Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001111.1 Hibiscus syriacus cultivar Beakdansim tig00002193_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: 3891333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 17
Found at i:1068164 original size:83 final size:83
Alignment explanation
Indices: 1068036--1068197 Score: 207
Period size: 83 Copynumber: 2.0 Consensus size: 83
1068026 TATTGCGACA
* * * *
1068036 TTTGTATAAAAACACCGCTAAAGTACTACTCTGGTGCTGCGTTTGTTGAAAAAACGCCACTATAT
1 TTTGTATAAAAACACCGCTAAAGTACTACTCTAGTGCAGCGTTTGTTGAAAAAACACCACTATAG
*
1068101 ATGAAATCTATTGCAAAG
66 ATGAAATATATTGCAAAG
* ** * * * *
1068119 TTTGTATAACAACGTCGCTAATGTACTATTCTATTGCAGCGTTTGTTGAAAAAATACCACTATAG
1 TTTGTATAAAAACACCGCTAAAGTACTACTCTAGTGCAGCGTTTGTTGAAAAAACACCACTATAG
*
1068184 ATGAATTATATTGC
66 ATGAAATATATTGC
1068198 GTCATTTTTA
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
83 66 1.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (83 bp):
TTTGTATAAAAACACCGCTAAAGTACTACTCTAGTGCAGCGTTTGTTGAAAAAACACCACTATAG
ATGAAATATATTGCAAAG
Found at i:1070761 original size:16 final size:18
Alignment explanation
Indices: 1070734--1070768 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1070724 ATAAGTCATG
1070734 TTTATATTTTTA-AAAAA
1 TTTATATTTTTAGAAAAA
1070751 TTTAT-TTTTTAGAAAAA
1 TTTATATTTTTAGAAAAA
1070768 T
1 T
1070769 ATTTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTATATTTTTAGAAAAA
Found at i:1070773 original size:30 final size:31
Alignment explanation
Indices: 1070741--1070798 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
1070731 ATGTTTATAT
*
1070741 TTTTAAAAA-ATTTATTTTT-TAGAAAAATA
1 TTTTAAAAATATTGATTTTTATAGAAAAATA
*
1070770 TTTTAAAAATATTGATTTTTATATAAAAA
1 TTTTAAAAATATTGATTTTTATAGAAAAA
1070799 AAATACAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 9 0.36
30 9 0.36
31 7 0.28
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (31 bp):
TTTTAAAAATATTGATTTTTATAGAAAAATA
Found at i:1092988 original size:23 final size:26
Alignment explanation
Indices: 1092948--1093023 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 26
1092938 ATTTGATTTT
* *
1092948 AATTTTAATATTATTTTTTAA-A-TA
1 AATTATAATATTAATTTTTAATATTA
1092972 AATTA-AATATTAATTTTTAATATTA
1 AATTATAATATTAATTTTTAATATTA
*
1092997 TATTATAGATATTAA-TTTTAATATTA
1 AATTATA-ATATTAATTTTTAATATTA
1093023 A
1 A
1093024 TTTTTTAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
23 14 0.32
24 5 0.11
25 6 0.14
26 12 0.27
27 7 0.16
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (26 bp):
AATTATAATATTAATTTTTAATATTA
Found at i:1093008 original size:14 final size:12
Alignment explanation
Indices: 1092972--1093025 Score: 56
Period size: 13 Copynumber: 4.3 Consensus size: 12
1092962 TTTTTAAATA
1092972 AATTA-AATATT
1 AATTATAATATT
*
1092983 AATTTTTAATATT
1 AA-TTATAATATT
1092996 ATATTATAGATATT
1 A-ATTATA-ATATT
*
1093010 AATTTTAATATT
1 AATTATAATATT
1093022 AATT
1 AATT
1093026 TTTTAAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
11 2 0.06
12 11 0.31
13 16 0.44
14 7 0.19
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (12 bp):
AATTATAATATT
Found at i:1093022 original size:12 final size:12
Alignment explanation
Indices: 1092923--1093027 Score: 83
Period size: 12 Copynumber: 8.7 Consensus size: 12
1092913 GGTTTTATAT
1092923 TTAATTTT-ATA
1 TTAATTTTAATA
* *
1092934 TT-ATATTTGATT
1 TTAAT-TTTAATA
1092946 TTAATTTTAATA
1 TTAATTTTAATA
*
1092958 TTATTTTTTAA-A
1 TTA-ATTTTAATA
* *
1092970 -TAAATTAAATA
1 TTAATTTTAATA
1092981 TTAATTTTTAATA
1 TTAA-TTTTAATA
*
1092994 TTATATTATAGATA
1 TTA-ATTTTA-ATA
1093008 TTAATTTTAATA
1 TTAATTTTAATA
1093020 TTAATTTT
1 TTAATTTT
1093028 TTAAATTTAT
Statistics
Matches: 74, Mismatches: 11, Indels: 17
0.73 0.11 0.17
Matches are distributed among these distances:
10 6 0.08
11 8 0.11
12 27 0.36
13 26 0.35
14 7 0.09
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (12 bp):
TTAATTTTAATA
Found at i:1093072 original size:20 final size:20
Alignment explanation
Indices: 1093028--1093097 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 20
1093018 TATTAATTTT
*
1093028 TTAAATTTATTCTATATCA-TA
1 TTAAA-TTATTTTATAT-ATTA
1093049 -TAAATTATTTTATATATTA
1 TTAAATTATTTTATATATTA
1093068 TTAAA-T-TTTTATAT-TTA
1 TTAAATTATTTTATATATTA
*
1093085 TTTTAATTATTTT
1 -TTAAATTATTTT
1093098 GATTTAAGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
17 3 0.07
18 13 0.31
19 14 0.33
20 12 0.29
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (20 bp):
TTAAATTATTTTATATATTA
Found at i:1093092 original size:18 final size:18
Alignment explanation
Indices: 1093028--1093086 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 18
1093018 TATTAATTTT
* *
1093028 TTAAATTTATTCTATATCA
1 TTAAATTT-TTATATATTA
1093047 TATAAATTATTTTATATATTA
1 T-TAAA-T-TTTTATATATTA
1093068 TTAAATTTTTATAT-TTA
1 TTAAATTTTTATATATTA
1093085 TT
1 TT
1093087 TTAATTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
17 5 0.14
18 8 0.23
19 2 0.06
20 8 0.23
21 10 0.29
22 2 0.06
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAAATTTTTATATATTA
Found at i:1094778 original size:2 final size:2
Alignment explanation
Indices: 1094766--1094801 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1094756 AATATGTAAG
* *
1094766 AT AT GT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1094802 GTAAAAACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1094798 original size:64 final size:64
Alignment explanation
Indices: 1094719--1094847 Score: 222
Period size: 64 Copynumber: 2.0 Consensus size: 64
1094709 ATTGTTGATG
*
1094719 TATATATACATATATATATGTAAAAAAATATTATGAAAATATGTAAGATATGTATATATATATA
1 TATATATACACATATATATGTAAAAAAATATTATGAAAATATGTAAGATATGTATATATATATA
* * *
1094783 TATATATATACATATATATGTAAAAACATATTATGTAAATATGTAAGATATGTATATATATATA
1 TATATATACACATATATATGTAAAAAAATATTATGAAAATATGTAAGATATGTATATATATATA
1094847 T
1 T
1094848 GTGTGTAAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (64 bp):
TATATATACACATATATATGTAAAAAAATATTATGAAAATATGTAAGATATGTATATATATATA
Found at i:1094819 original size:15 final size:16
Alignment explanation
Indices: 1094730--1094821 Score: 55
Period size: 16 Copynumber: 5.8 Consensus size: 16
1094720 ATATATACAT
*
1094730 ATATATATGTAAAAAA
1 ATATATATGTAAAAAC
*
1094746 ATAT-TATG-AAAATAT
1 ATATATATGTAAAA-AC
* * * * *
1094761 GTAAGATATGTATATAT
1 AT-ATATATGTAAAAAC
* * *
1094778 ATATATATATATATAC
1 ATATATATGTAAAAAC
1094794 ATATATATGTAAAAAC
1 ATATATATGTAAAAAC
1094810 ATAT-TATGTAAA
1 ATATATATGTAAA
1094822 TATGTAAGAT
Statistics
Matches: 60, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.07
15 14 0.23
16 33 0.55
17 7 0.12
18 2 0.03
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (16 bp):
ATATATATGTAAAAAC
Found at i:1095343 original size:5 final size:5
Alignment explanation
Indices: 1095333--1095363 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
1095323 TATGCGTTTC
1095333 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT T
1095364 GTTCGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:1103253 original size:14 final size:14
Alignment explanation
Indices: 1103234--1103260 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1103224 AATAAAAAAA
1103234 TTAAACCCTAAACT
1 TTAAACCCTAAACT
1103248 TTAAACCCTAAAC
1 TTAAACCCTAAAC
1103261 CATAGTTTAA
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:0.30, G:0.00, T:0.26
Consensus pattern (14 bp):
TTAAACCCTAAACT
Found at i:1103744 original size:101 final size:101
Alignment explanation
Indices: 1103620--1103816 Score: 268
Period size: 101 Copynumber: 2.0 Consensus size: 101
1103610 AAAAAGGCAC
* * *
1103620 TACCTACAATGTTATACGTATAAACCTATTTTGCCTTACTTTTGCATAACATAAATGGTTTCAAA
1 TACCTACAATGTTATACATATAAACATATTTTGCCTTACTTTTGCATAACATAAATAGTTTCAAA
*
1103685 CATATAACCTAAAAAATTGACAATTAAAAAAGGTGT
66 CATATAACCTAAAAAATTGACAAATAAAAAAGGTGT
* * * * ** *
1103721 TACCTATAATGTTATACATATAAACATGTTTTGTCTTACTTTTGTATATTATAAATAGTTTTAAA
1 TACCTACAATGTTATACATATAAACATATTTTGCCTTACTTTTGCATAACATAAATAGTTTCAAA
***
1103786 CATATAACCTAAATGGTTGACAAATAAAAAA
66 CATATAACCTAAAAAATTGACAAATAAAAAA
1103817 AAAGCACTAC
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
101 82 1.00
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (101 bp):
TACCTACAATGTTATACATATAAACATATTTTGCCTTACTTTTGCATAACATAAATAGTTTCAAA
CATATAACCTAAAAAATTGACAAATAAAAAAGGTGT
Found at i:1111061 original size:18 final size:18
Alignment explanation
Indices: 1110992--1111061 Score: 65
Period size: 18 Copynumber: 4.0 Consensus size: 18
1110982 TTTAATTGAG
*
1110992 CTAGTTTAATT-ATTGAA
1 CTAGTTTAATTGAATGAA
* * *
1111009 CCAGTTTAAATGAATAAA
1 CTAGTTTAATTGAATGAA
*
1111027 CTAGTTTAATT-AGTGAA
1 CTAGTTTAATTGAATGAA
1111044 CTAGCTTT-ATTGAATGAA
1 CTAG-TTTAATTGAATGAA
1111062 AAAACATACT
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
17 20 0.49
18 21 0.51
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (18 bp):
CTAGTTTAATTGAATGAA
Found at i:1112262 original size:21 final size:21
Alignment explanation
Indices: 1112238--1112278 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1112228 ATGAAATATA
1112238 GATATTTATT-ATATTCGTATT
1 GATA-TTATTCATATTCGTATT
*
1112259 GATATTATTCATATTTGTAT
1 GATATTATTCATATTCGTAT
1112279 CAATACTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (21 bp):
GATATTATTCATATTCGTATT
Found at i:1113197 original size:368 final size:372
Alignment explanation
Indices: 1112516--1113259 Score: 1442
Period size: 368 Copynumber: 2.0 Consensus size: 372
1112506 TTAAAAATGG
1112516 ATCATATTACATCAGGTAAAGTTAAGCCGAACGCATAATGTGAATAACTAGTTTGTGTCCCAAAA
1 ATCATATTACATCAGGTAAAGTTAAGCCGAACGCATAATGTGAATAACTAGTTTGTGTCCCAAAA
1112581 GTTGTTTGGGGTGCTATTTTCTTCTCGTGGTCAAGCTTGGGATTTTTATAGGGCATAAGTAAATA
66 GTTGTTTGGGGTGCTATTTTCTTCTCGTGGTCAAGCTTGGGATTTTTATAGGGCATAAGTAAATA
1112646 AGCATAGTTTTAGTGCATGACGAGGAATAACACGACTAGATAAGGAAGACAACGTCAAGTCATAA
131 AGCATAGTTTTAGTGCATGACGAGGAATAACACGACTAGATAAGGAAGACAACGTCAAGTCATAA
