTTCCGTGAAGAATCAAATAGAATGTCGA
66 AGAATCGAGCA--AA-AGATAC-GATGATCCAACTCTTTCTGTGAAGAATCAAATAGAATGTCGA
1333878 TGTT
127 TGTT
* * * * *
1333882 GATCTACCTCCTTCTGTGATAGAATTGAGTAAAATAAGGTTATGCTGATTCAACTCCTTTTGTGA
1 GATCTACCTCATTCTGTGATAGAATCGAGAAAAATAAGGTTATGCTGATTCAACTCCTTCTATGA
* * *
1333947 AGAATCGAGCAAAAGATTACGCTGATCCATCTCTTTCTGTGATGACATCAA
66 AGAATCGAGCAAAAGA-TACGATGATCCAACTCTTTCTGTGAAGA-ATCAA
1333998 GCACAAAAAA
Statistics
Matches: 206, Mismatches: 32, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
130 1 0.00
131 23 0.11
132 175 0.85
133 6 0.03
134 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (130 bp):
GATCTACCTCATTCTGTGATAGAATCGAGAAAAATAAGGTTATGCTGATTCAACTCCTTCTATGA
AGAATCGAGCAAAAGATACGATGATCCAACTCTTTCTGTGAAGAATCAAATAGAATGTCGATGTT
Found at i:1335144 original size:5 final size:5
Alignment explanation
Indices: 1335136--1335189 Score: 63
Period size: 5 Copynumber: 9.8 Consensus size: 5
1335126 CCATTTTATT
1335136 TTTTC TTTTC TTTTC TTTTC TTTTC ATTTCTC TTTTTC TTTTTC TTTTAC
1 TTTTC TTTTC TTTTC TTTTC TTTTC -TTT-TC -TTTTC -TTTTC TTTT-C
1335186 TTTT
1 TTTT
1335190 TCTTCTTTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
5 24 0.53
6 16 0.36
7 5 0.11
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:1335144 original size:6 final size:6
Alignment explanation
Indices: 1335135--1335193 Score: 63
Period size: 6 Copynumber: 10.3 Consensus size: 6
1335125 CCCATTTTAT
*
1335135 TTTTTC -TTTTC -TTTTC -TTTTC -TTTTC ATTTCTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC
*
1335180 TTTTAC TTTTTC TT
1 TTTTTC TTTTTC TT
1335194 CTTTAAGAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
5 20 0.43
6 23 0.49
7 4 0.09
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:1336221 original size:25 final size:24
Alignment explanation
Indices: 1336172--1336240 Score: 79
Period size: 25 Copynumber: 2.9 Consensus size: 24
1336162 TCTAAGGTAG
*
1336172 CATGAATTAAT--ATGCAATTCAA
1 CATGAATTAATACATGCAATGCAA
*
1336194 CATGAATTAATACCATGCAATGCCA
1 CATGAATTAATA-CATGCAATGCAA
*
1336219 CATGAATTCATAACATGCAATG
1 CATGAATTAAT-ACATGCAATG
1336241 AATTACTAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
22 11 0.28
25 28 0.70
26 1 0.03
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.28
Consensus pattern (24 bp):
CATGAATTAATACATGCAATGCAA
Found at i:1336886 original size:43 final size:44
Alignment explanation
Indices: 1336839--1336921 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
1336829 ATTCAACTCC
1336839 TTCTGTG-AAGAACCAAGCG-AAAGATTTTCACTGATCCAAGTTT
1 TTCTGTGAAAG-ACCAAGCGAAAAGATTTTCACTGATCCAAGTTT
* * *
1336882 TTCTGTGAAAGATCAAGTGAAAAGTTTTTCACTGATCCAA
1 TTCTGTGAAAGACCAAGCGAAAAGATTTTCACTGATCCAA
1336922 TTCTCTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
43 13 0.37
44 22 0.63
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (44 bp):
TTCTGTGAAAGACCAAGCGAAAAGATTTTCACTGATCCAAGTTT
Found at i:1337140 original size:132 final size:132
Alignment explanation
Indices: 1336957--1337341 Score: 427
Period size: 132 Copynumber: 2.9 Consensus size: 132
1336947 ATGAAAAATG
* * * * * * *
1336957 TTGATCCAACTCATTATGTGAAGAATCAAAACAATTTCCAATGTCGATCTACCTCATTATGGGAT
1 TTGATCCAACTCCTTATGTGAAGAATCAAAAGAATGT-CGATGTTGATCTACCTCATTCTGTGAT
* ** * **
1337022 ATAATCAAACAAAACGAGGTTATGCTGATTCAACTTCTTCTGTGAATAATCGAGCAG-AATGACG
65 AGAATCAAACAAAATAAGGTTATGCTGATTCAACTTCTTCTGTGAAGAATCGAGCAGAAATGAAA
*
1337086 CTA
130 CCA
* *
1337089 TTGATCCAAATCCTTTTGTGAAGAATCAAATAGAATGTCGATGTTGATCTACCTCATTCTGTGAT
1 TTGATCCAACTCCTTATGTGAAGAATCAAA-AGAATGTCGATGTTGATCTACCTCATTCTGTGAT
* * * * * *
1337154 AGAATCGAGA-AAAATAAGTTTATGGTGATTCAACTCCTTCTGTGAAGAATCAATC-GAAATGAA
65 AGAATC-AAACAAAATAAGGTTATGCTGATTCAACTTCTTCTGTGAAGAATCGAGCAGAAATGAA
1337217 ACCA
129 ACCA
* * * * * *
1337221 TTGATTCAACTCCTTCTGTGAAGACTCAAACAGAATGTCGATGATGATCTACCTCCTTCTATGAT
1 TTGATCCAACTCCTTATGTGAAGAATCAAA-AGAATGTCGATGTTGATCTACCTCATTCTGTGAT
* *
1337286 AGAATCAAGCAAAATAAGGTTATGCTGATTTAA-TTCCTTCTGTGAAGAATCGAGCA
65 AGAATCAAACAAAATAAGGTTATGCTGATTCAACTT-CTTCTGTGAAGAATCGAGCA
1337342 AAAGATTACG
Statistics
Matches: 209, Mismatches: 38, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
131 3 0.01
132 199 0.95
133 7 0.03
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (132 bp):
TTGATCCAACTCCTTATGTGAAGAATCAAAAGAATGTCGATGTTGATCTACCTCATTCTGTGATA
GAATCAAACAAAATAAGGTTATGCTGATTCAACTTCTTCTGTGAAGAATCGAGCAGAAATGAAAC
CA
Found at i:1337912 original size:22 final size:21
Alignment explanation
Indices: 1337873--1337953 Score: 90
Period size: 22 Copynumber: 3.6 Consensus size: 21
1337863 TCACTTTGGA
1337873 TTTTTCTTCTATTTTCCTTTTTC
1 TTTTTC-TCT-TTTTCCTTTTTC
1337896 TCTTTTCTCTTTTTCCTCATTTTC
1 T-TTTTCTCTTTTTCCT--TTTTC
*
1337920 TTTTTCTTTTTTTCTCTTTTTC
1 TTTTTCTCTTTTTC-CTTTTTC
*
1337942 TTCTTCTCTTTT
1 TTTTTCTCTTTT
