Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_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: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 78
Found at i:1201790 original size:20 final size:20
Alignment explanation
Indices: 1201767--1201861 Score: 111
Period size: 20 Copynumber: 4.8 Consensus size: 20
1201757 GAAACTTAAA
* *
1201767 ATCGCAACACGAAAATGATT
1 ATCGCAACGCGAAAATGACT
**
1201787 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
**
1201807 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
*
1201827 ATCGCAACGTG-AAATGACT
1 ATCGCAACGCGAAAATGACT
*
1201846 ATCGCAACGAGAAAAT
1 ATCGCAACGCGAAAAT
1201862 CGCAACGCGA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
19 16 0.24
20 50 0.76
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1201881 original size:19 final size:19
Alignment explanation
Indices: 1201857--1201893 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1201847 TCGCAACGAG
1201857 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
1201876 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
1201894 TAAATTCACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.30, G:0.16, T:0.05
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:1202040 original size:20 final size:20
Alignment explanation
Indices: 1202015--1202062 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1202005 CCGATTATCC
1202015 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAATCAAATTCG
* **
1202035 CGTTGCGGTAATCATTTTCG
1 CGTTGCGATAATCAAATTCG
*
1202055 TGTTGCGA
1 CGTTGCGA
1202063 CTATTCTTCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAATCAAATTCG
Found at i:1204053 original size:20 final size:20
Alignment explanation
Indices: 1204030--1204106 Score: 109
Period size: 20 Copynumber: 3.8 Consensus size: 20
1204020 TCTGAAACTT
1204030 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
1204050 AAAAATCGCAACACGAAAATG
1 -AAAATCGCAACACGAAAATG
*
1204071 AAAATCGCAACGCGAAAATG
1 AAAATCGCAACACGAAAATG
** *
1204091 ATTATCGCAACGCGAA
1 AAAATCGCAACACGAA
1204107 TTTGACTATC
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 33 0.62
21 20 0.38
ACGTcount: A:0.51, C:0.21, G:0.17, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:1204056 original size:21 final size:21
Alignment explanation
Indices: 1204030--1204091 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
1204020 TCTGAAACTT
1204030 AAAATCGCAACACGAAAATGA
1 AAAATCGCAACACGAAAATGA
1204051 AAAATCGCAACACGAAAATG-
1 AAAATCGCAACACGAAAATGA
*
1204071 AAAATCGCAACGCGAAAATGA
1 AAAATCGCAACACGAAAATGA
1204092 TTATCGCAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 19 0.49
21 20 0.51
ACGTcount: A:0.55, C:0.19, G:0.16, T:0.10
Consensus pattern (21 bp):
AAAATCGCAACACGAAAATGA
Found at i:1204116 original size:20 final size:19
Alignment explanation
Indices: 1204054--1204159 Score: 78
Period size: 20 Copynumber: 5.7 Consensus size: 19
1204044 AAAATGAAAA
* **
1204054 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCG-AAATGACT
*
1204074 ATCGCAACGCGAAAATGATT
1 ATCGCAACGCG-AAATGACT
*
1204094 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA-ATGACT
* *
1204114 ATCGC-A-TCGAGAT-A--
1 ATCGCAACGCGAAATGACT
*
1204128 ATCGCAACGCGAAATGGCT
1 ATCGCAACGCGAAATGACT
1204147 ATCGCAACGCGAA
1 ATCGCAACGCGAA
1204160 TTTTGTCGTT
Statistics
Matches: 69, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
14 5 0.07
15 1 0.01
16 6 0.09
17 1 0.01
18 3 0.04
19 16 0.23
20 37 0.54
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.17
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1204521 original size:22 final size:22
Alignment explanation
Indices: 1204496--1204571 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 22
1204486 GAGATAGACG
*
1204496 GATTTCGCCGAAGATGGGGATA
1 GATTTCGCCGAAGATGGGGACA
*
1204518 GATTTCGCCGGAA-ATTGGGACA
1 GATTTCGCC-GAAGATGGGGACA
* * * *
1204540 GATTTCGTCGGAGATGGAGACG
1 GATTTCGCCGAAGATGGGGACA
*
1204562 GATGTCGCCG
1 GATTTCGCCG
1204572 TAGAGAGTAA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
21 2 0.05
22 38 0.88
23 3 0.07
ACGTcount: A:0.24, C:0.17, G:0.37, T:0.22
Consensus pattern (22 bp):
GATTTCGCCGAAGATGGGGACA
Found at i:1204759 original size:20 final size:20
Alignment explanation
Indices: 1204734--1204830 Score: 133
Period size: 20 Copynumber: 4.8 Consensus size: 20
1204724 TTATCGCAAC
*
1204734 GCGATAGTCAGAATCTCGTT
1 GCGATAGTCAGAATCGCGTT
1204754 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
**
1204774 GCGATCACGT-ATTATCGCGTT
1 GCGAT-A-GTCAGAATCGCGTT
*
1204795 GCGATAGTCCGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
1204815 GCGATAGTCAGAATCG
1 GCGATAGTCAGAATCG
1204831 TTTCGAGATC
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
19 2 0.03
20 48 0.72
21 15 0.22
22 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (20 bp):
GCGATAGTCAGAATCGCGTT
Found at i:1204841 original size:61 final size:61
Alignment explanation
Indices: 1204734--1204860 Score: 184
Period size: 61 Copynumber: 2.1 Consensus size: 61
1204724 TTATCGCAAC
* * *
1204734 GCGATAGTCAGAATCTCGTTGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCGTT
1 GCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGAGATCAAGTATTATCGCGTT
* * *
1204795 GCGATAGTCCGAATCGCGTTGCGATAGTCAGAATCG-TTTCGAGATCAAGTGTTATCGCGTT
1 GCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTT-GAGATCAAGTATTATCGCGTT
1204856 GCGAT
1 GCGAT
1204861 TTACATATTC
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
60 2 0.03
61 57 0.97
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (61 bp):
GCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCGTTGAGATCAAGTATTATCGCGTT
Found at i:1204877 original size:20 final size:20
Alignment explanation
Indices: 1204849--1204901 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1204839 TCAAGTGTTA
*
1204849 TCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
1204869 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
* *
1204889 TCACATTACGATT
1 TCGCATTGCGATT
1204902 ATCTAAAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:1205011 original size:19 final size:19
Alignment explanation
Indices: 1204987--1205023 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1204977 TACGATAATG
*
1204987 GAGATCGCGTTACGATTTA
1 GAGATCGCATTACGATTTA
*
1205006 GAGATCGCATTGCGATTT
1 GAGATCGCATTACGATTT
1205024 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTACGATTTA
Found at i:1223269 original size:63 final size:60
Alignment explanation
Indices: 1223193--1223321 Score: 154
Period size: 63 Copynumber: 2.1 Consensus size: 60
1223183 TATTTGTTAC
1223193 TTATTTAACTTTGAATATTAAAGATAATTATATCCTTTTGAATATTTCAAATTAAAATAATA
1 TTATTTAA-TTTGAATATTAAAGATAATTATAT-CTTTTGAATATTTCAAATTAAAATAATA
* * **
1223255 TATATTTAAGTTTGAATAGTAAAAGATGACTT-TATCTTTTGAGCATTTCAAATTAAAAT-ATA
1 T-TATTTAA-TTTGAATA-TTAAAGAT-AATTATATCTTTTGAATATTTCAAATTAAAATAATA
1223317 TTATT
1 TTATT
1223322 ATCTGTTTAA
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
61 4 0.07
62 5 0.08
63 37 0.63
64 10 0.17
65 3 0.05
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (60 bp):
TTATTTAATTTGAATATTAAAGATAATTATATCTTTTGAATATTTCAAATTAAAATAATA
Found at i:1229180 original size:15 final size:16
Alignment explanation
Indices: 1229142--1229181 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
1229132 TTATGTTTTA
*
1229142 ATTTACCAAATATAAT
1 ATTTACTAAATATAAT
1229158 A-TTA-TAAA-ATAAT
1 ATTTACTAAATATAAT
1229171 ATTTACTAAAT
1 ATTTACTAAAT
1229182 TATGATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 6
0.74 0.04 0.22
Matches are distributed among these distances:
13 6 0.30
14 6 0.30
15 7 0.35
16 1 0.05
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTTACTAAATATAAT
Found at i:1229782 original size:16 final size:16
Alignment explanation
Indices: 1229750--1229790 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
1229740 GTTTACTTCA
*
1229750 GAATGATT-AAGTGTT
1 GAATGATTCAAATGTT
1229765 GAATGATTCAAATGTT
1 GAATGATTCAAATGTT
1229781 GAATGATTCA
1 GAATGATTCA
1229791 GAGGCTCTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (16 bp):
GAATGATTCAAATGTT
Found at i:1232187 original size:106 final size:107
Alignment explanation
Indices: 1232002--1232216 Score: 342
Period size: 106 Copynumber: 2.0 Consensus size: 107
1231992 ATATCAATAT
* * *
1232002 ATAAATCTTCATGTAAAATTGAAGAGGAGATTGAACTTCTCATCGCTCTTAACTCATTACTCTCA
1 ATAAATCTTCATGTAAAATTGAAGAGGAGATAGAACTTCTCATCGCTCTCAACTCATCACTCTCA
*
1232067 ATAAAAACAATTAATTGTGA-CTTCATCCAAATAATAATAAC
66 ATAAAAACAATTAATTGTGATCTTCATCCAAATAATAAAAAC
* *
1232108 ATAAATCTTCATGTAAGATTGAAGAGGAGATAGAACTTCTCATCGCTCTCGACTCATCACTCTCA
1 ATAAATCTTCATGTAAAATTGAAGAGGAGATAGAACTTCTCATCGCTCTCAACTCATCACTCTCA
* *
1232173 ATAAAAACAATTAATTGTGATTCTTCCTCCAAATCATAAAAAC
66 ATAAAAACAATTAATTGTGA-TCTTCATCCAAATAATAAAAAC
1232216 A
1 A
1232217 ACTTACTATG
Statistics
Matches: 99, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
106 80 0.81
108 19 0.19
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.31
Consensus pattern (107 bp):
ATAAATCTTCATGTAAAATTGAAGAGGAGATAGAACTTCTCATCGCTCTCAACTCATCACTCTCA
ATAAAAACAATTAATTGTGATCTTCATCCAAATAATAAAAAC
