Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007952.1 Hibiscus syriacus cultivar Beakdansim tig00110377_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: 3169409
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 16
Found at i:1160484 original size:75 final size:75
Alignment explanation
Indices: 1160387--1160584 Score: 210
Period size: 75 Copynumber: 2.6 Consensus size: 75
1160377 AATCATAAAT
* * * * *
1160387 AATGTCAAATATCAAGACTCAAACAACAATATTAAGTT-TATAACAGTAAAATCCATAA-ACAAA
1 AATGTCAAATTTCAATACTCAAAC-ATAATATTAAGTTCTAGAACAATAAAATCCATAATA-AAA
1160450 -CAACAATATTAA
64 TC-ACAATATTAA
* *
1160462 AATGTCAAATTTCAATATTCAAACCATAATATTAA-TTCTAGAATAATAAAATCCATAATAAAAT
1 AATGTCAAATTTCAATACTCAAA-CATAATATTAAGTTCTAGAACAATAAAATCCATAATAAAAT
*
1160526 CATAATATTAA
65 CACAATATTAA
* *
1160537 AGTGTCAAATCTT-AATACTCAAATCATAATATTAAG-TCTAGAAAAATA
1 AATGTCAAAT-TTCAATACTCAAA-CATAATATTAAGTTCTAGAACAATA
1160585 TTAAACTCAA
Statistics
Matches: 105, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
74 2 0.02
75 98 0.93
76 5 0.05
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (75 bp):
AATGTCAAATTTCAATACTCAAACATAATATTAAGTTCTAGAACAATAAAATCCATAATAAAATC
ACAATATTAA
Found at i:1160531 original size:11 final size:12
Alignment explanation
Indices: 1160504--1160532 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1160494 TAATTCTAGA
1160504 ATAATAAAATCC
1 ATAATAAAATCC
1160516 ATAATAAAAT-C
1 ATAATAAAATCC
1160527 ATAATA
1 ATAATA
1160533 TTAAAGTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (12 bp):
ATAATAAAATCC
Found at i:1160829 original size:21 final size:21
Alignment explanation
Indices: 1160804--1160847 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1160794 TTCCTCATCT
1160804 TCCCAAAG-TTCGAATCTTTCA
1 TCCCAAAGTTTC-AATCTTTCA
1160825 TCCCAAAGTTTCAATCTTTCA
1 TCCCAAAGTTTCAATCTTTCA
1160846 TC
1 TC
1160848 AATGGCTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.27, C:0.30, G:0.07, T:0.36
Consensus pattern (21 bp):
TCCCAAAGTTTCAATCTTTCA
Found at i:1167811 original size:51 final size:51
Alignment explanation
Indices: 1167728--1167855 Score: 168
Period size: 51 Copynumber: 2.5 Consensus size: 51
1167718 TTAACAGTAA
* *
1167728 AGCGTGCCCCCTGCACTGCGCTATACGATGATTTGGC-GCCACGTGGGGTAT
1 AGCGTGCCCCCTGCACCGCGCTATACGATGATTTGGCAGACACGT-GGGTAT
* * *
1167779 AGCGCGCCCCCTGCACCGCGCTATACGGTGATTTGGCATACACGTGGGTAT
1 AGCGTGCCCCCTGCACCGCGCTATACGATGATTTGGCAGACACGTGGGTAT
* * *
1167830 AGCGTGGCCCCTGCAACGCACTATAC
1 AGCGTGCCCCCTGCACCGCGCTATAC
1167856 CTGGATATCT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
51 62 0.93
52 5 0.07
ACGTcount: A:0.18, C:0.32, G:0.29, T:0.21
Consensus pattern (51 bp):
AGCGTGCCCCCTGCACCGCGCTATACGATGATTTGGCAGACACGTGGGTAT
Found at i:1168254 original size:110 final size:111
Alignment explanation
Indices: 1168115--1168335 Score: 399
Period size: 110 Copynumber: 2.0 Consensus size: 111
1168105 TGGAAATCAT
*
1168115 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
1168180 TATTTAGTT-ATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
1168225 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
1168290 TAATTAGTTGATTCATTTAATGCATTATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
1168336 TTTTTGTAAA
Statistics
Matches: 106, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
110 72 0.68
111 34 0.32
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:1169714 original size:26 final size:24
Alignment explanation
Indices: 1169642--1169714 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
1169632 TTATATTTGT
1169642 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
* *
1169667 ATTT-TTTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
1169690 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
1169715 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
23 4 0.11
24 10 0.27
25 12 0.32
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.63
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:1173417 original size:51 final size:51
Alignment explanation
Indices: 1173341--1173469 Score: 161
Period size: 51 Copynumber: 2.5 Consensus size: 51
1173331 CCCTACGTGG
* * * *
1173341 CGTATAGCGCGCTGCAGGGGCCGCGCTATA-CCCACGTGTATGCCAGATCAC
1 CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTG-ACGCCAAATCAC
* * *
1173392 CGTATAGCACGGTGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCAT
1 CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGACGCCAAATCAC
* *
1173443 CGTATAGCGCGGTGCATGGGGTGCGCT
1 CGTATAGCGCGGTGCAGGGGGCGCGCT
1173470 TTACTGCTAA
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
51 59 0.88
52 8 0.12
ACGTcount: A:0.19, C:0.30, G:0.33, T:0.18
Consensus pattern (51 bp):
CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGACGCCAAATCAC
Found at i:1173543 original size:30 final size:29
Alignment explanation
Indices: 1173481--1173556 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
1173471 TACTGCTAAG
* *
1173481 GGTGTTAGATCGAGAAATATAATCTGACC
1 GGTGTTAGATCGGGAAATATAATCTCACC
* *
1173510 GGTGTTAGATCGGGAAATATACTGTTCACC
1 GGTGTTAGATCGGGAAATATAAT-CTCACC
* *
1173540 GGTGATATATCGGGAAA
1 GGTGTTAGATCGGGAAA
1173557 ATCGCCCATT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 21 0.52
30 19 0.47
ACGTcount: A:0.32, C:0.13, G:0.28, T:0.28
Consensus pattern (29 bp):
GGTGTTAGATCGGGAAATATAATCTCACC
Found at i:1174993 original size:31 final size:31
Alignment explanation
Indices: 1174958--1175063 Score: 169
Period size: 31 Copynumber: 3.4 Consensus size: 31
1174948 CAAAAAAATA
*
1174958 TAAGTTTTGGTCACTTACATTATTATTTTAT
1 TAAGTTTTGGTCACTTACGTTATTATTTTAT
* *
1174989 TAAGTTTTGGTCACTGACGTTATCATTTTAT
1 TAAGTTTTGGTCACTTACGTTATTATTTTAT
1175020 TAAGTTTTGGTCACTTACGTTATCT-TTTTAT
1 TAAGTTTTGGTCACTTACGTTAT-TATTTTAT
1175051 TAAGTTTTGGTCA
1 TAAGTTTTGGTCA
1175064 TTTTGACGTT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
31 69 1.00
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.52
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACGTTATTATTTTAT
Found at i:1178652 original size:97 final size:97
Alignment explanation
Indices: 1178534--1178730 Score: 376
Period size: 97 Copynumber: 2.0 Consensus size: 97
1178524 TATATTTATT
*
1178534 ACAATCAATTTCATAGTTAGACACGCTTTCAATTAATTTTCAACCAAACAAGCAATTAAGCAACC
1 ACAATCAATTTCATAGTTAGACACGCTTTCAATTAATTTTCAACAAAACAAGCAATTAAGCAACC
1178599 AAACAAAATAATGTAGCATAGAATATATAGAC
66 AAACAAAATAATGTAGCATAGAATATATAGAC
*
1178631 ACAATCAATTTCATAGTTAGACATGCTTTCAATTAATTTTCAACAAAACAAGCAATTAAGCAACC
1 ACAATCAATTTCATAGTTAGACACGCTTTCAATTAATTTTCAACAAAACAAGCAATTAAGCAACC
1178696 AAACAAAATAATGTAGCATAGAATATATAGAC
66 AAACAAAATAATGTAGCATAGAATATATAGAC
1178728 ACA
1 ACA
1178731 CCTCGACAGA
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 98 1.00
ACGTcount: A:0.47, C:0.18, G:0.09, T:0.26
Consensus pattern (97 bp):
ACAATCAATTTCATAGTTAGACACGCTTTCAATTAATTTTCAACAAAACAAGCAATTAAGCAACC
AAACAAAATAATGTAGCATAGAATATATAGAC
Found at i:1181648 original size:13 final size:13
Alignment explanation
Indices: 1181630--1181686 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
1181620 ATTTAAGAAC
*
1181630 TTTCATATTTAAT
1 TTTCATATTTCAT
* * *
1181643 TTTCATCTTTTAC
1 TTTCATATTTCAT
1181656 TTT-ATA-TTCAT
1 TTTCATATTTCAT
*
1181667 TTTCACATTTCAT
1 TTTCATATTTCAT
1181680 TTTCATA
1 TTTCATA
1181687 ACCAATACTT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
11 6 0.18
12 4 0.12
13 24 0.71
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTCATATTTCAT
Found at i:1181761 original size:19 final size:19
Alignment explanation
Indices: 1181739--1181795 Score: 78
Period size: 19 Copynumber: 3.0 Consensus size: 19
1181729 CCTATTTCCT
*
1181739 TATTCAAAACTTACTTTCA
1 TATTCAAAACTTAATTTCA
*
1181758 TATTCATAACTTAATTTCA
1 TATTCAAAACTTAATTTCA
* *
1181777 TATTCATAGCTTAATTTCA
1 TATTCAAAACTTAATTTCA
1181796 AATTTCTAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.46
Consensus pattern (19 bp):
TATTCAAAACTTAATTTCA
Found at i:1181781 original size:38 final size:38
Alignment explanation
Indices: 1181739--1181814 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 38
1181729 CCTATTTCCT
* *
1181739 TATTCAAAACTTACTTTCATA-TTCATAACTTAATTTCA
1 TATTCAAAACTTAATTTCAAATTTC-TAACTTAATTTCA
* * *
1181777 TATTCATAGCTTAATTTCAAATTTCTAGCTTAATTTCA
1 TATTCAAAACTTAATTTCAAATTTCTAACTTAATTTCA
1181815 AATTTATAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 29 0.91
39 3 0.09
ACGTcount: A:0.34, C:0.17, G:0.03, T:0.46
Consensus pattern (38 bp):
TATTCAAAACTTAATTTCAAATTTCTAACTTAATTTCA
Found at i:1181805 original size:19 final size:20
Alignment explanation
Indices: 1181760--1181823 Score: 89
Period size: 19 Copynumber: 3.4 Consensus size: 20
1181750 TACTTTCATA
* *
1181760 TTCATAACTTAATTTCATA-
1 TTCATAGCTTAATTTCAAAT
1181779 TTCATAGCTTAATTTCAAAT
1 TTCATAGCTTAATTTCAAAT
1181799 TTC-TAGCTTAATTTCAAAT
1 TTCATAGCTTAATTTCAAAT
1181818 TT-ATAG
1 TTCATAG
1181824 TCCAATACAT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 38 0.93
20 3 0.07
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.47
Consensus pattern (20 bp):
TTCATAGCTTAATTTCAAAT
Found at i:1187543 original size:21 final size:20
Alignment explanation
Indices: 1187517--1187555 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
1187507 CTTTCAATAA
1187517 AATAATATAATTATTTAAAAT
1 AATAATATAA-TATTTAAAAT
1187538 AATAATATAATATTTAAA
1 AATAATATAATATTTAAA
1187556 CATTTGAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATAATATAATATTTAAAAT
Found at i:1192691 original size:20 final size:20
Alignment explanation
Indices: 1192666--1192713 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1192656 ATCAATTTTG
1192666 AACCAAACAAGCTATTAAGC
1 AACCAAACAAGCTATTAAGC
*
1192686 AACCAAACAAGCTATTAAGT
1 AACCAAACAAGCTATTAAGC
1192706 AACCAAAC
1 AACCAAAC