1337954 CTTTTCAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
22 22 0.43
23 16 0.31
24 13 0.25
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTCTCTTTTTCCTTTTTC
Found at i:1337918 original size:31 final size:32
Alignment explanation
Indices: 1337873--1337941 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 32
1337863 TCACTTTGGA
*
1337873 TTTTTCTTCTATTTTCCTTTTTC-TCTTTTCTC
1 TTTTTCCTCTATTTT-CTTTTTCTTCTTTTCTC
*
1337905 TTTTTCCTC-ATTTTCTTTTTCTTTTTTTCTC
1 TTTTTCCTCTATTTTCTTTTTCTTCTTTTCTC
1337936 TTTTTC
1 TTTTTC
1337942 TTCTTCTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 7 0.21
31 19 0.56
32 8 0.24
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (32 bp):
TTTTTCCTCTATTTTCTTTTTCTTCTTTTCTC
Found at i:1337943 original size:16 final size:16
Alignment explanation
Indices: 1337873--1337946 Score: 82
Period size: 15 Copynumber: 4.7 Consensus size: 16
1337863 TCACTTTGGA
1337873 TTTTTCTTCTATTT-TCC
1 TTTTTCTTCT-TTTCT-C
1337890 TTTTTC-TCTTTTCTC
1 TTTTTCTTCTTTTCTC
* *
1337905 TTTTTCCTCATTT-TC
1 TTTTTCTTCTTTTCTC
*
1337920 TTTTTCTTTTTTTCTC
1 TTTTTCTTCTTTTCTC
1337936 TTTTTCTTCTT
1 TTTTTCTTCTT
1337947 CTCTTTTCTT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
15 22 0.45
16 21 0.43
17 6 0.12
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTCTTCTTTTCTC
Found at i:1337952 original size:30 final size:31
Alignment explanation
Indices: 1337889--1337958 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
1337879 TTCTATTTTC
* *
1337889 CTTTTTC-TCTTTTCTCTTTTTCCTCATTTT
1 CTTTTTCTTTTTTTCTCTTTTTCCTCATTCT
*
1337919 CTTTTTCTTTTTTTCTCTTTTTCTTC-TTCT
1 CTTTTTCTTTTTTTCTCTTTTTCCTCATTCT
1337949 C-TTTTCTTTT
1 CTTTTTCTTTT
1337959 CAAAACTGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 9 0.25
30 11 0.31
31 16 0.44
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.74
Consensus pattern (31 bp):
CTTTTTCTTTTTTTCTCTTTTTCCTCATTCT
Found at i:1338656 original size:25 final size:23
Alignment explanation
Indices: 1338628--1338688 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 23
1338618 ACCCCCTTTA
1338628 TTTTTCTTTTCTTTTCTCTTTTACT
1 TTTTTCTTTTCTTTTCT-TTTT-CT
1338653 TTTTTCTTTT-TATTTCTTTTTCT
1 TTTTTCTTTTCT-TTTCTTTTTCT
1338676 TTTTT-TTCTTCTT
1 TTTTTCTT-TTCTT
1338689 CAAGCATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
22 2 0.06
23 10 0.30
24 6 0.18
25 15 0.45
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTCTTTTCTTTTCTTTTTCT
Found at i:1338674 original size:16 final size:15
Alignment explanation
Indices: 1338653--1338685 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
1338643 CTCTTTTACT
1338653 TTTTTCTTTTTATTTC
1 TTTTTCTTTTT-TTTC
1338669 TTTTTCTTTTTTTTC
1 TTTTTCTTTTTTTTC
1338684 TT
1 TT
1338686 CTTCAAGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTCTTTTTTTTC
Found at i:1339648 original size:25 final size:23
Alignment explanation
Indices: 1339598--1339674 Score: 97
Period size: 25 Copynumber: 3.3 Consensus size: 23
1339588 ACCTAAGGTA
1339598 ACATGAATTAAT--ATGCAATGC
1 ACATGAATTAATACATGCAATGC
1339619 AACATGAATTAATACCATGCAATGCC
1 -ACATGAATTAATA-CATGCAATG-C
1339645 ACATGAATTAATAACATGCAATG-
1 ACATGAATTAAT-ACATGCAATGC
1339668 ACATGAA
1 ACATGAA
1339675 AATACAATTA
Statistics
Matches: 50, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
22 12 0.24
23 7 0.14
25 29 0.58
26 2 0.04
ACGTcount: A:0.45, C:0.17, G:0.13, T:0.25
Consensus pattern (23 bp):
ACATGAATTAATACATGCAATGC
Found at i:1340609 original size:132 final size:132
Alignment explanation
Indices: 1340419--1340752 Score: 388
Period size: 132 Copynumber: 2.5 Consensus size: 132
1340409 TGCCAACGCC
* * *
1340419 GATCTACCTCCTTATGTTATAGAATCGAA-CAAAATAAGGTTATGCTGATTCAAATCCTTCTGTG
1 GATCTACCTCCTTTTGTGATAGAATC-AAGCAAAATAAGGTTATGCTGATTCAACTCCTTCTGTG
* * * *** * * *
1340483 AAGTATCGAACGGAATGACATTGTTGATCCAAATCCTTT-TGTGAAGAATCAAACAGATTTTCAA
65 AAGAATCGAACGGAAAGACACTACCGATCCAAAT-CTTTCTATGAAGAATCAAACAGAATGTCAA
1340547 TGT-T
129 T-TCT
* * *
1340551 GATCTACCTCGTTTTGTGATAGAATCAAGCAAAATAAGGTTATGGTGATTCAACTCCTTATGTGA
1 GATCTACCTCCTTTTGTGATAGAATCAAGCAAAATAAGGTTATGCTGATTCAACTCCTTCTGTGA
* * * * *
1340616 AGAATCGAGCGGAAAGACACTACCGATTCAACTCTTTCTATGAAGAATCAAATAGAATGTCGATT
66 AGAATCGAACGGAAAGACACTACCGATCCAAATCTTTCTATGAAGAATCAAACAGAATGTCAATT
1340681 CT
131 CT
* * * *
1340683 GATCTACCTCCTTCTT-TGATATAATCGAGAAAAATAAGGTTATGTTGATTCAACTCCTTCTGTG
1 GATCTACCTCCTT-TTGTGATAGAATCAAGCAAAATAAGGTTATGCTGATTCAACTCCTTCTGTG
1340747 AAGAAT
65 AAGAAT
1340753 TGAGCAAAAT
Statistics
Matches: 172, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
131 7 0.04
132 163 0.95
133 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (132 bp):
GATCTACCTCCTTTTGTGATAGAATCAAGCAAAATAAGGTTATGCTGATTCAACTCCTTCTGTGA
AGAATCGAACGGAAAGACACTACCGATCCAAATCTTTCTATGAAGAATCAAACAGAATGTCAATT
CT
Found at i:1341330 original size:42 final size:42