1112711 GAATTTTTTTGTTCAAAGCAAGGGTTTTGGAAATAAAAAGTGAATAATGATGATCATCAACGTGC
196 GAATTTTTTTGTTCAAAGCAAGGGTTTTGGAAATAAAAAGTGAATAATGATGATCATCAACGTGC
*
1112776 TCATTGGGCAGTTACAAAAATCGACTCAATGCTAGAATAGTAGTGAATGCAACAGAAACTGAAGA
261 TCATTGGACAGTTACAAAAATCGACTCAATGCTAGAATAGTAGTGAATGCAACAGAAACTGAAGA
*
1112841 TCAATGTTTTAGTTGTCATCGATGGGGATAGGGTTATGTAGAGGGCA
326 TCAATGTTTTAGTTGTCATCGATGGGGATAGGGCTATGTAGAGGGCA
1112888 ATCATATTACATCAGGTAAAGTTAAGCCGAACGCATAATGTGAATAACTAGTTTGTGTCCCAAAA
1 ATCATATTACATCAGGTAAAGTTAAGCCGAACGCATAATGTGAATAACTAGTTTGTGTCCCAAAA
1112953 GTTGTTTGGGGTGCTATTTT-TTCT-GTGGTCAAGCTTGGGA-TTTTATAGGGCATAAGT-AATA
66 GTTGTTTGGGGTGCTATTTTCTTCTCGTGGTCAAGCTTGGGATTTTTATAGGGCATAAGTAAATA
1113014 AGCATAGTTTTAGTGCATGACGAGGAATAACACGACTAGATAAGGAAGACAACGTCAAGTCATAA
131 AGCATAGTTTTAGTGCATGACGAGGAATAACACGACTAGATAAGGAAGACAACGTCAAGTCATAA
1113079 GAATTTTTTTGTTCAAAGCAAGGGTTTTGGAAATAAAAAGTGAATAATGATGATCATCAACGTGC
196 GAATTTTTTTGTTCAAAGCAAGGGTTTTGGAAATAAAAAGTGAATAATGATGATCATCAACGTGC
1113144 TCATTGGACAGTTACAAAAATCGACTCAATGCTAGAATAGTAGTGAATGCAACAGAAACTGAAGA
261 TCATTGGACAGTTACAAAAATCGACTCAATGCTAGAATAGTAGTGAATGCAACAGAAACTGAAGA
1113209 TCAATGTTTTAGTTGTCATCGATGGGGATAGGGCTATGTAGAGGGCA
326 TCAATGTTTTAGTTGTCATCGATGGGGATAGGGCTATGTAGAGGGCA
1113256 ATCA
1 ATCA
1113260 ATCTGTTGTC
Statistics
Matches: 370, Mismatches: 2, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
368 248 0.67
369 17 0.05
370 16 0.04
371 4 0.01
372 85 0.23
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (372 bp):
ATCATATTACATCAGGTAAAGTTAAGCCGAACGCATAATGTGAATAACTAGTTTGTGTCCCAAAA
GTTGTTTGGGGTGCTATTTTCTTCTCGTGGTCAAGCTTGGGATTTTTATAGGGCATAAGTAAATA
AGCATAGTTTTAGTGCATGACGAGGAATAACACGACTAGATAAGGAAGACAACGTCAAGTCATAA
GAATTTTTTTGTTCAAAGCAAGGGTTTTGGAAATAAAAAGTGAATAATGATGATCATCAACGTGC
TCATTGGACAGTTACAAAAATCGACTCAATGCTAGAATAGTAGTGAATGCAACAGAAACTGAAGA
TCAATGTTTTAGTTGTCATCGATGGGGATAGGGCTATGTAGAGGGCA
Found at i:1116986 original size:18 final size:19
Alignment explanation
Indices: 1116946--1116986 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
1116936 TATCTCACCT
* *
1116946 TTTATTTTTATATTTTTAA
1 TTTATTTTTATATCTTAAA
1116965 -TTATTTTT-TATCTTAAA
1 TTTATTTTTATATCTTAAA
1116982 TTTAT
1 TTTAT
1116987 CTCTATCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTATTTTTATATCTTAAA
Found at i:1122188 original size:21 final size:21
Alignment explanation
Indices: 1122162--1122204 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1122152 TTCCGTGTTC
1122162 ATTTAGTTTGTTTACATGCCT
1 ATTTAGTTTGTTTACATGCCT
1122183 ATTTAGTTTGTTTACATGCCT
1 ATTTAGTTTGTTTACATGCCT
1122204 A
1 A
1122205 ATAAATTAAT
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:0.21, C:0.14, G:0.14, T:0.51
Consensus pattern (21 bp):
ATTTAGTTTGTTTACATGCCT
Found at i:1122584 original size:24 final size:23
Alignment explanation
Indices: 1122557--1122601 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1122547 GGCTTCTTTT
* *
1122557 CAAAATTTAAAATATAAAAATATA
1 CAAAAATT-AAATAAAAAAATATA
1122581 CAAAAATTAAATAAAAAAATA
1 CAAAAATTAAATAAAAAAATA
1122602 CTAAAAGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (23 bp):
CAAAAATTAAATAAAAAAATATA
Found at i:1122596 original size:21 final size:21
Alignment explanation
Indices: 1122570--1122629 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
1122560 AATTTAAAAT
*
1122570 ATAAAAATATACAAAAATTAA
1 ATAAAAATATACTAAAATTAA
* *
1122591 ATAAAAAAATACTAAAAGTAA
1 ATAAAAATATACTAAAATTAA
*
1122612 A-ATAAAT-TACTAAAATTA
1 ATAAAAATATACTAAAATTA
1122630 TACATGTACA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
19 10 0.30
20 4 0.12
21 19 0.58
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (21 bp):
ATAAAAATATACTAAAATTAA
Found at i:1122598 original size:23 final size:24
Alignment explanation
Indices: 1122557--1122617 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 24
1122547 GGCTTCTTTT
* *
1122557 CAAAATTTAAAATATAAAAATATA
1 CAAAAATTAAAATAAAAAAATATA
1122581 CAAAAATT-AAAT-AAAAAA-ATA
1 CAAAAATTAAAATAAAAAAATATA
* *
1122602 CTAAAAGTAAAATAAA
1 CAAAAATTAAAATAAA
1122618 TTACTAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 9 0.29
22 9 0.29
23 6 0.19
24 7 0.23
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (24 bp):
CAAAAATTAAAATAAAAAAATATA
Found at i:1122607 original size:22 final size:21
Alignment explanation
Indices: 1122564--1122617 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
1122554 TTTCAAAATT
1122564 TAAAATATAAAAATATACAAAAA
1 TAAAATA-AAAAA-ATACAAAAA
* *
1122587 TTAAATAAAAAAATACTAAAAG
1 TAAAATAAAAAAATAC-AAAAA
1122609 TAAAATAAA
1 TAAAATAAA
1122618 TTACTAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.15
22 17 0.63
23 6 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (21 bp):
TAAAATAAAAAAATACAAAAA
Found at i:1122624 original size:19 final size:17
Alignment explanation
Indices: 1122592--1122626 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
1122582 AAAAATTAAA
1122592 TAAAAAAATACTAAAAG
1 TAAAAAAATACTAAAAG
1122609 TAAAATAAATTACTAAAA
1 TAAAA-AAA-TACTAAAA
1122627 TTATACATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.23
Consensus pattern (17 bp):
TAAAAAAATACTAAAAG
Found at i:1123920 original size:20 final size:20
Alignment explanation
Indices: 1123895--1123932 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1123885 TTTGGTTTAC
* *
1123895 AGAATATAATATTACCAGTG
1 AGAATAAAAGATTACCAGTG
1123915 AGAATAAAAGATTACCAG
1 AGAATAAAAGATTACCAG
1123933 GGAATAGGAT
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:0.50, C:0.11, G:0.16, T:0.24
Consensus pattern (20 bp):
AGAATAAAAGATTACCAGTG
Found at i:1129320 original size:22 final size:22
Alignment explanation
Indices: 1129295--1129345 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1129285 ATTTTGAGGA
*
1129295 TTTGGTGAAAGATTTTTATGCT
1 TTTGATGAAAGATTTTTATGCT
** *
1129317 TTTGATGTTAGATTTTTATGTT
1 TTTGATGAAAGATTTTTATGCT
1129339 TTTGATG
1 TTTGATG
1129346 TGGAGATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.20, C:0.02, G:0.22, T:0.57
Consensus pattern (22 bp):
TTTGATGAAAGATTTTTATGCT
Found at i:1129346 original size:22 final size:22
Alignment explanation
Indices: 1129304--1129346 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1129294 ATTTGGTGAA
1129304 AGATTTTTATGCTTTTGATGTT
1 AGATTTTTATGCTTTTGATGTT
*
1129326 AGATTTTTATGTTTTTGATGT
1 AGATTTTTATGCTTTTGATGT
1129347 GGAGATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.02, G:0.19, T:0.60
Consensus pattern (22 bp):
AGATTTTTATGCTTTTGATGTT
Found at i:1129352 original size:23 final size:22
Alignment explanation
Indices: 1129304--1129353 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
1129294 ATTTGGTGAA
*
1129304 AGATTTTTATGCTTTTGATGTT
1 AGATTTTTATGCTTTTGATGTG
*
1129326 AGATTTTTATGTTTTTGATGTGG
1 AGATTTTTATGCTTTTGATGT-G
1129349 AGATT
1 AGATT
1129354 AATTCTAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.20, C:0.02, G:0.22, T:0.56
Consensus pattern (22 bp):
AGATTTTTATGCTTTTGATGTG
Found at i:1131438 original size:19 final size:19
Alignment explanation
Indices: 1131362--1131444 Score: 78
Period size: 19 Copynumber: 4.4 Consensus size: 19
1131352 TATGCATCGG
*
1131362 GCTATGAATATGAAAATAA
1 GCTATGAATCTGAAAATAA
* * * *
1131381 ACTATGAATTTTAAAATTA
1 GCTATGAATCTGAAAATAA
*
1131400 GCTATGAATCT-AACAGTAA
1 GCTATGAATCTGAA-AATAA
*
1131419 GCTATGAGTCTGAAAATAA
1 GCTATGAATCTGAAAATAA
*
1131438 GTTATGA
1 GCTATGA
1131445 TTATGGAAAT
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
18 2 0.04
19 47 0.92
20 2 0.04
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.31
Consensus pattern (19 bp):
GCTATGAATCTGAAAATAA
Found at i:1131473 original size:19 final size:19
Alignment explanation
Indices: 1131429--1131475 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1131419 GCTATGAGTC
1131429 TGAAAATAAGTTATGATTA
1 TGAAAATAAGTTATGATTA
* *
1131448 TGGAAATAAGTTTTGATT-
1 TGAAAATAAGTTATGATTA
1131466 TAGAAAATAA
1 T-GAAAATAA
1131476 ATTCTGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 1 0.04
19 23 0.96
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.36
Consensus pattern (19 bp):
TGAAAATAAGTTATGATTA
Found at i:1137373 original size:19 final size:19
Alignment explanation
Indices: 1137348--1137461 Score: 115
Period size: 19 Copynumber: 6.0 Consensus size: 19
1137338 TATGCATTGG
*
1137348 GCTATGAATTTGAAAATAA
1 GCTATGAATCTGAAAATAA
* * *
1137367 TCTATGAGTTTGAAAATAA
1 GCTATGAATCTGAAAATAA
1137386 GCTATGAATCTGAAAGA-AA
1 GCTATGAATCTGAAA-ATAA
*
1137405 GCTATGAGTCTGAAAATAA
1 GCTATGAATCTGAAAATAA
* * *
1137424 GTTATGAATATGGAAATAA
1 GCTATGAATCTGAAAATAA
*
1137443 GTTATG-ATACTGAAAATAA
1 GCTATGAAT-CTGAAAATAA
1137462 ATTTTGAAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
18 3 0.04
19 76 0.95
20 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.18, T:0.30
Consensus pattern (19 bp):
GCTATGAATCTGAAAATAA
Found at i:1137400 original size:38 final size:38
Alignment explanation
Indices: 1137348--1137461 Score: 133
Period size: 38 Copynumber: 3.0 Consensus size: 38
1137338 TATGCATTGG
* * *
1137348 GCTATGAATTTGAAAATAATCTATGAGTTTGAAAATAA
1 GCTATGAATATGAAAATAAGCTATGAGTCTGAAAATAA
*
1137386 GCTATGAATCTGAAAGA-AAGCTATGAGTCTGAAAATAA
1 GCTATGAATATGAAA-ATAAGCTATGAGTCTGAAAATAA
* * *
1137424 GTTATGAATATGGAAATAAGTTATGA-TACTGAAAATAA
1 GCTATGAATATGAAAATAAGCTATGAGT-CTGAAAATAA
1137462 ATTTTGAAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
37 2 0.03
38 63 0.95
39 1 0.02
ACGTcount: A:0.46, C:0.06, G:0.18, T:0.30
Consensus pattern (38 bp):
GCTATGAATATGAAAATAAGCTATGAGTCTGAAAATAA
Found at i:1137441 original size:57 final size:57
Alignment explanation
Indices: 1137348--1137457 Score: 134
Period size: 57 Copynumber: 1.9 Consensus size: 57
1137338 TATGCATTGG
* * *
1137348 GCTATGAATTTGAAAATAATCTATGAGTTTGAAAATAAGCTATGA-ATCTGAAAGAAA
1 GCTATGAATCTGAAAATAATCTATGAATATGAAAATAAGCTATGATA-CTGAAAGAAA
* * *