Found at i:1234718 original size:25 final size:25
Alignment explanation
Indices: 1234685--1234743 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
1234675 TTATTCATAA
*
1234685 AAAGATCATAAATACCCGTAAGCTT
1 AAAGATCATAAATACCCGAAAGCTT
1234710 AAAGATCATAAATACCCGAAAGCTT
1 AAAGATCATAAATACCCGAAAGCTT
1234735 AAAGATCAT
1 AAAGATCAT
1234744 CCATTATCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (25 bp):
AAAGATCATAAATACCCGAAAGCTT
Found at i:1245687 original size:19 final size:20
Alignment explanation
Indices: 1245660--1245704 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1245650 ATTAGCAACA
*
1245660 TAAT-AAAAATGATTATATC
1 TAATAAAAAATGATCATATC
* *
1245679 TAATTAAAAATGATCCTATC
1 TAATAAAAAATGATCATATC
1245699 TAATAA
1 TAATAA
1245705 CTAATAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (20 bp):
TAATAAAAAATGATCATATC
Found at i:1245688 original size:20 final size:20
Alignment explanation
Indices: 1245663--1245702 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1245653 AGCAACATAA
*
1245663 TAAAAATGATTATATCTAAT
1 TAAAAATGATCATATCTAAT
*
1245683 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCATATCTAAT
1245703 AACTAATAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCATATCTAAT
Found at i:1245745 original size:20 final size:21
Alignment explanation
Indices: 1245716--1245755 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1245706 TAATAGAATA
*
1245716 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
1245737 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
1245756 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:1245797 original size:20 final size:20
Alignment explanation
Indices: 1245769--1245807 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1245759 TAATAGAATA
* *
1245769 AAAATTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
1245789 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
1245808 ATTTAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:1245798 original size:52 final size:51
Alignment explanation
Indices: 1245661--1245808 Score: 251
Period size: 53 Copynumber: 2.8 Consensus size: 51
1245651 TTAGCAACAT
*
1245661 AATAAAAATGATTATATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AATAAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1245712 AATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AAT-AAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
*
1245765 AATAAAAATTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 AATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATA
1245809 TTTAATTTAG
Statistics
Matches: 92, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 3 0.03
52 44 0.48
53 45 0.49
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (51 bp):
AATAAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
Found at i:1250373 original size:20 final size:20
Alignment explanation
Indices: 1250348--1250387 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1250338 AGCAACAGAA
*
1250348 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
1250368 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
1250388 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:1250430 original size:20 final size:21
Alignment explanation
Indices: 1250401--1250440 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1250391 TAATAGAATA
*
1250401 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
1250422 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
1250441 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:1250479 original size:20 final size:19
Alignment explanation
Indices: 1250454--1250491 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 19
1250444 TAATAGAATA
1250454 AAAACTGATTCTATCTAATT
1 AAAACTGA-TCTATCTAATT
1250474 AAAACTGATCTATCTAAT
1 AAAACTGATCTATCTAAT
1250492 ATTAATTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (19 bp):
AAAACTGATCTATCTAATT
Found at i:1250483 original size:52 final size:52
Alignment explanation
Indices: 1250344--1250492 Score: 266
Period size: 53 Copynumber: 2.9 Consensus size: 52
1250334 AATTAGCAAC
1250344 AGAATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1250395 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
*
1250448 AGAATAAAAACTGATTCTATCTAATTAAAACTGAT-CTATCTAATA
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
1250493 TTAATTAGAT
Statistics
Matches: 95, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
51 15 0.16
52 34 0.36
53 46 0.48
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (52 bp):
AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:1260628 original size:12 final size:12
Alignment explanation
Indices: 1260611--1260635 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1260601 ATTTTTGTCT
1260611 TTTGAAAATTAC
1 TTTGAAAATTAC
1260623 TTTGAAAATTAC
1 TTTGAAAATTAC
1260635 T
1 T
1260636 CCCCCACTCC
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTGAAAATTAC
Found at i:1262445 original size:20 final size:19
Alignment explanation
Indices: 1262417--1262461 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1262407 AGTTTTCATG
* *
1262417 AAAATAACATAATTAAATCA
1 AAAACAACA-AATTAAAACA
*
1262437 AAAACAACAATTTAAAACA
1 AAAACAACAAATTAAAACA
1262456 AAAACA
1 AAAACA
1262462 TTTTTTTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.69, C:0.13, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAACAACAAATTAAAACA
Found at i:1268973 original size:17 final size:18
Alignment explanation
Indices: 1268953--1268989 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
1268943 TGATATTCGA
1268953 ATAA-TTGAATCGAATAT
1 ATAATTTGAATCGAATAT
1268970 ATAATTTTGAATCGAATAT
1 ATAA-TTTGAATCGAATAT
1268989 A
1 A
1268990 AAATCTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
19 14 0.78
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (18 bp):
ATAATTTGAATCGAATAT
Found at i:1269009 original size:13 final size:13
Alignment explanation
Indices: 1268991--1269017 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1268981 TCGAATATAA
1268991 AATCTTAAAATTC
1 AATCTTAAAATTC
1269004 AATCTTAAAATTC
1 AATCTTAAAATTC
1269017 A
1 A
1269018 TTAACACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
AATCTTAAAATTC
Found at i:1277267 original size:31 final size:31
Alignment explanation
Indices: 1277209--1277267 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
1277199 ATTTGACTTA
*
1277209 TGGAAGATGATAAGGTTGATGTGTCTTGGTT
1 TGGAAGATGATAAGGTTGAGGTGTCTTGGTT
* * *
1277240 TGGAAGATTATAAGGTTTAGGTTTCTTG
1 TGGAAGATGATAAGGTTGAGGTGTCTTG
1277268 ATTTAATGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.24, C:0.03, G:0.32, T:0.41
Consensus pattern (31 bp):
TGGAAGATGATAAGGTTGAGGTGTCTTGGTT
Found at i:1277480 original size:20 final size:20
Alignment explanation
Indices: 1277455--1277494 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1277445 AAGAGCCCAA
*
1277455 TTAGGATAATATAGATGCAT
1 TTAGGAGAATATAGATGCAT
* *
1277475 TTAGGAGCATATAGTTGCAT
1 TTAGGAGAATATAGATGCAT
1277495 GTGGTGAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (20 bp):
TTAGGAGAATATAGATGCAT
Found at i:1282798 original size:60 final size:59
Alignment explanation
Indices: 1282664--1282794 Score: 192
Period size: 59 Copynumber: 2.2 Consensus size: 59
1282654 ATAGTTGAGT
* *
1282664 GACCATTTTGTAACTTTCAATAGTCGGGGACTCAATAAAGCAACACCCTATAGTCAAAG
1 GACCATTTTGTAACTTTCAATAGTCGGGGACTCAACAAAACAACACCCTATAGTCAAAG
* * **
1282723 GACCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAACATCACCCTATAGTC-GGG
1 GACCATTTTGTAACTTTCAATAGTCG-GGGACTCAACAAAACAACACCCTATAGTCAAAG
1282782 GACCATTTTGTAA
1 GACCATTTTGTAA
1282795 ACTTAACCCT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 39 0.60
60 26 0.40
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (59 bp):
GACCATTTTGTAACTTTCAATAGTCGGGGACTCAACAAAACAACACCCTATAGTCAAAG
Found at i:1283383 original size:12 final size:12
Alignment explanation
Indices: 1283362--1283401 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
1283352 GGCCAAAATA
1283362 TAAATTAAAGTT
1 TAAATTAAAGTT
* *
1283374 TAATTTAAAGGT
1 TAAATTAAAGTT
1283386 TAAATTAAAGTT
1 TAAATTAAAGTT
1283398 TAAA
1 TAAA
1283402 ATCAAATTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (12 bp):
TAAATTAAAGTT
Found at i:1284100 original size:20 final size:20
Alignment explanation
Indices: 1284063--1284101 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1284053 TTTAAAATCT
* *
1284063 AAATATTTAAATCCTAAAAA
1 AAATATTAAAATCATAAAAA
*
1284083 AAATATTAAAATTATAAAA
1 AAATATTAAAATCATAAAA
1284102 TTATAAATTC
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:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATATTAAAATCATAAAAA
Found at i:1291167 original size:18 final size:17
Alignment explanation
Indices: 1291144--1291177 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1291134 TGAGACCACA
1291144 ATATTATATTTTCATATT
1 ATATTATATTTT-ATATT
1291162 ATATTATATTTTATAT
1 ATATTATATTTTATAT
1291178 AAATAACTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:1292281 original size:28 final size:28
Alignment explanation
Indices: 1292222--1292310 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