Alignment explanation
Indices: 1341232--1341333 Score: 168
Period size: 42 Copynumber: 2.4 Consensus size: 42
1341222 TTTTAGGGCA
* *
1341232 TCACTTTAGATATTTCTTTTCTCAAAGTGCCTTTTCGTGTTT
1 TCACTTTAGATCTTTCTTTTCTCAAAGTGCCCTTTCGTGTTT
1341274 TCACTTTAGATCTTTCTTTTCTCAAAGTGCCCTTTCGTGTTT
1 TCACTTTAGATCTTTCTTTTCTCAAAGTGCCCTTTCGTGTTT
* *
1341316 TCACTTTGGTTCTTTCTT
1 TCACTTTAGATCTTTCTT
1341334 CTATTTTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.14, C:0.22, G:0.12, T:0.53
Consensus pattern (42 bp):
TCACTTTAGATCTTTCTTTTCTCAAAGTGCCCTTTCGTGTTT
Found at i:1341353 original size:21 final size:22
Alignment explanation
Indices: 1341328--1341398 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 22
1341318 ACTTTGGTTC
1341328 TTTCTTCT-ATTTTTTTTTTTT
1 TTTCTTCTCATTTTTTTTTTTT
1341349 TTTCTTTTTCCTCATTTTTATTTTCTTT
1 TTTC---TT-CTCATTTTT-TTTT-TTT
* *
1341377 TTT-TTCTGATTTTCTTTTTTT
1 TTTCTTCTCATTTTTTTTTTTT
1341398 T
1 T
1341399 CTTATTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
21 8 0.20
22 4 0.10
23 7 0.17
24 4 0.10
25 2 0.05
26 6 0.15
27 4 0.10
28 6 0.15
ACGTcount: A:0.06, C:0.13, G:0.01, T:0.80
Consensus pattern (22 bp):
TTTCTTCTCATTTTTTTTTTTT
Found at i:1341353 original size:25 final size:28
Alignment explanation
Indices: 1341325--1341383 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
1341315 TTCACTTTGG
*
1341325 TTCTTTCTT-CT-ATTTTT-TTTTTTTT
1 TTCTTTCTTCCTCATTTTTATTTTCTTT
1341350 TTCTTT-TTCCTCATTTTTATTTTCTTT
1 TTCTTTCTTCCTCATTTTTATTTTCTTT
1341377 TT-TTTCT
1 TTCTTTCT
1341384 GATTTTCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
24 2 0.07
25 8 0.28
26 9 0.31
27 10 0.34
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (28 bp):
TTCTTTCTTCCTCATTTTTATTTTCTTT
Found at i:1341381 original size:9 final size:9
Alignment explanation
Indices: 1341332--1341408 Score: 59
Period size: 9 Copynumber: 8.2 Consensus size: 9
1341322 TGGTTCTTTC
1341332 TTCTATTTTT
1 TTCT-TTTTT
1341342 TT-TTTTTT
1 TTCTTTTTT
*
1341350 TTCTTTTTC
1 TTCTTTTTT
*
1341359 CTCATTTTTATT
1 TTC--TTTT-TT
1341371 TTCTTTTTT
1 TTCTTTTTT
**
1341380 TTC-TGATT
1 TTCTTTTTT
1341388 TTCTTTTTT
1 TTCTTTTTT
1341397 TTCTTATTTT
1 TTCTT-TTTT
1341407 TT
1 TT
1341409 TTTCAAAAGT
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
8 13 0.25
9 21 0.40
10 12 0.23
11 4 0.08
12 3 0.06
ACGTcount: A:0.06, C:0.12, G:0.01, T:0.81
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:1341390 original size:17 final size:17
Alignment explanation
Indices: 1341368--1341411 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
1341358 CCTCATTTTT
1341368 ATTTTCTTTTTTTTCTG
1 ATTTTCTTTTTTTTCTG
*
1341385 ATTTTCTTTTTTTTCTT
1 ATTTTCTTTTTTTTCTG
1341402 ATTTT-TTTTT
1 ATTTTCTTTTT
1341412 CAAAAGTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 5 0.19
17 21 0.81
ACGTcount: A:0.07, C:0.09, G:0.02, T:0.82
Consensus pattern (17 bp):
ATTTTCTTTTTTTTCTG
Found at i:1341973 original size:18 final size:18
Alignment explanation
Indices: 1341934--1341973 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1341924 ACGTGAAGCT
* *
1341934 TCTCCCAAAATATCATAT
1 TCTCCCAAAATATCAGAC
1341952 TCTCCCAAAATATCAGAC
1 TCTCCCAAAATATCAGAC
1341970 TCTC
1 TCTC
1341974 GAGAGGGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.35, C:0.33, G:0.03, T:0.30
Consensus pattern (18 bp):
TCTCCCAAAATATCAGAC
Found at i:1342111 original size:6 final size:6
Alignment explanation
Indices: 1342097--1342144 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
1342087 TTAAACCCCC
* *
1342097 TTTTAT TTTTCT TTTTCA TTTTCT TTCTTCTTT TTTTCT TTTTCT TTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TT-TTC--T TTTTCT TTTTCT TTT
1342145 GTGTTTTCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
6 27 0.75
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:1353222 original size:23 final size:23
Alignment explanation
Indices: 1353196--1353239 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1353186 CTTTCAATAC
1353196 TTTAGAGTAAAAGAA-TATTCTTT
1 TTTA-AGTAAAAGAACTATTCTTT
*
1353219 TTTAATTAAAAGAACTATTCT
1 TTTAAGTAAAAGAACTATTCT
1353240 ACGCTTGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (23 bp):
TTTAAGTAAAAGAACTATTCTTT
Found at i:1355609 original size:21 final size:21
Alignment explanation
Indices: 1355585--1355630 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1355575 ACCCCTTCAC
1355585 AAAATGATCAAACCCTCGAAG
1 AAAATGATCAAACCCTCGAAG
* * *
1355606 AAAATGATCGATCCCTCGATG
1 AAAATGATCAAACCCTCGAAG
1355627 AAAA
1 AAAA
1355631 AAATAGATCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.46, C:0.22, G:0.15, T:0.17
Consensus pattern (21 bp):
AAAATGATCAAACCCTCGAAG
Found at i:1355639 original size:21 final size:21
Alignment explanation
Indices: 1355597--1355639 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1355587 AATGATCAAA