1137405 GCTATGAGTCTGAAAATAAGT-TATGAATATGGAAATAAGTTATGATACTGAAA
1 GCTATGAATCTGAAAATAA-TCTATGAATATGAAAATAAGCTATGATACTGAAA
1137458 ATAAATTTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
57 43 0.96
58 2 0.04
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.30
Consensus pattern (57 bp):
GCTATGAATCTGAAAATAATCTATGAATATGAAAATAAGCTATGATACTGAAAGAAA
Found at i:1137513 original size:12 final size:12
Alignment explanation
Indices: 1137496--1137541 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
1137486 TTTGAACATG
1137496 GAATATGAAAAT
1 GAATATGAAAAT
**
1137508 GAATATGTGAAT
1 GAATATGAAAAT
**
1137520 GAATATGTCAAT
1 GAATATGAAAAT
1137532 GAATATGAAA
1 GAATATGAAA
1137542 GTGGAAAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.50, C:0.02, G:0.20, T:0.28
Consensus pattern (12 bp):
GAATATGAAAAT
Found at i:1146541 original size:156 final size:156
Alignment explanation
Indices: 1146200--1146782 Score: 662
Period size: 156 Copynumber: 3.7 Consensus size: 156
1146190 AGGTGGATTC
* * *
1146200 AAAGAGGAATTGGAAGTACATA-AGTATTCTACAATGATTTAGGAGCATGTGGTTCAAATATGAT
1 AAAGAGGAATTGAAAGTACATATA-TATTCTACAATGATTTAGGAGCATGTGATTCAAATTTG-T
* *
1146264 AAAAACAA-ACTTAAAATAAATGATGAATTGAAGAAATAGGGAAATTATAAAAACATTGAGAGAC
64 AAAAA-AAGACTTAAAATAAAGGATGAATTGAAGAAATAAGGAAATTATAAAAA-ATTGAGAGAC
* * *
1146328 -AAATTGAAAAATAGATTTTTTTTTATCAA
127 TAAATTGAAAAATAGAATATTTGTTATCAA
* * * ** * * * * *
1146357 AAATAGGAAATGAAAATTTATATTTATTCTATATTGGTTTAGGAGCATGTGATTTAAATTTCGTA
1 AAAGAGGAATTGAAAGTACATATATATTCTACAATGATTTAGGAGCATGTGATTCAAATTT-GTA
*
1146422 AAAAAAGACTTAAAATAAAGGATGAATTGAA-AAATAAGAAAATTATAAAAAATTGAGAGACTAA
65 AAAAAAGACTTAAAATAAAGGATGAATTGAAGAAATAAGGAAATTATAAAAAATTGAGAGACTAA
1146486 ATTGAAAAATAGAATATTTGTTATCAA
130 ATTGAAAAATAGAATATTTGTTATCAA
* *
1146513 AAAGAGGAATTGAAAGTACATACATATTCTACAATGTTTTAGGAGCATGT-AGTTCAAATTTCGT
1 AAAGAGGAATTGAAAGTACATATATATTCTACAATGATTTAGGAGCATGTGA-TTCAAATTT-GT
* ** * *
1146577 AAAAAACGACTTAAAATAAAGGACAAATTGAAGAAATAAGGAAATTATAAAAAATTAAGGGACTA
64 AAAAAAAGACTTAAAATAAAGGATGAATTGAAGAAATAAGGAAATTATAAAAAATTGAGAGACTA
* * *
1146642 GATTG-AAAATAGAAAAATTGTTATCAA
129 AATTGAAAAATAGAATATTTGTTATCAA
* * * * *
1146669 AACGA-GAATTTGAAAGTACATATGTATTTTA-AGATGATTTAGGAGCATGTGGTTCAAATTT-A
1 AAAGAGGAA-TTGAAAGTACATATATATTCTACA-ATGATTTAGGAGCATGTGATTCAAATTTGT
* * * *
1146731 AGAAAAAATACTTAAAAATAAATGATGAATTGAAGGAATAATGAAATTATAA
64 A-AAAAAAGACTT-AAAATAAAGGATGAATTGAAGAAATAAGGAAATTATAA
1146783 CTAAATCATA
Statistics
Matches: 362, Mismatches: 53, Indels: 23
0.83 0.12 0.05
Matches are distributed among these distances:
154 1 0.00
155 24 0.07
156 227 0.63
157 109 0.30
158 1 0.00
ACGTcount: A:0.49, C:0.06, G:0.16, T:0.29
Consensus pattern (156 bp):
AAAGAGGAATTGAAAGTACATATATATTCTACAATGATTTAGGAGCATGTGATTCAAATTTGTAA
AAAAAGACTTAAAATAAAGGATGAATTGAAGAAATAAGGAAATTATAAAAAATTGAGAGACTAAA
TTGAAAAATAGAATATTTGTTATCAA
Found at i:1146780 original size:313 final size:312
Alignment explanation
Indices: 1146200--1146782 Score: 707
Period size: 313 Copynumber: 1.9 Consensus size: 312
1146190 AGGTGGATTC
* *
1146200 AAAGAGGAATTGGAAGTACATAAGTATTCTACAATGATTTAGGAGCATGTGGTTCAAATATGATA
1 AAAGAGGAATTGAAAGTACATAAGTATTCTACAATGATTTAGGAGCATGTAGTTCAAATATGATA
* ** * *
1146265 AAAACAAACTTAAAATAAATGATGAATTGAAGAAATAGGGAAATTATAAAAACATTGAGAGACAA
66 AAAACAAACTTAAAATAAAGGACAAATTGAAGAAATAAGGAAATTATAAAAACATTAAGAGACAA
**** * * ** * * *
1146330 ATTGAAAAATAGATTTTTTTTTATCAAAAATAGGAAATGAAAATTTATATTTATTCTATATTGGT
131 ATTGAAAAATAGAAAAATTGTTATCAAAAAGAGGAAATGAAAATACATATGTATTCTATAATGAT
* *
1146395 TTAGGAGCATGTGATTTAAATTTCGTAAAAAAAGACTTAAAATAAAGGATGAATTGAAAAATAAG
196 TTAGGAGCATGTGATTCAAATTTAG-AAAAAAAGACTTAAAATAAAGGATGAATTGAAAAATAAG
1146460 AAAATTATAAAAAATTGAGAGACTAAATTGAAAAATAGAATATTTGTTATCAA
260 AAAATTATAAAAAATTGAGAGACTAAATTGAAAAATAGAATATTTGTTATCAA
* *
1146513 AAAGAGGAATTGAAAGTACATACA-TATTCTACAATGTTTTAGGAGCATGTAGTTCAAATTTCG-
1 AAAGAGGAATTGAAAGTACATA-AGTATTCTACAATGATTTAGGAGCATGTAGTTCAAATAT-GA
* *
1146576 TAAAAA-ACGACTTAAAATAAAGGACAAATTGAAGAAATAAGGAAATTATAAAAA-ATTAAGGGA
64 TAAAAACA-AACTTAAAATAAAGGACAAATTGAAGAAATAAGGAAATTATAAAAACATTAAGAGA
* * * * *
1146639 CTAGATTG-AAAATAGAAAAATTGTTATCAAAACGA-GAATTTGAAAGTACATATGTATTTTA-A
128 C-AAATTGAAAAATAGAAAAATTGTTATCAAAAAGAGGAA-ATGAAAATACATATGTATTCTATA
* * *
1146701 GATGATTTAGGAGCATGTGGTTCAAATTTA-AGAAAAAATACTTAAAAATAAATGATGAATTGAA
191 -ATGATTTAGGAGCATGTGATTCAAATTTAGA-AAAAAAGACTT-AAAATAAAGGATGAATTGAA
*
1146765 GGAATAATG-AAATTATAA
253 -AAATAA-GAAAATTATAA
1146783 CTAAATCATA
Statistics
Matches: 227, Mismatches: 33, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
310 1 0.00
311 14 0.06
312 88 0.39
313 121 0.53
314 3 0.01
ACGTcount: A:0.49, C:0.06, G:0.16, T:0.29
Consensus pattern (312 bp):
AAAGAGGAATTGAAAGTACATAAGTATTCTACAATGATTTAGGAGCATGTAGTTCAAATATGATA
AAAACAAACTTAAAATAAAGGACAAATTGAAGAAATAAGGAAATTATAAAAACATTAAGAGACAA
ATTGAAAAATAGAAAAATTGTTATCAAAAAGAGGAAATGAAAATACATATGTATTCTATAATGAT
TTAGGAGCATGTGATTCAAATTTAGAAAAAAAGACTTAAAATAAAGGATGAATTGAAAAATAAGA
AAATTATAAAAAATTGAGAGACTAAATTGAAAAATAGAATATTTGTTATCAA
Found at i:1152534 original size:84 final size:84
Alignment explanation
Indices: 1152392--1152555 Score: 265
Period size: 84 Copynumber: 2.0 Consensus size: 84
1152382 TATGTATGAA
* * *
1152392 AATAATGCTTTCATGAATGTGGTAATGTGATTCATGCATATCCTTACTCTTTAAGGAGTGTCCTC
1 AATAATGCTCTCATGAATGCGGTAATGTGATTCATGCATATCCTTACTCCTTAAGGAGTGTCCTC
1152457 ATGAGAGGGGAAAAGTCTG
66 ATGAGAGGGGAAAAGTCTG
* **
1152476 AATAATGCTCTCATGAATGCGGTAATGTGATTCATGCATATCCTTAGTCCTTGGGGAGTGTCCTC
1 AATAATGCTCTCATGAATGCGGTAATGTGATTCATGCATATCCTTACTCCTTAAGGAGTGTCCTC
*
1152541 ATGAGAGGTGAAAAG
66 ATGAGAGGGGAAAAG
1152556 ATCTTTAGTA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 73 1.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (84 bp):
AATAATGCTCTCATGAATGCGGTAATGTGATTCATGCATATCCTTACTCCTTAAGGAGTGTCCTC
ATGAGAGGGGAAAAGTCTG
Found at i:1153113 original size:38 final size:37
Alignment explanation
Indices: 1153071--1153261 Score: 136
Period size: 38 Copynumber: 5.0 Consensus size: 37
1153061 AACTAAACTA
*
1153071 TCTAGGATACAAGTCCTAAGAAAGTCAAGATTGATGTT
1 TCTAGGA-ACAAGTCCTAAGAAAGTCAAGATTGAGGTT
* * * *
1153109 TCTAGAGAA-ATAGTCTTAAGAAAGACTAGATTGAGTTT
1 TCTAG-GAACA-AGTCCTAAGAAAGTCAAGATTGAGGTT
* *
1153147 TCTAGGACACAAGTCCTAAGAAAATCAAGAATGAGGTT
1 TCTAGGA-ACAAGTCCTAAGAAAGTCAAGATTGAGGTT
* * * * * * * **
1153185 CCTTGGGGAACAA-ACTTTAGAAAGACTAA-ACTGAACTT
1 TC-T-AGGAACAAGTCCTAAGAAAGTC-AAGATTGAGGTT
*
1153223 TCTAGGATACAAGTCCTAAGACAGTCAAGATTGAGGTT
1 TCTAGGA-ACAAGTCCTAAGAAAGTCAAGATTGAGGTT
1153261 T
1 T
1153262 ATAATAAAAA
Statistics
Matches: 112, Mismatches: 31, Indels: 20
0.69 0.19 0.12
Matches are distributed among these distances:
36 3 0.03
37 10 0.09
38 86 0.77
39 10 0.09
40 3 0.03
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (37 bp):
TCTAGGAACAAGTCCTAAGAAAGTCAAGATTGAGGTT
Found at i:1153136 original size:76 final size:76
Alignment explanation
Indices: 1152873--1153261 Score: 271
Period size: 76 Copynumber: 5.1 Consensus size: 76
1152863 AGAAGACCTA
* ** * * * * *
1152873 ATTGAGGTTTTTAGAGAAATGATCTTAAGAAAGATTAGATTGAGCTTTCTAGGATACAAGTCCTA
1 ATTGAGGTTTCTAGAGAAACAATCTTTAGAAAGACTAAACTGAACTTTCTAGGATACAAGTCCTA
* * *
1152938 GAGGAA--CGAT
66 -AGAAAGTCAAG
* * ** * * * * * * ** ** * *
1152948 CTTGAGGTTTCTAGAGCAATGAGCCTAAGAAGGAATAAAGTGAGTTTTCTACCAGACATGTCCTA
1 ATTGAGGTTTCTAGAGAAACAATCTTTAGAAAGACTAAACTGAACTTTCTAGGATACAAGTCCTA
*
1153013 AGAAAATCAAG
66 AGAAAGTCAAG
* * * * * * *
1153024 AATAAAGTTCCTCAG-GGAACAATCTTTAGAAAGACTAAACTAAACTATCTAGGATACAAGTCCT
1 ATTGAGGTTTCT-AGAGAAACAATCTTTAGAAAGACTAAACTGAACTTTCTAGGATACAAGTCCT
1153088 AAGAAAGTCAAG
65 AAGAAAGTCAAG
* * * * * * ** *
1153100 ATTGATGTTTCTAGAGAAATAGTCTTAAGAAAGACTAGATTGAGTTTTCTAGGACACAAGTCCTA
1 ATTGAGGTTTCTAGAGAAACAATCTTTAGAAAGACTAAACTGAACTTTCTAGGATACAAGTCCTA
*
1153165 AGAAAATCAAG
66 AGAAAGTCAAG
* * * * * *
1153176 AATGAGGTTCCTTGGGGAACAAACTTTAGAAAGACTAAACTGAACTTTCTAGGATACAAGTCCTA
1 ATTGAGGTTTCTAGAGAAACAATCTTTAGAAAGACTAAACTGAACTTTCTAGGATACAAGTCCTA
*
1153241 AGACAGTCAAG
66 AGAAAGTCAAG
1153252 ATTGAGGTTT
1 ATTGAGGTTT
1153262 ATAATAAAAA
Statistics
Matches: 235, Mismatches: 75, Indels: 7
0.74 0.24 0.02
Matches are distributed among these distances:
74 4 0.02
75 53 0.23
76 176 0.75
77 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.27
Consensus pattern (76 bp):
ATTGAGGTTTCTAGAGAAACAATCTTTAGAAAGACTAAACTGAACTTTCTAGGATACAAGTCCTA
AGAAAGTCAAG
Found at i:1153169 original size:152 final size:152
Alignment explanation
Indices: 1152949--1153261 Score: 439
Period size: 152 Copynumber: 2.1 Consensus size: 152
1152939 AGGAACGATC
* * * * * * * *
1152949 TTGAGGTTTCTAGAGCAATGAG-CCTAAGAAGGAATAAAGTGAGTTTTCTACCAGACATGTCCTA
1 TTGAGGTTTCTAGAGAAAT-AGTCTTAAGAAAGACTAGATTGAGTTTTCTACCACACAAGTCCTA
*
1153013 AGAAAATCAAGAATAAAGTTCCTCAGGGAACAATCTTTAGAAAGACTAAACTAAACTATCTAGGA
65 AGAAAATCAAGAATAAAGTTCCTCAGGGAACAAACTTTAGAAAGACTAAACTAAACTATCTAGGA
1153078 TACAAGTCCTAAGAAAGTCAAGA
130 TACAAGTCCTAAGAAAGTCAAGA
* **
1153101 TTGATGTTTCTAGAGAAATAGTCTTAAGAAAGACTAGATTGAGTTTTCTAGGACACAAGTCCTAA
1 TTGAGGTTTCTAGAGAAATAGTCTTAAGAAAGACTAGATTGAGTTTTCTACCACACAAGTCCTAA
* * ** * *
1153166 GAAAATCAAGAATGAGGTTCCTTGGGGAACAAACTTTAGAAAGACTAAACTGAACTTTCTAGGAT
66 GAAAATCAAGAATAAAGTTCCTCAGGGAACAAACTTTAGAAAGACTAAACTAAACTATCTAGGAT
*
1153231 ACAAGTCCTAAGACAGTCAAGA
131 ACAAGTCCTAAGAAAGTCAAGA
1153253 TTGAGGTTT
1 TTGAGGTTT
1153262 ATAATAAAAA
Statistics
Matches: 140, Mismatches: 20, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
151 2 0.01
152 138 0.99
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (152 bp):
TTGAGGTTTCTAGAGAAATAGTCTTAAGAAAGACTAGATTGAGTTTTCTACCACACAAGTCCTAA
GAAAATCAAGAATAAAGTTCCTCAGGGAACAAACTTTAGAAAGACTAAACTAAACTATCTAGGAT
ACAAGTCCTAAGAAAGTCAAGA
Found at i:1154141 original size:15 final size:16
Alignment explanation
Indices: 1154117--1154149 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1154107 AAGGCTTAGG