1292212 TTTTCAAACG
* *
1292222 TACAAGAACTAAAAT-ATCATTTT-TATA
1 TACAAGAACTAAAATGAAC-TTTTAAATA
1292249 GTACAAGAACTAAAATGAACTTTTAAATA
1 -TACAAGAACTAAAATGAACTTTTAAATA
* **
1292278 TACAATAGGGACTAAAATGAGTTTTTAAATA
1 TAC-A-A-GAACTAAAATGAACTTTTAAATA
1292309 TA
1 TA
1292311 GTACATAATC
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
28 22 0.43
29 6 0.12
30 1 0.02
31 22 0.43
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.33
Consensus pattern (28 bp):
TACAAGAACTAAAATGAACTTTTAAATA
Found at i:1293310 original size:14 final size:15
Alignment explanation
Indices: 1293291--1293329 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1293281 AAATGTGCGT
*
1293291 ATAAATAAAATTA-A
1 ATAAATAAAATAATA
1293305 ATAAATAAAATAATA
1 ATAAATAAAATAATA
*
1293320 ATAATTAAAA
1 ATAAATAAAA
1293330 CGTAAATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAAATAAAATAATA
Found at i:1294253 original size:84 final size:84
Alignment explanation
Indices: 1294148--1294367 Score: 273
Period size: 84 Copynumber: 2.6 Consensus size: 84
1294138 ACTCGACAAT
*
1294148 TTTA-TTGACAGATAGCCCTTCTTGCCTTGAGTTATGTTGTAAATGGTGTGCC-TAGGAGCTGAG
1 TTTAGTTGACAGATAGCCCTTCTAGCCTTGAGTTATGTTGTAAATGGTGTGCCTTA-GAGCTGAG
*
1294211 CGTAGTCAAACTCGAAGGTC
65 CATAGTCAAACTCGAAGGTC
* * * * * * * * * *
1294231 TTTAGTTGGCAGATAGCCCTTCTCGACTTAAGATACGCTGCAAATGATGTCCCTTAGAGCTGAGC
1 TTTAGTTGACAGATAGCCCTTCTAGCCTTGAGTTATGTTGTAAATGGTGTGCCTTAGAGCTGAGC
1294296 ATAGTCAAACTCGAAGGTC
66 ATAGTCAAACTCGAAGGTC
* * * *
1294315 TTTTGGTGACAAATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGGTGTGCC
1 TTTAGTTGACAGATAGCCCTTCTAGCCTTGAGTTATGTTGTAAATGGTGTGCC
1294368 CTCGAAGATG
Statistics
Matches: 110, Mismatches: 25, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
83 4 0.04
84 104 0.95
85 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.32
Consensus pattern (84 bp):
TTTAGTTGACAGATAGCCCTTCTAGCCTTGAGTTATGTTGTAAATGGTGTGCCTTAGAGCTGAGC
ATAGTCAAACTCGAAGGTC
Found at i:1294593 original size:30 final size:30
Alignment explanation
Indices: 1294557--1294615 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1294547 GTAAAACATA
*
1294557 TTCAAAGATTT-TGTTTCAA-ATGAAACTGTT
1 TTCAAAG-TTTATGCTTCAAGA-GAAACTGTT
1294587 TTCAAAGTTTATGCTTCAAGAGAAACTGT
1 TTCAAAGTTTATGCTTCAAGAGAAACTGT
1294616 CTCAATGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 3 0.12
30 22 0.85
31 1 0.04
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (30 bp):
TTCAAAGTTTATGCTTCAAGAGAAACTGTT
Found at i:1294656 original size:37 final size:36
Alignment explanation
Indices: 1294601--1294684 Score: 89
Period size: 37 Copynumber: 2.3 Consensus size: 36
1294591 AAGTTTATGC
* * **
1294601 TTCAAGAGAAACTGTCTCAATG-GAGACAAAATTTTGT
1 TTCAAGGGAAACTATCTCAA-GAGAGACAAAA-TTCAT
* *
1294638 TTCAAGGGAACCTATCTCAAGAGAGGCAAAATTCAT
1 TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT
1294674 TTCAAGGGAAA
1 TTCAAGGGAAA
1294685 TGTTTTCAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
36 14 0.36
37 25 0.64
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.25
Consensus pattern (36 bp):
TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT
Found at i:1294707 original size:102 final size:102
Alignment explanation
Indices: 1294578--1294951 Score: 412
Period size: 102 Copynumber: 3.7 Consensus size: 102
1294568 TGTTTCAAAT
* * *
1294578 GAAACTGTTTTCAAAGTTTATGCTTCAAGAGAAACTGTCTCAATGGAGACAAAATTTTGTTTCAA
1 GAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAA
* *
1294643 GGGAACCTATCTCAAGAGAGGCAAAATTCATTTCAAGG
65 GGGAACATATCTCAAGAGAGACAAAATTCATTTCAAGG
1294681 GAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAG
1 GAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAG
* *
1294746 GGAACATATCTCAAGATATACAAAATTCATTTCAAGG
66 GGAACATATCTCAAGAGAGACAAAATTCATTTCAAGG
* * * * * * * *
1294783 GAAATGTTTTTAATGTTTATGTTTCAAGAGAAACTATCTTAAGAGAGAGAAAACTTAGTTCCAA-
1 GAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAG
** * * * * ** *
1294847 AAAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAAG
66 GGAACATATCTCAAGAGAGACAAAATTCATTTCAAGG
** * * * * * **
1294884 GAAACATATTCAAAGATTT-TGTTTTAAGAGAAACTATCTCAAGAGAGACAAAA-TTCATTTCAA
1 GAAATGTTTTCAATG-TTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAA
1294947 GGGAA
65 GGGAA
1294952 ATGTTTTCAA
Statistics
Matches: 230, Mismatches: 39, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
100 7 0.03
101 69 0.30
102 150 0.65
103 4 0.02
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (102 bp):
GAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAG
GGAACATATCTCAAGAGAGACAAAATTCATTTCAAGG
Found at i:1294961 original size:65 final size:65
Alignment explanation
Indices: 1294855--1294983 Score: 152
Period size: 65 Copynumber: 2.0 Consensus size: 65
1294845 AAAAAAAATG
* * ** *
1294855 TCTCAAGGGAGACGAAATTTGTTTCAAAGGAAACATATTCAAAGATTT-TGTTTTAAGAGAAACT
1 TCTCAAGAGAGACAAAATTCATTTCAAAGGAAACATATTCAAAG-TTTATGTTTCAAGAGAAACT
1294919 A
65 A
* ** * *
1294920 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACT
1 TCTCAAGAGAGACAAAATTCATTTCAAAGGAAACATATTCAAAGTTTATGTTTCAAGAGAAACT
1294984 GTAACATCCC
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
64 3 0.06
65 50 0.94
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.32
Consensus pattern (65 bp):
TCTCAAGAGAGACAAAATTCATTTCAAAGGAAACATATTCAAAGTTTATGTTTCAAGAGAAACTA
Found at i:1297554 original size:99 final size:99
Alignment explanation
Indices: 1297383--1297571 Score: 333
Period size: 99 Copynumber: 1.9 Consensus size: 99
1297373 CGGTCTTTCG
** * *
1297383 GGACATATATGTATTCTTTGGAACATGTGTGAAGTTTGGTGAGACACATACTTGATCCTTGGCAT
1 GGACATATATGTATTCTTTGGAACATGTGTGAAGTCAGGTGAGACACATACTTGATCCCTAGCAT
1297448 ATGTATATGATTCTTAAGGAATGATGTGTCCTTC
66 ATGTATATGATTCTTAAGGAATGATGTGTCCTTC
*
1297482 GGACATATATGTATTCTTTGGAACATGTGTGAAGTCAGGTGAGACACATACTTGATCCCTAGTAT
1 GGACATATATGTATTCTTTGGAACATGTGTGAAGTCAGGTGAGACACATACTTGATCCCTAGCAT
1297547 ATGTATATGATTCTTAAGGAATGAT
66 ATGTATATGATTCTTAAGGAATGAT
1297572 ATGTAGTCCT
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 85 1.00
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.36
Consensus pattern (99 bp):
GGACATATATGTATTCTTTGGAACATGTGTGAAGTCAGGTGAGACACATACTTGATCCCTAGCAT
ATGTATATGATTCTTAAGGAATGATGTGTCCTTC
Found at i:1297633 original size:23 final size:23
Alignment explanation
Indices: 1297599--1297666 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
1297589 ATTATTATAT
*
1297599 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
*
1297622 GGCACT-CTGGTGCAATTCTACGT
1 GGCACTAC-GGTGCAATTCTACGC
* *
1297645 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
1297667 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
22 1 0.03
23 38 0.95
24 1 0.03
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1302850 original size:103 final size:103
Alignment explanation
Indices: 1302666--1302878 Score: 363
Period size: 103 Copynumber: 2.1 Consensus size: 103
1302656 GGGTCTACAC
* *
1302666 GGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCAGGTGAGACACATACTTGAT
* * *
1302731 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAAGAATGATATGT
1302769 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCAGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCAGGTGAGACACATACTTGAT
*
1302834 CCCTAGTATATGTATATGATTCTTAAAGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAAGAATGATATGT
*
1302872 AGTCCTT
1 GGTCCTT
1302879 ATGGACATTA
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCAGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAAGAATGATATGT
Found at i:1302956 original size:23 final size:23
Alignment explanation
Indices: 1302894--1302962 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 23
1302884 CATTATTATA
*
1302894 TGGCACTACGGTGCAATTCTACG
1 TGGCACTATGGTGCAATTCTACG
* * * *
1302917 CGACACTCCT-GTACAATTCTACG
1 TGGCACT-ATGGTGCAATTCTACG
* *
1302940 TGGCACTTTGGTGCAATTATACG
1 TGGCACTATGGTGCAATTCTACG
1302963 AGCTGTGGTG
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
22 1 0.03
23 33 0.97
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (23 bp):
TGGCACTATGGTGCAATTCTACG
Found at i:1303803 original size:36 final size:36
Alignment explanation
Indices: 1303756--1304420 Score: 467
Period size: 36 Copynumber: 19.0 Consensus size: 36
1303746 ATTCAAAGAT
1303756 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
1303792 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
1303828 TTTGTTTCTAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** * * *
1303864 CTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * * ** *
1303901 TTAGTTTCAAAGAAAACAGAT-T----A-A-A-TTAT
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAA
*
1303930 TTTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
1303966 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* ** *
1304002 TTTGTTTAAAAAGAAACTGTCTCAAGAGAGTCAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** * * *
1304038 CTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * ** *
1304075 TTAGTTTCAAGGAAAACATAT-TC-----A-A-TTAT
1 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAA
*
1304104 TTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
1304140 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
1304176 TTTATTTCAAGAGAAACTGTCTTAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** * * *
1304212 CTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
1304249 TTTGTTTCAAGGGAAACAGAT-TC-----A-A-ATAT
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAA
* *
1304278 TTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
1304314 TTTGTTGTTTCAAGGGAAACAGAT-TC-----A-A-ATAT
1 --T-TTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAA
* *
1304346 TTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1304382 TTTGTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 --T-TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1304421 CTTGGAAAAT
Statistics
Matches: 490, Mismatches: 94, Indels: 87
0.73 0.14 0.13
Matches are distributed among these distances:
28 5 0.01
29 72 0.15
30 4 0.01
31 3 0.01
32 2 0.00
33 2 0.00
34 5 0.01
35 4 0.01
36 249 0.51
37 90 0.18
38 2 0.00
39 51 0.10
40 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:1303934 original size:138 final size:139
Alignment explanation
Indices: 1303792--1304054 Score: 386
Period size: 138 Copynumber: 1.9 Consensus size: 139
1303782 AGAGACAAAA
* *
1303792 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCTAGAGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
* * * * *
1303857 GACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAA-TTAGTTTC-AAAGAAAACAG
66 GACAAAA-TTAGTTCAAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAACAG
1303920 ATTAAATTAT
130 ATTAAATTAT
* * *
1303930 TTTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
* * *
1303995 GACAAAATTTGTTTAAAAAGAAACTGTCTCAAGAGAGTCAAAACTTAGTTCCAAAAGAAA
66 GACAAAATTAGTTCAAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAA
1304055 TTGTCTCAAG
Statistics
Matches: 110, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
137 29 0.26
138 74 0.67
139 7 0.06
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.27
Consensus pattern (139 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
GACAAAATTAGTTCAAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAACAGA
TTAAATTAT
Found at i:1303955 original size:174 final size:174
Alignment explanation
Indices: 1303665--1304333 Score: 1088
Period size: 174 Copynumber: 3.8 Consensus size: 174
1303655 GGGGTGTTAC
* * * * * *
1303665 AGAAACTGTCTCATGGGAGACAAAATTTAGTTCTAAAAGAAAATGTCTCAAGGGAGATGAAATTA
1 AGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAATTA
*
1303730 GTTTCAAAGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
66 GTTTCAAAGAAAACAGATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
1303795 GTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCTAG
131 GTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAG
1303839 AGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAATTA
1 AGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAATTA
*
1303904 GTTTCAAAGAAAACAGATT-AAATTATTTTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAATT
66 GTTTCAAAGAAAACAGATTCAAA-TATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
1303968 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTAAAA
130 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAG
*
1304013 AGAAACTGTCTCAAGAGAGTCAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAATTA
1 AGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAATTA
* * * *
1304078 GTTTCAAGGAAAACATATTCAATTATTTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAATTT
66 GTTTCAAAGAAAACAGATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
1304143 GTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTATTTCAAG
131 GTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAG
* *
1304187 AGAAACTGTCTTAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAATTT
1 AGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAATTA
* * * *
1304252 GTTTCAAGGGAAACAGATTCAAATATTTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTT
66 GTTTCAAAGAAAACAGATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--T
1304317 GTTGTTTCAAGGGAAAC
129 -TTGTTTCAAGGGAAAC
1304334 AGATTCAAAT
Statistics
Matches: 461, Mismatches: 29, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
173 3 0.01
174 439 0.95
175 2 0.00
176 1 0.00
177 16 0.03
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.27
Consensus pattern (174 bp):
AGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAATTA
GTTTCAAAGAAAACAGATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
GTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAG
Found at i:1304108 original size:138 final size:138
Alignment explanation
Indices: 1303966--1304218 Score: 364
Period size: 138 Copynumber: 1.8 Consensus size: 138
1303956 AGAGACAAAA
**
1303966 TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTAAAAAGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAATTTGTTTAAAAAGAAACTGTCTCAAGAGA
* * * *
1304031 GTCAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAA-TTAGTTTCAAGGAAAACATA
66 GACAAAACTTA-TTCCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTTCAAGGAAAACATA
1304095 TTCAATTAT
130 TTCAATTAT
* ** *
1304104 TTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGA
1 TTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAATTTGTTTAAAAAGAAACTGTCTCAAGAGA
* * * *
1304169 GACAAAATTTATTTCAAGAGAAACTGTCTTAAGAGAGACAAAACTTAGTT
66 GACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTT
1304219 CCAAAAGAAA
Statistics
Matches: 100, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
137 26 0.26
138 74 0.74
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (138 bp):
TTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAATTTGTTTAAAAAGAAACTGTCTCAAGAGA
GACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTTCAAGGAAAACATAT
TCAATTAT
Found at i:1304285 original size:29 final size:29
Alignment explanation
Indices: 1304249--1304362 Score: 113
Period size: 29 Copynumber: 3.6 Consensus size: 29
1304239 GGAGACGAAA
1304249 TTTGTTTCAAGGGAAACAGATTCAAATAT
1 TTTGTTTCAAGGGAAACAGATTCAAATAT
*
1304278 TTTGTTTCAAGGGAAAC-TATCTCAAGAGAGATAAAATT
1 TTTGTTTCAAGGGAAACAGAT-TC---A-A-AT---A-T
1304316 TGTTGTTTCAAGGGAAACAGATTCAAATAT
1 T-TTGTTTCAAGGGAAACAGATTCAAATAT
1304346 TTTGTTTCAAGGGAAAC
1 TTTGTTTCAAGGGAAAC
1304363 TATCTCAAGA
Statistics
Matches: 71, Mismatches: 2, Indels: 24
0.73 0.02 0.25
Matches are distributed among these distances:
28 2 0.03
29 35 0.49
30 2 0.03
31 1 0.01
32 1 0.01
33 1 0.01
34 4 0.06
35 1 0.01
36 1 0.01
37 1 0.01
38 2 0.03
39 18 0.25
40 2 0.03
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (29 bp):
TTTGTTTCAAGGGAAACAGATTCAAATAT
Found at i:1304333 original size:39 final size:39
Alignment explanation
Indices: 1304279--1304420 Score: 171
Period size: 39 Copynumber: 3.9 Consensus size: 39
1304269 TTCAAATATT
1304279 TTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTG
1 TTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTG
*
1304318 TTGTTTCAAGGGAAACAGAT-TC---A-A-AT---A-TT-
1 TTGTTTCAAGGGAAAC-TATCTCAAGAGAGATAAAATTTG
1304347 TTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTG
1 TTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTG
* *
1304386 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAA
1304421 CTTGGAAAAT
Statistics
Matches: 87, Mismatches: 4, Indels: 24
0.76 0.03 0.21
Matches are distributed among these distances:
28 2 0.02
29 18 0.21
30 2 0.02
31 1 0.01
32 1 0.01
33 1 0.01
34 4 0.05
35 1 0.01
36 1 0.01
37 1 0.01
38 2 0.02
39 51 0.59
40 2 0.02
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (39 bp):
TTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTG
Found at i:1304338 original size:68 final size:68
Alignment explanation
Indices: 1304250--1304401 Score: 304
Period size: 68 Copynumber: 2.2 Consensus size: 68
1304240 GAGACGAAAT
1304250 TTGTTTCAAGGGAAACAGATTCAAATATTTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAAT
1 TTGTTTCAAGGGAAACAGATTCAAATATTTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAAT
1304315 TTG
66 TTG
1304318 TTGTTTCAAGGGAAACAGATTCAAATATTTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAAT
1 TTGTTTCAAGGGAAACAGATTCAAATATTTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAAT
1304383 TTG
66 TTG
1304386 TTGTTTCAAGGGAAAC
1 TTGTTTCAAGGGAAAC
1304402 TGTCTCAAGA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 84 1.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.32
Consensus pattern (68 bp):
TTGTTTCAAGGGAAACAGATTCAAATATTTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAAT
TTG
Found at i:1305327 original size:32 final size:32
Alignment explanation
Indices: 1305260--1305353 Score: 136
Period size: 32 Copynumber: 2.9 Consensus size: 32
1305250 ATTCCCAAAG
*
1305260 ATGCCCCAATATTCGATGTTGAATCT-AAAAA
1 ATGCCCCAATATTTGATGTTGAATCTCAAAAA
*
1305291 ATGCCCCAATATTTGATGTTAAATCTCAAAAA
1 ATGCCCCAATATTTGATGTTGAATCTCAAAAA
**
1305323 ATGCCCCAGCATTTGATGTTGAATCTTCAAA
1 ATGCCCCAATATTTGATGTTGAATC-TCAAA
1305354 GATGCCGTCA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 24 0.43
32 27 0.48
