Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000402.1 Hibiscus syriacus cultivar Beakdansim tig00000738_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: 1701760
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 7
Found at i:917390 original size:12 final size:12
Alignment explanation
Indices: 917373--917401 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
917363 TAGTTGTTTG
917373 TGTTCGTTCGTT
1 TGTTCGTTCGTT
917385 TGTTCGTTCGTT
1 TGTTCGTTCGTT
917397 TGTTC
1 TGTTC
917402 TGTTAAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.24, T:0.59
Consensus pattern (12 bp):
TGTTCGTTCGTT
Found at i:919450 original size:22 final size:22
Alignment explanation
Indices: 919420--919471 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
919410 ATTCCCGTAT
*
919420 GTTTTTCTGCAGAAAAACATCA
1 GTTTCTCTGCAGAAAAACATCA
919442 GTTTCTCTGCAGAAAAACATCA
1 GTTTCTCTGCAGAAAAACATCA
919464 GTTTCTCT
1 GTTTCTCT
919472 CCTCCAGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (22 bp):
GTTTCTCTGCAGAAAAACATCA
Found at i:922109 original size:24 final size:24
Alignment explanation
Indices: 922082--922133 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
922072 ATCTTACCTA
922082 GATTCTGATC-GAATACTTGACATG
1 GATTCTGATCTG-ATACTTGACATG
* *
922106 GATTTTGATCTGATACTTGACCTG
1 GATTCTGATCTGATACTTGACATG
922130 GATT
1 GATT
922134 ATATTTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
GATTCTGATCTGATACTTGACATG
Found at i:924909 original size:158 final size:157
Alignment explanation
Indices: 924615--925034 Score: 490
Period size: 158 Copynumber: 2.7 Consensus size: 157
924605 TTAGTCCATG
* * * * * * * *
924615 ATTTCATTATTCCTTCAATTCATCGTTCATTTCAAGTCTATTTTTAACCAAATTTGAACCATATG
1 ATTTCCTTATTTCTTCAATTCATCATTTATTTTAAGTCTGTTTTTAACCAAATTTGAATCACATG
** * ** *
924680 CT-TCTAATTCATCGTAGAACGCATATGTACTTTCAATTCCTCTTTTCGATAACAAGTGTTCTAT
66 CTCT-TAAACCATCATAGAATACATATGTACTTTCAATTCCTCTTTTCGATAACAAGTGTTCTAC
*
924744 TTTCAATTTAGTCCCTCAATTCTTCATA
130 TTCCAATTTAGTCCCTCAATTCTTCATA
* * * *
924772 TTTTCCTTATTTCTTCAATTCATCATTTATTTTAAGTCTGTTGTTTTATCAAATTTAAATCACAT
1 ATTTCCTTATTTCTTCAATTCATCATTTATTTTAAGTCTGTT-TTTAACCAAATTTGAATCACAT
*
924837 GCTCTTAAACCATCATAGAATACATATGTACTTTCAATTCCTCTTTTCGATAACAAGTTTTCTAC
65 GCTCTTAAACCATCATAGAATACATATGTACTTTCAATTCCTCTTTTCGATAACAAGTGTTCTAC
* *
924902 TTCCAATTTAGTTCCTCAATTTTTCATA
130 TTCCAATTTAGTCCCTCAATTCTTCATA
* * *
924930 ATTTCCTTTTTTTTCTTCAATTCATTATTTATTTTAAGT-TCG-TTTTCACCAAATTTGAATCAC
1 ATTTCC--TTATTTCTTCAATTCATCATTTATTTTAAGTCT-GTTTTTAACCAAATTTGAATCAC
* * *
924993 ATGCTCATATACCA-CTATAGAATACCTATGTAAC-TTCAATTC
63 ATGCTCTTAAACCATC-ATAGAATACATATGT-ACTTTCAATTC
925035 TTATATTTTT
Statistics
Matches: 225, Mismatches: 31, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
157 36 0.16
158 154 0.68
159 5 0.02
160 30 0.13
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.45
Consensus pattern (157 bp):
ATTTCCTTATTTCTTCAATTCATCATTTATTTTAAGTCTGTTTTTAACCAAATTTGAATCACATG
CTCTTAAACCATCATAGAATACATATGTACTTTCAATTCCTCTTTTCGATAACAAGTGTTCTACT
TCCAATTTAGTCCCTCAATTCTTCATA
Found at i:928932 original size:106 final size:106
Alignment explanation
Indices: 928747--928964 Score: 400
Period size: 106 Copynumber: 2.1 Consensus size: 106
928737 TGTGTGAGAA
*
928747 TTGCATCGGGAGGTGAGTTTCATTTTCGAAGCATCAACATTTACGAGAGCAATGTTTTAGAGTAG
1 TTGCATCGAGAGGTGAGTTTCATTTTCGAAGCATCAACATTTACGAGAGCAATGTTTTAGAGTAG
*
928812 AGAGATCTAGTTGACTGATTGTCTTAGCATACTTAGTAAAT
66 AGAGATCTAGTTGACTGATTATCTTAGCATACTTAGTAAAT
* *
928853 TTGCATCGAGAGGTGAGTTTCATTTTCGAAGCATCAACATTTACTAGAGTAATGTTTTAGAGTAG
1 TTGCATCGAGAGGTGAGTTTCATTTTCGAAGCATCAACATTTACGAGAGCAATGTTTTAGAGTAG
928918 AGAGATCTAGTTGACTGATTATCTTAGCATACTTAGTAAAT
66 AGAGATCTAGTTGACTGATTATCTTAGCATACTTAGTAAAT
928959 TTGCAT
1 TTGCAT
928965 AACATTGGTG
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 108 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (106 bp):
TTGCATCGAGAGGTGAGTTTCATTTTCGAAGCATCAACATTTACGAGAGCAATGTTTTAGAGTAG
AGAGATCTAGTTGACTGATTATCTTAGCATACTTAGTAAAT
Found at i:932961 original size:64 final size:63
Alignment explanation
Indices: 932893--933049 Score: 163
Period size: 64 Copynumber: 2.4 Consensus size: 63
932883 TTCAGTGTGT
* * * *
932893 ATCGATGCACAGGAAGTGGATCGATGCACCCCTTAAAAAT-AGAAACATCGAATGCAATTGGTGC
1 ATCGATGCAAAGG-AGTGCATCGATGCACCCCTTAAAAATGA-AAACATCAAAGGCAATTGGTGC
* * * * * *
932957 ATCGATGCATAAGGAGTGCATCGATGCATCCCTTTAAGATGAAAACATCAAAGGTAATTTGTGT