1154117 CCCAAACCTAA-TTAA
1 CCCAAACCTAAGTTAA
*
1154132 CCCAACCCTAAGTTAA
1 CCCAAACCTAAGTTAA
1154148 CC
1 CC
1154150 AAAAATGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.39, C:0.39, G:0.03, T:0.18
Consensus pattern (16 bp):
CCCAAACCTAAGTTAA
Found at i:1154420 original size:2 final size:2
Alignment explanation
Indices: 1154413--1154441 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1154403 AAGAAACATA
1154413 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1154442 TAAAGCTATC
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:1155390 original size:9 final size:9
Alignment explanation
Indices: 1155352--1155405 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
1155342 TACAATAACA
*
1155352 ATTTTATTA
1 ATTTTATTT
*
1155361 ATTTTAATT
1 ATTTTATTT
*
1155370 ATTGTTA-AT
1 ATT-TTATTT
1155379 ATTTTATTT
1 ATTTTATTT
1155388 A--TTATTT
1 ATTTTATTT
1155395 ATTTTATTT
1 ATTTTATTT
1155404 AT
1 AT
1155406 ATTTCAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 7 0.19
8 3 0.08
9 24 0.65
10 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (9 bp):
ATTTTATTT
Found at i:1155397 original size:16 final size:16
Alignment explanation
Indices: 1155355--1155409 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
1155345 AATAACAATT
* *
1155355 TTATTAATTTTAATTA
1 TTATTTATTTTATTTA
*
1155371 TTGTTAATATTTTATTTA
1 TTATT--TATTTTATTTA
1155389 TTATTTATTTTATTTA
1 TTATTTATTTTATTTA
1155405 -TATTT
1 TTATTT
1155410 CAATTTCGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
15 5 0.15
16 15 0.45
18 13 0.39
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
TTATTTATTTTATTTA
Found at i:1156960 original size:21 final size:21
Alignment explanation
Indices: 1156936--1156983 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1156926 GCCATTTCAT
1156936 ATGCCACTGCAGCCAAGTCAG
1 ATGCCACTGCAGCCAAGTCAG
*
1156957 ATGCCACTGCAGCCAGGTCAG
1 ATGCCACTGCAGCCAAGTCAG
1156978 ATGCCA
1 ATGCCA
1156984 TTGCTTCCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.33, G:0.25, T:0.15
Consensus pattern (21 bp):
ATGCCACTGCAGCCAAGTCAG
Found at i:1157303 original size:3 final size:3
Alignment explanation
Indices: 1157297--1157322 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1157287 ATAATGATGA
1157297 TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TG
1157323 ATGATGATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:1157588 original size:25 final size:25
Alignment explanation
Indices: 1157528--1157588 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
1157518 ATTTTGTTTC
* *
1157528 TTAATTTCTTTATTACTTAATTGTT
1 TTAATTTTTTTATTACTTAATTATT
* * * *
1157553 TGAATTGTTTTATTATTTAGTTATT
1 TTAATTTTTTTATTACTTAATTATT
1157578 TTAATTTTTTT
1 TTAATTTTTTT
1157589 GTTGTATAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.67
Consensus pattern (25 bp):
TTAATTTTTTTATTACTTAATTATT
Found at i:1163620 original size:15 final size:15
Alignment explanation
Indices: 1163600--1163629 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1163590 ACTTCATAGG
*
1163600 GTAAGAAGACAACGT
1 GTAAGAAGAAAACGT
1163615 GTAAGAAGAAAACGT
1 GTAAGAAGAAAACGT
1163630 CAAAGAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.10, G:0.27, T:0.13
Consensus pattern (15 bp):
GTAAGAAGAAAACGT
Found at i:1167333 original size:37 final size:38
Alignment explanation
Indices: 1167277--1167361 Score: 113
Period size: 37 Copynumber: 2.2 Consensus size: 38
1167267 AAAAAGAAAC
1167277 AAAAATAAGAGGGGAAAGGAGAAGGGACACCGCAA-A-GG
1 AAAAA-AAGAGGGGAAAGGAGAAGGGACACCG-AAGAGGG
*
1167315 AAAAAAAGAGGAGG-AAGGAGAAGGGACACTGAAGAGGG
1 AAAAAAAGAGG-GGAAAGGAGAAGGGACACCGAAGAGGG
1167353 AAAAAAAGA
1 AAAAAAAGA
1167362 AAGAAAATGA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
36 2 0.05
37 23 0.53
38 18 0.42
ACGTcount: A:0.54, C:0.07, G:0.36, T:0.02
Consensus pattern (38 bp):
AAAAAAAGAGGGGAAAGGAGAAGGGACACCGAAGAGGG
Found at i:1167355 original size:38 final size:37
Alignment explanation
Indices: 1167277--1167391 Score: 117
Period size: 38 Copynumber: 3.0 Consensus size: 37
1167267 AAAAAGAAAC
1167277 AAAAATAAGAGGGGAAAGGAGAAGGGACACCGCAAAGG
1 AAAAA-AAGAGGGGAAAGGAGAAGGGACACCGCAAAGG
*
1167315 AAAAAAAGAGGAGG-AAGGAGAAGGGACACTG-AAGAGGG
1 AAAAAAAGAGG-GGAAAGGAGAAGGGACACCGCAA-A-GG
** * * *
1167353 AAAAAAAGAAAGAAAATGAGGAGGGAACACCGCAAAGG
1 AAAAAAAGAGGGGAAAGGAGAAGGG-ACACCGCAAAGG
1167391 A
1 A
1167392 GGAGGACGAG
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
36 2 0.03
37 24 0.38
38 30 0.47
39 6 0.09
40 2 0.03
ACGTcount: A:0.53, C:0.09, G:0.36, T:0.03
Consensus pattern (37 bp):
AAAAAAAGAGGGGAAAGGAGAAGGGACACCGCAAAGG
Found at i:1169754 original size:163 final size:163
Alignment explanation
Indices: 1169480--1169809 Score: 651
Period size: 163 Copynumber: 2.0 Consensus size: 163
1169470 TATATATAAA
1169480 ATTGGTCATTTTAGTACTCTTTGATAGTTAATTATATACTTCACTTTAAATAAGTATAAATTATA
1 ATTGGTCATTTTAGTACTCTTTGATAGTTAATTATATACTTCACTTTAAATAAGTATAAATTATA
*
1169545 TACTCTTTGCATAATGTATATGTCGTGATATTTTGTATCGACATATGATTAATACAATATTTTTG
66 TACTCTTTGCATAATGTATATGTCGTGATATTTTGTATCAACATATGATTAATACAATATTTTTG
1169610 ATAACTTAATGTGAATATATTGTATGCACATGG
131 ATAACTTAATGTGAATATATTGTATGCACATGG
1169643 ATTGGTCATTTTAGTACTCTTTGATAGTTAATTATATACTTCACTTTAAATAAGTATAAATTATA
1 ATTGGTCATTTTAGTACTCTTTGATAGTTAATTATATACTTCACTTTAAATAAGTATAAATTATA
1169708 TACTCTTTGCATAATGTATATGTCGTGATATTTTGTATCAACATATGATTAATACAATATTTTTG
66 TACTCTTTGCATAATGTATATGTCGTGATATTTTGTATCAACATATGATTAATACAATATTTTTG
1169773 ATAACTTAATGTGAATATATTGTATGCACATGG
131 ATAACTTAATGTGAATATATTGTATGCACATGG
1169806 ATTG
1 ATTG
1169810 CTTAAATATA
Statistics
Matches: 166, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
163 166 1.00
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (163 bp):
ATTGGTCATTTTAGTACTCTTTGATAGTTAATTATATACTTCACTTTAAATAAGTATAAATTATA
TACTCTTTGCATAATGTATATGTCGTGATATTTTGTATCAACATATGATTAATACAATATTTTTG
ATAACTTAATGTGAATATATTGTATGCACATGG
Found at i:1169967 original size:24 final size:24
Alignment explanation
Indices: 1169940--1169986 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1169930 CTCAATGAAC
1169940 GTCATAAATGCA-CATCATAAATGT
1 GTCATAAATG-AGCATCATAAATGT
* *
1169964 GTCATACATGAGTATCATAAATG
1 GTCATAAATGAGCATCATAAATG
1169987 CACGTCATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (24 bp):
GTCATAAATGAGCATCATAAATGT
Found at i:1184555 original size:15 final size:16
Alignment explanation
Indices: 1184527--1184557 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1184517 TTAAATTGAA
1184527 TTATTAATTAAGAAAT
1 TTATTAATTAAGAAAT
1184543 TTATTAATT-AGAAAT
1 TTATTAATTAAGAAAT
1184558 AAATTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
TTATTAATTAAGAAAT
Found at i:1191396 original size:20 final size:19
Alignment explanation
Indices: 1191373--1191412 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1191363 TTTAATTTGA
1191373 ATTAATTAAATAAGAAATTT
1 ATTAATTAAA-AAGAAATTT
* *
1191393 ATTAATTCAAAATAAATTT
1 ATTAATTAAAAAGAAATTT
1191412 A
1 A
1191413 AAACCCTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (19 bp):
ATTAATTAAAAAGAAATTT
Found at i:1198070 original size:281 final size:281
Alignment explanation
Indices: 1197566--1198121 Score: 848
Period size: 281 Copynumber: 2.0 Consensus size: 281
1197556 AAAGGTCTCC
* *
1197566 CTAAACATCATTTACATACAAGATCAATCAAATACATATAAATTTATATTCAAATCAAATCATTC
1 CTAAACATCATTTACATACAAGATCAATCAAATACATATAAATTTACATTCAAATAAAATCATTC
* * * *
1197631 CACAAGACCCTACTTAACCAAACTTTGATTCAATTATTTCTTATTGTTTTTAATCATCATACAAG
66 CACAAGACCCTAATAAACCAAACTTTGATTCAACTATTTCTAATTGTTTTTAATCATCATACAAG
*
1197696 ATTGAAAATGAATCAACCACATCCCTAACATCAAAATCCACCCTTAAATCATCAAAATTAATTCC
131 ATTGAAAATGAATCAACCACATCACTAACATCAAAATCCACCCTTAAATCATCAAAATTAATTCC
* * * *
1197761 CCCTTCATCCATAAAATTCATGAACTTTTGATTTCAAGCATGGAAAACAAGAACAAATTACATCA
196 CCCTTCATCCACAAAATTCATAAACTTTTGATTTCAAGCATGAAAAACAAGAACAAATTACACCA
1197826 AATGATAGAGAATTTCAAACT
261 AATGATAGAGAATTTCAAACT
* * * * * *
1197847 CTAAACATCATTT-CAATACAAGAAT-AATTAGATACATATCAATTTCCATTCATATAAAATCTT
1 CTAAACATCATTTAC-ATACAAG-ATCAATCAAATACATATAAATTTACATTCAAATAAAATCAT
* *
1197910 TCCATAATACCCTAATAAACCAAACTTTGATTCAACTATTTCTAATTGTTTTTAATCATCATACA
64 TCCACAAGACCCTAATAAACCAAACTTTGATTCAACTATTTCTAATTGTTTTTAATCATCATACA
* ** *
1197975 AGCTTGAAAATGAATCAGGCACATCACTAACATCAAAATCCATCCTTAAATCATCAAAATTAACT
129 AGATTGAAAATGAATCAACCACATCACTAACATCAAAATCCACCCTTAAATCATCAAAATTAA-T
*
1198040 T-CCCCTTCATCCACAAAATTCATAAACTTTTGATTTCAAGCATGAAAAACAATAACAAATTACA
193 TCCCCCTTCATCCACAAAATTCATAAACTTTTGATTTCAAGCATGAAAAACAAGAACAAATTACA
1198104 CCAAATGATAGAGAATTT
258 CCAAATGATAGAGAATTT
1198122 AATGTAGGTA
Statistics
Matches: 248, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
280 1 0.00
281 243 0.98
282 4 0.02
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.31
Consensus pattern (281 bp):
CTAAACATCATTTACATACAAGATCAATCAAATACATATAAATTTACATTCAAATAAAATCATTC
CACAAGACCCTAATAAACCAAACTTTGATTCAACTATTTCTAATTGTTTTTAATCATCATACAAG
ATTGAAAATGAATCAACCACATCACTAACATCAAAATCCACCCTTAAATCATCAAAATTAATTCC
CCCTTCATCCACAAAATTCATAAACTTTTGATTTCAAGCATGAAAAACAAGAACAAATTACACCA
AATGATAGAGAATTTCAAACT
Found at i:1198709 original size:20 final size:20
Alignment explanation
Indices: 1198671--1198709 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1198661 CAGAGAATTA
**
1198671 ATCCCCAATGACTCCAAATC
1 ATCCCCAATGACTAAAAATC
*
1198691 ATCCTCAATGACTAAAAAT
1 ATCCCCAATGACTAAAAAT
1198710 GGCCAAAAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.31, G:0.05, T:0.23
Consensus pattern (20 bp):
ATCCCCAATGACTAAAAATC
Found at i:1199975 original size:280 final size:281
Alignment explanation
Indices: 1199474--1200034 Score: 1115
Period size: 280 Copynumber: 2.0 Consensus size: 281
1199464 TGATTGGAGT
1199474 GATGAAGAGAAGAAGAAGTTCCAACTGAATGCAAAGGATATGCACATTCTATTTTGTACTTTAGG
1 GATGAAGAGAAGAAGAAGTTCCAACTGAATGCAAAGGATATGCACATTCTATTTTGTACTTTAGG