33 5 0.09
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (32 bp):
ATGCCCCAATATTTGATGTTGAATCTCAAAAA
Found at i:1305359 original size:32 final size:31
Alignment explanation
Indices: 1305255--1305359 Score: 129
Period size: 32 Copynumber: 3.3 Consensus size: 31
1305245 ATTTAATTCC
* *
1305255 CAAAGATGCCCCAATATTCGATGTTGAATCT
1 CAAAAATGCCCCAATATTTGATGTTGAATCT
* *
1305286 AAAAAATGCCCCAATATTTGATGTTAAATCT
1 CAAAAATGCCCCAATATTTGATGTTGAATCT
**
1305317 CAAAAAATGCCCCAGCATTTGATGTTGAATCTT
1 C-AAAAATGCCCCAATATTTGATGTTGAATC-T
*
1305350 CAAAGATGCC
1 CAAAAATGCC
1305360 GTCATTGTTC
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
31 27 0.43
32 34 0.54
33 2 0.03
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (31 bp):
CAAAAATGCCCCAATATTTGATGTTGAATCT
Found at i:1306356 original size:61 final size:63
Alignment explanation
Indices: 1306283--1306412 Score: 183
Period size: 69 Copynumber: 2.0 Consensus size: 63
1306273 TGTCTCTCTC
1306283 TTGATGCTCTATGATCTTC-AAGTGG-AGTGATTCAGAAATGATTGTGCTTGATCAATCTCAT
1 TTGATGCTCTATGATCTTCGAAGTGGTAGTGATTCAGAAATGATTGTGCTTGATCAATCTCAT
*
1306344 TTGATGCTCTATGATCTTCGAGTGAAGTGGTTCAGTGATTCAGAAATTATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTC----GAAGTGG-T-AGTGATTCAGAAATGATTGTGCTTGATCAATC
1306409 TCAT
60 TCAT
1306413 AGTTTGAATC
Statistics
Matches: 60, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
61 19 0.32
66 6 0.10
69 35 0.58
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (63 bp):
TTGATGCTCTATGATCTTCGAAGTGGTAGTGATTCAGAAATGATTGTGCTTGATCAATCTCAT
Found at i:1306485 original size:26 final size:26
Alignment explanation
Indices: 1306451--1306511 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
1306441 ACATCTTGTC
1306451 TTCT-TTTTTCTTTAAT-TTTCCTTTTT
1 TTCTCTTTTT-TTT-ATCTTTCCTTTTT
* *
1306477 TTC-CTTTTTTTTCTCTTTGCTTTTT
1 TTCTCTTTTTTTTATCTTTCCTTTTT
1306502 TTCTCTTTTT
1 TTCTCTTTTT
1306512 GTTCTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 1 0.03
25 15 0.50
26 14 0.47
ACGTcount: A:0.03, C:0.18, G:0.02, T:0.77
Consensus pattern (26 bp):
TTCTCTTTTTTTTATCTTTCCTTTTT
Found at i:1306499 original size:25 final size:26
Alignment explanation
Indices: 1306471--1306521 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1306461 TTTAATTTTC
*
1306471 CTTTTTTTC-CTTTTTTTTCTCTTTG
1 CTTTTTTTCTCTTTTTGTTCTCTTTG
*
1306496 CTTTTTTTCTCTTTTTGTTCTGTTTG
1 CTTTTTTTCTCTTTTTGTTCTCTTTG
1306522 AATTTTCACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.00, C:0.18, G:0.08, T:0.75
Consensus pattern (26 bp):
CTTTTTTTCTCTTTTTGTTCTCTTTG
Found at i:1306512 original size:17 final size:16
Alignment explanation
Indices: 1306474--1306512 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1306464 AATTTTCCTT
*
1306474 TTTTTCCTTTTTTTTC
1 TTTTTGCTTTTTTTTC
*
1306490 TCTTTGCTTTTTTTCTC
1 TTTTTGCTTTTTTT-TC
1306507 TTTTTG
1 TTTTTG
1306513 TTCTGTTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.77
Consensus pattern (16 bp):
TTTTTGCTTTTTTTTC
Found at i:1306527 original size:26 final size:25
Alignment explanation
Indices: 1306473--1306527 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
1306463 TAATTTTCCT
* **
1306473 TTTTTTCCTTTTTTTTCTCTTTGCT
1 TTTTTTCCTTTTTGTTCTCTTTGAA
*
1306498 TTTTTTCTCTTTTTGTTCTGTTTGAA
1 TTTTTTC-CTTTTTGTTCTCTTTGAA
1306524 TTTT
1 TTTT
1306528 CACACTTGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.04, C:0.15, G:0.07, T:0.75
Consensus pattern (25 bp):
TTTTTTCCTTTTTGTTCTCTTTGAA
Found at i:1308479 original size:17 final size:18
Alignment explanation
Indices: 1308453--1308488 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1308443 TGCAAACGAT
*
1308453 GAAAACAAAAT-AAAAGA
1 GAAAAAAAAATGAAAAGA
1308470 GAAAAAAAAATGAAAAGA
1 GAAAAAAAAATGAAAAGA
1308488 G
1 G
1308489 GTTAGTGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.06
Consensus pattern (18 bp):
GAAAAAAAAATGAAAAGA
Found at i:1309598 original size:28 final size:24
Alignment explanation
Indices: 1309562--1309624 Score: 63
Period size: 28 Copynumber: 2.4 Consensus size: 24
1309552 AAAAACTAAC
*
1309562 AAAATATAAAACTAATGAAATAGAGAAG
1 AAAA-ATAAAACAAAT-AAA-AGA-AAG
1309590 ATAAAATAAAACAAATAAAAGAAAG
1 A-AAAATAAAACAAATAAAAGAAAG
*
1309615 AAAAAGAAAA
1 AAAAATAAAA
1309625 GAATAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 8 0.25
25 4 0.12
26 3 0.09
27 3 0.09
28 11 0.34
29 3 0.09
ACGTcount: A:0.73, C:0.03, G:0.11, T:0.13
Consensus pattern (24 bp):
AAAAATAAAACAAATAAAAGAAAG
Found at i:1309698 original size:21 final size:21
Alignment explanation
Indices: 1309654--1309718 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
1309644 CAAGTAAATT
* *
1309654 AAATAAAAATAAAGAAGCAAAAG
1 AAAT-AAAATAAATAA-AAAAAG
1309677 AAA-ATAAATAAATAAAAAAAG
1 AAATA-AAATAAATAAAAAAAG
* *
1309698 ACATAAAATAAATAAATAAAG
1 AAATAAAATAAATAAAAAAAG
1309719 TCCATAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 23 0.64
22 10 0.28
23 3 0.08
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.14
Consensus pattern (21 bp):
AAATAAAATAAATAAAAAAAG
Found at i:1309727 original size:21 final size:20
Alignment explanation
Indices: 1309680--1309731 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
1309670 GCAAAAGAAA
1309680 ATAAATAAATAAAAAAAGAC
1 ATAAATAAATAAAAAAAGAC
* *
1309700 ATAAAATAAATAAATAAAGTCC
1 AT-AAATAAATAAAAAAAG-AC
1309722 ATAAATAAAT
1 ATAAATAAAT
1309732 GGAATAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 23 0.82
22 3 0.11
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.21
Consensus pattern (20 bp):
ATAAATAAATAAAAAAAGAC
Found at i:1309865 original size:2 final size:2
Alignment explanation
Indices: 1309858--1309886 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1309848 CGAAATGATA
1309858 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1309887 AATAAATAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1309928 original size:19 final size:18
Alignment explanation
Indices: 1309806--1309956 Score: 70
Period size: 16 Copynumber: 8.5 Consensus size: 18
1309796 AAGAGAGAAA
1309806 AAATATA-AAATTAAT-T
1 AAATATATAAATTAATAT
*
1309822 AAATAAATAAA-TAGATAT
1 AAATATATAAATTA-ATAT
* *
1309840 AAGATAAACGAAATGATAATAT
1 AA-ATATA-TAAAT--TAATAT
* *
1309862 ATATATATATA-T-ATAT
1 AAATATATAAATTAATAT
*
1309878 ATATATATAAA-TAA-AT
1 AAATATATAAATTAATAT
* * *
1309894 AAAAACATAAA-AAATAGT
1 AAATATATAAATTAATA-T
1309912 AAATATATAAATTAATA-
1 AAATATATAAATTAATAT
1309929 AAATATAATGAAATT-ATAT
1 AAATAT-AT-AAATTAATAT
*
1309948 ATATATATA
1 AAATATATA
1309957 TTTGTAATCT
Statistics
Matches: 105, Mismatches: 15, Indels: 29
0.70 0.10 0.19
Matches are distributed among these distances:
16 35 0.33
17 15 0.14
18 20 0.19
19 19 0.18
20 5 0.05
21 4 0.04
22 5 0.05
23 2 0.02
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (18 bp):
AAATATATAAATTAATAT
Found at i:1309952 original size:34 final size:33
Alignment explanation
Indices: 1309874--1309954 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 33
1309864 ATATATATAT
1309874 ATATATATATATAAATAAATAAAAACATAAAAA
1 ATATATATATATAAATAAATAAAAACATAAAAA
* * *
1309907 ATAGTAAATATATAAATTAAT-AAAATATAATGAAA
1 ATA-TATATATATAAATAAATAAAAACATAA--AAA
*
1309942 TTATATATATATA
1 ATATATATATATA
1309955 TATTTGTAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
33 11 0.28
34 24 0.60
35 5 0.12
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.33
Consensus pattern (33 bp):
ATATATATATATAAATAAATAAAAACATAAAAA
Found at i:1325214 original size:26 final size:26
Alignment explanation
Indices: 1325168--1325222 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
1325158 CTGAAATTAG
*
1325168 AAAATTTAGGGATTTGAATTTCTTTT
1 AAAATTTAGGAATTTGAATTTCTTTT
* *
1325194 AAAATTTAGTGAATTT-TATTTTTTTT
1 AAAATTTAG-GAATTTGAATTTCTTTT
1325220 AAA
1 AAA
1325223 TTAATAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.35, C:0.02, G:0.11, T:0.53
Consensus pattern (26 bp):
AAAATTTAGGAATTTGAATTTCTTTT
Found at i:1329476 original size:2 final size:2
Alignment explanation
Indices: 1329469--1329515 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1329459 CTTTGTAAGG
1329469 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
1329511 AT AT A
1 AT AT A
1329516 CACTCAAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1334372 original size:20 final size:20
Alignment explanation
Indices: 1334349--1334390 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1334339 CAACACGAAC
* *
1334349 TCCAATTTCGCAACACAGTT
1 TCCAAATTCACAACACAGTT
*
1334369 TCCAAATTCACAACTCAGTT
1 TCCAAATTCACAACACAGTT
1334389 TC
1 TC
1334391 TGCAATCATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.07, T:0.31
Consensus pattern (20 bp):
TCCAAATTCACAACACAGTT
Found at i:1334493 original size:21 final size:20
Alignment explanation
Indices: 1334400--1334494 Score: 68
Period size: 21 Copynumber: 4.7 Consensus size: 20
1334390 CTGCAATCAT
*
1334400 AACGCGAATTTCT-TTCTCGC
1 AACGCGAATTTCTAAT-TCGC
* * *
1334420 AACGCGATTTTCCAAATTCCC
1 AACGCGAATTT-CTAATTCGC
*
1334441 AACACGAAATTTC-AATTCGC
1 AACGCG-AATTTCTAATTCGC
** *
1334461 AATTCGATTTTCTGAATTCGC
1 AACGCGAATTTCT-AATTCGC
1334482 AACGCGAATTTCT
1 AACGCGAATTTCT
1334495 TTTACGCAAC