1 ATCGATGCA-AAGGAGTGCATCGATGCACCCCTTAAAAATGAAAACATCAAAGGCAATTGGTGC
**
933021 ATCGATGCATGGGTAGTGCATCGATGCAC
1 ATCGATGCAAAGG-AGTGCATCGATGCAC
933050 ATGTTAAAGA
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
63 2 0.03
64 71 0.92
65 4 0.05
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (63 bp):
ATCGATGCAAAGGAGTGCATCGATGCACCCCTTAAAAATGAAAACATCAAAGGCAATTGGTGC
Found at i:933082 original size:20 final size:22
Alignment explanation
Indices: 933037--933094 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
933027 GCATGGGTAG
933037 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
933061 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
933081 TGCATCGATGCACT
1 TGCATCGATGCACT
933095 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:934601 original size:23 final size:23
Alignment explanation
Indices: 934533--934593 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
934523 ACATTTTATA
*
934533 TGGCATTTCAGTGCAATTCTACG
1 TGGCACTTCAGTGCAATTCTACG
* **
934556 CGGCACTTTGGTGCAATTCTACG
1 TGGCACTTCAGTGCAATTCTACG
934579 TGGCACTTCAGTGCA
1 TGGCACTTCAGTGCA
934594 TTTATACGAG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.31
Consensus pattern (23 bp):
TGGCACTTCAGTGCAATTCTACG
Found at i:939729 original size:23 final size:23
Alignment explanation
Indices: 939699--939759 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
939689 ACATTTTATA
*
939699 TGGCACTTTGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
939722 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
939745 TGGCACTTCAGTGCA
1 TGGCACTTCGGTGCA
939760 TTTATATGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:944228 original size:26 final size:26
Alignment explanation
Indices: 944184--944233 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
944174 CAGAAGGCGC
*
944184 GCTGACTAGATCTTATAGAAACTGAT
1 GCTGACTAGACCTTATAGAAACTGAT
* *
944210 GCTGACTGGACCTTCTAGAAACTG
1 GCTGACTAGACCTTATAGAAACTG
944234 CCACGTCAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (26 bp):
GCTGACTAGACCTTATAGAAACTGAT
Found at i:945113 original size:21 final size:18
Alignment explanation
Indices: 945071--945144 Score: 94
Period size: 18 Copynumber: 3.9 Consensus size: 18
945061 ACTGAATATT
*
945071 TGTCCTGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
945089 TGTCCCGAAGGACCACTGATA
1 TGTCCCGAAGGACCAC---TA
* *
945110 TGTCCTGAAGGACTACTA
1 TGTCCCGAAGGACCACTA
945128 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
945145 GATAATCCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
18 32 0.67
21 16 0.33
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:945117 original size:39 final size:39
Alignment explanation
Indices: 945071--945148 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
945061 ACTGAATATT
945071 TGTCCTGAAGGACCACTATGTCCCGAAGGACCACTGATA
1 TGTCCTGAAGGACCACTATGTCCCGAAGGACCACTGATA
*
945110 TGTCCTGAAGGACTACTATGTCCCGAAGGACCACTGATA
1 TGTCCTGAAGGACCACTATGTCCCGAAGGACCACTGATA
945149 ATCCCTCGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.22
Consensus pattern (39 bp):
TGTCCTGAAGGACCACTATGTCCCGAAGGACCACTGATA
Found at i:946787 original size:63 final size:64
Alignment explanation
Indices: 946700--946841 Score: 155
Period size: 63 Copynumber: 2.2 Consensus size: 64
946690 TCCTTAACGT
* ** *
946700 GTGCATCGATGCACTACCTGTGCATCGGTACACAAATCACCTTCGAT-GTT-TATTCTTAAGGGG
1 GTGCATCGATGCACTACCTATGCATCAATACACAAATCACATTCGATAGTTGTATT-TTAAGGGG
* * * ** *
946763 GTGCATCGATGCACT-CCTTATGCATTAATGCACTAATTGCATTCGATATTTGTATTTTAAGGGG
1 GTGCATCGATGCACTACC-TATGCATCAATACACAAATCACATTCGATAGTTGTATTTTAAGGGG
946827 GTGCATCGATGCACT
1 GTGCATCGATGCACT
946842 GATGGCATTC
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
62 2 0.03
63 35 0.53
64 25 0.38
65 4 0.06
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCACTACCTATGCATCAATACACAAATCACATTCGATAGTTGTATTTTAAGGGG
Found at i:949188 original size:63 final size:63
Alignment explanation
Indices: 949084--949227 Score: 216
Period size: 63 Copynumber: 2.3 Consensus size: 63
949074 GGCTAGGTCC
* * *
949084 GGGTCACAAAGCATCAACCTTTGCCAAGTTAGCCTACCCCTCTATGATACTTAAAACACATTT
1 GGGTCACAAAGCATCAACCTTTGCCAAGTTAGCCTACCCCTCTAGGATACTCAAAACAAATTT
* * * *
949147 GGGTCAAAAAGCATCAACCTTTGCCAAGTTGGTCTATCCCTCTAGGATACTCAAAACAAATTT
1 GGGTCACAAAGCATCAACCTTTGCCAAGTTAGCCTACCCCTCTAGGATACTCAAAACAAATTT
*
949210 GGGTCACATAGCATCAAC
1 GGGTCACAAAGCATCAAC
949228 AACAAGACGT