1199539 TCTGGATGAATATGGAATAATCTTCTTTTATTCTAATGCCAAGGAGATTTGGCACAATATCCAAG
66 TCTGGATGAATATGGAATAATCTTCTTTTATTCTAATGCCAAGGAGATTTGGCACAATATCCAAG
1199604 TCACTCATGAAGGAACCAATGAAGTGAGAGAAACTAAAATTAGTCTTCTCAATCATAGCTTTGAG
131 TCACTCATGAAGGAACCAATGAAGTGAGAGAAACTAAAATTAGTCTTCTCAATCATAGCTTTGAG
1199669 AATTTCAAGATGAAACCGGATGAAGACATCAAAGCTATAACGGATAGATTTTCTGTGA-TGTCAA
196 AATTTCAAGATGAAACCGGATGAAGACATCAAAGCTATAACGGATAGATTTTCTGTGATTGTCAA
1199733 CGGTCTCAAGGGATTTGGATA
261 CGGTCTCAAGGGATTTGGATA
1199754 GATGAAGAGAAGAAGAAGTTCCAACTGAATGCAAAGGATATGCACATTCTATTTTGTACTTTAGG
1 GATGAAGAGAAGAAGAAGTTCCAACTGAATGCAAAGGATATGCACATTCTATTTTGTACTTTAGG
1199819 TCTGGATGAATATGGAATAATCTTCTTTTATTCTAATGCCAAGGAGATTTGGCACAATATCCAAG
66 TCTGGATGAATATGGAATAATCTTCTTTTATTCTAATGCCAAGGAGATTTGGCACAATATCCAAG
1199884 TCACTCATGAAGGAACCAATGAAGTGAGAGAAACTAAAATTAGTCTTCTCAATCATAGCTTTGAG
131 TCACTCATGAAGGAACCAATGAAGTGAGAGAAACTAAAATTAGTCTTCTCAATCATAGCTTTGAG
1199949 AATTTCAAGATGAAACCGGATGAAGACATCAAAGCTATAACGGATAGATTTTCTGTGATTGTCAA
196 AATTTCAAGATGAAACCGGATGAAGACATCAAAGCTATAACGGATAGATTTTCTGTGATTGTCAA
1200014 CGGTCTCAAGGGATTTGGATA
261 CGGTCTCAAGGGATTTGGATA
1200035 AGTGATTTCT
Statistics
Matches: 280, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
280 253 0.90
281 27 0.10
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.29
Consensus pattern (281 bp):
GATGAAGAGAAGAAGAAGTTCCAACTGAATGCAAAGGATATGCACATTCTATTTTGTACTTTAGG
TCTGGATGAATATGGAATAATCTTCTTTTATTCTAATGCCAAGGAGATTTGGCACAATATCCAAG
TCACTCATGAAGGAACCAATGAAGTGAGAGAAACTAAAATTAGTCTTCTCAATCATAGCTTTGAG
AATTTCAAGATGAAACCGGATGAAGACATCAAAGCTATAACGGATAGATTTTCTGTGATTGTCAA
CGGTCTCAAGGGATTTGGATA
Found at i:1210141 original size:81 final size:81
Alignment explanation
Indices: 1210028--1210277 Score: 401
Period size: 81 Copynumber: 3.1 Consensus size: 81
1210018 AAGCATTTAG
1210028 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
* *
1210093 ATAACTAGGCAATTAA
66 ACAGCTAGGCAATTAA
* * *
1210109 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCGTGATTGAAATCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
*
1210174 ACAGCTAGACAATTAA
66 ACAGCTAGGCAATTAA
* * * *
1210190 TCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGACATGATTGACACATTTCTATCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
*
1210255 ACAGCTACGCAATTAA
66 ACAGCTAGGCAATTAA
1210271 TCTTTTA
1 TCTTTTA
1210278 TTTTAAAACA
Statistics
Matches: 154, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 154 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
ACAGCTAGGCAATTAA
Found at i:1218007 original size:48 final size:48
Alignment explanation
Indices: 1217940--1218088 Score: 210
Period size: 48 Copynumber: 3.1 Consensus size: 48
1217930 ACATACTTTG
*
1217940 TGTATGATGGTTATCGATCGATTTTGTTTAATGCATAAGTTGCATTTT
1 TGTATGATGGTTATCGATCGATTTTGTTTAATGCATAAGTTTCATTTT
* * *
1217988 TGTACGATGATTATCGATCGAATTTGTTTAATGCATAA-TCTTCATTTT
1 TGTATGATGGTTATCGATCGATTTTGTTTAATGCATAAGT-TTCATTTT
* * *
1218036 CGTATGATGGTTATTGATCGATTTTGTTTAATGCATATGTTTCATTTT
1 TGTATGATGGTTATCGATCGATTTTGTTTAATGCATAAGTTTCATTTT
*
1218084 CGTAT
1 TGTAT
1218089 CATTACTATT
Statistics
Matches: 89, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
47 1 0.01
48 87 0.98
49 1 0.01
ACGTcount: A:0.23, C:0.10, G:0.18, T:0.48
Consensus pattern (48 bp):
TGTATGATGGTTATCGATCGATTTTGTTTAATGCATAAGTTTCATTTT
Found at i:1220057 original size:3 final size:3
Alignment explanation
Indices: 1220049--1220080 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
1220039 AATTTTTACC
1220049 TAA TAA TAA TAA TAA TAA TAA TAA TAA CTAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA T
1220081 CGATCGCCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1229443 original size:24 final size:23
Alignment explanation
Indices: 1229402--1229510 Score: 76
Period size: 24 Copynumber: 4.5 Consensus size: 23
1229392 GAATATTTTA
* *
1229402 TCTGATTTATGATTTGAATTCTGT
1 TCTGA-TTCTGATCTGAATTCTGT
* * *
1229426 TTTGACATCTGATCTGAAATCTGT
1 TCTGA-TTCTGATCTGAATTCTGT
* *
1229450 TCTGATTCCT-AACATGGATTCTGT
1 TCTGATT-CTGATC-TGAATTCTGT
*
1229474 TCTGATTTCTGATCTGAATTATGT
1 TCTGA-TTCTGATCTGAATTCTGT
*
1229498 TTTGATTTCTGAT
1 TCTGA-TTCTGAT
1229511 ATCTCCGTTT
Statistics
Matches: 66, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
23 3 0.05
24 59 0.89
25 4 0.06
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.49
Consensus pattern (23 bp):
TCTGATTCTGATCTGAATTCTGT
Found at i:1234347 original size:24 final size:23
Alignment explanation
Indices: 1234315--1234406 Score: 60
Period size: 24 Copynumber: 3.9 Consensus size: 23
1234305 ATCTGATTTA
*
1234315 TGATTTGAATTCTGTTTTGACATC
1 TGATCTGAATTCTGTTTTGA-ATC
* * *
1234339 TGATCTGAAATCTGTTCTGATTCC
1 TGATCTGAATTCTGTTTTGAAT-C
* * *
1234363 TAACCT-AGATTCTGTTATGATATC
1 TGATCTGA-ATTCTGTTTTGA-ATC
**
1234387 TGATCTGAATTAAGTTTTGA
1 TGATCTGAATTCTGTTTTGA
1234407 TTTCCGATAT
Statistics
Matches: 50, Mismatches: 14, Indels: 8
0.69 0.19 0.11
Matches are distributed among these distances:
23 2 0.04
24 46 0.92
25 2 0.04
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (23 bp):
TGATCTGAATTCTGTTTTGAATC
Found at i:1246575 original size:2 final size:2
Alignment explanation
Indices: 1246568--1246609 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1246558 TGAATAAATA
1246568 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
1246610 GATTAAGTAA
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:1247887 original size:3 final size:3
Alignment explanation
Indices: 1247881--1247922 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
1247871 ATTAATTATT
1247881 TAA TAA TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1247923 TAAGCAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1247911 original size:22 final size:22
Alignment explanation
Indices: 1247883--1247925 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1247873 TAATTATTTA
1247883 ATAATAATAATAATAATATAAT
1 ATAATAATAATAATAATATAAT
1247905 ATAATAATAATAATAATATAA
1 ATAATAATAATAATAATATAA
1247926 GCAAATAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
ATAATAATAATAATAATATAAT
Found at i:1247932 original size:22 final size:22
Alignment explanation
Indices: 1247883--1247933 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
1247873 TAATTATTTA
*
1247883 ATAATAATAATAATAATATAAT
1 ATAATAATAATAATAATATAAC
1247905 ATAATAATAATAATAATATAAGC
1 ATAATAATAATAATAATATAA-C
1247928 A-AATAA
1 ATAATAA
1247934 GAAAAAAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 26 0.96
23 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
ATAATAATAATAATAATATAAC
Found at i:1247933 original size:19 final size:16
Alignment explanation
Indices: 1247883--1247925 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1247873 TAATTATTTA
*
1247883 ATAATAATAATAATAAT
1 ATAAT-ATAAAAATAAT
*
1247900 ATAATATAATAATAAT
1 ATAATATAAAAATAAT
1247916 AATAATATAA
1 -ATAATATAA
1247926 GCAAATAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAATATAAAAATAAT
Found at i:1248441 original size:118 final size:119
Alignment explanation
Indices: 1248290--1248562 Score: 380
Period size: 116 Copynumber: 2.3 Consensus size: 119
1248280 GTTGAACAAG
* *
1248290 TTCTTCCTCTTCAATGAGTTCTTCTCATTATGAACTTCTTCTGGAAATGCTGATGCTGATCTATC
1 TTCTTCCTCTTCAATAAGTTCTTCTCATTATGAACTTCTTCTGAAAATGCTGATGCTGATC--TC
* *
1248355 TCCTTCTGTGATAGAATC-ATACAAAAAGTTGAATAAGTTC-T-TC-TTATGAACTTC
64 TCCTTCTGTGATAGAATCGA-AC-AAAAGTTGAACAAATTCTTCTCATTATGAACTTC
*
1248409 TTCTTCCTCTTCAATAAG-TCTTCTCATTATGAAC--CTTCTGAAAATGTTGATGCTGATCTCTC
1 TTCTTCCTCTTCAATAAGTTCTTCTCATTATGAACTTCTTCTGAAAATGCTGATGCTGATCTCTC
* *
1248471 CTTCTGTGATAGAATCGAGCAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
66 CTTCTGTGATAGAATCGAACAAAAGTTGAACAAATTCTTCTCATTATGAACTTC
*
1248525 TTCTTCCTTTTCAGATAAGTTCTTCTCATTATGAACTT
1 TTCTTCCTCTTCA-ATAAGTTCTTCTCATTATGAACTT
1248563 TATGGAAAAG
Statistics
Matches: 138, Mismatches: 8, Indels: 15
0.86 0.05 0.09
Matches are distributed among these distances:
113 14 0.10
114 22 0.16
115 3 0.02
116 45 0.33
117 5 0.04
118 32 0.23
119 17 0.12
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.41
Consensus pattern (119 bp):
TTCTTCCTCTTCAATAAGTTCTTCTCATTATGAACTTCTTCTGAAAATGCTGATGCTGATCTCTC
CTTCTGTGATAGAATCGAACAAAAGTTGAACAAATTCTTCTCATTATGAACTTC
Found at i:1248831 original size:109 final size:108
Alignment explanation
Indices: 1248704--1248972 Score: 332
Period size: 109 Copynumber: 2.5 Consensus size: 108
1248694 CAAACTCTTC
*
1248704 TCTTCAGAT-AGTTCTTCTCATTATGAACTTTCTCTGGTATGTTGATCCATCAAATGAT-GATTC
1 TCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAATGTTGATCCATCAAATGATGGATT-
* *
1248767 AACAAAAAGTTGAATAA-TTCTTCTCATTATGAA-TTCCTTCTTCCT
65 --CAAAAAGTTGAACAAGCTCTTCTCATTATGAACTT-CTTCTTCCT
* * *
1248812 TCTTCAGATGAGTTCTTCTCATTATGAACTTTCTATGGAAAAGTTGATCCATCAAGTGATGGATT
1 TCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG-AATGTTGATCCATCAAATGATGGATT
** * *
1248877 TGAGAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCT
65 CAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCT
* *
1248921 TTTTCAGATGAGTTCTTCTCATTATGAACTCTT-TCTAGAAATGTTGATCCAT
1 TCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCT-GGAATGTTGATCCAT
1248973 TGTGATGGAT
Statistics
Matches: 140, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
108 19 0.14
109 94 0.67
110 23 0.16
111 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (108 bp):
TCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAATGTTGATCCATCAAATGATGGATTC
AAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCT
Found at i:1250124 original size:20 final size:20
Alignment explanation
Indices: 1250090--1250154 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
1250080 ATGTTAATCC
*
1250090 ATTTACAAAAGAATAAATTGA
1 ATTT-CAAAAAAATAAATTGA
*
1250111 ATTTCAAAAAAATAAATTAA
1 ATTTCAAAAAAATAAATTGA
1250131 ATTTCAAAAATAAT-AATTGA
1 ATTTCAAAAA-AATAAATTGA
1250151 ATTT
1 ATTT