1192714 TAATAATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.52, C:0.25, G:0.08, T:0.15
Consensus pattern (20 bp):
AACCAAACAAGCTATTAAGC
Found at i:1197257 original size:24 final size:26
Alignment explanation
Indices: 1197208--1197268 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 26
1197198 TTAAATTAAT
*
1197208 TTTTTAATAATTTAATTTTTTTAGTA
1 TTTTTAATAATTTAATTTTTTGAGTA
1197234 TTTTT-AT-ATTT-ATTTTATTGAGTA
1 TTTTTAATAATTTAATTTT-TTGAGTA
*
1197258 -TCTTAATAATT
1 TTTTTAATAATT
1197269 GTTTATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
23 8 0.27
24 12 0.40
25 5 0.17
26 5 0.17
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (26 bp):
TTTTTAATAATTTAATTTTTTGAGTA
Found at i:1197911 original size:30 final size:30
Alignment explanation
Indices: 1197859--1197916 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
1197849 ATGTTTCCTA
*
1197859 ATTTTCAAAATAAAAATAAAAATGAAAACT
1 ATTTTCAAAATAAAAATAAAAATAAAAACT
1197889 ATTTTCTAAAA-AAAACAT-AAAATAAAAA
1 ATTTTC-AAAATAAAA-ATAAAAATAAAAA
1197917 TAGAAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.26
Consensus pattern (30 bp):
ATTTTCAAAATAAAAATAAAAATAAAAACT
Found at i:1198053 original size:24 final size:25
Alignment explanation
Indices: 1198021--1198069 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1198011 AATGATTTTC
* *
1198021 AAAAAATGATAACA-AAAATAAGTG
1 AAAAAATGAAAACATAAAAAAAGTG
*
1198045 AAAATATGAAAACATAAAAAAAGTG
1 AAAAAATGAAAACATAAAAAAAGTG
1198070 TTTTCAGTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.67, C:0.04, G:0.12, T:0.16
Consensus pattern (25 bp):
AAAAAATGAAAACATAAAAAAAGTG
Found at i:1198414 original size:29 final size:29
Alignment explanation
Indices: 1198361--1198420 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
1198351 TTTTTAAATT
* * *
1198361 TTTCTAAAAGATTAAATAAGTCCTCAGAC
1 TTTCTAAAAAATTAAATAAGCCCTCAAAC
1198390 TTTCTAAAAAATT-AATCAAGCCCTCAAAC
1 TTTCTAAAAAATTAAAT-AAGCCCTCAAAC
1198419 TT
1 TT
1198421 AGTCGAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 3 0.11
29 24 0.89
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.32
Consensus pattern (29 bp):
TTTCTAAAAAATTAAATAAGCCCTCAAAC
Found at i:1201182 original size:155 final size:156
Alignment explanation
Indices: 1200900--1201210 Score: 615
Period size: 155 Copynumber: 2.0 Consensus size: 156
1200890 TCATGGAGCC
1200900 CCACCACCGGAACAAGAGCAACTGCTTTGTCCGCGCTGTGACTCCACCAACACTAAGTTTTGCTA
1 CCACCACCGGAACAAGAGCAACTGCTTTGTCCGCGCTGTGACTCCACCAACACTAAGTTTTGCTA
1200965 CTACAACAACTATAACTTCTCTCAGCCTCGCTATTTCTGTAAGTCCTGTCGCCGTTACTGGACTC
66 CTACAACAACTATAACTTCTCTCAGCCTCGCTATTTCTGTAAGTCCTGTCGCCGTTACTGGACTC
1201030 ATGG-GGCACCCTTAGGGACATCCCT
131 ATGGTGGCACCCTTAGGGACATCCCT
1201055 CCACCACCGGAACAAGAGCAACTGCTTTGTCCGCGCTGTGACTCCACCAACACTAAGTTTTGCTA
1 CCACCACCGGAACAAGAGCAACTGCTTTGTCCGCGCTGTGACTCCACCAACACTAAGTTTTGCTA
1201120 CTACAACAACTATAACTTCTCTCAGCCTCGCTATTTCTGTAAGTCCTGTCGCCGTTACTGGACTC
66 CTACAACAACTATAACTTCTCTCAGCCTCGCTATTTCTGTAAGTCCTGTCGCCGTTACTGGACTC
1201185 ATGGTGGCACCCTTAGGGACATCCCT
131 ATGGTGGCACCCTTAGGGACATCCCT
1201211 ATTGGCGGTG
Statistics
Matches: 155, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
155 134 0.86
156 21 0.14
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.26
Consensus pattern (156 bp):
CCACCACCGGAACAAGAGCAACTGCTTTGTCCGCGCTGTGACTCCACCAACACTAAGTTTTGCTA
CTACAACAACTATAACTTCTCTCAGCCTCGCTATTTCTGTAAGTCCTGTCGCCGTTACTGGACTC
ATGGTGGCACCCTTAGGGACATCCCT
Found at i:1202861 original size:18 final size:18
Alignment explanation
Indices: 1202838--1202873 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1202828 ATAACGTGAA
1202838 TTCCATGTTGAAGTTGAT
1 TTCCATGTTGAAGTTGAT
1202856 TTCCATGTTGAAGTTGAT
1 TTCCATGTTGAAGTTGAT
1202874 ATCTTGAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.44
Consensus pattern (18 bp):
TTCCATGTTGAAGTTGAT
Found at i:1204435 original size:18 final size:18
Alignment explanation
Indices: 1204412--1204448 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1204402 ACTTGTACCG
*
1204412 GTCTGAGTAGTCTGATAA
1 GTCTGAGTAGTCTAATAA
1204430 GTCTGAGTAGTCTAATAA
1 GTCTGAGTAGTCTAATAA
1204448 G
1 G
1204449 AAAGCATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.32
Consensus pattern (18 bp):
GTCTGAGTAGTCTAATAA
Found at i:1205394 original size:24 final size:24
Alignment explanation
Indices: 1205349--1205409 Score: 88
Period size: 26 Copynumber: 2.5 Consensus size: 24
1205339 TCTATAAGAG
1205349 GAGGGTTGAAAAGAGAGAGAGAATAA
1 GAGGGTTGAAAAGAGAGAGA-AA-AA
*
1205375 AAGGGTTGAAAAGAGAGAGAAAAA
1 GAGGGTTGAAAAGAGAGAGAAAAA
1205399 GAGGGTT-AAAA
1 GAGGGTTGAAAA
1205410 CTTTATAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 4 0.12
24 8 0.24
25 2 0.06
26 19 0.58
ACGTcount: A:0.52, C:0.00, G:0.36, T:0.11
Consensus pattern (24 bp):
GAGGGTTGAAAAGAGAGAGAAAAA
Found at i:1206739 original size:3 final size:3
Alignment explanation
Indices: 1206648--1206726 Score: 90
Period size: 3 Copynumber: 26.7 Consensus size: 3
1206638 TTCATTTGAA
* *
1206648 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT AAT TAT TAT AAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
1206693 AAT AAT AAT TAT TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1206727 ATAAATATTA
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
2 3 0.04
3 63 0.94
4 1 0.01
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1208350 original size:20 final size:19
Alignment explanation
Indices: 1208325--1208366 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1208315 TTATTTTATA
1208325 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
1208345 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
1208364 AAT
1 AAT
1208367 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:1208352 original size:119 final size:117
Alignment explanation
Indices: 1208223--1208457 Score: 285
Period size: 120 Copynumber: 2.0 Consensus size: 117
1208213 TTTAATCCTA
* * * * *
1208223 TTTTAATATTTATTTATTTTCCAATAT-TAAGAAATG-GCAGTCTTAAAATAACTGGATGTTCAT
1 TTTTAATATTTATTTATTTTCCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAG-TCAT
* *
1208286 TTTCTGATATTTTTAAATAAATAAATATCTTATTTTATAAATTATATATTAATTG
65 TTTCTGATATTTCTAAATAAATAAATATCTTA-TTTATAAA-TATATATAAATTG
** * ** *
1208341 TTTTAATTATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCAT
1 TTTTAA-TATTTATTTATTTTCCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCAT
* *
1208406 TTTCTGATATTTCTAAATAAATTAATATTTTATTTATAAATATATATAAATT
65 TTTCTGATATTTCTAAATAAATAAATATCTTATTTATAAATATATATAAATT
1208458 AATATATATA
Statistics
Matches: 99, Mismatches: 15, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
118 17 0.17
119 27 0.27
120 40 0.40
121 15 0.15
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (117 bp):
TTTTAATATTTATTTATTTTCCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCATT
TTCTGATATTTCTAAATAAATAAATATCTTATTTATAAATATATATAAATTG
Found at i:1211328 original size:36 final size:36
Alignment explanation
Indices: 1211281--1211362 Score: 155
Period size: 36 Copynumber: 2.3 Consensus size: 36
1211271 TTGAAGATCT
*
1211281 GAAAGGAAAGAATAGCTGTCTACTCAAAAGCCTTGA
1 GAAAGGAAAGAATAGCCGTCTACTCAAAAGCCTTGA
1211317 GAAAGGAAAGAATAGCCGTCTACTCAAAAGCCTTGA
1 GAAAGGAAAGAATAGCCGTCTACTCAAAAGCCTTGA
1211353 GAAAGGAAAG
1 GAAAGGAAAG
1211363 CAAAAAATGG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (36 bp):
GAAAGGAAAGAATAGCCGTCTACTCAAAAGCCTTGA
Found at i:1212324 original size:15 final size:15
Alignment explanation
Indices: 1212304--1212335 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1212294 GATCAATACC
1212304 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
1212319 TTTTGCATACATTCA
1 TTTTGCATACATGCA
1212334 TT
1 TT
1212336 ATTCATTGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:1219514 original size:9 final size:9
Alignment explanation
Indices: 1219500--1219583 Score: 70
Period size: 8 Copynumber: 9.7 Consensus size: 9
1219490 GAAGAAAAAG
1219500 AAAAGAAGA
1 AAAAGAAGA
*
1219509 AAAAGAAAAA
1 AAAAG-AAGA
1219519 AAAGAGAAGA
1 AAA-AGAAGA
1219529 AAAA-AAGA
1 AAAAGAAGA
*
1219537 AAAAAAAG-
1 AAAAGAAGA
*
1219545 AGAAGAA-A
1 AAAAGAAGA
*
1219553 AAAAGAAAA
1 AAAAGAAGA
1219562 AAAAGAA-A
1 AAAAGAAGA
*
1219570 AAGAGAA-A
1 AAAAGAAGA
1219578 AAAAGA
1 AAAAGA
1219584 GGGGGTCAAG
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
8 32 0.51
9 17 0.27
10 12 0.19
11 2 0.03
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
AAAAGAAGA
Found at i:1219520 original size:23 final size:22
Alignment explanation
Indices: 1219494--1219580 Score: 129
Period size: 22 Copynumber: 3.8 Consensus size: 22
1219484 ATGCTTGAAG
1219494 AAAAAGAAAAGAAGAAAAAGAAA
1 AAAAAGAAAAGAA-AAAAAGAAA
*
1219517 AAAAAGAGAAGAAAAAAAGAAA
1 AAAAAGAAAAGAAAAAAAGAAA
*
1219539 AAAAAGAGAAGAAAAAAAGAAA
1 AAAAAGAAAAGAAAAAAAGAAA
1219561 AAAAAGAAAAAGAGAAAAAA
1 AAAAAG-AAAAGA-AAAAAA
1219581 AGAGGGGGTC
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
22 37 0.62
23 17 0.28
24 6 0.10
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAGAAAAAAAGAAA
Found at i:1219578 original size:14 final size:14
Alignment explanation
Indices: 1219492--1219579 Score: 64
Period size: 14 Copynumber: 6.5 Consensus size: 14
1219482 TTATGCTTGA
1219492 AGAAAAAG-AAAAG
1 AGAAAAAGAAAAAG
1219505 AAGAAAAAGAAAAA-
1 -AGAAAAAGAAAAAG
1219519 A-AAGAGAAGAAAAA-
1 AGAA-A-AAGAAAAAG
*
1219533 A-AGAAA-AAAAAG
1 AGAAAAAGAAAAAG
*
1219545 AGAAGAA-AAAAAG
1 AGAAAAAGAAAAAG
*
1219558 AAAAAAAAGAAAAAG
1 -AGAAAAAGAAAAAG
1219573 AGAAAAA
1 AGAAAAA
1219580 AAGAGGGGGT
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
11 5 0.08
12 5 0.08
13 12 0.20
14 29 0.48
15 10 0.16
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AGAAAAAGAAAAAG
Found at i:1219578 original size:22 final size:22
Alignment explanation