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 72 1.00
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (63 bp):
GGGTCACAAAGCATCAACCTTTGCCAAGTTAGCCTACCCCTCTAGGATACTCAAAACAAATTT
Found at i:951538 original size:95 final size:95
Alignment explanation
Indices: 951375--951555 Score: 326
Period size: 95 Copynumber: 1.9 Consensus size: 95
951365 ACAAGGAATT
* *
951375 GGAGATTGTTTGTGTTTTCTTCTCTCAGCTCTATTCTTTTATACTTTATATGTGTACCATCTCGA
1 GGAGATTGTTTGTGTTTACTTCTCTCAGCTCTATTCTTTTATACTTTATATGTGCACCATCTCGA
*
951440 AGTGTCACGTGTTAGGCACAAGGAGTTGAA
66 AGTGTCACGTGTTACGCACAAGGAGTTGAA
*
951470 GGAGATTGTTTGTGTTTACTTCTCTCAGCTCTATTCTTTTGTACTTTATATGTGCACCATCTCGA
1 GGAGATTGTTTGTGTTTACTTCTCTCAGCTCTATTCTTTTATACTTTATATGTGCACCATCTCGA
951535 AGTGTCACGTGTTACGCACAA
66 AGTGTCACGTGTTACGCACAA
951556 ATTGACGGGT
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
95 82 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (95 bp):
GGAGATTGTTTGTGTTTACTTCTCTCAGCTCTATTCTTTTATACTTTATATGTGCACCATCTCGA
AGTGTCACGTGTTACGCACAAGGAGTTGAA
Found at i:953558 original size:20 final size:20
Alignment explanation
Indices: 953533--953573 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
953523 GATTATAGAG
*
953533 CCTGTAATCTTTACTTCTTT
1 CCTGTAATCTTTACATCTTT
953553 CCTGTAATCTTTACATCTTT
1 CCTGTAATCTTTACATCTTT
953573 C
1 C
953574 ATCATAGCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.27, G:0.05, T:0.51
Consensus pattern (20 bp):
CCTGTAATCTTTACATCTTT
Found at i:956417 original size:18 final size:18
Alignment explanation
Indices: 956394--956464 Score: 106
Period size: 18 Copynumber: 3.9 Consensus size: 18
956384 AGGGATTATC
*
956394 AGTGGTCCTTCGAGACAT
1 AGTGGTCCTTCGGGACAT
* *
956412 AGTGGTTCTTCGGGATAT
1 AGTGGTCCTTCGGGACAT
956430 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
956448 AGTGATCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
956465 AATATTCAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:956434 original size:36 final size:38
Alignment explanation
Indices: 956385--956462 Score: 115
Period size: 36 Copynumber: 2.1 Consensus size: 38
956375 TAAGAGTCGA
* *
956385 GGGATTATCAGTGGTCCTTCGAGACATAGTGGTTCTTC
1 GGGATTATCAGTGGTCCTTCGAGACATAGTGATCCTTC
*
956423 GGGA-TAT-AGTGGTCCTTCGGGACATAGTGATCCTTC
1 GGGATTATCAGTGGTCCTTCGAGACATAGTGATCCTTC
956459 GGGA
1 GGGA
956463 CAAATATTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 30 0.81
37 3 0.08
38 4 0.11
ACGTcount: A:0.19, C:0.18, G:0.32, T:0.31
Consensus pattern (38 bp):
GGGATTATCAGTGGTCCTTCGAGACATAGTGATCCTTC
Found at i:958858 original size:18 final size:18
Alignment explanation
Indices: 958812--958858 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
958802 TTAAGGATTG
*
958812 ATATAGAAGAGTAAGGTA
1 ATATAAAAGAGTAAGGTA
*
958830 ATATGAAAAGAGTGAGG-A
1 ATAT-AAAAGAGTAAGGTA
958848 AGTATAAAAGA
1 A-TATAAAAGA
958859 AAAGATATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.53, C:0.00, G:0.28, T:0.19
Consensus pattern (18 bp):
ATATAAAAGAGTAAGGTA
Found at i:960666 original size:2 final size:2
Alignment explanation
Indices: 960659--960708 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
960649 AATCATATGA
960659 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
960701 AT AT AT AT
1 AT AT AT AT
960709 CTAATTCATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:961686 original size:18 final size:18
Alignment explanation
Indices: 961663--961733 Score: 106
Period size: 18 Copynumber: 3.9 Consensus size: 18
961653 AGGGATTATC
*
961663 AGTGGTTCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
961681 AGTGGTTCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
961699 AGTGGTCCTTTGGGACAT
1 AGTGGTCCTTCGGGACAT
*
961717 AGTGGTCCTTTGGGACA
1 AGTGGTCCTTCGGGACA
961734 AATATTCAGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 51 1.00
ACGTcount: A:0.17, C:0.17, G:0.34, T:0.32
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:967091 original size:20 final size:20
Alignment explanation
Indices: 967066--967105 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
967056 ATTCATCTCA
* *
967066 GTTCATCTAGTATTGATACT
1 GTTCATCCAGTATCGATACT
967086 GTTCATCCAGTATCGATACT
1 GTTCATCCAGTATCGATACT
967106 CGAACCTAAA
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:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (20 bp):
GTTCATCCAGTATCGATACT
Found at i:975502 original size:2 final size:2
Alignment explanation