** *
1355597 CCCTCGAAGAAAATGATCGAT
1 CCCTCGAAGAAAAAAATAGAT
*
1355618 CCCTCGATGAAAAAAATAGAT
1 CCCTCGAAGAAAAAAATAGAT
1355639 C
1 C
1355640 TCTTTCCTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (21 bp):
CCCTCGAAGAAAAAAATAGAT
Found at i:1357036 original size:24 final size:23
Alignment explanation
Indices: 1356959--1357036 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 23
1356949 GACGATAATC
1356959 AAAGAA-AAGAAAATAAAGAAGAGA
1 AAAGAAGAAGAAAATAAAG-AG-GA
* *
1356983 AGAAGAAGAA-AAAGAAAAATAGGA
1 A-AAGAAGAAGAAA-ATAAAGAGGA
*
1357007 GCAAGAAGAAGAAAATAAAGAGGTA
1 -AAAGAAGAAGAAAATAAAGAGG-A
1357032 AAAGA
1 AAAGA
1357037 GGAGCAATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
24 22 0.52
25 14 0.33
26 6 0.14
ACGTcount: A:0.69, C:0.01, G:0.24, T:0.05
Consensus pattern (23 bp):
AAAGAAGAAGAAAATAAAGAGGA
Found at i:1357040 original size:33 final size:33
Alignment explanation
Indices: 1356998--1357060 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
1356988 AAGAAAAAGA
*
1356998 AAAATAGGAGCAAGAAGAAGAAAATAAAGAGGT
1 AAAAGAGGAGCAAGAAGAAGAAAATAAAGAGGT
*
1357031 AAAAGAGGAGCAATAAGAAGAAAATAAAGA
1 AAAAGAGGAGCAAGAAGAAGAAAATAAAGA
1357061 AGAGAAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.63, C:0.03, G:0.25, T:0.08
Consensus pattern (33 bp):
AAAAGAGGAGCAAGAAGAAGAAAATAAAGAGGT
Found at i:1361638 original size:21 final size:21
Alignment explanation
Indices: 1361572--1361639 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
1361562 AAATTTTATT
1361572 TCATTGTAAAATATTCCTTTA
1 TCATTGTAAAATATTCCTTTA
* *
1361593 TCAACTT-TAAAGCTATT--TACT-
1 TC-A-TTGTAAA-ATATTCCT-TTA
1361614 TCATTGTAAAATATTCCTTTA
1 TCATTGTAAAATATTCCTTTA
1361635 TCATT
1 TCATT
1361640 CAAAACAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
19 6 0.17
20 6 0.17
21 11 0.31
22 6 0.17
23 6 0.17
ACGTcount: A:0.32, C:0.16, G:0.04, T:0.47
Consensus pattern (21 bp):
TCATTGTAAAATATTCCTTTA
Found at i:1367982 original size:22 final size:22
Alignment explanation
Indices: 1367940--1367982 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1367930 TGTGAAATAC
*
1367940 TAAATAAAATAATAAACACAAT
1 TAAATAAAATAATAAAAACAAT
*
1367962 TAAATAAATTAA-AATAAACAA
1 TAAATAAAATAATAA-AAACAA
1367983 GCAAAAAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (22 bp):
TAAATAAAATAATAAAAACAAT
Found at i:1368095 original size:10 final size:10
Alignment explanation
Indices: 1368080--1368109 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
1368070 AATGAGGGCT
1368080 AAATTAAAAC
1 AAATTAAAAC
1368090 AAATTAAAAC
1 AAATTAAAAC
1368100 AAATTAAAAC
1 AAATTAAAAC
1368110 TTAATGAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (10 bp):
AAATTAAAAC
Found at i:1368497 original size:109 final size:109
Alignment explanation
Indices: 1368266--1368470 Score: 241
Period size: 109 Copynumber: 1.9 Consensus size: 109
1368256 CCACATATGT
*
1368266 CCAAAATGTAAAAACACACTAAACTTACAGGAACTAAACAGTAAATAAACTAAAAATTATATAAC
1 CCAAAATGTAAAAACACACTAAACATACAGGAACTAAACAGTAAATAAACTAAAAATTATATAAC
* * * * * * **
1368331 ATGCACATGAAAGGGGAAATAATGATTTTAGTCCTCATAGATAA
66 ATGAAAATAAAAGAGAAAATAAAGATTCGAGTCCTCATAGATAA
** * * * * *
1368375 ATAGAATATAAAAACACACTAAACATAGAGGGACTAAATAGTAAATAAAAC-AAAAATTATATAA
1 CCAAAATGTAAAAACACACTAAACATACAGGAACTAAACAGTAAAT-AAACTAAAAATTATATAA
1368439 CATGAAAATAAAAGAGAAAATAACAGATTCGA
65 CATGAAAATAAAAGAGAAAATAA-AGATTCGA
1368471 TCCCTACAAC
Statistics
Matches: 78, Mismatches: 16, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
109 69 0.88
110 9 0.12
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.21
Consensus pattern (109 bp):
CCAAAATGTAAAAACACACTAAACATACAGGAACTAAACAGTAAATAAACTAAAAATTATATAAC
ATGAAAATAAAAGAGAAAATAAAGATTCGAGTCCTCATAGATAA
Found at i:1369867 original size:139 final size:138
Alignment explanation
Indices: 1369608--1370197 Score: 618
Period size: 139 Copynumber: 4.3 Consensus size: 138
1369598 TCAAGATGTG
* * * * * * * *
1369608 AGTTTTTCTCATTATGATCTCTCTACTGGAAATGTTGATCTCTCGAGTGAGGCGTCGGTGATTCG
1 AGTTCTTCTCATTATGAACTCTCCACT-GAAATGTTGGTCTCTCGAGCGAGGTGTCGCTGATTCA
* * * * * * * * * * * *
1369673 ACTACATATGCGATGAATCAAACTAACGTTGAAAAAGTTATTCTCGTTATAAACTTTTTATTCCT
65 AATTCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCT
1369738 CATCGGATA
130 CATCGGATA
* * *
1369747 AGTTCTTATCATTATGAACTCTCAACATGAAATGTTGG-CATCTCAAGCGAGGTGTCGCTGATTC
1 AGTTCTTCTCATTATGAACTCTCCAC-TGAAATGTTGGTC-TCTCGAGCGAGGTGTCGCTGATTC
*
1369811 AAATTCATATGCGATGAATCGAGCTAATGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCC
64 AAATTCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCC
*
1369876 TCATCGGATG
129 TCATCGGATA
* * * *
1369886 AGTTCTTCTCATTATGAACTCTCCACTTGAAATGTTGGTCCCTTGAGTGAGGTGTCGCTAATTCA
1 AGTTCTTCTCATTATGAACTCTCCAC-TGAAATGTTGGTCTCTCGAGCGAGGTGTCGCTGATTCA
* * * * *