Indices: 1219494--1219567 Score: 130
Period size: 22 Copynumber: 3.3 Consensus size: 22
1219484 ATGCTTGAAG
*
1219494 AAAAAGAAAAGAAGAAAAAGAAA
1 AAAAAGAGAAGAA-AAAAAGAAA
1219517 AAAAAGAGAAGAAAAAAAGAAA
1 AAAAAGAGAAGAAAAAAAGAAA
1219539 AAAAAGAGAAGAAAAAAAGAAA
1 AAAAAGAGAAGAAAAAAAGAAA
1219561 AAAAAGA
1 AAAAAGA
1219568 AAAAGAGAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 38 0.76
23 12 0.24
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (22 bp):
AAAAAGAGAAGAAAAAAAGAAA
Found at i:1221371 original size:3 final size:3
Alignment explanation
Indices: 1221363--1221410 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
1221353 TTTACTTTTA
*
1221363 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1221411 TAACCATAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1221698 original size:114 final size:112
Alignment explanation
Indices: 1221501--1221711 Score: 255
Period size: 114 Copynumber: 1.9 Consensus size: 112
1221491 TTTAATCCTA
* * * * *
1221501 TTTTAATATTTATTTATTTTCTAATATTAAGAAAGGGCAGTCTTAAAATAACTGGATGTCCATTT
1 TTTTAATATTTATTTATTTTCTAATATAAAGAAAGAGCAGTCTTAAAACAACTAGAAGTCCATTT
* *
1221566 TCTTATATTTTTAAATAAATAAATATCTTATTTTATTTATATTAATTG
66 TCTGATATTTCTAAATAAATAAAT-TCTTATTTTATTTATATTAATTG
* * ** *
1221614 TTTTAATTATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCC-
1 TTTTAA-TATTTATTTATTTTCTAATAT-AAAG-AAAGAGCAGTCTTAAAACAACTAGAAGTCCA
*
1221678 TTTTCTGATA-TTCTAAATAAATAAATTTTTATTT
63 TTTTCTGATATTTCTAAATAAATAAATTCTTATTT
1221712 ATAATATATA
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
113 13 0.16
114 35 0.43
115 12 0.15
116 22 0.27
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.48
Consensus pattern (112 bp):
TTTTAATATTTATTTATTTTCTAATATAAAGAAAGAGCAGTCTTAAAACAACTAGAAGTCCATTT
TCTGATATTTCTAAATAAATAAATTCTTATTTTATTTATATTAATTG
Found at i:1221722 original size:2 final size:2
Alignment explanation
Indices: 1221711--1221758 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
1221701 AATTTTTATT
*
1221711 TA TA -A TA TA TA TA AA T- TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1221750 TA TA TA TA T
1 TA TA TA TA T
1221759 TTTTCATAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1223400 original size:40 final size:41
Alignment explanation
Indices: 1223345--1223452 Score: 137
Period size: 40 Copynumber: 2.7 Consensus size: 41
1223335 ATAATCGTAC
1223345 TTTAATAGTGTTTTTATATAAACGCCGCTAAAGACT-GAAA
1 TTTAATAGTGTTTTTATATAAACGCCGCTAAAGACTCGAAA
* * * ** * *
1223385 TTTAGTAGCGTTTTTATACAAAAACCGCTAAAGACTCGTAC
1 TTTAATAGTGTTTTTATATAAACGCCGCTAAAGACTCGAAA
*
1223426 TTTAATAGTATTTTTATATAAACGCCG
1 TTTAATAGTGTTTTTATATAAACGCCG
1223453 TTACTTTAGT
Statistics
Matches: 54, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
40 31 0.57
41 23 0.43
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (41 bp):
TTTAATAGTGTTTTTATATAAACGCCGCTAAAGACTCGAAA
Found at i:1224099 original size:17 final size:17
Alignment explanation
Indices: 1224073--1224107 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1224063 GGGGTCGGAA
*
1224073 TGTTGGAAATTCTAGAT
1 TGTTGAAAATTCTAGAT
1224090 TGTTGAAAATTCTAGAT
1 TGTTGAAAATTCTAGAT
1224107 T
1 T
1224108 TTCTAGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (17 bp):
TGTTGAAAATTCTAGAT
Found at i:1227465 original size:23 final size:23
Alignment explanation
Indices: 1227421--1227465 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1227411 AATCTTATAT
*
1227421 GGCACTACGATACAATTCTACGC
1 GGCACTACGATACAATTATACGC
* * *
1227444 GGCACTTCGATGCATTTATACG
1 GGCACTACGATACAATTATACG
1227466 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (23 bp):
GGCACTACGATACAATTATACGC
Found at i:1237003 original size:17 final size:17
Alignment explanation
Indices: 1236981--1237015 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1236971 CAATCTAGAA
*
1236981 AATCTAGAATTTTCAAC
1 AATCTAGAATTTCCAAC
1236998 AATCTAGAATTTCCAAC
1 AATCTAGAATTTCCAAC
1237015 A
1 A
1237016 CGGAATGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (17 bp):
AATCTAGAATTTCCAAC
Found at i:1237518 original size:27 final size:27
Alignment explanation
Indices: 1237480--1237549 Score: 140
Period size: 27 Copynumber: 2.6 Consensus size: 27
1237470 ATATGGGAAG
1237480 AATATTGACTAGCAAAACGAAGGCCTT
1 AATATTGACTAGCAAAACGAAGGCCTT
1237507 AATATTGACTAGCAAAACGAAGGCCTT
1 AATATTGACTAGCAAAACGAAGGCCTT
1237534 AATATTGACTAGCAAA
1 AATATTGACTAGCAAA
1237550 TGATAATAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (27 bp):
AATATTGACTAGCAAAACGAAGGCCTT
Found at i:1240134 original size:17 final size:18
Alignment explanation
Indices: 1240107--1240154 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 18
1240097 TTAAATAAAC
1240107 ATCGAATGCACTG-AGTGT
1 ATCG-ATGCACTGTAGTGT
1240125 ATCGATGCACATGTAGTGT
1 ATCGATGCAC-TGTAGTGT
1240144 ATCGATGCACT
1 ATCGATGCACT
1240155 CCCTTAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.21
18 7 0.25
19 15 0.54
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (18 bp):
ATCGATGCACTGTAGTGT
Found at i:1240207 original size:63 final size:62
Alignment explanation
Indices: 1240058--1240216 Score: 169
Period size: 63 Copynumber: 2.5 Consensus size: 62
1240048 TCTGGGCAAG
*
1240058 GTGCATCGATGCATAAGTAGTGCACCGATGCACACCTAATTAAATAAACATCGAATGCACTGA
1 GTGCATCGATGCATAAGTAGTGTACCGATGCACACC-AATTAAATAAACATCGAATGCACTGA
* * * * * * *
1240121 GTGTATCGATGCACATGTAGTGTATCGATGCACTCC-CTTAAGATGAAACATCGAATGCA-TATA
1 GTGCATCGATGCATAAGTAGTGTACCGATGCACACCAATTAA-AT-AAACATCGAATGCACT-GA
* * *
1240184 GTGCATCGATGCATAGGTTGTGTACCAATGCAC
1 GTGCATCGATGCATAAGTAGTGTACCGATGCAC
1240217 CAGTGAGAGG
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
61 4 0.05
62 3 0.04
63 72 0.91
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (62 bp):
GTGCATCGATGCATAAGTAGTGTACCGATGCACACCAATTAAATAAACATCGAATGCACTGA
Found at i:1240641 original size:58 final size:59
Alignment explanation
Indices: 1240561--1240892 Score: 227
Period size: 59 Copynumber: 5.7 Consensus size: 59
1240551 GCACTTTGTT
* * * * *
1240561 TGCTAAAATGTTAAGTAAATCATACTGAGTGTATAGATTTCCATAT-GGAGCA-CTGAGTG
1 TGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGG-GCATATGA-TG
* * * *
1240620 TGC-CAAATGATAAGGAAATCATATTGAAAT-TATGGATTTCCAGATAGGGCATATTATG
1 TGCTAAAATGATAAGGAAATCATACTG-AGTGTATGGATTTCCAGATAGGGCATATGATG
* * * * * *
1240678 TGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGGTTTCCAGATAAGGCACTAAG-GG
1 TGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGGGCA-TATGATG
* ** * *** *
1240737 TGCT-AACTGATAAATAAATCATATTGAAAATATGGATTTCCAGATAGGGCATATTATG
1 TGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGGGCATATGATG
* ** * * *
1240795 TGCTAAAATGGTAATAAAATCATACT-AATAGTATGGATTTTC-GAATAGGGCACTTTG-TG
1 TGCTAAAATGATAAGGAAATCATACTGAGT-GTATGGATTTCCAG-ATAGGGCA-TATGATG
* * *
1240854 TGGTAAAATGAAAAGGGAAA-CATACTAAGTGTAT-GATTT
1 TGCTAAAATGATAA-GGAAATCATACTGAGTGTATGGATTT
1240893 TCCTAATGGA
Statistics
Matches: 211, Mismatches: 49, Indels: 27
0.74 0.17 0.09
Matches are distributed among these distances:
57 2 0.01
58 91 0.43
59 109 0.52
60 9 0.04
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (59 bp):
TGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGGGCATATGATG
Found at i:1240771 original size:117 final size:117
Alignment explanation
Indices: 1240561--1240820 Score: 360
Period size: 117 Copynumber: 2.2 Consensus size: 117
1240551 GCACTTTGTT
* * * * * *
1240561 TGCTAAAATGTTAAGTAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGAGTGTGCCAA
1 TGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCAGATAGAGCACTAAGGGTGCCAA
* *
1240626 ATGATAAGGAAATCATATTGAAATTATGGATTTCCAGATAGGGCATATTATG
66 ATGATAAAGAAATCATATTGAAAATATGGATTTCCAGATAGGGCATATTATG
* * * *
1240678 TGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGGTTTCCAGATA-AGGCACTAAGGGTGCTA
1 TGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCAGATAGA-GCACTAAGGGTGCCA
* *
1240742 ACTGATAAATAAATCATATTGAAAATATGGATTTCCAGATAGGGCATATTATG
65 AATGATAAAGAAATCATATTGAAAATATGGATTTCCAGATAGGGCATATTATG
**
1240795 TGCTAAAATGGTAATAAAATCATACT
1 TGCTAAAATGGTAAGGAAATCATACT
1240821 AATAGTATGG
Statistics
Matches: 125, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
116 1 0.01
117 124 0.99
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (117 bp):
TGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCAGATAGAGCACTAAGGGTGCCAA
ATGATAAAGAAATCATATTGAAAATATGGATTTCCAGATAGGGCATATTATG
Found at i:1246710 original size:17 final size:18
Alignment explanation
Indices: 1246683--1246730 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
1246673 TTAAATTAAC
1246683 ATCGAATGCACTG-AGTGT
1 ATCG-ATGCACTGTAGTGT
*
1246701 ATCGATGCACAGGTAGTGT
1 ATCGATGCAC-TGTAGTGT
1246720 ATCGATGCACT
1 ATCGATGCACT
1246731 CCCTTAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 6 0.23
18 5 0.19
19 15 0.58
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (18 bp):
ATCGATGCACTGTAGTGT
Found at i:1247198 original size:59 final size:60
Alignment explanation
Indices: 1247135--1247287 Score: 163
Period size: 58 Copynumber: 2.6 Consensus size: 60
1247125 ATGGCACTTT
* * * *
1247135 GTGTGCTAAAATGTTAAAGAAATCATACTGAGTGTATAGATTTCCATAT-GGAGCA-CTGA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCAGATAGG-GCATATGA
* * * *
1247194 GTGTGCT-AAATGATAAGGAAATCATATTGAAAT-TATGGATTTCCAGATAGGGCATATTA
1 GTGTGCTAAAATGATAAGGAAATCATACTG-AGTGTATAGATTTCCAGATAGGGCATATGA
* *
1247253 -TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTA
1247288 GCCCCCTAGA
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
58 43 0.56
59 34 0.44
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.31
Consensus pattern (60 bp):
GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCAGATAGGGCATATGA
Found at i:1248961 original size:30 final size:29
Alignment explanation