Indices: 975497--975537 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
975487 TCCTTTTTAA
975497 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
975538 AACAAATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:979478 original size:83 final size:83
Alignment explanation
Indices: 979338--979861 Score: 600
Period size: 83 Copynumber: 6.3 Consensus size: 83
979328 TTAATGGAAC
* * * *
979338 ATGCGCCTTTCATTTCAGATGGGATGGAACACTATGAAATTGCAGAGTTTCTTTGAATAATAATG
1 ATGCGCCTTTCATTTCAGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATG
* ** *
979403 GAAAACGCTTCTTCTAGA
66 GAAAACACTTCCCCTGGA
* *
979421 GTGCGCCTTTCATTTCAGATGGGATGTAACACTATGACATGGCAGAGATTCTCTGAATAATAATG
1 ATGCGCCTTTCATTTCAGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATG
* * *
979486 GAATACGCTTCCCCTAGA
66 GAAAACACTTCCCCTGGA
** * ** * *
979504 ACACACCTTTCATTTTGGATGGAATGGAACACTATGACATGGTAGAGATTCTCTGAATAATAATG
1 ATGCGCCTTTCATTTCAGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATG
979569 GAAAACACTTCCCCTGGA
66 GAAAACACTTCCCCTGGA
* * * ** * *
979587 ATGTGCCTTTCATTTCGGATGAGATATAACACTATGACATGGCAGAGATTATCTAAATAATAATG
1 ATGCGCCTTTCATTTCAGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATG
***
979652 GAAAATGTTTCCCCTGGA
66 GAAAACACTTCCCCTGGA
* * * * * * * *
979670 ACGCCCCATTAATTTCGGATGAGATGGAACACTTTGACATGGTAGAGATTCTCTGAATAATAATA
1 ATGCGCCTTTCATTTCAGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAAT-
* *
979735 GG-AAACACTTGCCCTTGA
65 GGAAAACACTTCCCCTGGA
* * * * * *
979753 ATGCGTCTTTCATTTCATATGAGATGAAACACTATGACATGACAGAGATTCTCTGAATAATAATT
1 ATGCGCCTTTCATTTCAGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATG
979818 GAAAACACTTCCCCTGGA
66 GAAAACACTTCCCCTGGA
* *
979836 ATGCGCCTTTGATTTAAGATGGGATG
1 ATGCGCCTTTCATTTCAGATGGGATG
979862 AAATACTTGA
Statistics
Matches: 368, Mismatches: 71, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
82 1 0.00
83 365 0.99
84 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (83 bp):
ATGCGCCTTTCATTTCAGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATG
GAAAACACTTCCCCTGGA
Found at i:982226 original size:26 final size:26
Alignment explanation
Indices: 982195--982245 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
982185 GAAAGTTTAG
*
982195 GGATTTAAATGA-AAAGTATTGAAGTT
1 GGATTTAAATAACAAAGT-TTGAAGTT
982221 GGATTTAAATAACAAAGTTTGAAGT
1 GGATTTAAATAACAAAGTTTGAAGT
982246 AACAAGGGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.43, C:0.02, G:0.22, T:0.33
Consensus pattern (26 bp):
GGATTTAAATAACAAAGTTTGAAGTT
Found at i:993006 original size:4 final size:4
Alignment explanation
Indices: 992997--993021 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
992987 GTTTCTCTTC
992997 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
993022 CTATGTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1002153 original size:24 final size:22
Alignment explanation
Indices: 1002121--1002169 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
1002111 TTACCATTAT
* *
1002121 ATATATATTTATGAATATATAAAA
1 ATATATATTCAT-AA-AAATAAAA
*
1002145 ATATTTATTCATAAAAATAAAA
1 ATATATATTCATAAAAATAAAA
1002167 ATA
1 ATA
1002170 CTATTAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 10 0.45
23 2 0.09
24 10 0.45
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
ATATATATTCATAAAAATAAAA
Found at i:1003604 original size:3 final size:3
Alignment explanation
Indices: 1003596--1003695 Score: 157
Period size: 3 Copynumber: 33.7 Consensus size: 3
1003586 TTAATATATT
*
1003596 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA AAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1003643 TAA TAA TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1003691 TAA TA
1 TAA TA
1003696 TGGATAAAAA
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
2 2 0.02
3 86 0.98
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1003981 original size:117 final size:116
Alignment explanation
Indices: 1003850--1004489 Score: 1037
Period size: 117 Copynumber: 5.4 Consensus size: 116
1003840 TTCTCCAGAT
** ** * *
1003850 GAGTTCTTCTCATTACAAACTTTCTGCTGGGGATGATGTTCCATCAAATGATGAATTCAAGCAAA
1 GAGTTCTTCTCATTATGAACTTTCT-CTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAAA
1003915 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
65 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
1003967 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAA
1 GAGTTCTTCTCATTATGAACT-TT-CTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAA
1004032 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
64 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
*
1004085 GAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAA
1 GAGTTCTTCTCATTATGAACTTTCTCTGGAAATG-ATGATCCATCAAGTGATGAATTCAAGCAAA
*
1004150 AGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAC
65 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
* *
1004202 GAGTTCTTCTCATTATGAACTTCCTCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAA
1 GAGTTCTTCTCATTATGAACTTTCTCTGGAAATG-ATGATCCATCAAGTGATGAATTCAAGCAAA
1004267 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
65 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
* *
1004319 GAGTTCTTCTCATTATGAACTCTTCCTCTAGAAATGATGATCCATCAATTTGATGAATTCAAGCA
1 GAGTTCTTCTCATTATGAACT-TT-CTCTGGAAATGATGATCCATCAA-GTGATGAATTCAAGCA
*
1004384 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAC
63 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
* ** * * *
1004438 GAGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCATCAAATGATG
1 GAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAGTGATG
1004490 GATTTGAGTC
Statistics
Matches: 495, Mismatches: 22, Indels: 13
0.93 0.04 0.02
Matches are distributed among these distances:
116 15 0.03
117 256 0.52
118 124 0.25
119 100 0.20
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (116 bp):
GAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAAAA
GGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
Found at i:1004361 original size:235 final size:232
Alignment explanation
Indices: 1003850--1004489 Score: 1050
Period size: 235 Copynumber: 2.7 Consensus size: 232
1003840 TTCTCCAGAT
** * ** *
1003850 GAGTTCTTCTCATTACAAACTTTCTGCTGGGGATGATGTTCCATCAAATGATGAATTCAAGCAAA
1 GAGTTCTTCTCATTATGAACTTTCT-CTAGAAATGATGATCCATCAAATGATGAATTCAAGCAAA
*
1003915 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCAT
65 AGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGACGAGTTCTTCTCAT
*
1003980 TATGAACTCTTCCTCTGGAAATGATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAG
130 TATGAA--CTTCCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAG
1004045 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
193 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
* * *
1004085 GAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAA
1 GAGTTCTTCTCATTATGAACTTTCTCTAGAAATG-ATGATCCATCAAATGATGAATTCAAGCAAA
1004150 AGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGACGAGTTCTTCTCAT
65 AGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGACGAGTTCTTCTCAT
1004215 TATGAACTTCCTCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGT
130 TATGAACTTCCTCTGGAAAAG-ATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGT
1004280 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
194 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
*
1004319 GAGTTCTTCTCATTATGAACTCTTCCTCTAGAAATGATGATCCATCAATTTGATGAATTCAAGCA
1 GAGTTCTTCTCATTATGAACT-TT-CTCTAGAAATGATGATCCATCAA-ATGATGAATTCAAGCA
1004384 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGACGAGTTCTTCTC
63 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGACGAGTTCTTCTC
* *
1004449 ATTATGAAC-T-CTAACTGGAAAAGCTGATCCATCAAATGATG
128 ATTATGAACTTCCT--CTGGAAAAGATGATCCATCAAGTGATG
1004490 GATTTGAGTC
Statistics
Matches: 384, Mismatches: 14, Indels: 14
0.93 0.03 0.03
Matches are distributed among these distances:
233 14 0.04
234 111 0.29
235 152 0.40
236 107 0.28
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (232 bp):
GAGTTCTTCTCATTATGAACTTTCTCTAGAAATGATGATCCATCAAATGATGAATTCAAGCAAAA
GGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGACGAGTTCTTCTCATT
ATGAACTTCCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGTTC
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
Found at i:1005206 original size:52 final size:52
Alignment explanation
Indices: 1005131--1005479 Score: 644
Period size: 52 Copynumber: 6.7 Consensus size: 52
1005121 ATTCTGTCCA
* *
1005131 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTTTGTCTAACCAG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
1005183 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
1005235 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
* * *
1005287 ATTAGATAACTCAAAGAACACTTCCAAAAGATGTTATGTTCTGTCCAACCAG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
*