Statistics
Matches: 57, Mismatches: 13, Indels: 9
0.72 0.16 0.11
Matches are distributed among these distances:
19 5 0.09
20 20 0.35
21 27 0.47
22 5 0.09
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
AACGCGAATTTCTAATTCGC
Found at i:1334503 original size:41 final size:40
Alignment explanation
Indices: 1334400--1334504 Score: 111
Period size: 41 Copynumber: 2.5 Consensus size: 40
1334390 CTGCAATCAT
1334400 AACGCGAATTTCTTTCTCGCAACGCGATTTTCCAAATTCCC
1 AACGCGAATTTCTTT-TCGCAACGCGATTTTCCAAATTCCC
* ** ** ** *
1334441 AACACGAAATTTCAATTCGCAATTCGATTTTCTGAATTCGC
1 AACGCG-AATTTCTTTTCGCAACGCGATTTTCCAAATTCCC
1334482 AACGCGAATTTCTTTTACGCAAC
1 AACGCGAATTTCTTTT-CGCAAC
1334505 ACAAGTTTCC
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
40 8 0.16
41 35 0.70
42 7 0.14
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (40 bp):
AACGCGAATTTCTTTTCGCAACGCGATTTTCCAAATTCCC
Found at i:1334561 original size:20 final size:20
Alignment explanation
Indices: 1334538--1334586 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1334528 ATTTTCTAAA
**
1334538 TCGCAACACGAATTTTGTTT
1 TCGCAACACGAATTTTGAAT
* *
1334558 TCGCAACTCGATTTTTGAAT
1 TCGCAACACGAATTTTGAAT
1334578 TCGCAACAC
1 TCGCAACAC
1334587 AAATGTTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (20 bp):
TCGCAACACGAATTTTGAAT
Found at i:1334700 original size:22 final size:22
Alignment explanation
Indices: 1334675--1334735 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
1334665 TATCACTCTC
*
1334675 TCCAGCGACATCCATTCCTATA
1 TCCAACGACATCCATTCCTATA
1334697 TCCAACGACATCCATTCCTATA
1 TCCAACGACATCCATTCCTATA
*
1334719 TCTAACGACATCC-TTCC
1 TCCAACGACATCCATTCC
1334736 CCATCTCTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
21 4 0.11
22 33 0.89
ACGTcount: A:0.28, C:0.38, G:0.07, T:0.28
Consensus pattern (22 bp):
TCCAACGACATCCATTCCTATA
Found at i:1335547 original size:24 final size:24
Alignment explanation
Indices: 1335520--1335573 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1335510 GTATTCGAAA
1335520 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1335544 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1335568 TTTGAT
1 TTTGAT
1335574 GATGTTCAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1338315 original size:20 final size:20
Alignment explanation
Indices: 1338273--1338318 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1338263 ATAATCGTAA
* *
1338273 TGCGAATTTGACTTTTGTAT
1 TGCGAATTTGACTTTCGCAT
*
1338293 TGCGAATTTGACTTTCGCGT
1 TGCGAATTTGACTTTCGCAT
1338313 TGCGAA
1 TGCGAA
1338319 AGTGTACCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (20 bp):
TGCGAATTTGACTTTCGCAT
Found at i:1339665 original size:21 final size:21
Alignment explanation
Indices: 1339615--1339752 Score: 131
Period size: 21 Copynumber: 6.7 Consensus size: 21
1339605 GTGAATCGGG
* *
1339615 CTCTTGAACGGT-AGGAGGGAC
1 CTCTTGAACGATGA-GAGGGGC
1339636 CTC-TGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
** * *
1339656 CTCTTGAACGGGGGGAGAGGC
1 CTCTTGAACGATGAGAGGGGC
* *
1339677 CTCTTAAAAGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
1339698 CTCTTGAATGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
**
1339719 CTCTTGAACGAT-AGGAGAAGC
1 CTCTTGAACGATGA-GAGGGGC
1339740 CTCTT-AACGATGA
1 CTCTTGAACGATGA
1339753 CAGGTGATCG
Statistics
Matches: 96, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
20 23 0.24
21 73 0.76
ACGTcount: A:0.27, C:0.18, G:0.36, T:0.20
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:1339721 original size:63 final size:62
Alignment explanation
Indices: 1339629--1339746 Score: 173
Period size: 63 Copynumber: 1.9 Consensus size: 62
1339619 TGAACGGTAG
* * *
1339629 GAGGGACCTCTGAACGATGAGAGGGGCCTCTTGAACGGGGGGAGAGGCCTCTTAAAAGATGA
1 GAGGGACCTCTGAACGATGAGAGGGGCCTCTTGAACGAGAGGAGAAGCCTCTTAAAAGATGA
* * *
1339691 GAGGGGCCTCTTGAATGATGAGAGGGGCCTCTTGAACGATAGGAGAAGCCTCTTAA
1 GAGGGACCTC-TGAACGATGAGAGGGGCCTCTTGAACGAGAGGAGAAGCCTCTTAA
1339747 CGATGACAGG
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
62 9 0.18
63 40 0.82
ACGTcount: A:0.27, C:0.18, G:0.36, T:0.19
Consensus pattern (62 bp):
GAGGGACCTCTGAACGATGAGAGGGGCCTCTTGAACGAGAGGAGAAGCCTCTTAAAAGATGA
Found at i:1341842 original size:19 final size:20
Alignment explanation
Indices: 1341804--1341847 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
1341794 TGAAACTAAT
*
1341804 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATCAAAA
1341824 TCGCAACGCG-AAATCAAAA
1 TCGCAACGCGAAAATCAAAA
1341843 TCGCA
1 TCGCA
1341848 TTGCGAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.45, C:0.25, G:0.18, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAATCAAAA
Found at i:1341871 original size:20 final size:20
Alignment explanation
Indices: 1341843--1341911 Score: 60
Period size: 20 Copynumber: 3.8 Consensus size: 20
1341833 GAAATCAAAA
*
1341843 TCGCATTGCGAATTTCATTT
1 TCGCGTTGCGAATTTCATTT
1341863 TCGCGTTGCG------ATTT
1 TCGCGTTGCGAATTTCATTT
*
1341877 TCGTGTTGCGAATTTCATTT
1 TCGCGTTGCGAATTTCATTT
* *
1341897 TTGTGTTGCGAATTT
1 TCGCGTTGCGAATTT
1341912 AAGTTTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 13 0.32
20 27 0.68
ACGTcount: A:0.14, C:0.16, G:0.22, T:0.48
Consensus pattern (20 bp):
TCGCGTTGCGAATTTCATTT
Found at i:1341878 original size:14 final size:14
Alignment explanation
Indices: 1341859--1341892 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1341849 TGCGAATTTC
1341859 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
*
1341873 ATTTTCGTGTTGCG
1 ATTTTCGCGTTGCG
*
1341887 AATTTC
1 ATTTTC
1341893 ATTTTTGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:1342446 original size:19 final size:19
Alignment explanation
Indices: 1342410--1342449 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1342400 TTCGAATTCA
**
1342410 AAAATAAATTCGCGTTGCG
1 AAAATAAACGCGCGTTGCG
*
1342429 AAAATAAACGCGCTTTGCG
1 AAAATAAACGCGCGTTGCG
1342448 AA
1 AA
1342450 TTTGACTTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (19 bp):
AAAATAAACGCGCGTTGCG
Found at i:1349896 original size:27 final size:27
Alignment explanation
Indices: 1349842--1349896 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
1349832 TTTATTAGAG
* **
1349842 AATTTAACACACATATATATATGTAAT
1 AATTTAAAACACATATATATATAAAAT
1349869 AATTTAAAACACA-ATATGATATAAAAT
1 AATTTAAAACACATATAT-ATATAAAAT
1349896 A
1 A
1349897 TATAAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.33
Consensus pattern (27 bp):
AATTTAAAACACATATATATATAAAAT
Found at i:1357734 original size:31 final size:31
Alignment explanation
Indices: 1357667--1357767 Score: 84
Period size: 31 Copynumber: 3.3 Consensus size: 31
1357657 TAAGTAGCGC
* * *
1357667 AAAAAATAATTA-ATTAATA-AATTTAAAT-
1 AAAAAATAATTATATAAATATTATTTTAATA
*
1357695 AAATAATAATTATATAAATATTATTTTAATA
1 AAAAAATAATTATATAAATATTATTTTAATA
* * *
1357726 AAAAAATAA-TATTTATATAATTATATTAATA
1 AAAAAATAATTATATAAAT-ATTATTTTAATA
*
1357757 TAAAATATAAT
1 -AAAAAATAAT
1357768 AACTATTTTA
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
28 11 0.19
29 6 0.10
30 14 0.24
31 19 0.33
32 8 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
AAAAAATAATTATATAAATATTATTTTAATA
Found at i:1358500 original size:15 final size:15
Alignment explanation
Indices: 1358480--1358531 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
1358470 CTAGAATTTG
1358480 AATTATTGAAAAATT
1 AATTATTGAAAAATT
* *
1358495 AATTATTG-GAATTT
1 AATTATTGAAAAATT
*
1358509 AAATTACTGAAAAATT
1 -AATTATTGAAAAATT
1358525 AATTATT
1 AATTATT
1358532 AGAATTTGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 4 0.14
15 21 0.72
16 4 0.14
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (15 bp):
AATTATTGAAAAATT
Found at i:1358507 original size:30 final size:30
Alignment explanation
Indices: 1358471--1358559 Score: 126
Period size: 30 Copynumber: 3.0 Consensus size: 30
1358461 ACATTTTTAC
*
1358471 TAGAATTTGAATTATTGAAAAATTAATTAT
1 TAGAATTTGAATTACTGAAAAATTAATTAT
* *
1358501 TGGAATTTAAATTACTGAAAAATTAATTAT
1 TAGAATTTGAATTACTGAAAAATTAATTAT
* *
1358531 TAGAATTTGAATT-CTGGAAAATGAATTAT
1 TAGAATTTGAATTACTGAAAAATTAATTAT
1358560 ATTTTTGGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
29 14 0.27
30 38 0.73
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.40
Consensus pattern (30 bp):
TAGAATTTGAATTACTGAAAAATTAATTAT
Found at i:1358828 original size:28 final size:27
Alignment explanation
Indices: 1358772--1358830 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
1358762 TAAAAATTTA
* **
1358772 TTTATTATTAAATATTATTTTTATAAT
1 TTTATTATAAAATATTATTGGTATAAT
1358799 TTTATTAATAAAATATTAATTGGTAT-AT
1 TTTATT-ATAAAATATT-ATTGGTATAAT
1358827 TTTA
1 TTTA
1358831 GTGAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 6 0.22
28 15 0.56
29 6 0.22
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (27 bp):
TTTATTATAAAATATTATTGGTATAAT
Found at i:1359082 original size:26 final size:25
Alignment explanation
Indices: 1358966--1359084 Score: 80
Period size: 26 Copynumber: 4.6 Consensus size: 25
1358956 AATATATCAT
1358966 AATATATTCATTATTA-AATATAAAAA
1 AATATATT-A-TATTATAATATAAAAA
* * *
1358992 AAT-TATTATATATTTATTAAAATAAA