Indices: 1248926--1249019 Score: 100
Period size: 29 Copynumber: 3.2 Consensus size: 29
1248916 CACATTCAAA
*
1248926 AATTACAAAAATATCAACTTTATTAAAAAT
1 AATTACAAAAATATCAACATT-TTAAAAAT
* * *
1248956 AATTACCAAAATATCACCATTTTACAAAT
1 AATTACAAAAATATCAACATTTTAAAAAT
* * *
1248985 AATT-CACAAAATGTCATCGTTTTAAAAAT
1 AATTACA-AAAATATCAACATTTTAAAAAT
1249014 AATTAC
1 AATTAC
1249020 CAGAATGTCA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
28 1 0.02
29 33 0.62
30 19 0.36
ACGTcount: A:0.50, C:0.15, G:0.02, T:0.33
Consensus pattern (29 bp):
AATTACAAAAATATCAACATTTTAAAAAT
Found at i:1248994 original size:29 final size:29
Alignment explanation
Indices: 1248948--1249117 Score: 168
Period size: 29 Copynumber: 5.9 Consensus size: 29
1248938 ATCAACTTTA
*
1248948 TTAAAAATAATT-ACCAAAATATCACCATT
1 TTAAAAATAATTCA-CAAAATGTCACCATT
* * *
1248977 TTACAAATAATTCACAAAATGTCATCGTT
1 TTAAAAATAATTCACAAAATGTCACCATT
* *
1249006 TTAAAAATAATT-ACCAGAATGTCACCGTT
1 TTAAAAATAATTCA-CAAAATGTCACCATT
* *
1249035 TCTAAAAAAAATTCTCAAAATGTCA-CATTT
1 T-TAAAAATAATTCACAAAATGTCACCA-TT
* *
1249065 TTCAAAATAATTCACAAAATGTCA-CTTT
1 TTAAAAATAATTCACAAAATGTCACCATT
* *
1249093 TTCAAAATAATTCCCAAAATGTCAC
1 TTAAAAATAATTCACAAAATGTCAC
1249118 TGGGTCGATT
Statistics
Matches: 119, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
28 26 0.22
29 70 0.59
30 23 0.19
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (29 bp):
TTAAAAATAATTCACAAAATGTCACCATT
Found at i:1249073 original size:59 final size:56
Alignment explanation
Indices: 1248948--1249117 Score: 189
Period size: 59 Copynumber: 2.9 Consensus size: 56
1248938 ATCAACTTTA
* *
1248948 TTAAAAATAATTACCAAAATATCACCATTTTACAAATAATTCACAAAATGTCATCGTT
1 TTAAAAATAATTACCAAAATGTCACC-TTTTAAAAATAATTCACAAAATGTCA-CGTT
* * * *
1249006 TTAAAAATAATTACCAGAATGTCACCGTTTCTAAAAAAAATTCTCAAAATGTCACATTT
1 TTAAAAATAATTACCAAAATGTCACC-TTT-TAAAAATAATTCACAAAATGTCAC-GTT
* * * *
1249065 TTCAAAATAATT-CACAAAATGTCACTTTTTCAAAATAATTCCCAAAATGTCAC
1 TTAAAAATAATTAC-CAAAATGTCACCTTTTAAAAATAATTCACAAAATGTCAC
1249118 TGGGTCGATT
Statistics
Matches: 96, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
57 21 0.22
58 32 0.33
59 43 0.45
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (56 bp):
TTAAAAATAATTACCAAAATGTCACCTTTTAAAAATAATTCACAAAATGTCACGTT
Found at i:1249075 original size:88 final size:87
Alignment explanation
Indices: 1248949--1249117 Score: 234
Period size: 88 Copynumber: 1.9 Consensus size: 87
1248939 TCAACTTTAT
*
1248949 TAAAAATAATTACCAAAATATCACCATTTTACAAATAATTCACAAAATGTCATCGTTTTAAAAAT
1 TAAAAAAAATTACCAAAATATCACCATTTTACAAATAATTCACAAAATGTCA-CGTTTTAAAAAT
*
1249014 AATTACCAGAATGTCACCGTTTC
65 AATTACCAAAATGTCACCGTTTC
* * * *
1249037 TAAAAAAAATT-CTCAAAATGTCA-CATTTTTCAAAATAATTCACAAAATGTCACTTTTTCAAAA
1 TAAAAAAAATTAC-CAAAATATCACCATTTTAC-AAATAATTCACAAAATGTCACGTTTTAAAAA
*
1249100 TAATTCCCAAAATGTCAC
64 TAATTACCAAAATGTCAC
1249118 TGGGTCGATT
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
87 33 0.46
88 39 0.54
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (87 bp):
TAAAAAAAATTACCAAAATATCACCATTTTACAAATAATTCACAAAATGTCACGTTTTAAAAATA
ATTACCAAAATGTCACCGTTTC
Found at i:1256559 original size:58 final size:57
Alignment explanation
Indices: 1256497--1256695 Score: 215
Period size: 58 Copynumber: 3.4 Consensus size: 57
1256487 ATCACCTTTA
* *
1256497 TTAAAAATAATTATCAAAATTTCA-T-TGTTTTACAAATAATTCAAAAAATGTCATCGTT
1 TTAAAAATAATTACCAAAATGTCACTAT-TTTTA-AAATAATTCAAAAAATGTCA-CGTT
* * *
1256555 TTAAAAATAATTACCAGAATGTCACTATTTTTAAAATAATTCCAAAAATGTCACTTT
1 TTAAAAATAATTACCAAAATGTCACTATTTTTAAAATAATTCAAAAAATGTCACGTT
* * ** *
1256612 TTTAAAATAATTCCCAAAATGTCAC-ATTTTTTCAAAATAATTCCCAAAATGTCACCTT
1 TTAAAAATAATTACCAAAATGTCACTA-TTTTT-AAAATAATTCAAAAAATGTCACGTT
* *
1256670 TTCCAAAATAATTCCCAAAATGTCAC
1 TT-AAAAATAATTACCAAAATGTCAC
1256696 CGGGTCGGGT
Statistics
Matches: 125, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
56 1 0.01
57 30 0.24
58 65 0.52
59 28 0.22
60 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.36
Consensus pattern (57 bp):
TTAAAAATAATTACCAAAATGTCACTATTTTTAAAATAATTCAAAAAATGTCACGTT
Found at i:1256603 original size:87 final size:86
Alignment explanation
Indices: 1256475--1256695 Score: 216
Period size: 87 Copynumber: 2.5 Consensus size: 86
1256465 CACATTCGAA
* * ** * *
1256475 AATTACAAAAATATCACCTTTATTAAAAATAATTATC-AAAATTTCA-TTGTTTTACAAATAATT
1 AATTACCAAAATGTCACCTTT-TCCAAAATAATT-CCAAAAATGTCACTT-TTTTA-AAATAATT
1256538 CAAAAAATGTCATC-GTTTTAAAAAT
62 CAAAAAATGTCA-CAGTTTTAAAAAT
* ** **
1256563 AATTACCAGAATGTCA-CTATTTTTAAAATAATTCCAAAAATGTCACTTTTTTAAAATAATTCCC
1 AATTACCAAAATGTCACCT-TTTCCAAAATAATTCCAAAAATGTCACTTTTTTAAAATAATTCAA
* *
1256627 AAAATGTCACATTTTTTCAAAAT
65 AAAATGTCACA-GTTTTAAAAAT
* *
1256650 AATTCCCAAAATGTCACCTTTTCCAAAATAATTCCCAAAATGTCAC
1 AATTACCAAAATGTCACCTTTTCCAAAATAATTCCAAAAATGTCAC
1256696 CGGGTCGGGT
Statistics
Matches: 112, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
85 1 0.01
86 19 0.17
87 73 0.65
88 19 0.17
ACGTcount: A:0.43, C:0.17, G:0.04, T:0.36
Consensus pattern (86 bp):
AATTACCAAAATGTCACCTTTTCCAAAATAATTCCAAAAATGTCACTTTTTTAAAATAATTCAAA
AAATGTCACAGTTTTAAAAAT
Found at i:1256696 original size:29 final size:29
Alignment explanation
Indices: 1256482--1256696 Score: 195
Period size: 29 Copynumber: 7.4 Consensus size: 29
1256472 GAAAATTACA
* * **
1256482 AAAATATCACCTTTATTAAAAATAATTATC
1 AAAATGTCACCTTT-TTCAAAATAATTCCC
* * **
1256512 AAAATTTCA--TTGTTTTACAAATAATTCAA
1 AAAATGTCACCTT-TTTCA-AAATAATTCCC
* * * *
1256541 AAAATGTCATCGTTTTAAAAATAATTACC
1 AAAATGTCACCTTTTTCAAAATAATTCCC
* * *
1256570 AGAATGTCA-CTATTTTTAAAATAATTCCA
1 AAAATGTCACCT-TTTTCAAAATAATTCCC
*
1256599 AAAATGTCA-CTTTTTTAAAATAATTCCC
1 AAAATGTCACCTTTTTCAAAATAATTCCC
*
1256627 AAAATGTCACATTTTTTCAAAATAATTCCC
1 AAAATGTCAC-CTTTTTCAAAATAATTCCC
*
1256657 AAAATGTCACCTTTTCCAAAATAATTCCC
1 AAAATGTCACCTTTTTCAAAATAATTCCC
1256686 AAAATGTCACC
1 AAAATGTCACC
1256697 GGGTCGGGTC
Statistics
Matches: 156, Mismatches: 22, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
28 31 0.20
29 85 0.54
30 39 0.25
31 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.04, T:0.36
Consensus pattern (29 bp):
AAAATGTCACCTTTTTCAAAATAATTCCC
Found at i:1264513 original size:2 final size:2
Alignment explanation
Indices: 1264506--1264534 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1264496 GCTTAGTGTT
1264506 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 T
1264535 GGGATTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1265438 original size:7 final size:8
Alignment explanation
Indices: 1265419--1265455 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
1265409 GTAATTTACT
1265419 TTTTTCCC
1 TTTTTCCC
1265427 TTTTTCCC
1 TTTTTCCC
1265435 TTTTTCCC
1 TTTTTCCC
*
1265443 TTTTCCCC
1 TTTTTCCC
1265451 TTTTT
1 TTTTT
1265456 TGTCATCCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTTTCCC
Found at i:1269809 original size:23 final size:19
Alignment explanation
Indices: 1269794--1269831 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1269784 TATACATATG
1269794 AAAAGAAAGAAAATATAAAT
1 AAAA-AAAGAAAATATAAAT
*
1269814 AAAAAATGAAAATATAAA
1 AAAAAAAGAAAATATAAA
1269832 AAACATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (19 bp):
AAAAAAAGAAAATATAAAT
Found at i:1271221 original size:79 final size:81
Alignment explanation
Indices: 1271123--1271280 Score: 221
Period size: 79 Copynumber: 2.0 Consensus size: 81
1271113 TTTTGTTGAC
* * * *
1271123 AGATAACCCTTCTCGCCTTGAGCTATGCTGTGAATGATGTG-CCTTG-AGCTGAATGGAATTGAA
1 AGATAACCCTTATAGCCTTGAGCTATGCTGTAAATGATGTGCCCTTGAAGCTGAATGGAATCGAA
*
1271186 CTCTAAGGTCTTTGGT
66 CTCGAAGGTCTTTGGT
* * * *
1271202 AGATAACCCTTATAGCCTTGAGTTATGCTGTAAATGATGTGCCCTTGAAGCTGAGTGTAGTCGAA
1 AGATAACCCTTATAGCCTTGAGCTATGCTGTAAATGATGTGCCCTTGAAGCTGAATGGAATCGAA
1271267 CTCGAAGGTCTTTG
66 CTCGAAGGTCTTTG
1271281 TGTTTCAAGA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
79 37 0.54
80 5 0.07
81 26 0.38
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (81 bp):
AGATAACCCTTATAGCCTTGAGCTATGCTGTAAATGATGTGCCCTTGAAGCTGAATGGAATCGAA
CTCGAAGGTCTTTGGT
Found at i:1271384 original size:33 final size:34
Alignment explanation
Indices: 1271277--1271396 Score: 208
Period size: 34 Copynumber: 3.6 Consensus size: 34
1271267 CTCGAAGGTC
1271277 TTTGTGTTTCAAGAGAAAC-ATTTTCAAAGGTTTT
1 TTTGTGTTTCAAGAGAAACGA-TTTCAAAGGTTTT
1271311 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
*
1271345 TTTGTGTTTCAAGAGAAACGGTTTCAAAGG-TTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
1271378 TTTGTGTTTCAAGAGAAAC
1 TTTGTGTTTCAAGAGAAAC
1271397 TGTCTCCAGG
Statistics
Matches: 84, Mismatches: 1, Indels: 3
0.95 0.01 0.03
Matches are distributed among these distances:
33 22 0.26
34 61 0.73
35 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (34 bp):
TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
Found at i:1271429 original size:37 final size:36
Alignment explanation
Indices: 1271382--1271737 Score: 339
Period size: 36 Copynumber: 10.1 Consensus size: 36
1271372 AGGTTTTTTG
* * *
1271382 TGTTTCAAGAGAAACTGTCTCCAGGGAGGCAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* ***
1271419 TGTTTCAAGAGAAACATAT-TC-A-A-AGA-TTGA--
1 TGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAATT
1271449 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * **
1271486 TATTTCAAGGGAAACAATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1271522 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * *
1271559 AGCTCCAAAAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
1271595 TGTTTCAAG-GAAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
* *
1271624 TGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
1271660 TGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1271696 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