1005339 ATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGTTCTGTCCAACCAG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
1005391 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
1005443 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1005480 TGGCATATTC
Statistics
Matches: 289, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 289 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (52 bp):
ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
Found at i:1006671 original size:20 final size:20
Alignment explanation
Indices: 1006633--1006717 Score: 84
Period size: 20 Copynumber: 4.2 Consensus size: 20
1006623 CTTGACCCCC
* *
1006633 TTTCTTTTTCTTCTC-TTTT
1 TTTCATTTTCTTTTCTTTTT
*
1006652 TTTCATTTTCTATT-TTTTT
1 TTTCATTTTCTTTTCTTTTT
* *
1006671 TTTCTTTTTTCTTTTCTTTCT
1 TTTC-ATTTTCTTTTCTTTTT
*
1006692 TTTCTTTTTCTTTTCTTTTT
1 TTTCATTTTCTTTTCTTTTT
1006712 TCTTCA
1 T-TTCA
1006718 AGCATAATAT
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
19 19 0.35
20 24 0.44
21 11 0.20
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTCATTTTCTTTTCTTTTT
Found at i:1006678 original size:5 final size:5
Alignment explanation
Indices: 1006633--1006710 Score: 58
Period size: 5 Copynumber: 15.6 Consensus size: 5
1006623 CTTGACCCCC
* *
1006633 TTTCT TTT-T CTTCT CTTT-T TTTCAT TTTCT ATTT-T TTT-T TTCTTT
1 TTTCT TTTCT TTTCT -TTTCT TTTC-T TTTCT -TTTCT TTTCT TT-TCT
1006678 TTTCT TTTC- TTTCT TTTCTT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTC-T TTTCT TTTCT TTT
1006711 TTCTTCAAGC
Statistics
Matches: 61, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
4 16 0.26
5 27 0.44
6 18 0.30
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:1006689 original size:39 final size:39
Alignment explanation
Indices: 1006633--1006715 Score: 116
Period size: 39 Copynumber: 2.2 Consensus size: 39
1006623 CTTGACCCCC
*
1006633 TTTC-TTTTTCTTCTCTTT-TTTTCATTTTCTATTTTTTT
1 TTTCTTTTTTCTTCTCTTTCTTTTCATTTTCT-TTTCTTT
* *
1006671 TTTCTTTTTTCTTTTCTTTCTTTTCTTTTTCTTTTCTTT
1 TTTCTTTTTTCTTCTCTTTCTTTTCATTTTCTTTTCTTT
1006710 TTTCTT
1 TTTCTT
1006716 CAAGCATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
38 4 0.10
39 25 0.62
40 11 0.28
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (39 bp):
TTTCTTTTTTCTTCTCTTTCTTTTCATTTTCTTTTCTTT
Found at i:1006713 original size:32 final size:33
Alignment explanation
Indices: 1006633--1006715 Score: 100
Period size: 32 Copynumber: 2.5 Consensus size: 33
1006623 CTTGACCCCC
* *
1006633 TTTCTTTT-TCTTCTCTTTTTTTCATTTTCTATT
1 TTTCTTTTCTTTTTTCTTTTTTTCATTTTC-ATT
*
1006666 TTTTTTTTCTTTTTTCTTTTCTTTC-TTTTC-TT
1 TTTCTTTTCTTTTTTCTTTT-TTTCATTTTCATT
1006698 TTTCTTTTCTTTTTTCTT
1 TTTCTTTTCTTTTTTCTT
1006716 CAAGCATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
32 19 0.43
33 7 0.16
34 14 0.32
35 4 0.09
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (33 bp):
TTTCTTTTCTTTTTTCTTTTTTTCATTTTCATT
Found at i:1006715 original size:27 final size:28
Alignment explanation
Indices: 1006633--1006715 Score: 89
Period size: 27 Copynumber: 2.9 Consensus size: 28
1006623 CTTGACCCCC
*
1006633 TTTCTTTTTCTTCTCTTTTTTTCATTTTCTAT
1 TTTCTTTTTCTTTTC-TTTTTTC--TTTC-AT
*
1006665 TTTTTTTTTCTTTT-TTCTTTTCTTTC-T
1 TTTCTTTTTCTTTTCTT-TTTTCTTTCAT
1006692 TTTCTTTTTCTTTTCTTTTTTCTT
1 TTTCTTTTTCTTTTCTTTTTTCTT
1006716 CAAGCATAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
27 21 0.46
28 2 0.04
29 4 0.09
30 2 0.04
31 5 0.11
32 12 0.26
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (28 bp):
TTTCTTTTTCTTTTCTTTTTTCTTTCAT
Found at i:1018065 original size:24 final size:22
Alignment explanation
Indices: 1018033--1018081 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
1018023 TTACCATTAT
* *
1018033 ATATATATTTATGAATATATAAAA
1 ATATATATTCAT-AA-AAATAAAA
*
1018057 ATATTTATTCATAAAAATAAAA
1 ATATATATTCATAAAAATAAAA
1018079 ATA
1 ATA
1018082 CTATTAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 10 0.45
23 2 0.09
24 10 0.45
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
ATATATATTCATAAAAATAAAA
Found at i:1019028 original size:6 final size:6
Alignment explanation
Indices: 1019017--1019043 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1019007 TCTCTCCGGT
1019017 TCTGTC TCTGTC TCTGTC TCTGTC TCT
1 TCTGTC TCTGTC TCTGTC TCTGTC TCT
1019044 TTTTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.15, T:0.52
Consensus pattern (6 bp):
TCTGTC
Found at i:1019519 original size:3 final size:3