1250155 AGAGAAATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
20 33 0.82
21 7 0.17
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.34
Consensus pattern (20 bp):
ATTTCAAAAAAATAAATTGA
Found at i:1261861 original size:2 final size:2
Alignment explanation
Indices: 1261849--1261882 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1261839 TGAATAAATA
*
1261849 AT AT TT 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
1261883 TAAGTAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1263280 original size:3 final size:3
Alignment explanation
Indices: 1263272--1263310 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
1263262 ATTAATTATT
*
1263272 TAA TAA TAA TAA T-A TAA -CA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1263311 TAAGAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 3 0.09
3 29 0.91
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1263320 original size:25 final size:25
Alignment explanation
Indices: 1263272--1263321 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1263262 ATTAATTATT
*
1263272 TAATAATAATAATATAACATAATAA
1 TAATAATAATAATATAACAAAATAA
*
1263297 TAATAATAATAATATAAGAAAATAA
1 TAATAATAATAATATAACAAAATAA
1263322 GAAAAAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (25 bp):
TAATAATAATAATATAACAAAATAA
Found at i:1278422 original size:3 final size:3
Alignment explanation
Indices: 1278409--1278508 Score: 159
Period size: 3 Copynumber: 33.7 Consensus size: 3
1278399 GGGATATAAA
*
1278409 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT GAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1278455 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1278503 GTAT TA
1 -TAT TA
1278509 CAACTATTTG
Statistics
Matches: 90, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
2 4 0.04
3 83 0.92
4 3 0.03
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1282438 original size:55 final size:54
Alignment explanation
Indices: 1282354--1282495 Score: 185
Period size: 55 Copynumber: 2.6 Consensus size: 54
1282344 ACATTCAAGT
* ** *
1282354 GATTCATGAAGAATGACGTCCGATGAATGAAGAAATTTGAACCTAATTGAAGAAC
1 GATTCATGAAG-ATGACATCCGATGAATGAAGAAACCTGAAACTAATTGAAGAAC
* *
1282409 GATTCATGAAGATGGACATCCGATGAATGAAGAAACCTGAAACTGATTGAAGATC
1 GATTCATGAAGAT-GACATCCGATGAATGAAGAAACCTGAAACTAATTGAAGAAC
* *
1282464 GATCCATGAAGAAAGACATCCGATGAATGAAG
1 GATTCATGAAG-ATGACATCCGATGAATGAAG
1282496 TCCGATCCAT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
54 2 0.03
55 74 0.96
56 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (54 bp):
GATTCATGAAGATGACATCCGATGAATGAAGAAACCTGAAACTAATTGAAGAAC
Found at i:1283580 original size:50 final size:51
Alignment explanation
Indices: 1283526--1283622 Score: 142
Period size: 52 Copynumber: 1.9 Consensus size: 51
1283516 TTTGTAAAAA
* * *
1283526 AAAACTTGTAAATGCTAGAA-TACCTTTTTATAAATGAACTTTAGGATTAG
1 AAAACATGTAAATGCTAGAAGGACCTTTTTATAAATCAACTTTAGGATTAG
*
1283576 AAAACATGTAAATTCTAGAAGGGACCTTTTTATAAATCAACTTTAGG
1 AAAACATGTAAATGCTAGAA-GGACCTTTTTATAAATCAACTTTAGG
1283623 GTTTAAATCA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 18 0.44
52 23 0.56
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.34
Consensus pattern (51 bp):
AAAACATGTAAATGCTAGAAGGACCTTTTTATAAATCAACTTTAGGATTAG
Found at i:1287827 original size:34 final size:33
Alignment explanation
Indices: 1287789--1287872 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 33
1287779 GTAATAAACA
*
1287789 AAATTAACCAAAATACATTAACAA-AAAGTCCAA-C
1 AAATTAA-CAAAATAAATTAA-AATAAA-TCCAACC
1287823 AAATTTAACAAAATAAATTAAAATAAATCCAACC
1 AAA-TTAACAAAATAAATTAAAATAAATCCAACC
**
1287857 AAATTAATGAAATAAA
1 AAATTAACAAAATAAA
1287873 GTATTAAATG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
33 18 0.41
34 22 0.50
35 4 0.09
ACGTcount: A:0.62, C:0.14, G:0.02, T:0.21
Consensus pattern (33 bp):
AAATTAACAAAATAAATTAAAATAAATCCAACC
Found at i:1287872 original size:33 final size:34
Alignment explanation
Indices: 1287785--1287861 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 34
1287775 AATGGTAATA
* *
1287785 AACAAAATTAACCAAAATACATTAACAAAAAGTCC
1 AACAAATTTAA-CAAAATAAATTAACAAAAAGTCC
1287820 AACAAATTTAACAAAATAAATTAA-AATAAA-TCC
1 AACAAATTTAACAAAATAAATTAACAA-AAAGTCC
1287853 AACCAAATT
1 AA-CAAATT
1287862 AATGAAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
33 7 0.18
34 21 0.55
35 10 0.26
ACGTcount: A:0.61, C:0.17, G:0.01, T:0.21
Consensus pattern (34 bp):
AACAAATTTAACAAAATAAATTAACAAAAAGTCC
Found at i:1287904 original size:15 final size:15
Alignment explanation
Indices: 1287886--1287920 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
1287876 TTAAATGATA
1287886 AATAAAAAAAATTAC
1 AATAAAAAAAATTAC
1287901 AAT--AAAAAATTAC
1 AATAAAAAAAATTAC
1287914 AATAAAA
1 AATAAAA
1287921 TCTAATAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
13 13 0.72
15 5 0.28
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (15 bp):
AATAAAAAAAATTAC
Found at i:1287920 original size:12 final size:13
Alignment explanation
Indices: 1287891--1287920 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1287881 TGATAAATAA
1287891 AAAAAATTACAAT
1 AAAAAATTACAAT
1287904 AAAAAATTACAAT
1 AAAAAATTACAAT
1287917 AAAA
1 AAAA
1287921 TCTAATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAAAATTACAAT
Found at i:1287944 original size:23 final size:22
Alignment explanation
Indices: 1287914--1287961 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
1287904 AAAAAATTAC
* * *
1287914 AATAAAATCTAATAAACAACTA
1 AATAAAATATAATAAAAAACAA
1287936 AATACAAATATAATAAAAAACAA
1 AATA-AAATATAATAAAAAACAA
1287959 AAT
1 AAT
1287962 CTATCGATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (22 bp):
AATAAAATATAATAAAAAACAA
Found at i:1290047 original size:24 final size:24
Alignment explanation
Indices: 1290008--1290070 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
1289998 ACTAAATAAA
*
1290008 TAAA-TAAATTATAACTAATAATT
1 TAAATTAAATTAAAACTAATAATT
1290031 TAAATTAAATTAAAACTAATAATT
1 TAAATTAAATTAAAACTAATAATT
1290055 TAAATTAAATTAAAAC
1 TAAATTAAATTAAAAC
1290071 GTTAAAACGT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 4 0.11
24 34 0.89
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (24 bp):
TAAATTAAATTAAAACTAATAATT
Found at i:1290794 original size:25 final size:23
Alignment explanation
Indices: 1290746--1290806 Score: 79
Period size: 25 Copynumber: 2.6 Consensus size: 23
1290736 AGTATAAAGT
1290746 AATAATAAAAATAAATAAATATA
1 AATAATAAAAATAAATAAATATA
*
1290769 ATTATAATAAAAATAAATAGGA-ATA
1 A--ATAATAAAAATAAATA-AATATA
1290794 AATAATAAAAATA
1 AATAATAAAAATA
1290807 GCAAAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
23 13 0.38
25 20 0.59
26 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.26
Consensus pattern (23 bp):
AATAATAAAAATAAATAAATATA
Found at i:1292559 original size:105 final size:105
Alignment explanation
Indices: 1292367--1293234 Score: 1406
Period size: 105 Copynumber: 8.3 Consensus size: 105
1292357 ATATTGTTCC
* * * * * * **
1292367 GAGTCC-ATATCCTCCGCTGGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATCGTCGGTTGACA
1 GAGTCCAATATCCTTCG-TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-CGTTTGTTGACA
** * * **** *
1292431 GTCAGCGGCCCCTTCGTCTTGAAGTTGAACTTATACTGTCTT
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1292473 GAGTCCAATATCCTTCGTTGTGAAGTTGAAACTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAACGTTTGTTGACAAC
1292538 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1292578 GAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTGAAATTGAGAAACGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAACGTTTGTTGACAAC
1292643 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1292683 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAATTGAGAAACGTTTGTTGACAAT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAACGTTTGTTGACAAC
*
1292748 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTCGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1292788 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAACGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAACGTTTGTTGACAAC
1292853 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-G
1292894 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAACGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAACGTTTGTTGACAAC
1292959 CA--GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1292997 GAGTCCAATATCC-TCGTTGTGAAGTTGAAATTGACTCTGGAATTGAGAAACGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAACGTTTGTTGACAAC
*
1293061 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTCGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1293101 GAGTCC-ATATCCTTCG-TGTGAAGTTGAAATTGGCTCTGAAATTGAAAAACGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAACGTTTGTTGACAAC
1293164 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1293204 GAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1293235 ATTTGACTCT
Statistics
Matches: 715, Mismatches: 40, Indels: 15
0.93 0.05 0.02
Matches are distributed among these distances:
102 51 0.07
103 109 0.15
104 89 0.12
105 356 0.50
106 101 0.14
107 9 0.01
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.32
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAACGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1294090 original size:6 final size:6
Alignment explanation
Indices: 1294079--1294117 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
1294069 CGTTCTTCTC
1294079 TTTTTG TTTTTG TTTTT- TTTTTG TTTTTG TTTTT- TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
1294118 CCAACTTAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 10 0.31
6 22 0.69
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (6 bp):
TTTTTG
Found at i:1294099 original size:11 final size:12
Alignment explanation
Indices: 1294079--1294117 Score: 64
Period size: 11 Copynumber: 3.4 Consensus size: 12
1294069 CGTTCTTCTC
1294079 TTTTTGTTTTTG