1271733 TGTTT
1 TGTTT
1271738 TGAGTAAATT
Statistics
Matches: 262, Mismatches: 35, Indels: 44
0.77 0.10 0.13
Matches are distributed among these distances:
28 1 0.00
29 20 0.08
30 19 0.07
31 2 0.01
32 3 0.01
33 6 0.02
34 3 0.01
35 2 0.01
36 117 0.45
37 87 0.33
38 2 0.01
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:1271539 original size:73 final size:73
Alignment explanation
Indices: 1271449--1271737 Score: 323
Period size: 73 Copynumber: 4.1 Consensus size: 73
1271439 CAAAGATTGA
* *
1271449 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTATTTCAAGGGAAACAATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTATTTCAAGAGAAACAGTCTCAAGAGAG
1271514 ACAAAATT
66 ACAAAATT
* * * * *
1271522 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC-TTAGCTCCAAAAGAAACTGTCTCAAGGGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTA-TTTCAAGAGAAACAGTCTCAAGAGA
1271586 GACAAAATT
65 GACAAAATT
* * * *
1271595 TGTTTCAAG-GAAAACATAT-TC-A-A-AG-----ATTTTGTTTCAAGGGAAACAGTCTCAAGAG
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAACTTTATTTCAAGAGAAACAGTCTCAAGAG
1271650 AGACAAAATT
64 AGACAAAATT
* * * *
1271660 TGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTATTTCAAGAGAAACAGTCTCAAGAGAG
1271724 ACAAAACTT
66 ACAAAA-TT
1271733 TGTTT
1 TGTTT
1271738 TGAGTAAATT
Statistics
Matches: 181, Mismatches: 20, Indels: 30
0.78 0.09 0.13
Matches are distributed among these distances:
64 1 0.01
65 44 0.24
66 4 0.02
67 1 0.01
68 2 0.01
70 2 0.01
71 1 0.01
72 39 0.22
73 85 0.47
74 2 0.01
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.25
Consensus pattern (73 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTATTTCAAGAGAAACAGTCTCAAGAGAG
ACAAAATT
Found at i:1271663 original size:138 final size:138
Alignment explanation
Indices: 1271488--1271737 Score: 412
Period size: 138 Copynumber: 1.8 Consensus size: 138
1271478 CAAAACTTTA
*
1271488 TTTCAAGGGAAACAATCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
1 TTTCAAGGGAAACAATCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAGTCTCAAGAGAGACA
*
1271553 AAACTTAGCTCCAAAAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGAAAACATATTCA
66 AAA-TTAGCTCCAAAAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGAAAACATATTCA
1271617 AAGATTTTG
130 AAGATTTTG
* *
1271626 TTTCAAGGGAAACAGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAGTCTCAAGAGAGACA
1 TTTCAAGGGAAACAATCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAGTCTCAAGAGAGACA
* * * *
1271691 AAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
66 AAATTAGCTCCAAAAGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
1271738 TGAGTAAATT
Statistics
Matches: 103, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
137 31 0.30
138 72 0.70
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (138 bp):
TTTCAAGGGAAACAATCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAGTCTCAAGAGAGACA
AAATTAGCTCCAAAAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGAAAACATATTCAA
AGATTTTG
Found at i:1271705 original size:21 final size:21
Alignment explanation
Indices: 1271643--1271707 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
1271633 GGAAACAGTC
1271643 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
* *
1271664 TCAAG-G-GA-AACA---GTC
1 TCAAGAGAGACAAAATTTGTT
1271679 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
1271700 TCAAGAGA
1 TCAAGAGA
1271708 AACTGTCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 7 0.21
16 1 0.03
17 2 0.06
18 6 0.18
19 2 0.06
20 1 0.03
21 15 0.44
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:1271753 original size:37 final size:34
Alignment explanation
Indices: 1271634--1271762 Score: 134
Period size: 36 Copynumber: 3.6 Consensus size: 34
1271624 TGTTTCAAGG
* *
1271634 GAAACAGTCTCAAGAGAGACAAAATTTGTTTCAAGG
1 GAAATAGTCTCAAGAGAGACAAAATTTGTTT--AGA
*
1271670 GAAACAGTCTCAAGAGAGACAAAATTTGTTTCAAGA
1 GAAATAGTCTCAAGAGAGACAAAATTTGTTT--AGA
*
1271706 GAAACT-GTCTCAAGAGAGACAAAACTTTGTTTTGA
1 GAAA-TAGTCTCAAGAGAGACAAAA-TTTGTTTAGA
*
1271741 GTAAATTAGTCTCAAGCGAGAC
1 G-AAA-TAGTCTCAAGAGAGAC
1271763 GACCCTTTGT
Statistics
Matches: 84, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
35 3 0.04
36 61 0.73
37 20 0.24
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (34 bp):
GAAATAGTCTCAAGAGAGACAAAATTTGTTTAGA
Found at i:1271756 original size:174 final size:177
Alignment explanation
Indices: 1271391--1271732 Score: 584
Period size: 174 Copynumber: 1.9 Consensus size: 177
1271381 GTGTTTCAAG
* *
1271391 AGAAACTGTCTCCAGGGAGGCAAAATTTTGTTTCAAGAGAAACATATTCAAAGATTGATGTTTCA
1 AGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACATATTCAAAGATTGATGTTTCA
*
1271456 AGAGAAACTGTCTCAAGAGAGACAAAACTTTATTTCAAGGGAAACAATCTCAAGAGAGACAAAAT
66 AGAGAAACAGTCTCAAGAGAGACAAAACTTTATTTCAAGGGAAACAATCTCAAGAGAGACAAAAT
1271521 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGCTCCAAA
131 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGCTCCAAA
*
1271568 AGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAG-GAAAACATATTCAAAGATT-TTGTTTC
1 AGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAG-AAACATATTCAAAGATTGATGTTTC
* * *
1271630 AAGGGAAACAGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAA
65 AAGAGAAACAGTCTCAAGAGAGACAAAACTTTATTTCAAGGGAAACAATCTCAAGAGAGACAAAA
1271694 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
130 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1271733 TGTTTTGAGT
Statistics
Matches: 157, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
174 73 0.46
175 33 0.21
176 28 0.18
177 23 0.15
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (177 bp):
AGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACATATTCAAAGATTGATGTTTCA
AGAGAAACAGTCTCAAGAGAGACAAAACTTTATTTCAAGGGAAACAATCTCAAGAGAGACAAAAT
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGCTCCAAA
Found at i:1273424 original size:83 final size:86
Alignment explanation
Indices: 1273293--1273519 Score: 282
Period size: 95 Copynumber: 2.6 Consensus size: 86
1273283 GGCTAGCTGA
* *
1273293 ATCCATAAAGTCGGGGTGTTTAACCAATTGCTCTAGAGGGACAGCTCAA-TAT-GTA-AA-CACC
1 ATCCATAAAG-CGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATTATAGTATAATCACC
* *
1273354 TTTATCAGGTTAGCTGAATCTT
65 TTTATCAGGCTAGCTGAATATT
*
1273376 ATCCATAAAGCGGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATAGTA
1 ATCCATAAAGC-GGGGCGTTTAACCAATTGCTCTAGAGGGACAACTC-A-----A-T-TATAGTA
1273441 TAATCACCTTTATCAGGCTAGCTGAATATT
57 TAATCACCTTTATCAGGCTAGCTGAATATT
1273471 ATCCATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA
1 ATCCATAAAGC-GGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA
1273520 GCTTTATTGT
Statistics
Matches: 124, Mismatches: 7, Indels: 20
0.82 0.05 0.13
Matches are distributed among these distances:
82 1 0.01
83 42 0.34
84 1 0.01
89 2 0.02
92 3 0.02
93 3 0.02
94 3 0.02
95 69 0.56
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (86 bp):
ATCCATAAAGCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATTATAGTATAATCACCT
TTATCAGGCTAGCTGAATATT
Found at i:1273513 original size:95 final size:94
Alignment explanation
Indices: 1273341--1273536 Score: 329
Period size: 95 Copynumber: 2.1 Consensus size: 94
1273331 GGACAGCTCA
* * * *
1273341 ATATGTAAACACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGCGGGGGCGTTTAACCAATTG
1 ATATATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCGGGGGCGTTTAACCAATTG
*
1273406 CTTTAGAGGGACAACTCAAGCTTTATTGT
66 CTCTAGAGGGACAACTCAAGCTTTATTGT
*
1273435 ATAGTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCTGGGGCGTTTAACCAATT
1 ATA-TATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCGGGGGCGTTTAACCAATT
1273500 GCTCTAGAGGGACAACTCAAGCTTTATTGT
65 GCTCTAGAGGGACAACTCAAGCTTTATTGT
1273530 ATATATA
1 ATATATA
1273537 TATAATATTA
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
94 7 0.07
95 88 0.93
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (94 bp):
ATATATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCGGGGGCGTTTAACCAATTG
CTCTAGAGGGACAACTCAAGCTTTATTGT
Found at i:1274168 original size:23 final size:23
Alignment explanation
Indices: 1274138--1274189 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
1274128 AATACAACCA
* * *
1274138 AACTCCTGATGGATGCCCTAATC
1 AACTCCTGAAGGATACCCCAATC
1274161 AACTCCTGAAGGATACCCCAATC
1 AACTCCTGAAGGATACCCCAATC
1274184 AACTCC
1 AACTCC
1274190 CGATCAGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.35, G:0.13, T:0.21
Consensus pattern (23 bp):
AACTCCTGAAGGATACCCCAATC
Found at i:1277619 original size:19 final size:20
Alignment explanation
Indices: 1277576--1277624 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1277566 AAAATTAAAA
1277576 AAATAACAT-ATATATATAT
1 AAATAACATAATATATATAT
* *
1277595 ATATAACATAATATCTA-AT
1 AAATAACATAATATATATAT
*
1277614 AAATAAAATAA
1 AAATAACATAA
1277625 AAAAGAGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATAACATAATATATATAT
Found at i:1281962 original size:13 final size:13
Alignment explanation
Indices: 1281944--1281968 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1281934 GGGTACCTAA
1281944 AAAATTAAAATAG
1 AAAATTAAAATAG
1281957 AAAATTAAAATA
1 AAAATTAAAATA
1281969 AGTAAAAACG
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:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
AAAATTAAAATAG
Found at i:1291171 original size:15 final size:17
Alignment explanation
Indices: 1291153--1291191 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
1291143 AGTTTTAAAA
*
1291153 TTTTTTATTAT-TA-AT
1 TTTTTTATAATATATAT
1291168 TTTTTTATAATATATAT
1 TTTTTTATAATATATAT
1291185 TTTTTTA
1 TTTTTTA
1291192 AAAAGTTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.48
16 2 0.10
17 9 0.43