Alignment explanation
Indices: 1019511--1019610 Score: 157
Period size: 3 Copynumber: 33.7 Consensus size: 3
1019501 TTAATATATT
*
1019511 TAA TAA TAA -AA TAA TAA TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1019558 TAA TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1019606 TAA TA
1 TAA TA
1019611 TGGATAAAAA
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
2 2 0.02
3 86 0.98
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1025590 original size:24 final size:24
Alignment explanation
Indices: 1025563--1025610 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1025553 GTCTTGAGGG
1025563 AGCTGGTAGAAACGTGGACTGTTC
1 AGCTGGTAGAAACGTGGACTGTTC
1025587 AGCTGGTAGAAACGTGGACTGTTC
1 AGCTGGTAGAAACGTGGACTGTTC
1025611 GGTGGAGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (24 bp):
AGCTGGTAGAAACGTGGACTGTTC
Found at i:1034445 original size:28 final size:28
Alignment explanation
Indices: 1034405--1034469 Score: 130
Period size: 28 Copynumber: 2.3 Consensus size: 28
1034395 TTGGTTTTAA
1034405 AAGGCGCGCCTAGGCGCTCCTAAAGCAC
1 AAGGCGCGCCTAGGCGCTCCTAAAGCAC
1034433 AAGGCGCGCCTAGGCGCTCCTAAAGCAC
1 AAGGCGCGCCTAGGCGCTCCTAAAGCAC
1034461 AAGGCGCGC
1 AAGGCGCGC
1034470 ATGGACTCCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.25, C:0.35, G:0.31, T:0.09
Consensus pattern (28 bp):
AAGGCGCGCCTAGGCGCTCCTAAAGCAC
Found at i:1035857 original size:21 final size:22
Alignment explanation
Indices: 1035811--1035857 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
1035801 TTATGTTTCT
*
1035811 TTGTTTAGGCAATCTTTTGTAA
1 TTGTTTAGGCAATCTTATGTAA
*
1035833 -TGTTT-GGTAATCTTATGTAA
1 TTGTTTAGGCAATCTTATGTAA
1035853 TTGTT
1 TTGTT
1035858 GGTTATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.21, C:0.06, G:0.19, T:0.53
Consensus pattern (22 bp):
TTGTTTAGGCAATCTTATGTAA
Found at i:1042941 original size:164 final size:162
Alignment explanation
Indices: 1042657--1042958 Score: 498
Period size: 164 Copynumber: 1.9 Consensus size: 162
1042647 GGCAATTATT
* * *
1042657 TGTAATGTTTGGTTCTTATGTAATTGTTGGTTATTAATATACTAAGGCACTCTTTTCCTCCTTCC
1 TGTAATGGTTGGTTCTTATGTAATTATGGGTTATTAATATACTAAGGCACTCTTTTCCTCCTTCC
*
1042722 GCTACTTGTCTCCTTAATAGAGACAACTATGAGGGAGGTTTTTAATGAGGCCTTCTATTCCTATC
66 GCTACTTGTCTCCTTAATAGAGACAACTATGAGGGAGGTTTTTAATGAGGCCTTCTATTCCTATA
1042787 AAAAAAAACTGTTTCTATGTTAGGTAATTTTA
131 AAAAAAAACTGTTTCTATGTTAGGTAATTTTA
*
1042819 TGTAATGGTTGGTAATCTTATGTAATTATGGGTTATTAATATATTAAGGCACTCTTTTCCTCCTT
1 TGTAATGGTTGGT--TCTTATGTAATTATGGGTTATTAATATACTAAGGCACTCTTTTCCTCCTT
* * *
1042884 CCGCTATTTGTCTCTTTACA-AGAGGCAACTATGAGGGAGGTTTTTAATGAGGCCTTCTATTCCT
64 CCGCTACTTGTCTCCTTA-ATAGAGACAACTATGAGGGAGGTTTTTAATGAGGCCTTCTATTCCT
1042948 ATAAAAAAAAA
128 ATAAAAAAAAA
1042959 TAAGCTTGTC
Statistics
Matches: 129, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
162 12 0.09
164 116 0.90
165 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (162 bp):
TGTAATGGTTGGTTCTTATGTAATTATGGGTTATTAATATACTAAGGCACTCTTTTCCTCCTTCC
GCTACTTGTCTCCTTAATAGAGACAACTATGAGGGAGGTTTTTAATGAGGCCTTCTATTCCTATA
AAAAAAAACTGTTTCTATGTTAGGTAATTTTA
Found at i:1057256 original size:3 final size:3
Alignment explanation
Indices: 1057250--1057298 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
1057240 ATATTTTTTT
*
1057250 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1057297 TT
1 TT
1057299 TTCCACACTC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1062849 original size:18 final size:18
Alignment explanation
Indices: 1062826--1062860 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1062816 AAGGTTCTAC
*
1062826 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCAGGACATA
1062844 GTGGTCCTTCAGGACAT
1 GTGGTCCTTCAGGACAT
1062861 TTCTACGCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (18 bp):
GTGGTCCTTCAGGACATA
Found at i:1068435 original size:16 final size:16
Alignment explanation
Indices: 1068414--1068445 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1068404 GACTGTTGAG
*
1068414 GATGATAGAACCAACT
1 GATGATAGAAACAACT
1068430 GATGATAGAAACAACT
1 GATGATAGAAACAACT
1068446 CTAAGACTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.19
Consensus pattern (16 bp):
GATGATAGAAACAACT
Found at i:1068837 original size:11 final size:11
Alignment explanation
Indices: 1068821--1068846 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1068811 TAGCAGTGTT
1068821 AAAAAAAAGAA
1 AAAAAAAAGAA
1068832 AAAAAAAAGAA