1 TTTTTGTTTTTG
1294091 TTTTT-TTTTTG
1 TTTTTGTTTTTG
1294102 TTTTTGTTTTT-
1 TTTTTGTTTTTG
1294113 TTTTT
1 TTTTT
1294118 CCAACTTAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (12 bp):
TTTTTGTTTTTG
Found at i:1294101 original size:17 final size:17
Alignment explanation
Indices: 1294079--1294117 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
1294069 CGTTCTTCTC
1294079 TTTTTGTTTTTGTTTTT
1 TTTTTGTTTTTGTTTTT
1294096 TTTTTGTTTTTGTTTTT
1 TTTTTGTTTTTGTTTTT
1294113 TTTTT
1 TTTTT
1294118 CCAACTTAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (17 bp):
TTTTTGTTTTTGTTTTT
Found at i:1304210 original size:16 final size:18
Alignment explanation
Indices: 1304189--1304225 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1304179 AAGTAAAGAC
1304189 AAAAAT-GAACAA-AATA
1 AAAAATAGAACAATAATA
*
1304205 AAAAATAGAATAATAATA
1 AAAAATAGAACAATAATA
1304223 AAA
1 AAA
1304226 CATATATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (18 bp):
AAAAATAGAACAATAATA
Found at i:1304654 original size:25 final size:23
Alignment explanation
Indices: 1304606--1304666 Score: 79
Period size: 25 Copynumber: 2.6 Consensus size: 23
1304596 AGTATAAAGT
1304606 AATAATAAAAATAAATAAATATA
1 AATAATAAAAATAAATAAATATA
*
1304629 ATTATAATAAAAATAAATAGGA-ATA
1 A--ATAATAAAAATAAATA-AATATA
1304654 AATAATAAAAATA
1 AATAATAAAAATA
1304667 GCAAAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
23 13 0.38
25 20 0.59
26 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.26
Consensus pattern (23 bp):
AATAATAAAAATAAATAAATATA
Found at i:1305811 original size:29 final size:29
Alignment explanation
Indices: 1305778--1305834 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1305768 AAAAAATTAA
*
1305778 TTAAATAAAGTATTAAAAAAT-TTAAATAC
1 TTAAATAAAGTA-AAAAAAATATTAAATAC
*
1305807 TTAAATAAATTAAAAAAAATATTAAATA
1 TTAAATAAAGTAAAAAAAATATTAAATA
1305835 TAATAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (29 bp):
TTAAATAAAGTAAAAAAAATATTAAATAC
Found at i:1305831 original size:21 final size:22
Alignment explanation
Indices: 1305801--1305842 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1305791 TAAAAAATTT
1305801 AAATACTTAAATA-AATTAAAAA
1 AAATACTTAAATATAA-TAAAAA
1305823 AAATA-TTAAATATAATAAAA
1 AAATACTTAAATATAATAAAA
1305843 TATACATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATACTTAAATATAATAAAAA
Found at i:1306125 original size:16 final size:16
Alignment explanation
Indices: 1306104--1306161 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
1306094 AGCACGCCTT
1306104 ATCAACGTGGCTCCAG
1 ATCAACGTGGCTCCAG
** * **
1306120 ATCAACGTAAAACGCCTT
1 ATCAACGT--GGCTCCAG
1306138 ATCAACGTGGCTCCAG
1 ATCAACGTGGCTCCAG
1306154 ATCAACGT
1 ATCAACGT
1306162 AAAACGCATT
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
16 19 0.63
18 11 0.37
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (16 bp):
ATCAACGTGGCTCCAG
Found at i:1306135 original size:34 final size:34
Alignment explanation
Indices: 1306097--1306168 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
1306087 TTCAGGGAGC
1306097 ACGCCTTATCAACGTGGCTCCAGATCAACGTAAA
1 ACGCCTTATCAACGTGGCTCCAGATCAACGTAAA
1306131 ACGCCTTATCAACGTGGCTCCAGATCAACGTAAA
1 ACGCCTTATCAACGTGGCTCCAGATCAACGTAAA
1306165 ACGC
1 ACGC
1306169 ATTGCAAGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.32, C:0.31, G:0.18, T:0.19
Consensus pattern (34 bp):
ACGCCTTATCAACGTGGCTCCAGATCAACGTAAA
Found at i:1306520 original size:16 final size:16
Alignment explanation
Indices: 1306489--1306529 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
1306479 TTTTATTACG
1306489 TATTAATTATTAAATAT
1 TATTAA-TATTAAATAT
*
1306506 TATTAATATTTAATAT
1 TATTAATATTAAATAT
1306522 TATTAATA
1 TATTAATA
1306530 ATTCAATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATTAATATTAAATAT
Found at i:1306687 original size:14 final size:14
Alignment explanation
Indices: 1306668--1306694 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1306658 GTATTTTATT
1306668 TTTTTATTAATTAG
1 TTTTTATTAATTAG
1306682 TTTTTATTAATTA
1 TTTTTATTAATTA
1306695 TTAATATTCA
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:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (14 bp):
TTTTTATTAATTAG
Found at i:1308026 original size:3 final size:3
Alignment explanation
Indices: 1308018--1308061 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1308008 TTATATAATA
1308018 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1308062 CATTTATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1310210 original size:13 final size:13
Alignment explanation
Indices: 1310171--1310210 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1310161 ATTAACACCT
1310171 TTTGCATCTGCATA
1 TTTGCAT-TGCATA
* *
1310185 TTTGTATTTCATA
1 TTTGCATTGCATA
1310198 TTTGCATTGCATA
1 TTTGCATTGCATA
1310211 AATTTAAGCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (13 bp):
TTTGCATTGCATA
Found at i:1313202 original size:30 final size:31
Alignment explanation
Indices: 1313167--1313228 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
1313157 TATCACCATT
*
1313167 AAACCAAGACACATAA-CCTTATCATCTTCC
1 AAACCAAGACACATAACCCTTAGCATCTTCC
*
1313197 AAACCAAGACACCTAACCCTTAGCATCTTCC
1 AAACCAAGACACATAACCCTTAGCATCTTCC
1313228 A
1 A
1313229 TAAGTCAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 15 0.52
31 14 0.48
ACGTcount: A:0.39, C:0.35, G:0.05, T:0.21
Consensus pattern (31 bp):
AAACCAAGACACATAACCCTTAGCATCTTCC
Found at i:1313662 original size:29 final size:30
Alignment explanation
Indices: 1313577--1313663 Score: 81
Period size: 29 Copynumber: 2.9 Consensus size: 30
1313567 GCCAAAATGT
** *
1313577 AACTTTTAAAATTACCATTTTAGTC-CCTA
1 AACTTTTAAAATTTTCATTTTGGTCACCTA
* *
1313606 AACTTTTCCAAAGTTTAT-ACTTTGGTCACC-A
1 AACTTTT--AAAATTT-TCATTTTGGTCACCTA
1313637 AACTTTTAAAATTTTCATTTTGGTCAC
1 AACTTTTAAAATTTTCATTTTGGTCAC
1313664 TATCTAAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
28 1 0.02
29 23 0.50
31 20 0.43
32 2 0.04
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.43
Consensus pattern (30 bp):
AACTTTTAAAATTTTCATTTTGGTCACCTA
Found at i:1315197 original size:2 final size:2
Alignment explanation
Indices: 1315190--1315216 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1315180 AAGACAAATA
1315190 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 A
1315217 ATAAATCTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1315831 original size:25 final size:24
Alignment explanation
Indices: 1315797--1315888 Score: 121
Period size: 25 Copynumber: 3.7 Consensus size: 24
1315787 TTTTCGAAAC
*
1315797 TTCATCAAACATTGTTCAAAATTCT
1 TTCATAAAACATT-TTCAAAATTCT
* *
1315822 TTCATAAAACATTTCTCATAATTTT
1 TTCATAAAACATTT-TCAAAATTCT
*
1315847 TTCATTAAACATTTTTCAAAATTCT
1 TTCATAAAACA-TTTTCAAAATTCT
1315872 TTCATAAAACATTTTCA
1 TTCATAAAACATTTTCA
1315889 GTCAAGACAA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
24 7 0.12
25 48 0.83
26 3 0.05
ACGTcount: A:0.37, C:0.17, G:0.01, T:0.45
Consensus pattern (24 bp):
TTCATAAAACATTTTCAAAATTCT
Found at i:1319687 original size:34 final size:32
Alignment explanation
Indices: 1319634--1319703 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1319624 CCTTACAAAC
*
1319634 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
1319666 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
1319700 TCCC
1 TCCC
1319704 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:1327055 original size:13 final size:14
Alignment explanation
Indices: 1327027--1327060 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
1327017 TACATAATAA
1327027 ATGCACTCACCTAGT
1 ATGC-CTCACCTAGT
1327042 ATGCCTCA-CTAGT
1 ATGCCTCACCTAGT
1327055 ATGCCT
1 ATGCCT
1327061 TATTATCGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.58
14 4 0.21
15 4 0.21
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (14 bp):
ATGCCTCACCTAGT
Found at i:1334140 original size:82 final size:82
Alignment explanation
Indices: 1334000--1334152 Score: 263
Period size: 82 Copynumber: 1.9 Consensus size: 82
1333990 CTTCTTATTA
*
1334000 ACTAAATATTTGATAGCTGAGTGATCACTGTGAATAATAACTTTGGTCCCTATAAAGTATGCCCT
1 ACTAAATATTTGATAGCTAAGTGATCACTGTGAATAATAACTTTGGTCCCTATAAAGTATGCCCT
1334065 AAACTTTGGTGCCTATC
66 AAACTTTGGTGCCTATC
* *
1334082 ACTAAATATTTGATAGCTAAGTGATCAGTGTGAATAATAACTTTGGTGCCC-ATCAAGTATGCCC
1 ACTAAATATTTGATAGCTAAGTGATCACTGTGAATAATAACTTTGGT-CCCTATAAAGTATGCCC
1334146 TAAACTT
65 TAAACTT
1334153 GTCAAATGCA
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
82 64 0.96
83 3 0.04
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (82 bp):
ACTAAATATTTGATAGCTAAGTGATCACTGTGAATAATAACTTTGGTCCCTATAAAGTATGCCCT
AAACTTTGGTGCCTATC
Found at i:1336948 original size:53 final size:53
Alignment explanation
Indices: 1336868--1337167 Score: 458
Period size: 53 Copynumber: 5.7 Consensus size: 53
1336858 CTAAGGTAAT
*
1336868 GAAATAGTAATTCACAAACTCATTATGAATACCAT-GAGTGCACACATAGTGTC
1 GAAATAGTAATTCACAAACTCATTATGAATACCATGGA-TGCACACATAGTGCC
* *
1336921 GAAATAGTAATTCACAAACTCATTATGAATACCCTGGATGCACATATAGTGCC
1 GAAATAGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCC
* *
1336974 GAAATAGTAATTCACAAACTCATTATGAATACCATGGATGTAAACATAGTGCC
1 GAAATAGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCC
* *
1337027 GAAATGGTAATTCACAAACTCATTATGAATACCATGGATTCACACATAGTGCC
1 GAAATAGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCC
* * * * *
1337080 TAAATGGTAATTCAAAAACTCATTATGAATACCTTGGATGCACACATAATGCC
1 GAAATAGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCC
* *
1337133 AAAATGGTAATTCACAAACTCATTATGAATACCAT
1 GAAATAGTAATTCACAAACTCATTATGAATACCAT
1337168 CATAAGAAAA
Statistics
Matches: 227, Mismatches: 19, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
53 225 0.99
54 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (53 bp):
GAAATAGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCC
Found at i:1337226 original size:48 final size:48