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTTATAATATATAT
Found at i:1292966 original size:18 final size:18
Alignment explanation
Indices: 1292943--1292978 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1292933 GGATTACATA
1292943 CTTCAGAATAAATATATG
1 CTTCAGAATAAATATATG
*
1292961 CTTCAGAATTAATATATG
1 CTTCAGAATAAATATATG
1292979 TCTAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (18 bp):
CTTCAGAATAAATATATG
Found at i:1298473 original size:18 final size:18
Alignment explanation
Indices: 1298450--1298487 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1298440 ATCAGATTAC
1298450 ATGCTTCAGAATAAATAT
1 ATGCTTCAGAATAAATAT
*
1298468 ATGCTTCAGAATTAATAT
1 ATGCTTCAGAATAAATAT
1298486 AT
1 AT
1298488 AACTCGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (18 bp):
ATGCTTCAGAATAAATAT
Found at i:1301080 original size:24 final size:25
Alignment explanation
Indices: 1301051--1301101 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
1301041 AATATTTTTG
* *
1301051 TCCTC-TAAAATTTTATAAATTGAT
1 TCCTCTTAAAATTCTAAAAATTGAT
*
1301075 TCCTCTTAAAATTCTAAAAATTTAT
1 TCCTCTTAAAATTCTAAAAATTGAT
1301100 TC
1 TC
1301102 TAAAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.37, C:0.16, G:0.02, T:0.45
Consensus pattern (25 bp):
TCCTCTTAAAATTCTAAAAATTGAT
Found at i:1301287 original size:76 final size:76
Alignment explanation
Indices: 1301161--1301315 Score: 292
Period size: 76 Copynumber: 2.0 Consensus size: 76
1301151 CTCTTAAACC
*
1301161 ACACTTTTCCTCTTGCAGTTAAAGGAAGATTAAAGAGTATGCAATGAAGCTATTATAATAAAAAG
1 ACACTTTTCCCCTTGCAGTTAAAGGAAGATTAAAGAGTATGCAATGAAGCTATTATAATAAAAAG
1301226 CTCAAGGGACA
66 CTCAAGGGACA
1301237 ACACTTTTCCCCTTGCAGTTAAAGGAAGATTAAAGAGTATGCAATGAAGCTATTATAATAAAAAG
1 ACACTTTTCCCCTTGCAGTTAAAGGAAGATTAAAGAGTATGCAATGAAGCTATTATAATAAAAAG
*
1301302 TTCAAGGGACA
66 CTCAAGGGACA
1301313 ACA
1 ACA
1301316 TCTCCCTAGG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (76 bp):
ACACTTTTCCCCTTGCAGTTAAAGGAAGATTAAAGAGTATGCAATGAAGCTATTATAATAAAAAG
CTCAAGGGACA
Found at i:1302984 original size:23 final size:24
Alignment explanation
Indices: 1302946--1302990 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
1302936 AAAATATTAA
1302946 TTATTAATATATTTAA-AATATGT
1 TTATTAATATATTTAATAATATGT
1302969 TTATTAATAT-TGTTAATAATAT
1 TTATTAATATAT-TTAATAATAT
1302991 AATATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 1 0.05
23 14 0.70
24 5 0.25
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (24 bp):
TTATTAATATATTTAATAATATGT
Found at i:1302996 original size:23 final size:24
Alignment explanation
Indices: 1302970--1303016 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
1302960 AAAATATGTT
*
1302970 TATTAATATTGTT-AATAATATAA
1 TATTAATATTATTAAATAATATAA
1302993 TATTAATATTATTACAATAATATA
1 TATTAATATTATTA-AATAATATA
1303017 CTCAATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.57
25 9 0.43
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (24 bp):
TATTAATATTATTAAATAATATAA
Found at i:1326338 original size:16 final size:16
Alignment explanation
Indices: 1326317--1326347 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1326307 TAATAAATAA
1326317 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1326333 ACGAACATAAACGAA
1 ACGAACATAAACGAA
1326348 ATTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1326765 original size:24 final size:26
Alignment explanation
Indices: 1326736--1326785 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
1326726 CCTTTATTCA
*
1326736 AACATAAATGAACATA-AAT-GAACG
1 AACATAAACGAACATATAATCGAACG
1326760 AACATAAACGAACATATAATCGAACG
1 AACATAAACGAACATATAATCGAACG
1326786 TTTACAAACG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 15 0.65
25 3 0.13
26 5 0.22
ACGTcount: A:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (26 bp):
AACATAAACGAACATATAATCGAACG
Found at i:1328816 original size:14 final size:15
Alignment explanation
Indices: 1328778--1328819 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1328768 ATTGGAACTC
1328778 GAAAA-TGAATTACT
1 GAAAATTGAATTACT
* *
1328792 GGAATTTGAATT-CT
1 GAAAATTGAATTACT
1328806 GAAAATTGAATTAC
1 GAAAATTGAATTAC
1328820 ATTTCTAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (15 bp):
GAAAATTGAATTACT
Found at i:1328860 original size:14 final size:14
Alignment explanation
Indices: 1328827--1328861 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1328817 TACATTTCTA
*
1328827 GAAAACGTTTTCCG
1 GAAAATGTTTTCCG
1328841 GAAAATGTTTTCCG
1 GAAAATGTTTTCCG
*
1328855 TAAAATG
1 GAAAATG
1328862 AATTACATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.31
Consensus pattern (14 bp):
GAAAATGTTTTCCG
Found at i:1328975 original size:16 final size:16
Alignment explanation
Indices: 1328954--1329001 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
1328944 AGAGTTTTTT
1328954 AAATATTATTTATTAA
1 AAATATTATTTATTAA
* *
1328970 AAATATTAAATATAATAA
1 AAATATT--ATTTATTAA
1328988 ATAATATTATTTAT
1 A-AATATTATTTAT
1329002 CATAAAACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
16 7 0.28
17 4 0.16
18 8 0.32
19 6 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATATTATTTATTAA
Found at i:1329006 original size:19 final size:17
Alignment explanation
Indices: 1328954--1329008 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 17
1328944 AGAGTTTTTT
1328954 AAATATTATTTAT-TAA
1 AAATATTATTTATATAA
**
1328970 AAATATTAAATATAATAA
1 AAATATTATTTAT-ATAA
1328988 ATAATATTATTTATCATAA
1 A-AATATTATTTAT-ATAA
1329007 AA
1 AA
1329009 CTTAATATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 11 0.35
18 5 0.16
19 15 0.48
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATATTATTTATATAA
Found at i:1329116 original size:29 final size:28
Alignment explanation
Indices: 1329045--1329117 Score: 87
Period size: 30 Copynumber: 2.6 Consensus size: 28
1329035 AAATAATTTA
1329045 TTTATTATT-AAATATTATTTTTATAAT
1 TTTATTATTAAAATATTATTTTTATAAT
* *
1329072 TTTATTAATAACAATATTAATTTTTGTATAT
1 TTTATTATTAA-AATATT-ATTTTTATA-AT
1329103 TTTA-TATTAAAATAT
1 TTTATTATTAAAATAT
1329118 ATTATATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
27 8 0.21
28 1 0.03
29 11 0.28
30 13 0.33
31 6 0.15
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (28 bp):
TTTATTATTAAAATATTATTTTTATAAT
Found at i:1329248 original size:19 final size:20
Alignment explanation
Indices: 1329196--1329248 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
1329186 TTAAATATCT
1329196 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
1329215 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
1329236 TTATTAAATATAT
1 TTATTAAATATAT
1329249 AAAACATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 6 0.21
22 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:1329261 original size:30 final size:27
Alignment explanation
Indices: 1329204--1329293 Score: 80
Period size: 28 Copynumber: 3.3 Consensus size: 27
1329194 CTTTATTAAA
1329204 ATATTATTTAAATATATAAATAATATTAT
1 ATATTA-TTAAATATATAAA-AATATTAT
1329233 -TCATTATTAAATATATAAAACATTTATTAT
1 AT-ATTATTAAATATATAAAA-A--TATTAT
*
1329263 ATATTATT-AA-A-ATAAAAATATAAT
1 ATATTATTAAATATATAAAAATATTAT
*
1329287 ATCTTAT
1 ATATTAT
1329294 ATTATATTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
24 11 0.20
26 1 0.02
27 7 0.13
28 16 0.30
29 6 0.11
30 12 0.22
31 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (27 bp):
ATATTATTAAATATATAAAAATATTAT
Found at i:1329317 original size:18 final size:18
Alignment explanation
Indices: 1329290--1329336 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
1329280 ATATAATATC
* * *
1329290 TTATATTATATTTTATTA
1 TTATAATATAATTGATTA
1329308 TTATAATATAATTGATTA
1 TTATAATATAATTGATTA
*
1329326 TT-TTATATAAT
1 TTATAATATAAT
1329337 ATTAAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TTATAATATAATTGATTA
Found at i:1329616 original size:42 final size:42
Alignment explanation
Indices: 1329565--1329684 Score: 197
Period size: 42 Copynumber: 2.9 Consensus size: 42
1329555 ATGAATTACA
*
1329565 TTCCGGAAAATC-AATTACGTGAAACAAACATGGGAAAACATT
1 TTCCGGAAAA-CGAATTACGTGAAACAAACACGGGAAAACATT
*
1329607 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
1329649 TTTCGGAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
1329685 TTCGGGGAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
41 1 0.01
42 72 0.99
ACGTcount: A:0.46, C:0.17, G:0.18, T:0.18
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:1330696 original size:5 final size:5
Alignment explanation
Indices: 1330686--1330717 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
1330676 TTTACCCTAA
1330686 ACCCG ACCCG ACCCG ACCCG ACCCG AACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG -ACCCG A
1330718 AATTTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.25, C:0.56, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:1332983 original size:25 final size:25
Alignment explanation
Indices: 1332955--1333006 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
1332945 AAAATTATAT
*
1332955 TGTCATGAGTTGTTAAGACCATCGA
1 TGTCATGAGTTATTAAGACCATCGA
*
1332980 TGTCGTGAGTTATTAAGACCATCGA
1 TGTCATGAGTTATTAAGACCATCGA
1333005 TG
1 TG
1333007 AAGTGGGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (25 bp):
TGTCATGAGTTATTAAGACCATCGA
Found at i:1341219 original size:3 final size:3
Alignment explanation
Indices: 1341211--1341257 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
1341201 GGATTTTAAC
* * *
1341211 TTA TTA TTA TTG TTG TTG TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1341258 ATAAATTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1343639 original size:17 final size:17
Alignment explanation
Indices: 1343617--1343650 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1343607 AAACGCAGAC
1343617 CAATTTTTGTCTTAAAA
1 CAATTTTTGTCTTAAAA
*
1343634 CAATTTTTTTCTTAAAA