1 AATATATTATAT-TATAATATAA-AAA
* * * *
1359018 AATATAATATCTTATATTATAATAA
1 AATATATTATATTATAATATAAAAA
* * *
1359043 ATTGATTTTTTATTATAATATAAAAA
1 AAT-ATATTATATTATAATATAAAAA
1359069 AATAATATTATATTAT
1 AAT-ATATTATATTAT
1359085 TATAAATATT
Statistics
Matches: 69, Mismatches: 19, Indels: 10
0.70 0.19 0.10
Matches are distributed among these distances:
23 3 0.04
24 2 0.03
25 13 0.19
26 45 0.65
27 6 0.09
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (25 bp):
AATATATTATATTATAATATAAAAA
Found at i:1359380 original size:42 final size:42
Alignment explanation
Indices: 1359324--1359418 Score: 163
Period size: 42 Copynumber: 2.3 Consensus size: 42
1359314 TTCCTCCAAC
* * *
1359324 CAAACACTGGAAAACATTTTCCGGAAAACGAATTACATGAAA
1 CAAACACGGGAAAACAATTTCCAGAAAACGAATTACATGAAA
1359366 CAAACACGGGAAAACAATTTCCAGAAAACGAATTACATGAAA
1 CAAACACGGGAAAACAATTTCCAGAAAACGAATTACATGAAA
1359408 CAAACACGGGA
1 CAAACACGGGA
1359419 TTTTGAGGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.49, C:0.20, G:0.16, T:0.15
Consensus pattern (42 bp):
CAAACACGGGAAAACAATTTCCAGAAAACGAATTACATGAAA
Found at i:1360252 original size:19 final size:20
Alignment explanation
Indices: 1360228--1360278 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1360218 AATGACCAAT
1360228 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
1360247 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
1360267 AAAATCGCAACG
1 AAAATCGCAACG
1360279 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:1360272 original size:20 final size:20
Alignment explanation
Indices: 1360228--1360545 Score: 147
Period size: 20 Copynumber: 15.6 Consensus size: 20
1360218 AATGACCAAT
* *
1360228 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
1360247 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
1360267 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
1360287 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
1360307 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
1360328 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1360351 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * * *
1360371 AGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
1360391 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
1360411 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
1360431 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1360454 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
1360474 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
1360494 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
1360514 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
1360534 AGAATCGCAACG
1 AAAATCGCAACG
1360546 TTAAAAAGAA
Statistics
Matches: 244, Mismatches: 43, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
19 17 0.07
20 184 0.75
21 14 0.06
23 29 0.12
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:1360404 original size:40 final size:40
Alignment explanation
Indices: 1360353--1360543 Score: 256
Period size: 40 Copynumber: 4.7 Consensus size: 40
1360343 TTTAGAAGAA
* *
1360353 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
* *
1360393 AATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
* * * *
1360433 AGTCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGA-TT-G-AGAGAATCGCAATGCGATTGAGAG
* * *
1360476 AATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
1360516 AATCGCAATGCGATTGAGAGAATCGCAA
1 AATCGCAATGCGATTGAGAGAATCGCAA
1360544 CGTTAAAAAG
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
40 96 0.73
41 3 0.02
42 1 0.01
43 32 0.24
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (40 bp):
AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
Found at i:1360460 original size:83 final size:83
Alignment explanation
Indices: 1360373--1360530 Score: 235
Period size: 83 Copynumber: 1.9 Consensus size: 83
1360363 CGATTGATAG
* * * * * *
1360373 AATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAGTCG
1 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCG
1360438 CAACGCGATTTAGAAGAA
66 CAACGCGATTTAGAAGAA
* *
1360456 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATCG
1 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCG
*
1360521 CAATGCGATT
66 CAACGCGATT
1360531 GAGAGAATCG
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
83 66 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.22
Consensus pattern (83 bp):
AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATCG
CAACGCGATTTAGAAGAA
Found at i:1360464 original size:103 final size:103
Alignment explanation
Indices: 1360332--1360545 Score: 383
Period size: 103 Copynumber: 2.1 Consensus size: 103
1360322 GCTTCCAAGT
* * * *
1360332 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
*
1360397 GCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAG
66 GCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAA
1360435 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1360500 GCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAA
66 GCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAA
1360538 TCGCAACG
1 TCGCAACG
1360546 TTAAAAAGAA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (103 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
GCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAA
Found at i:1360559 original size:20 final size:20
Alignment explanation
Indices: 1360536--1360575 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1360526 CGATTGAGAG
*
1360536 AATCGCAACGTTAAAAAGAA
1 AATCGCAACGGTAAAAAGAA
*
1360556 AATCGCAACGGTCAAAAGAA
1 AATCGCAACGGTAAAAAGAA
1360576 TAGTTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.17, G:0.17, T:0.12
Consensus pattern (20 bp):
AATCGCAACGGTAAAAAGAA
Found at i:1360663 original size:6 final size:6
Alignment explanation
Indices: 1360652--1360717 Score: 111
Period size: 6 Copynumber: 11.5 Consensus size: 6
1360642 GACACGTATT
1360652 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1360700 ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACC
1360718 CGAGATGAGA
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.25
6 45 0.75
ACGTcount: A:0.30, C:0.53, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1361414 original size:6 final size:6
Alignment explanation
Indices: 1361393--1361447 Score: 96
Period size: 6 Copynumber: 9.5 Consensus size: 6
1361383 CGTCTCGGGC
1361393 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1361439 GGTCGT GGT
1 GGTCGT GGT
1361448 AATACGTGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.20
6 39 0.80
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:1361578 original size:20 final size:20
Alignment explanation
Indices: 1361555--1361721 Score: 182
Period size: 20 Copynumber: 8.3 Consensus size: 20
1361545 ATTTTCAACG
*
1361555 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTATCAATCGCA
* *
1361575 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTATCAATCGCA
* *
1361595 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTATCAATCGCA
1361615 TTGCGATTTTCT-TCTAAATCGCA
1 TTGCGA--TTCTATC--AATCGCA
1361638 TTGCG-TTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
1361657 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
*
1361677 TTGCAATTCTATCAAT-GC-
1 TTGCGATTCTATCAATCGCA
*
1361695 TTGCGATTTCT-TCTAATCGCG
1 TTGCGA-TTCTATC-AATCGCA
1361716 TTGCGA
1 TTGCGA
1361722 ACTTGGAAGC
Statistics
Matches: 131, Mismatches: 6, Indels: 19
0.84 0.04 0.12
Matches are distributed among these distances:
18 7 0.05
19 21 0.16
20 78 0.60
21 10 0.08
22 4 0.03
23 11 0.08
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTATCAATCGCA
Found at i:1361654 original size:82 final size:79
Alignment explanation
Indices: 1361555--1361721 Score: 228
Period size: 82 Copynumber: 2.1 Consensus size: 79
1361545 ATTTTCAACG
* * * * *
1361555 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCATTGCG
1 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCAATTCTATCAAT-GC-TTGCG
1361620 ATTTTCTTCTAAATCGCA
64 A-TTTCTTCT-AATCGCA
*
1361638 TTGCG-TTCTATCAATCGCATTGCGATTCTATCAATCGCATTGCAATTCTATCAATGCTTGCGAT
1 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCAATTCTATCAATGCTTGCGAT
*
1361702 TTCTTCTAATCGCG
66 TTCTTCTAATCGCA
1361716 TTGCGA
1 TTGCGA
1361722 ACTTGGAAGC
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
78 11 0.14
79 8 0.11
80 6 0.08
81 2 0.03
82 44 0.58
83 5 0.07
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.38
Consensus pattern (79 bp):
TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCAATTCTATCAATGCTTGCGAT
TTCTTCTAATCGCA
Found at i:1361779 original size:21 final size:19
Alignment explanation
Indices: 1361755--1361806 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
1361745 TTCTTTTTAA
*
1361755 CGTTGCCGATTTTCTAAATCG
1 CGTTG-CGATTTT-GAAATCG
*
1361776 CGTTGCGATTTTGATATCG
1 CGTTGCGATTTTGAAATCG
1361795 CGTTGCGATTTT
1 CGTTGCGATTTT
1361807 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 7 0.24
21 5 0.17
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTGAAATCG
Found at i:1373310 original size:17 final size:18
Alignment explanation