Alignment explanation
Indices: 1337163--1337274 Score: 136
Period size: 48 Copynumber: 2.3 Consensus size: 48
1337153 CATTATGAAT
* *
1337163 ACCATCATA-AGAAAATGCAAATCATGCATTAAACAAATTTGATCGATA
1 ACCATCATACA-AAAATGCAAATCATGCATTAAACAAAATTAATCGATA
* ** * *
1337211 ATCATCATACAAAAATGCACCTTATGCATTACACAAAATTAATCGATA
1 ACCATCATACAAAAATGCAAATCATGCATTAAACAAAATTAATCGATA
*
1337259 ACCATCATACACAAAT
1 ACCATCATACAAAAAT
1337275 TATTTCGAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
48 53 0.98
49 1 0.02
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.25
Consensus pattern (48 bp):
ACCATCATACAAAAATGCAAATCATGCATTAAACAAAATTAATCGATA
Found at i:1337802 original size:22 final size:23
Alignment explanation
Indices: 1337762--1337804 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1337752 AGTGTCGACA
1337762 CTCTTCCTATAGTACCGATACTT
1 CTCTTCCTATAGTACCGATACTT
* *
1337785 CTCTT-CTATGGTATCGATAC
1 CTCTTCCTATAGTACCGATAC
1337805 CATTTTGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.21, C:0.28, G:0.12, T:0.40
Consensus pattern (23 bp):
CTCTTCCTATAGTACCGATACTT
Found at i:1337865 original size:20 final size:20
Alignment explanation
Indices: 1337839--1337889 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1337829 CTTTACTTAC
*
1337839 AGTATCGATACCTTAACCTT
1 AGTATCGATACCTTAACATT
* *
1337859 GGTATCGATACCTTCACATT
1 AGTATCGATACCTTAACATT
1337879 AGTATCGATAC
1 AGTATCGATAC
1337890 TTCTTCAACC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (20 bp):
AGTATCGATACCTTAACATT
Found at i:1347993 original size:12 final size:12
Alignment explanation
Indices: 1347976--1348000 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1347966 ATTCTTGTGT
1347976 AAACACACACAC
1 AAACACACACAC
1347988 AAACACACACAC
1 AAACACACACAC
1348000 A
1 A
1348001 TCCTATAATT
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:0.60, C:0.40, G:0.00, T:0.00
Consensus pattern (12 bp):
AAACACACACAC
Found at i:1349887 original size:19 final size:19
Alignment explanation
Indices: 1349863--1349902 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1349853 CGCCCCGTAT
*
1349863 CCGCCCCGCATCCACCCGC
1 CCGCCCCACATCCACCCGC
*
1349882 CCGCCCCACATCCGCCCGC
1 CCGCCCCACATCCACCCGC
1349901 CC
1 CC
1349903 AACTAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.10, C:0.70, G:0.15, T:0.05
Consensus pattern (19 bp):
CCGCCCCACATCCACCCGC
Found at i:1352961 original size:53 final size:53
Alignment explanation
Indices: 1352824--1353190 Score: 571
Period size: 53 Copynumber: 7.0 Consensus size: 53
1352814 ACTAAGTTAA
* *
1352824 CGAAATGGTAATTCACAAACTCATTAAGAATACCATGGGTGCACACATAGTGT
1 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGT
* * *
1352877 C-AAATGGTAATTCATAAATTCATTATGAATACCATGGATGCATACATAGTGT
1 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGT
* *
1352929 CGAAATGGTAATTCACAAACTCATTATAAATACCATGGATGCACACATAATGT
1 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGT
* *
1352982 CCAAATGGTAATTCACAAACTCATTATGAATACTATGGATGCACACATAGTGT
1 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGT
*
1353035 CCAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTG-
1 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGT
1353087 CTGAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTG-
1 C-GAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGT
* * *
1353140 CTAAAATGGTAATTCACAAACTCATTATCAATACCATAGATGCAC-CATAGT
1 C-GAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGT
1353191 ACCGAAAGTA
Statistics
Matches: 293, Mismatches: 19, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
52 54 0.18
53 239 0.82
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (53 bp):
CGAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGT
Found at i:1353272 original size:48 final size:47
Alignment explanation
Indices: 1353213--1353360 Score: 172
Period size: 48 Copynumber: 3.1 Consensus size: 47
1353203 CATAGTACTG
**
1353213 ATACGAAAATGCAACATATGTATTAAACAAAACCGATCGATAAACATC
1 ATACGAAAATGCAACATATG-ATTAAACAAAATTGATCGATAAACATC
* * *
1353261 ATACGATAATGCAA-ATCATGCATTAAACAAATTTGATCGATAATCATC
1 ATACGAAAATGCAACAT-ATG-ATTAAACAAAATTGATCGATAAACATC
* * * *
1353309 ATACAAAAATGCAACTTATGATTTAAACAAAATTGATCGATAACCAAC
1 ATACGAAAATGCAACATATGA-TTAAACAAAATTGATCGATAAACATC
1353357 ATAC
1 ATAC
1353361 ACAAAGTATG
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
47 3 0.04
48 81 0.95
49 1 0.01
ACGTcount: A:0.48, C:0.18, G:0.09, T:0.25
Consensus pattern (47 bp):
ATACGAAAATGCAACATATGATTAAACAAAATTGATCGATAAACATC
Found at i:1361017 original size:18 final size:17
Alignment explanation
Indices: 1360990--1361024 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1360980 AAATCAAATT
1360990 AATTCAAATTTTATCAAA
1 AATTCAAATTTT-TCAAA
*
1361008 AATTCTAATTTTTCAAA
1 AATTCAAATTTTTCAAA
1361025 TAAAATCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTCAAATTTTTCAAA
Found at i:1386190 original size:10 final size:8
Alignment explanation
Indices: 1386149--1386186 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1386139 AATAAATGAT
1386149 TATTTTAA
1 TATTTTAA
1386157 -ATTTT-A
1 TATTTTAA
*
1386163 TTTTTTAA
1 TATTTTAA
1386171 TATTTTAA
1 TATTTTAA
1386179 TATTTTAA
1 TATTTTAA
1386187 AATAACTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
6 1 0.04
7 9 0.35
8 16 0.62
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TATTTTAA
Found at i:1386363 original size:32 final size:32
Alignment explanation
Indices: 1386327--1386392 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
1386317 ACATCACTCG
1386327 AAGTGATTATATGCCATGTTCCATGTCACCCA
1 AAGTGATTATATGCCATGTTCCATGTCACCCA
* * * *
1386359 AAGTGTTTATATGGCATGTTCTATGTCACTCA
1 AAGTGATTATATGCCATGTTCCATGTCACCCA
1386391 AA
1 AA
1386393 ATAATGAGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.35
Consensus pattern (32 bp):
AAGTGATTATATGCCATGTTCCATGTCACCCA
Found at i:1389483 original size:3 final size:3
Alignment explanation
Indices: 1389475--1389499 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1389465 CATTACCTTA
1389475 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1389500 TTAATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1389510 original size:2 final size:2
Alignment explanation
Indices: 1389503--1389530 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1389493 TATTATTTTA
1389503 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
1389531 TACAAACCCA
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:1389596 original size:23 final size:24
Alignment explanation
Indices: 1389569--1389621 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
1389559 CCCAACAATA
1389569 CAAACCCGGGCCCAAACT-AAACC
1 CAAACCCGGGCCCAAACTAAAACC
* *
1389592 CAAACCCGGGTCCAAATTAAAACC
1 CAAACCCGGGCCCAAACTAAAACC
*
1389616 CTAACC
1 CAAACC
1389622 ACTAAAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.40, C:0.40, G:0.11, T:0.09
Consensus pattern (24 bp):
CAAACCCGGGCCCAAACTAAAACC
Found at i:1390225 original size:36 final size:36
Alignment explanation
Indices: 1390115--1390292 Score: 146
Period size: 36 Copynumber: 4.7 Consensus size: 36
1390105 AAATATTTTT
* * * *
1390115 GAAAA-ATATAATATATGATTTTTAGAAAACGGTTTTT
1 GAAAATATATATTATAT-AGTTTT-GAAAACGGTATTC
* * * * *
1390152 GAAAACATATA--ATATACTTTTCAAAAATCAGTTTTC
1 GAAAATATATATTATATAGTTTT-GAAAA-CGGTATTC
1390188 GAAAATATATATTATATAGTTTTGAAAACGGTATTC
1 GAAAATATATATTATATAGTTTTGAAAACGGTATTC
*
1390224 GAAAATATATATATATCATATAGTTTTGAAAAACGATATTC
1 G-AAA-ATATATAT-T-ATATAGTTTTG-AAAACGGTATTC
1390265 GAAAATATATATATTATATAGTTTTGAA
1 G-AAA-ATATATATTATATAGTTTTGAA
1390293 CATTTTGAAA
Statistics
Matches: 121, Mismatches: 11, Indels: 17
0.81 0.07 0.11
Matches are distributed among these distances:
35 9 0.07
36 27 0.22
37 12 0.10
38 24 0.20
39 12 0.10
40 12 0.10
41 25 0.21
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (36 bp):
GAAAATATATATTATATAGTTTTGAAAACGGTATTC
Found at i:1390354 original size:37 final size:38
Alignment explanation
Indices: 1390189--1390692 Score: 441
Period size: 41 Copynumber: 13.6 Consensus size: 38
1390179 TCAGTTTTCG
* *
1390189 AAAATATATAT--TATATAG-TTTTGAAAACGGTATTCG-
1 AAAATATATATAATATATAGTTTTTGAAAAC-AT-TTTGA
*
1390225 AAAATATATATATATCATATAG-TTTTGAAAAACGATATTCG-
1 AAAATATATATA-AT-ATATAGTTTTTG-AAAAC-AT-TTTGA
*
1390266 AAAATATATATATTATATAG-TTTTG--AACATTTTGAA
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTG-A
1390302 AAAATATATATAATATATAGTTTTTGAAAACATTTTGA
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTGA
**
1390340 AAACGATATA-AATATAATTAG-TTTTG---ACATTTTGA
1 AAAATATATATAATAT-A-TAGTTTTTGAAAACATTTTGA
1390375 AAAATA-ATATAATA-ATA--TTTTG-AAACATTTTG-
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTGA
** *
1390407 -AAACGTATATAATTTATA-TTTTTGAAAAC-------
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTGA
*
1390436 ---ATATATATAATATACAGTTTTTGAAAACATTTTGA
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTGA
1390471 ATATATATATATATATATATATAGTTTTTGAAAACATTTTGAA
1 A-A-A-ATATATATA-ATATATAGTTTTTGAAAACATTTTG-A
1390514 AAAATATATATAATATATAG-TTTTGAAAACATTTTGA
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTGA
1390551 ATATATATATATATAATATATAGTTTTTGAAAACATTTTGA
1 A-A-A-ATATATATAATATATAGTTTTTGAAAACATTTTGA
*
1390592 AAAA-ATATATAATATATAATTTTTGAAAACATTTTGA
1 AAAATATATATAATATATAGTTTTTGAAAACATTTTGA
*
1390629 AAATATATATATATATAATATAG-TTTTGGAAACATTTTTGA
1 AAA-ATATATATA-AT-ATATAGTTTTTGAAAACA-TTTTGA
*
1390670 AAACT-TATATAATATATAGTTTT
1 AAAATATATATAATATATAGTTTT
1390693 GACAATCAAT
Statistics
Matches: 403, Mismatches: 20, Indels: 88
0.79 0.04 0.17
Matches are distributed among these distances:
27 12 0.03
28 11 0.03
31 8 0.02
32 9 0.02
33 12 0.03
34 11 0.03
35 23 0.06
36 33 0.08
37 53 0.13
38 39 0.10
39 47 0.12
40 52 0.13
41 66 0.16
42 25 0.06
43 2 0.00
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.42
Consensus pattern (38 bp):
AAAATATATATAATATATAGTTTTTGAAAACATTTTGA
Done.