1 CAATTTTTGTCTTAAAA
1343651 TTGTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.50
Consensus pattern (17 bp):
CAATTTTTGTCTTAAAA
Found at i:1346324 original size:31 final size:31
Alignment explanation
Indices: 1346286--1346439 Score: 247
Period size: 31 Copynumber: 5.0 Consensus size: 31
1346276 GAGTCGAGGG
*
1346286 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGA
** *
1346317 TTACCTATGTTCTTCAGG-ACATATAAACTGT
1 TTACCTATGTTCTTC-GGAACATATGGACTGA
*
1346348 TTACCTATGTTCTTCGGAACGTATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGA
1346379 TTACCTATGTTCTTCGGAACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGA
1346410 TTACCTATGTTCTTCGGAACATATGGACTG
1 TTACCTATGTTCTTCGGAACATATGGACTG
1346440 GTCCTTTGGG
Statistics
Matches: 113, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
30 2 0.02
31 109 0.96
32 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.36
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGA
Found at i:1349204 original size:15 final size:15
Alignment explanation
Indices: 1349186--1349234 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 15
1349176 CAAAGAAATA
1349186 AAGAAAAAAGCAAAG
1 AAGAAAAAAGCAAAG
1349201 AAGAAAAAAAAGCAAAG
1 AAG--AAAAAAGCAAAG
*
1349218 AAAAAATAAAG-AAAG
1 AAGAAA-AAAGCAAAG
1349233 AA
1 AA
1349235 AATATGACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 12 0.40
16 4 0.13
17 14 0.47
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.02
Consensus pattern (15 bp):
AAGAAAAAAGCAAAG
Found at i:1349235 original size:15 final size:15
Alignment explanation
Indices: 1349168--1349236 Score: 70
Period size: 15 Copynumber: 4.4 Consensus size: 15
1349158 CAAAGCAAAG
1349168 AGAAAAAACAAAG-AA
1 AGAAAAAA-AAAGCAA
*
1349183 ATAAAGAAAAAAGCAA
1 AGAAA-AAAAAAGCAA
1349199 AGAAGAAAAAAAAGCAA
1 AG-A-AAAAAAAAGCAA
1349216 AGAAAAAATAAAG-AA
1 AGAAAAAA-AAAGCAA
1349231 AGAAAA
1 AGAAAA
1349237 TATGACAAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
15 21 0.45
16 11 0.23
17 13 0.28
18 2 0.04
ACGTcount: A:0.78, C:0.04, G:0.14, T:0.03
Consensus pattern (15 bp):
AGAAAAAAAAAGCAA
Found at i:1352038 original size:102 final size:99
Alignment explanation
Indices: 1351875--1352115 Score: 231
Period size: 102 Copynumber: 2.4 Consensus size: 99
1351865 ACATGAACAC
* * * *
1351875 TTGAGATTGTTTCTCTTAAAAAAATTTGTCTCACTTGAGACAGTTTCCCCTACGAATACAAATTT
1 TTGAGATTGTTTCTCTCAAAAAAATTTGTCTCACTTGAGACAG-ATCCCCTACGAACACAAATTG
* *
1351940 TGAAATTGTTT-CACTTGAAACAAAATTTTCATCAT
65 TGAAATT-TTTGCACCTAAAACAAAATTTTCATCAT
* * * *
1351975 TTGAGCTTGTTTCTCTCAAAACAAATTTTGTTTCGCTTGAGACA-ATCCTCCTTCGAAACACAAA
1 TTGAGATTGTTTCTCTCAAAA-AAA-TTTGTCTCACTTGAGACAGATCC-CCTACG-AACACAAA
* *
1352039 TTGTGAAATTTTTGCACCTAAAACAAAATTGATC-TCAC
62 TTGTGAAATTTTTGCACCTAAAACAAAATT-TTCATCAT
* * *
1352077 TTGAGATAGTCTTC-CT-AAAAAAGTGTTGTCTCGCTTGAG
1 TTGAGATTGT-TTCTCTCAAAAAAAT-TTGTCTCACTTGAG
1352116 GCAGTTTCCC
Statistics
Matches: 117, Mismatches: 16, Indels: 16
0.79 0.11 0.11
Matches are distributed among these distances:
99 1 0.01
100 37 0.32
101 15 0.13
102 59 0.50
103 5 0.04
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (99 bp):
TTGAGATTGTTTCTCTCAAAAAAATTTGTCTCACTTGAGACAGATCCCCTACGAACACAAATTGT
GAAATTTTTGCACCTAAAACAAAATTTTCATCAT
Found at i:1352315 original size:66 final size:67
Alignment explanation
Indices: 1352096--1352800 Score: 900
Period size: 67 Copynumber: 10.6 Consensus size: 67
1352086 TCTTCCTAAA
* * * * * *
1352096 AAAGTGTTGTCTCGCTTGAGGCAGTTTCCCTAGAAACATAAACCTTTGAGATCGTTTCACTTGAA
1 AAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTTGAA
1352161 AC
66 AC
* * ** ** *
1352163 AAATTTTTGTCTCTCTACAGACAGTTTCTCTTGAAACATAAACCTTTGAGATCATTTATCTTGAA
1 AAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTTGAA
1352228 AC
66 AC
* * * * * * * *
1352230 AAAGTTCTGTCTCCCTTGAGACA-ATTCTCCTGACACATAAAACCATTGAAATTATTTCTCTTGA
1 AAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACAT-AAACCTTTGAGATTGTTTCTCTTGA
1352294 AAC
65 AAC
* * *
1352297 AAA-TTTTGTCTCGTTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAAATTGTTTCTATTGAA
1 AAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTTGAA
*
1352361 AT
66 AC
* **
1352363 AAA-ATTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCAAA
1 AAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCT-TGA
*
1352427 AAA
65 AAC
* *
1352430 AAAGTTTTGTCTCGCTTGAGACAATTTCTCTTTAAACATAAACCTTTGAGATTGTTTCTCTTGAA
1 AAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTTGAA
1352495 AC
66 AC
* * * * *
1352497 AAAGTTTTGTCTCACTTGAGACATTTTCTTTTGAAACATAAACCTTTGAGATTATTTCTCTCGAA
1 AAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTTGAA
1352562 AC
66 AC
* * *
1352564 AAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTAAAACATAAACCTTTGAGATTATTTCTCTCGAA
1 AAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTTGAA
*
1352629 AT
66 AC
* * * *
1352631 AAAATTTTGTCTCGTTTGAGACATTTTCTCTTGAAACATAAACCTTTGATATTGTTTCTCTTGAA
1 AAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTTGAA
1352696 A-
66 AC
* * *
1352697 TAATTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCATTGAGATTGTTTC-CTTTGA
1 AAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTC-TTGA
1352761 AAC
65 AAC
* *
1352764 AAA-TTTTGTCTCGCTTGGGACAGTTTCTGTTGAAACA
1 AAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACA
1352801 AAATTAATCT
Statistics
Matches: 559, Mismatches: 73, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
65 1 0.00
66 198 0.35
67 306 0.55
68 54 0.10
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (67 bp):
AAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTTGAA
AC
Found at i:1352419 original size:30 final size:30
Alignment explanation
Indices: 1352310--1352422 Score: 84
Period size: 30 Copynumber: 3.6 Consensus size: 30
1352300 TTTTGTCTCG
1352310 TTTGAGACAGTTTCTCTTGAAACATAAACC
1 TTTGAGACAGTTTCTCTTGAAACATAAACC
* ** * *
1352340 TTTGAAATTGTTTCTATTGAAATA-AAATTTGTCTC
1 TTTGAGACAGTTTCTCTTGAAACATAAA-----C-C
*
1352375 GCTTGAGACAGTTTCTCTTGAAACATAAACC
1 -TTTGAGACAGTTTCTCTTGAAACATAAACC
**
1352406 TTTGAGATTGTTTCTCT
1 TTTGAGACAGTTTCTCT
1352423 CAAAAAAAAA
Statistics
Matches: 61, Mismatches: 14, Indels: 16
0.67 0.15 0.18
Matches are distributed among these distances:
29 3 0.05
30 33 0.54
31 1 0.02
32 1 0.02
34 1 0.02
35 1 0.02
36 18 0.30
37 3 0.05
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (30 bp):
TTTGAGACAGTTTCTCTTGAAACATAAACC
Found at i:1353153 original size:139 final size:139
Alignment explanation
Indices: 1352821--1353393 Score: 627
Period size: 139 Copynumber: 4.1 Consensus size: 139
1352811 CACTTGAGAT
* * * * * *
1352821 TGTTATCTCCAAATTATCCCTAAAGATGGCTAGACGTCCTCATCACATAGGAACAATATCGTCCA
1 TGTTATCTCCAAATTATCCCTAAAGACGGCTAGACATCCTCATCACGTAGAAACAATGTAGTCCA
* * *
1352886 CCGACCAAATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAAGCT-ATCAAACTTCCTCATCAC
66 CCGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCT-AAGATAACCAAACTTCCTCATCAC
*
1352950 -TAGGAACCA
130 GTAGGAACCG
* * * * * *
1352959 TGTTGTCTCTAAATTATCTCTAAATACGGCTAGACATCCTCATAACGTATG-AACAATGTAGTCG
1 TGTTATCTCCAAATTATCCCTAAAGACGGCTAGACATCCTCATCACGTA-GAAACAATGTAGTCC
* * * *
1353023 ACCGACCATATCTCCTCAACGTGTAGGAGCAGAGTCATCCTAAGATAACCAAAATTCCTCATCAC
65 ACCGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTAAGATAACCAAACTTCCTCATCAC
*
1353088 GTAGGAACTG
130 GTAGGAACCG
* * * *
1353098 TGTTGTCTCCAAATTATCCCTAAAGACGGCTATACGTCCTCATCACGTAGAAACAATGTCGTCCA
1 TGTTATCTCCAAATTATCCCTAAAGACGGCTAGACATCCTCATCACGTAGAAACAATGTAGTCCA
* * * *
1353163 ACGACCAGATCTCCTCAACGCGTATGAGCAGCT-TCATCCTCAGATAACCAGACTTCCTCATCAC
66 CCGACCAGATCTCCTCAACGCGTAGGAGCAG-TGTCATCCTAAGATAACCAAACTTCCTCATCAC
*
1353227 ATAGGAACCG
130 GTAGGAACCG
* * * * * * * *
1353237 AGTTATCTCCAAATTATCCCTAAAGATGGTTATATATCTTTATCGCGTA-AGAACAATGTCA-TC
1 TGTTATCTCCAAATTATCCCTAAAGACGGCTAGACATCCTCATCACGTAGA-AACAATGT-AGTC
* * * * * * *
1353300 CACCGACCAGATCTTCTCAACGCGTAGGAGCAGTTTCATTCTCAGACAATCAGACTTCCTCATCA
64 CACCGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTAAGATAACCAAACTTCCTCATCA
*
1353365 CGTAAGAACCG
129 CGTAGGAACCG
* *
1353376 TGTTTTCACCAAATTATC
1 TGTTATCTCCAAATTATC
1353394 TTCATATTGA
Statistics
Matches: 369, Mismatches: 58, Indels: 15
0.83 0.13 0.03
Matches are distributed among these distances:
137 4 0.01
138 108 0.29
139 257 0.70
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (139 bp):
TGTTATCTCCAAATTATCCCTAAAGACGGCTAGACATCCTCATCACGTAGAAACAATGTAGTCCA
CCGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTAAGATAACCAAACTTCCTCATCACG
TAGGAACCG
Found at i:1353642 original size:3 final size:3
Alignment explanation
Indices: 1353634--1353665 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1353624 GGGTTTTAAC
*
1353634 TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1353666 TACAGATCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1355281 original size:2 final size:2
Alignment explanation
Indices: 1355274--1355316 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1355264 TCTTTAATAC
1355274 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1355316 T
1 T
1355317 TATTATTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1357730 original size:6 final size:6
Alignment explanation
Indices: 1357719--1357764 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
1357709 GACACGTATT
* * *
1357719 ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCACG ACCAGG ACCA
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCA
1357765 TGAGCCGAGC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.30, C:0.48, G:0.17, T:0.04
Consensus pattern (6 bp):
ACCACG
Found at i:1357776 original size:5 final size:5
Alignment explanation
Indices: 1357766--1357818 Score: 54
Period size: 5 Copynumber: 10.6 Consensus size: 5
1357756 CCAGGACCAT