Indices: 1373267--1373307 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1373257 GAATTATATT
1373267 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
1373284 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
1373302 ATTAAA
1 AGTAAA
1373308 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:1375973 original size:17 final size:17
Alignment explanation
Indices: 1375951--1375983 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1375941 AAGAACTTTG
1375951 AAAATATGTAAACAAAT
1 AAAATATGTAAACAAAT
1375968 AAAATATGTAAACAAA
1 AAAATATGTAAACAAA
1375984 AATGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.21
Consensus pattern (17 bp):
AAAATATGTAAACAAAT
Found at i:1376006 original size:15 final size:15
Alignment explanation
Indices: 1375988--1376040 Score: 63
Period size: 16 Copynumber: 3.5 Consensus size: 15
1375978 AACAAAAATG
1375988 AAAAAAACTTTAATT
1 AAAAAAACTTTAATT
*
1376003 -AAAAAACTTTTATTT
1 AAAAAAAC-TTTAATT
*
1376018 AAAATAAAATTTAATT
1 AAAA-AAACTTTAATT
1376034 AAAAAAA
1 AAAAAAA
1376041 TTCATTCATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 7 0.22
15 9 0.28
16 13 0.41
17 3 0.09
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAAAACTTTAATT
Found at i:1376008 original size:14 final size:14
Alignment explanation
Indices: 1375989--1376039 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
1375979 ACAAAAATGA
1375989 AAAAAACTTTAATT
1 AAAAAACTTTAATT
*
1376003 AAAAAACTTTTATTT
1 AAAAAAC-TTTAATT
*
1376018 AAAATAAAATTTAATT
1 -AAA-AAACTTTAATT
1376034 AAAAAA
1 AAAAAA
1376040 ATTCATTCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 10 0.32
15 9 0.29
16 9 0.29
17 3 0.10
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAAAACTTTAATT
Found at i:1376035 original size:16 final size:15
Alignment explanation
Indices: 1375988--1376040 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
1375978 AACAAAAATG
*
1375988 AAAAAAACTTTAATT
1 AAAAAAAATTTAATT
** *
1376003 AAAAAACTTTTATTT
1 AAAAAAAATTTAATT
1376018 AAAATAAAATTTAATT
1 AAAA-AAAATTTAATT
1376034 AAAAAAA
1 AAAAAAA
1376041 TTCATTCATA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
15 19 0.61
16 12 0.39
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAAAAATTTAATT
Found at i:1376508 original size:11 final size:11
Alignment explanation
Indices: 1376494--1376523 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1376484 TTGAAAATTT
1376494 AAAAAATTTGA
1 AAAAAATTTGA
1376505 AAAAAATTTGA
1 AAAAAATTTGA
1376516 AAAAAATT
1 AAAAAATT
1376524 CCATGGAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (11 bp):
AAAAAATTTGA
Found at i:1376509 original size:10 final size:10
Alignment explanation
Indices: 1376487--1376520 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 10
1376477 TTATTTTTTG
1376487 AAAATTT-AA
1 AAAATTTGAA
1376496 AAAATTTGAAA
1 AAAATTTG-AA
1376507 AAAATTTGAA
1 AAAATTTGAA
1376517 AAAA
1 AAAA
1376521 ATTCCATGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.30
10 6 0.26
11 10 0.43
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (10 bp):
AAAATTTGAA
Found at i:1377485 original size:21 final size:22
Alignment explanation
Indices: 1377453--1377498 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1377443 AAATAATACA
*
1377453 AGTTAGAAAAAATCATAGTTAC
1 AGTTAGAAAAAAACATAGTTAC
*
1377475 AGTTA-AAAAAAACCTAGTTAC
1 AGTTAGAAAAAAACATAGTTAC
1377496 AGT
1 AGT
1377499 ACATAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (22 bp):
AGTTAGAAAAAAACATAGTTAC
Found at i:1381703 original size:13 final size:13
Alignment explanation
Indices: 1381685--1381709 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1381675 GAGTTTTTGC
1381685 CAAAGTCAATGGT
1 CAAAGTCAATGGT
1381698 CAAAGTCAATGG
1 CAAAGTCAATGG
1381710 GTTGACTCGA
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:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (13 bp):
CAAAGTCAATGGT
Found at i:1384659 original size:28 final size:30
Alignment explanation
Indices: 1384626--1384690 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 30
1384616 TTTTGATAAT
1384626 TTTAAAATTA-AAAAAAAA-C-CCTAATTTA
1 TTTAAAATTACAAAAAAAATCTCC-AATTTA
1384654 TTT-AAATTACAAAAAAAATCTCCAATTTA
1 TTTAAAATTACAAAAAAAATCTCCAATTTA
*
1384683 TTAAAAAT
1 TTTAAAAT
1384691 CCTAAATCCT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 6 0.19
28 11 0.34
29 9 0.28
30 6 0.19
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (30 bp):
TTTAAAATTACAAAAAAAATCTCCAATTTA
Found at i:1384662 original size:27 final size:29
Alignment explanation
Indices: 1384630--1384684 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1384620 GATAATTTTA
1384630 AAATTA-AAAAAAAA-C-CCTAATTTATTT
1 AAATTACAAAAAAAATCTCC-AATTTATTT
1384657 AAATTACAAAAAAAATCTCCAATTTATT
1 AAATTACAAAAAAAATCTCCAATTTATT
1384685 AAAAATCCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 6 0.24
28 8 0.32
29 9 0.36
30 2 0.08
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.33
Consensus pattern (29 bp):
AAATTACAAAAAAAATCTCCAATTTATTT
Found at i:1390046 original size:16 final size:17
Alignment explanation
Indices: 1390008--1390039 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1389998 AAGAAATTTA
1390008 ATATA-TAAATATAGAT
1 ATATATTAAATATAGAT
1390024 ATATATTAAATA-AGAT
1 ATATATTAAATATAGAT
1390040 TTTTATTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
ATATATTAAATATAGAT
Found at i:1390361 original size:2 final size:2
Alignment explanation
Indices: 1390354--1390385 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1390344 TACATTTTTA
1390354 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
1390386 TAAATAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1396609 original size:5 final size:5
Alignment explanation
Indices: 1396595--1396653 Score: 59
Period size: 5 Copynumber: 11.8 Consensus size: 5
1396585 GTCCGTCCGT
* *
1396595 CTCGT CTCGG CTCGG CACGG -TACGG CAT-GG CTCGG CTCGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CT-CGG C-TCGG CTCGG CTCGG CTCGG CTCGG
*
1396645 CTCAG CTCG
1 CTCGG CTCG
1396654 AGTCGTGGTC
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
4 1 0.02
5 43 0.96
7 1 0.02
ACGTcount: A:0.07, C:0.37, G:0.36, T:0.20
Consensus pattern (5 bp):
CTCGG
Found at i:1396970 original size:22 final size:22
Alignment explanation
Indices: 1396945--1396999 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1396935 TCAGGAGTTA
* *
1396945 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1396967 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
1396989 CAGGAGTTATA
1 CAGGAGTTATA
1397000 ACAACTGAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1405246 original size:36 final size:36
Alignment explanation
Indices: 1405206--1405274 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
1405196 TTAACAAGTC
* *
1405206 TATTCACCAAGTGACATGACTTATTATTATCATTTA
1 TATTCACCAAATGACATAACTTATTATTATCATTTA
*
1405242 TATTCACCAAATTACATAACTTATTATTATCAT
1 TATTCACCAAATGACATAACTTATTATTATCAT
1405275 CAATATTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.36, C:0.17, G:0.04, T:0.42
Consensus pattern (36 bp):
TATTCACCAAATGACATAACTTATTATTATCATTTA
Found at i:1405281 original size:36 final size:36
Alignment explanation
Indices: 1405206--1405289 Score: 107
Period size: 36 Copynumber: 2.4 Consensus size: 36
1405196 TTAACAAGTC
* * * **
1405206 TATTCACCAAGTGACATGACTTATTATTATCATTTA
1 TATTCACCAAATTACATAACTTATTATTATCATCAA
1405242 TATTCACCAAATTACATAACTTATTATTATCATCAA
1 TATTCACCAAATTACATAACTTATTATTATCATCAA
*
1405278 TATT-ACTAAATT
1 TATTCACCAAATT
1405290 TATCCATTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 7 0.17
36 35 0.83
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.42
Consensus pattern (36 bp):
TATTCACCAAATTACATAACTTATTATTATCATCAA
Found at i:1411746 original size:20 final size:20
Alignment explanation
Indices: 1411721--1411794 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
1411711 TTTTCCCAAT
*
1411721 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
** *
1411741 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAA-TAAGTAAA
*
1411762 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
1411782 TCGCAACGCGAAT
1 TCGCAACGCGAAT
1411795 TGGGAAAATC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:1411813 original size:21 final size:21
Alignment explanation
Indices: 1411738--1411805 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
1411728 GCGAATAAGT
1411738 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
1411759 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
1411779 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
1411800 AAATCG
1 AAATCG
1411806 TAATGCGATA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 16 0.42
21 22 0.58
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:1411828 original size:41 final size:41
Alignment explanation
Indices: 1411721--1411813 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
1411711 TTTTCCCAAT
1411721 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1411762 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
1411803 TCGTAATGCGA
1 TCGCAATGCGA
1411814 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Done.