1369951 ACTCCATATAC-ATGAATCGAGCTAAGGTTGAA-AACGTTTTTCTCATTATGAAATTATTCTCCC
65 AATTCATATGCGATGAATCGAGCTAAGGTTGAACAA-GTTCTTCTCATTATGAACTTATTCTCCC
*
1370014 TCATTGGA-A
129 TCATCGGATA
* * *
1370023 AGTTCATCTCATTATGAACTCTCCACTGAAAATTTTGGTC-CATCCAGCGAGGTGTCGCTGATT-
1 AGTTCTTCTCATTATGAACTCTCCACTG-AAATGTTGGTCTC-TCGAGCGAGGTGTCGCTGATTC
* * * *
1370086 TAACTCAATATG-TATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
64 AAATTC-ATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCC
* *
1370150 CTCATCGGGTT
128 CTCATCGGATA
* * * *
1370161 AGGTCTTCTCATTATGAAATGTTCACTGGAAATGTTG
1 AGTTCTTCTCATTATGAACTCTCCACT-GAAATGTTG
1370198 ATTGGTTTAT
Statistics
Matches: 378, Mismatches: 62, Indels: 23
0.82 0.13 0.05
Matches are distributed among these distances:
136 5 0.01
137 110 0.29
138 85 0.22
139 176 0.47
140 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (138 bp):
AGTTCTTCTCATTATGAACTCTCCACTGAAATGTTGGTCTCTCGAGCGAGGTGTCGCTGATTCAA
ATTCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTC
ATCGGATA
Found at i:1370132 original size:275 final size:278
Alignment explanation
Indices: 1369606--1370199 Score: 745
Period size: 275 Copynumber: 2.1 Consensus size: 278
1369596 CTTCAAGATG
* * * * * *
1369606 TGAGTTTTTCTCATTATGATCTCTCTACTGGAAATGTTGATCTCTCGAGTGAGGCGTCGGTGATT
1 TGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGCGTCGCTAATT
* * * * *
1369671 CGACTACATATGCGATGAATCAAACTAACGTTGAAAAAGTTATTCTCGTTATAAACTTTTTATTC
66 CAACTACATATACGATGAATCAAACTAACGTTGAAAAAGTTATTCTCATTATAAACTTATTATCC
*
1369736 CTCATCGGATAAGTTCTTATCATTATGAACTCTCAACATGAAATGTTGGCATCTCAAGCGAGGTG
131 CTCATCGGATAAGTTCATATCATTATGAACTCTCAACATGAAATGTTGGCATCTCAAGCGAGGTG
* *
1369801 TCGCTGATTCAAATTCATATGCGATGAATCGAGCTAATGTTGAACAAGTTCTTCTCATTATGAAC
196 TCGCTGATTCAAACTCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAAC
1369866 TTATTCTCCCTCATCGGA
261 TTATTCTCCCTCATCGGA
* * * *
1369884 TGAGTTCTTCTCATTATGAACTCTCCACTTGAAATGTTGGTCCCTTGAGTGAGGTGTCGCTAATT
1 TGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGCGTCGCTAATT
* * * * * * *
1369949 CAACTCCATATAC-ATGAATCGAGCTAAGGTTGAAAACGTTTTTCTCATTATGAAA-TTATTCTC
66 CAACTACATATACGATGAATCAAACTAACGTTGAAAAAGTTATTCTCATTAT-AAACTTATTATC
* * * *
1370012 CCTCATTGGA-AAGTTCATCTCATTATGAACTCTCCAC-TGAAAATTTTGGTCCATC-C-AGCGA
130 CCTCATCGGATAAGTTCATATCATTATGAACTCTCAACATG-AAATGTTGG--CATCTCAAGCGA
* *
1370073 GGTGTCGCTGATT-TAACTCAATATG-TATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTA
192 GGTGTCGCTGATTCAAACTC-ATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTA
* *
1370136 TGAACTTCTTCTCCCTCATCGGG
256 TGAACTTATTCTCCCTCATCGGA
* * * * *
1370159 TTAGGTCTTCTCATTATGAAATGTTCACTGGAAATGTTGAT
1 TGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGAT
1370200 TGGTTTATCC
Statistics
Matches: 271, Mismatches: 40, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
275 97 0.36
276 55 0.20
277 47 0.17
278 72 0.27
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (278 bp):
TGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGCGTCGCTAATT
CAACTACATATACGATGAATCAAACTAACGTTGAAAAAGTTATTCTCATTATAAACTTATTATCC
CTCATCGGATAAGTTCATATCATTATGAACTCTCAACATGAAATGTTGGCATCTCAAGCGAGGTG
TCGCTGATTCAAACTCATATGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAAC
TTATTCTCCCTCATCGGA
Found at i:1378554 original size:18 final size:18
Alignment explanation
Indices: 1378531--1378569 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1378521 CACAATGCAT
1378531 AAGCACTTCAGGTAAAGA
1 AAGCACTTCAGGTAAAGA
1378549 AAGCACTTCAGGTAAAGA
1 AAGCACTTCAGGTAAAGA
1378567 AAG
1 AAG
1378570 TACATCCGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.15, G:0.23, T:0.15
Consensus pattern (18 bp):
AAGCACTTCAGGTAAAGA
Found at i:1380034 original size:24 final size:20
Alignment explanation
Indices: 1379977--1380014 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1379967 TTCCCCTTGA
1379977 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
*
1379997 AGTGTATCGATGCATTCT
1 AGTGCATCGATGCATTCT
1380015 TTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1380109 original size:64 final size:64
Alignment explanation
Indices: 1380022--1380159 Score: 179
Period size: 64 Copynumber: 2.2 Consensus size: 64
1380012 TCTTTAACAT
* * * *
1380022 GTGCATCGTTGCACTACTCATGCATCGATACACAAATTACCTTCGATGTTTTCA-TTTTAAGGG
1 GTGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCCATTTTTAAGAG
* * * * *
1380085 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCCATTTTTAAGAG
1 G-TGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCCATTTTTAAGAG
1380150 GTGCATCGAT
1 GTGCATCGAT
1380160 ACACACTGAA
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
63 1 0.02
64 54 0.84
65 9 0.14
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCCATTTTTAAGAG
Found at i:1383975 original size:7 final size:7
Alignment explanation