* * * *
1357766 GAGCC GAGCC GAGCC GAGCC GAGCC GTGCC GTA-CT GTGCC GAGCC GAGAC
1 GAGCC GAGCC GAGCC GAGCC GAGCC GAGCC G-AGCC GAGCC GAGCC GAGCC
1357816 GAG
1 GAG
1357819 ACGGACGGAC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.19, C:0.34, G:0.40, T:0.08
Consensus pattern (5 bp):
GAGCC
Found at i:1366446 original size:40 final size:39
Alignment explanation
Indices: 1366402--1366491 Score: 126
Period size: 40 Copynumber: 2.3 Consensus size: 39
1366392 TCTAGAATAT
1366402 TCTGGAGATGTGTAAAAGCTTGTGGAAGAGTACGAAATCC
1 TCTGGA-ATGTGTAAAAGCTTGTGGAAGAGTACGAAATCC
* ** *
1366442 TCTGGATATGTGTAGAAGCTTGTGGAAGAGTGTGGAATCC
1 TCTGGA-ATGTGTAAAAGCTTGTGGAAGAGTACGAAATCC
1366482 TCTGGAATGT
1 TCTGGAATGT
1366492 TCTAGAGATG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 4 0.09
40 41 0.91
ACGTcount: A:0.28, C:0.11, G:0.32, T:0.29
Consensus pattern (39 bp):
TCTGGAATGTGTAAAAGCTTGTGGAAGAGTACGAAATCC
Found at i:1366506 original size:40 final size:40
Alignment explanation
Indices: 1366402--1366508 Score: 101
Period size: 40 Copynumber: 2.7 Consensus size: 40
1366392 TCTAGAATAT
* * * *
1366402 TCTGGAGATGTGTAAAAGCTTGTGGAAGAGTACGAAATCC
1 TCTGGATATGTCTAGAAGATTGTGGAAGAGTACGAAATCC
* * ** *
1366442 TCTGGATATGTGTAGAAGCTTGTGGAAGAGTGTGGAATCC
1 TCTGGATATGTCTAGAAGATTGTGGAAGAGTACGAAATCC
1366482 TCTGGA-ATGTTCTAG-AGATGTGTGGAA
1 TCTGGATATG-TCTAGAAGAT-TGTGGAA
1366509 CCTTATGGAA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 6 0.10
40 52 0.90
ACGTcount: A:0.28, C:0.10, G:0.33, T:0.29
Consensus pattern (40 bp):
TCTGGATATGTCTAGAAGATTGTGGAAGAGTACGAAATCC
Found at i:1366547 original size:90 final size:90
Alignment explanation
Indices: 1366367--1366549 Score: 197
Period size: 90 Copynumber: 2.0 Consensus size: 90
1366357 AACTCTCTAC
* * * *
1366367 AAGCTTGTGGAAGAGTATGGAATCCTCTAGAATATTCTGGAGATGTGTAAAAGCTTGTGGAAGAG
1 AAGCTTGTGGAAGAGTATGGAATCCTCTAGAATATTCTAGAGATGTGTAAAACCTTATGGAAGAA
*** * *
1366432 TACGAAATCCTCTGGATATGTGTAG
66 TACGAAAGAATATGGATATGAGTAG
* * * ** *
1366457 AAGCTTGTGGAAGAGTGTGGAATCCTCTGGAATGTTCTAGAGATGTGTGGAACCTTATGGAATAA
1 AAGCTTGTGGAAGAGTATGGAATCCTCTAGAATATTCTAGAGATGTGTAAAACCTTATGGAAGAA
* *
1366522 TATGGAAGAATATGGA-ATTGAGTAG
66 TACGAAAGAATATGGATA-TGAGTAG
1366547 AAG
1 AAG
1366550 AGTGTAGAGT
Statistics
Matches: 75, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
89 1 0.01
90 74 0.99
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.28
Consensus pattern (90 bp):
AAGCTTGTGGAAGAGTATGGAATCCTCTAGAATATTCTAGAGATGTGTAAAACCTTATGGAAGAA
TACGAAAGAATATGGATATGAGTAG
Found at i:1369985 original size:50 final size:50
Alignment explanation
Indices: 1369931--1370075 Score: 209
Period size: 50 Copynumber: 2.9 Consensus size: 50
1369921 TGGAAGAGTT
*
1369931 TGGAATATTATGGAGATGTGTAGAAGCTTGTGGAAGAGTATGGAATCCTC
1 TGGAATATTCTGGAGATGTGTAGAAGCTTGTGGAAGAGTATGGAATCCTC
* *
1369981 TGGAATATTCTGGAGATATGTAGAAGCTTGTGGAAGAGTGTGGAATCCTC
1 TGGAATATTCTGGAGATGTGTAGAAGCTTGTGGAAGAGTATGGAATCCTC
* * * * * *
1370031 TTGAATATTCTGGAGATGTGTGGAACCTTATGGAAAAATATGGAA
1 TGGAATATTCTGGAGATGTGTAGAAGCTTGTGGAAGAGTATGGAA
1370076 GAATATGGAA
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 84 1.00
ACGTcount: A:0.31, C:0.08, G:0.30, T:0.30
Consensus pattern (50 bp):
TGGAATATTCTGGAGATGTGTAGAAGCTTGTGGAAGAGTATGGAATCCTC
Found at i:1377302 original size:16 final size:16
Alignment explanation
Indices: 1377281--1377315 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1377271 AAAGCAGAAG
1377281 CAAGAAATATACTAAA
1 CAAGAAATATACTAAA
*
1377297 CAAGAAATATACTGAA
1 CAAGAAATATACTAAA
1377313 CAA
1 CAA
1377316 TAATACCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.60, C:0.14, G:0.09, T:0.17
Consensus pattern (16 bp):
CAAGAAATATACTAAA
Found at i:1390780 original size:30 final size:30
Alignment explanation
Indices: 1390717--1390780 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
1390707 GTTGATAGCT
* * **
1390717 GTGAGTTGGTTATGGGGGTTCATGGGTTAC
1 GTGAGTTGATTATGGGGGTGCATGAATTAC
* *
1390747 GTGAGTTGATTATTGGGGTGCATGAATTGC
1 GTGAGTTGATTATGGGGGTGCATGAATTAC
1390777 GTGA
1 GTGA
1390781 TCTCATACCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.17, C:0.06, G:0.41, T:0.36
Consensus pattern (30 bp):
GTGAGTTGATTATGGGGGTGCATGAATTAC
Found at i:1398622 original size:20 final size:20
Alignment explanation
Indices: 1398597--1398665 Score: 75
Period size: 20 Copynumber: 3.2 Consensus size: 20
1398587 ATTCGACTCG
*
1398597 ACTCGACTTGAATTTTATAA
1 ACTCGACTTGAATTTCATAA
1398617 ACTCGACTTGACTCGAATTTCATAA
1 ACTCGAC-T---T-GAATTTCATAA
*
1398642 ACTCGACTCGAATTTCATAA
1 ACTCGACTTGAATTTCATAA
1398662 ACTC
1 ACTC
1398666 AACTCGACTC
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
20 22 0.52
21 1 0.02
24 2 0.05
25 17 0.40
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ACTCGACTTGAATTTCATAA
Found at i:1398629 original size:25 final size:25
Alignment explanation
Indices: 1398592--1398678 Score: 103
Period size: 25 Copynumber: 3.7 Consensus size: 25
1398582 CAAAAATTCG
* *
1398592 ACTCGACTCGACTTGAATTTTATAA
1 ACTCGACTCGACTCGAATTTCATAA
*
1398617 ACTCGACTTGACTCGAATTTCAT-A
1 ACTCGACTCGACTCGAATTTCATAA
1398641 A----ACTCGACTCGAATTTCATAA
1 ACTCGACTCGACTCGAATTTCATAA
*
1398662 ACTCAACTCGACTCGAA
1 ACTCGACTCGACTCGAA
1398679 AAAATTTCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
20 17 0.32
21 2 0.04
24 2 0.04
25 32 0.60
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.30
Consensus pattern (25 bp):
ACTCGACTCGACTCGAATTTCATAA
Found at i:1398670 original size:20 final size:20
Alignment explanation
Indices: 1398627--1398672 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1398617 ACTCGACTTG
*
1398627 ACTCGAATTTCATAAACTCG
1 ACTCGAATTTCATAAACTCA
1398647 ACTCGAATTTCATAAACTCA
1 ACTCGAATTTCATAAACTCA
1398667 ACTCGA
1 ACTCGA
1398673 CTCGAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.26, G:0.09, T:0.28
Consensus pattern (20 bp):
ACTCGAATTTCATAAACTCA
Found at i:1408381 original size:16 final size:16
Alignment explanation
Indices: 1408353--1408386 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1408343 TTTCAACGAG
1408353 TTTAATTTCTATAAAT
1 TTTAATTTCTATAAAT
1408369 TTTATATTT-TATAAAT
1 TTTA-ATTTCTATAAAT
1408385 TT
1 TT
1408387 ATCATCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTAATTTCTATAAAT
Found at i:1411923 original size:5 final size:5
Alignment explanation
Indices: 1411913--1411942 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1411903 ATATGACACA
*
1411913 AATTT AATTT AATTT AAATT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT AATTT
1411943 TAAAATAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
AATTT
Found at i:1415079 original size:8 final size:7
Alignment explanation
Indices: 1415060--1415098 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
1415050 TTCATTCTTC
1415060 CTTTTTA
1 CTTTTTA
1415067 CTTTTTA
1 CTTTTTA
1415074 CTTTTT-
1 CTTTTTA
*
1415080 CATTTT-
1 CTTTTTA
1415086 CTTTTTA
1 CTTTTTA
1415093 CTTTTT
1 CTTTTT
1415099 CATTTCCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 10 0.34
7 19 0.66
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.74
Consensus pattern (7 bp):
CTTTTTA
Found at i:1415091 original size:19 final size:19
Alignment explanation
Indices: 1415062--1415116 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
1415052 CATTCTTCCT
1415062 TTTTACTTTTTACTTTTTCA
1 TTTT-CTTTTTACTTTTTCA
1415082 TTTTCTTTTTACTTTTTCA
1 TTTTCTTTTTACTTTTTCA
* *
1415101 TTTCCTTTTTCCTTTT
1 TTTTCTTTTTACTTTT
1415117 GAATCTCAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 29 0.88
20 4 0.12
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTCTTTTTACTTTTTCA
Found at i:1415111 original size:7 final size:6
Alignment explanation
Indices: 1415060--1415116 Score: 51
Period size: 7 Copynumber: 8.8 Consensus size: 6
1415050 TTCATTCTTC
* * *
1415060 CTTTTT ACTTTTT ACTTTTT CATTTT CTTTTT ACTTTTT CATTTC CTTTTT
1 CTTTTT -CTTTTT -CTTTTT CTTTTT CTTTTT -CTTTTT CTTTTT CTTTTT
1415111 CCTTTT
1 -CTTTT
1415117 GAATCTCAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
6 18 0.43
7 24 0.57
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:1415115 original size:26 final size:27
Alignment explanation
Indices: 1415052--1415116 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 27
1415042 AAAACATATT
* *
1415052 CATTCTTCCTTTTTACTTTTTACTTTTT
1 CATT-TTCCTTTTTACTTTTTACATTTC
1415080 CATTTT-CTTTTTACTTTTT-CATTTC
1 CATTTTCCTTTTTACTTTTTACATTTC
*
1415105 CTTTTTCCTTTT
1 CATTTTCCTTTT
1415117 GAATCTCAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 9 0.27
26 18 0.55
27 2 0.06
28 4 0.12
ACGTcount: A:0.09, C:0.22, G:0.00, T:0.69
Consensus pattern (27 bp):
CATTTTCCTTTTTACTTTTTACATTTC
Found at i:1416684 original size:21 final size:21
Alignment explanation
Indices: 1416658--1416702 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1416648 GATTTCTGGG
* *
1416658 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1416679 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1416700 CAA
1 CAA
1416703 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1418077 original size:32 final size:31
Alignment explanation
Indices: 1418035--1418162 Score: 136
Period size: 31 Copynumber: 4.1 Consensus size: 31
1418025 AGAGTCGAGG
1418035 GTTTACCTATGTTCTACAGAACATATGGACA
1 GTTTACCTATGTTCTACAGAACATATGGACA
*
1418066 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACAGA-ACATATGGACA
*
1418098 GTATACCTATGTTCTA-AGGAACATATGGACA
1 GTTTACCTATGTTCTACA-GAACATATGGACA
* * * * *
1418129 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACAGAACATATGGACA
1418160 GTT
1 GTT
1418163 ACCGAGGATC
Statistics
Matches: 81, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
31 53 0.65
32 28 0.35
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACAGAACATATGGACA
Done.