Indices: 1383963--1383992 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
1383953 GTTTTAGTTG
1383963 GGTGAGC
1 GGTGAGC
1383970 GGTGAGC
1 GGTGAGC
1383977 GGTGAGC
1 GGTGAGC
1383984 GGGTGAGC
1 -GGTGAGC
1383992 G
1 G
1383993 ACTTCTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.13, C:0.13, G:0.60, T:0.13
Consensus pattern (7 bp):
GGTGAGC
Found at i:1383982 original size:14 final size:15
Alignment explanation
Indices: 1383963--1383992 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1383953 GTTTTAGTTG
1383963 GGTGAGC-GGTGAGC
1 GGTGAGCGGGTGAGC
1383977 GGTGAGCGGGTGAGC
1 GGTGAGCGGGTGAGC
1383992 G
1 G
1383993 ACTTCTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.13, C:0.13, G:0.60, T:0.13
Consensus pattern (15 bp):
GGTGAGCGGGTGAGC
Found at i:1385974 original size:11 final size:11
Alignment explanation
Indices: 1385958--1385982 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1385948 GAAATTGAAA
1385958 AAATAAAGAAT
1 AAATAAAGAAT
1385969 AAATAAAGAAT
1 AAATAAAGAAT
1385980 AAA
1 AAA
1385983 AGAAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (11 bp):
AAATAAAGAAT
Found at i:1394259 original size:20 final size:20
Alignment explanation
Indices: 1394234--1394272 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1394224 TCCAGGCGAC
1394234 ATACGAGCCATACAAGCCAT
1 ATACGAGCCATACAAGCCAT
*
1394254 ATACGAGCCATACGAGCCA
1 ATACGAGCCATACAAGCCA
1394273 ATGGAGAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.31, G:0.18, T:0.13
Consensus pattern (20 bp):
ATACGAGCCATACAAGCCAT
Found at i:1394266 original size:9 final size:9
Alignment explanation
Indices: 1394233--1394272 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
1394223 ATCCAGGCGA
1394233 CATACGAGC
1 CATACGAGC
*
1394242 CATACAAGC
1 CATACGAGC
1394251 CATATACGAGC
1 C--ATACGAGC
1394262 CATACGAGC
1 CATACGAGC
1394271 CA
1 CA
1394273 ATGGAGAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 19 0.70
11 8 0.30
ACGTcount: A:0.38, C:0.33, G:0.17, T:0.12
Consensus pattern (9 bp):
CATACGAGC
Found at i:1394315 original size:28 final size:28
Alignment explanation
Indices: 1394275--1394331 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
1394265 ACGAGCCAAT
* *
1394275 GGAGAGGTCGCCATGCAGTCTTATACGA
1 GGAGAGGTCGCCATGCAGGCTTAGACGA
1394303 GGAGAGGTCGCCATGCAGGCTTAGACGA
1 GGAGAGGTCGCCATGCAGGCTTAGACGA
1394331 G
1 G
1394332 TCGTACGAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.21, G:0.37, T:0.18
Consensus pattern (28 bp):
GGAGAGGTCGCCATGCAGGCTTAGACGA
Found at i:1394400 original size:29 final size:29
Alignment explanation
Indices: 1394350--1394429 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 29
1394340 GCCAATAGAG
* * *
1394350 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTAT
1394379 AGGTCGCCATGTAGTCCCGGCGACCTTAT
1 AGGTCGCCATGTAGTCCCGGCGACCTTAT
*
1394408 AGGTCGCCATGTAGTCTCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
1394430 CCATTCCCAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 44 0.96
30 2 0.04
ACGTcount: A:0.16, C:0.30, G:0.31, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTAT
Found at i:1394537 original size:27 final size:27
Alignment explanation
Indices: 1394505--1394560 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1394495 CCTACAGCTC
1394505 CCAATGCATGCATGTGAACCATTTGAG
1 CCAATGCATGCATGTGAACCATTTGAG
1394532 CCAATGCATGCATGTGAACCATTTGAG
1 CCAATGCATGCATGTGAACCATTTGAG
1394559 CC
1 CC
1394561 GTGAATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (27 bp):
CCAATGCATGCATGTGAACCATTTGAG
Found at i:1394733 original size:27 final size:23
Alignment explanation
Indices: 1394706--1394751 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1394696 AAAAGAAAGA
1394706 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
1394729 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
1394752 CCGAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.39, T:0.09
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:1394766 original size:25 final size:23
Alignment explanation
Indices: 1394706--1394766 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
1394696 AAAAGAAAGA
**
1394706 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
1394729 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
1394752 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
1394767 AGGGAGAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 23 0.70
25 10 0.30
ACGTcount: A:0.51, C:0.07, G:0.36, T:0.07
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:1395009 original size:46 final size:48
Alignment explanation
Indices: 1394946--1395037 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 48
1394936 TTATATAGTT
*
1394946 AAAAAATAATTAATTAGTTTGT-TTTGTT-AATAGTT-AGTTATATAA
1 AAAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATATAA
*
1394991 AAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAA-TAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1395038 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 6 0.15
46 15 0.37
47 5 0.12
48 7 0.17
49 8 0.20
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (48 bp):
AAAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATATAA
Found at i:1397543 original size:25 final size:26
Alignment explanation
Indices: 1397515--1397574 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
1397505 AGATTAAAAA
*
1397515 ATTAGATAAGATAAT-TTCATAAATT
1 ATTAAATAAGATAATATTCATAAATT
* * *
1397540 ATTAAATAATATAATATTTATAAATG
1 ATTAAATAAGATAATATTCATAAATT
*
1397566 ATCAAATAA
1 ATTAAATAA
1397575 AATTTATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 13 0.45
26 16 0.55
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.38
Consensus pattern (26 bp):
ATTAAATAAGATAATATTCATAAATT
Found at i:1397672 original size:26 final size:24
Alignment explanation
Indices: 1397614--1397672 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
1397604 CTAATAAACC
*
1397614 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
1397638 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
1397666 TAATAAT
1 TAATAAT
1397673 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:1398536 original size:21 final size:21
Alignment explanation
Indices: 1398510--1398560 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1398500 TAAACTAATA
1398510 TAATAACTTAAACTAACAAAC
1 TAATAACTTAAACTAACAAAC
* *
1398531 TAATAATTTATACTAACAAAC
1 TAATAACTTAAACTAACAAAC
1398552 TAATTAACT
1 TAA-TAACT
1398561 AGATTTTAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
TAATAACTTAAACTAACAAAC
Found at i:1399214 original size:29 final size:29
Alignment explanation
Indices: 1399172--1399233 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
1399162 AAATACACAC
*
1399172 AGGTCGCTCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
1399201 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
1399230 AGGT
1 AGGT
1399234 TACTGTAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.18, C:0.34, G:0.32, T:0.16
Consensus pattern (29 bp):
AGGTCGCCCGGATGCCATGGCGACCTCCA
Found at i:1400600 original size:181 final size:183
Alignment explanation
Indices: 1400296--1400654 Score: 607
Period size: 181 Copynumber: 2.0 Consensus size: 183
1400286 TGAAACGGTG
* *
1400296 GAGAGTATAAGATTTGTCCACCATGTAATTAAGCAAAGAAAAAATCAATCTTTACTTACTGTTTG
1 GAGAGTATAAGATTTGTCCACCATGCAATTAAACAAAGAAAAAATCAATCTTTACTTACTGTTTG
* * *
1400361 CTGTCAATATCCACAACTACAGCCCTTTCACTTCAATTCATAACCCTCAATTCTTTGCTTGGACA
66 CTGTCAATATCCACAACTAAAACCCTTTCACTTCAATTCATAACCCTAAATTCTTTGCTTGGACA
1400426 TCCCCC-CTCTATCTCTCT-T-ATGAATTGGAAAGACAAAAAAGTGCAAAGGTA
131 -CCCCCTCTCTATCTCTCTCTCATGAATTGGAAAGACAAAAAAGTGCAAAGGTA
* * *
1400477 GAGAGTATAAGATTTGTCCACCCTGCAATTAAACAAAGTAGAAATCAATCTTTACTTACTGTTTG
1 GAGAGTATAAGATTTGTCCACCATGCAATTAAACAAAGAAAAAATCAATCTTTACTTACTGTTTG
1400542 CTGTCAATATCCACAACTAAAACCCTTTCACTTCAATTCATAACCCTAAATTCTTTGCTTGGACA
66 CTGTCAATATCCACAACTAAAACCCTTTCACTTCAATTCATAACCCTAAATTCTTTGCTTGGACA
*
1400607 CCCCCTCTCTCTCTCTCTCTCATGAATTGGAAAGACAAAAAAGTGCAA
131 CCCCCTCTCTATCTCTCTCTCATGAATTGGAAAGACAAAAAAGTGCAA
1400655 GGTCTCTTTT
Statistics
Matches: 166, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
180 5 0.03
181 133 0.80
182 1 0.01
183 27 0.16
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.30
Consensus pattern (183 bp):
GAGAGTATAAGATTTGTCCACCATGCAATTAAACAAAGAAAAAATCAATCTTTACTTACTGTTTG
CTGTCAATATCCACAACTAAAACCCTTTCACTTCAATTCATAACCCTAAATTCTTTGCTTGGACA
CCCCCTCTCTATCTCTCTCTCATGAATTGGAAAGACAAAAAAGTGCAAAGGTA
Found at i:1402173 original size:30 final size:30
Alignment explanation
Indices: 1402137--1402204 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
1402127 TTTGACTTTT
*
1402137 TCGGTCAAAGTCAACGGTCAAGGGGTTGAC
1 TCGGTCAAAGTCAACGGTCAAGGAGTTGAC
*
1402167 TCGGTCAAAGTCAACGGTCAATGAGTTGAC
1 TCGGTCAAAGTCAACGGTCAAGGAGTTGAC
*
1402197 TAGGTCAA
1 TCGGTCAA
1402205 GCAGGTCGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.22
Consensus pattern (30 bp):
TCGGTCAAAGTCAACGGTCAAGGAGTTGAC
Found at i:1404285 original size:14 final size:14
Alignment explanation
Indices: 1404266--1404292 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1404256 CGAGTGACGA
1404266 TTATTATATATATG
1 TTATTATATATATG
1404280 TTATTATATATAT
1 TTATTATATATAT
1404293 AATAATATTA
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:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (14 bp):
TTATTATATATATG
Found at i:1411597 original size:22 final size:22
Alignment explanation
Indices: 1411567--1411619 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1411557 CTACATTCTG
*
1411567 CAAAAATGATAGATTCTCTTTT
1 CAAAGATGATAGATTCTCTTTT
1411589 CAAAGATGATAGATTCTCTTTT
1 CAAAGATGATAGATTCTCTTTT
1411611 CAAAGATGA
1 CAAAGATGA
1411620 AAGCTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (22 bp):
CAAAGATGATAGATTCTCTTTT
Found at i:1412892 original size:16 final size:16
Alignment explanation
Indices: 1412850--1412909 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 16
1412840 GAATGATGAT
1412850 TATTATATATAAGTTATTA
1 TATTATA-ATAA--TATTA
1412869 TATATATAATAATATTA
1 TAT-TATAATAATATTA
*
1412886 TATTATAAATATTATTA
1 TATTAT-AATAATATTA
1412903 T-TTATAA
1 TATTATAA
1412910 ACCCGGAAGG
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
15 2 0.05
16 7 0.18
17 18 0.47
19 7 0.18
20 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
TATTATAATAATATTA
Found at i:1412898 original size:14 final size:14
Alignment explanation
Indices: 1412850--1412910 Score: 52
Period size: 14 Copynumber: 4.0 Consensus size: 14
1412840 GAATGATGAT
*
1412850 TATTATA-TATAAGT
1 TATTATATTATAA-A
1412864 TATTATATATATAATAA
1 TATTATAT-TAT-A-AA
1412881 TATTATATTATAAA
1 TATTATATTATAAA
1412895 TATTATTATTTATAAA
1 TATTA-TA-TTATAAA
1412911 CCCGGAAGGC
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 14 0.35
15 3 0.08
16 13 0.32
17 9 0.22
18 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
TATTATATTATAAA
Found at i:1419648 original size:23 final size:23
Alignment explanation
Indices: 1419618--1419690 Score: 74
Period size: 30 Copynumber: 2.9 Consensus size: 23
1419608 CAATCAAAAA
1419618 CAAAGTCAACGGGTTGACTCGGT
1 CAAAGTCAACGGGTTGACTCGGT
1419641 CAAAGTCAACGGTCAACCAGTTGACTCGGT
1 CAAAGTCAACGG-------GTTGACTCGGT
*
1419671 CAAAGTCAACGAGTTGACTC
1 CAAAGTCAACGGGTTGACTC
1419691 AACCAAGTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 14
0.74 0.02 0.25
Matches are distributed among these distances:
23 20 0.48
30 22 0.52
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.21
Consensus pattern (23 bp):
CAAAGTCAACGGGTTGACTCGGT
Found at i:1427474 original size:49 final size:49
Alignment explanation
Indices: 1427398--1427499 Score: 177
Period size: 49 Copynumber: 2.1 Consensus size: 49
1427388 GCTACCAACC
*
1427398 TGCTAAGATATGGTACTAAACAATAGGCACATATATGGTCTTGATCAAA
1 TGCTAAGATATGGTACTAAACAATAGGCACATAAATGGTCTTGATCAAA
* *
1427447 TGCTAAGATATGGTGCTAAACAGTAGGCACATAAATGGTCTTGATCAAA
1 TGCTAAGATATGGTACTAAACAATAGGCACATAAATGGTCTTGATCAAA
1427496 TGCT
1 TGCT
1427500 GCCTACTTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (49 bp):
TGCTAAGATATGGTACTAAACAATAGGCACATAAATGGTCTTGATCAAA
Found at i:1431524 original size:49 final size:49
Alignment explanation
Indices: 1431452--1431553 Score: 204
Period size: 49 Copynumber: 2.1 Consensus size: 49
1431442 GCTACCAACC
1431452 TGCTAAGATATGGTACTAAACAGTAGGCACATAAATGGTCTTGATCAAA
1 TGCTAAGATATGGTACTAAACAGTAGGCACATAAATGGTCTTGATCAAA
1431501 TGCTAAGATATGGTACTAAACAGTAGGCACATAAATGGTCTTGATCAAA
1 TGCTAAGATATGGTACTAAACAGTAGGCACATAAATGGTCTTGATCAAA
1431550 TGCT
1 TGCT
1431554 GCCTACTTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (49 bp):
TGCTAAGATATGGTACTAAACAGTAGGCACATAAATGGTCTTGATCAAA
Found at i:1443162 original size:17 final size:18
Alignment explanation
Indices: 1443127--1443163 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
1443117 CTTGGAGAAT
1443127 AAGAAAAGAAAATAAATG
1 AAGAAAAGAAAATAAATG
1443145 AAGAAAA-AAAGA-AAATG
1 AAGAAAAGAAA-ATAAATG
1443162 AA
1 AA
1443164 AAGTGATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (18 bp):
AAGAAAAGAAAATAAATG
Found at i:1472788 original size:21 final size:21
Alignment explanation
Indices: 1472762--1472804 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1472752 TCAAGTAATA
1472762 TAGGGTAAGTGAGTTATCATC
1 TAGGGTAAGTGAGTTATCATC
1472783 TAGGGTAAGTGAGTTATCATC
1 TAGGGTAAGTGAGTTATCATC
1472804 T
1 T
1472805 CCTCAGGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.35
Consensus pattern (21 bp):
TAGGGTAAGTGAGTTATCATC
Found at i:1479004 original size:21 final size:21
Alignment explanation
Indices: 1478980--1479044 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 21
1478970 CCCTTTGATT
**
1478980 AAAAGACTTCTCCTTTTAATG
1 AAAAGACTTAACCTTTTAATG
* *
1479001 AAAAGGCTTAACCTTTTCATG
1 AAAAGACTTAACCTTTTAATG
* * * *
1479022 AAAGGATTTAATCTTTTCATG
1 AAAAGACTTAACCTTTTAATG
1479043 AA
1 AA
1479045 GAGAATTGTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.37
Consensus pattern (21 bp):
AAAAGACTTAACCTTTTAATG
Found at i:1482024 original size:20 final size:18
Alignment explanation
Indices: 1481982--1482024 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1481972 ATTTGGAGGA
*
1481982 CTAAAAACCTAAATTATC
1 CTAAAAACCTAAATTACC
1482000 CTAAAAACCTAATATATACC
1 CTAAAAACCTAA-AT-TACC
1482020 CTAAA
1 CTAAA
1482025 TAAAACAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.55
19 2 0.09
20 8 0.36
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (18 bp):
CTAAAAACCTAAATTACC
Done.