1 AAAAAAAAGAA
1068843 AAAA
1 AAAA
1068847 GGAAAAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:1073143 original size:63 final size:63
Alignment explanation
Indices: 1073039--1073166 Score: 211
Period size: 63 Copynumber: 2.0 Consensus size: 63
1073029 CTACAACTGG
*
1073039 TATGGAAAAGCTAATAGTGTGTTACCCATATTCTTTAGATGCTAGAACACTTCTTGAATCAAC
1 TATGGAAAAGCTAATAGTGTGTTACCCAGATTCTTTAGATGCTAGAACACTTCTTGAATCAAC
** * *
1073102 TATGGAAAAGCTAATAGTGTGTTACCTGGATTTTTTGGATGCTAGAACACTTCTTGAATCAAC
1 TATGGAAAAGCTAATAGTGTGTTACCCAGATTCTTTAGATGCTAGAACACTTCTTGAATCAAC
1073165 TA
1 TA
1073167 GGGATTTACT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (63 bp):
TATGGAAAAGCTAATAGTGTGTTACCCAGATTCTTTAGATGCTAGAACACTTCTTGAATCAAC
Found at i:1074652 original size:15 final size:16
Alignment explanation
Indices: 1074599--1074645 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 16
1074589 AATTAGAGAA
*
1074599 TTTTTATTAAAGTATAAA
1 TTTTTATTAAA--ATAAC
*
1074617 ATTTTATTAAAATAAC
1 TTTTTATTAAAATAAC
1074633 TTTTTA-TAAAATA
1 TTTTTATTAAAATA
1074646 GTTTTTTTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 7 0.27
16 9 0.35
18 10 0.38
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (16 bp):
TTTTTATTAAAATAAC
Found at i:1079742 original size:13 final size:13
Alignment explanation
Indices: 1079724--1079755 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1079714 TGTTTAATTG
1079724 TACCAAGTCATGC
1 TACCAAGTCATGC
1079737 TACCAAGTCATGC
1 TACCAAGTCATGC
*
1079750 AACCAA
1 TACCAA
1079756 TTCAACTAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.38, C:0.31, G:0.12, T:0.19
Consensus pattern (13 bp):
TACCAAGTCATGC
Found at i:1084483 original size:15 final size:15
Alignment explanation
Indices: 1084463--1084492 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1084453 AAACTGTTCC
1084463 TGGTCTGTTTAACAT
1 TGGTCTGTTTAACAT
1084478 TGGTCTGTTTAACAT
1 TGGTCTGTTTAACAT
1084493 CCGTGATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (15 bp):
TGGTCTGTTTAACAT
Found at i:1090081 original size:17 final size:17
Alignment explanation
Indices: 1090059--1090092 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1090049 TTAATATTTT
1090059 TTTAAA-AAATAATATAA
1 TTTAAAGAAA-AATATAA
1090076 TTTAAAGAAAAATATAA
1 TTTAAAGAAAAATATAA
1090093 AAAATTATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
TTTAAAGAAAAATATAA
Found at i:1091104 original size:23 final size:24
Alignment explanation
Indices: 1091078--1091123 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1091068 TTCTACTACT
*
1091078 GTACATTTTC-TGATGTCTCAACC
1 GTACATGTTCTTGATGTCTCAACC
*
1091101 GTACCTGTTCTTGATGTCTCAAC
1 GTACATGTTCTTGATGTCTCAAC
1091124 AAGTGCGTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.20, C:0.26, G:0.15, T:0.39
Consensus pattern (24 bp):
GTACATGTTCTTGATGTCTCAACC
Found at i:1094815 original size:27 final size:27
Alignment explanation
Indices: 1094776--1094843 Score: 109
Period size: 28 Copynumber: 2.5 Consensus size: 27
1094766 AAAAATCGGG
* *
1094776 TCGGGACGAGTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTAAGTGTGATAT
1094803 TCGGGTCGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGG-TTTTTTAAGTGTGATAT
1094831 TCGGGTCGGGTTT
1 TCGGGTCGGGTTT
1094844 AGGGTGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 11 0.29
28 27 0.71
ACGTcount: A:0.15, C:0.09, G:0.34, T:0.43
Consensus pattern (27 bp):
TCGGGTCGGGTTTTTTAAGTGTGATAT
Found at i:1094825 original size:28 final size:28
Alignment explanation
Indices: 1094786--1094843 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
1094776 TCGGGACGAG
1094786 TTTTTTAAGTGTGATATTCGGGTCGGGT
1 TTTTTTAAGTGTGATATTCGGGTCGGGT
1094814 TTTTTTAAGTGTGATATTCGGGTCGGGT
1 TTTTTTAAGTGTGATATTCGGGTCGGGT
1094842 TT
1 TT
1094844 AGGGTGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.14, C:0.07, G:0.31, T:0.48
Consensus pattern (28 bp):
TTTTTTAAGTGTGATATTCGGGTCGGGT
Found at i:1094850 original size:23 final size:25
Alignment explanation
Indices: 1094788--1094850 Score: 67
Period size: 28 Copynumber: 2.5 Consensus size: 25
1094778 GGGACGAGTT
*
1094788 TTTTAAGTGTGATATTCGGGTCGGG
1 TTTTAAGGGTGATATTCGGGTCGGG
*
1094813 TTTTTTTAAGTGTGATATTCGGGTCGGG
1 ---TTTTAAGGGTGATATTCGGGTCGGG
1094841 -TTT-AGGGTGA
1 TTTTAAGGGTGA
1094851 AAAATACCCG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
23 6 0.18
24 3 0.09
28 25 0.74
ACGTcount: A:0.16, C:0.06, G:0.35, T:0.43
Consensus pattern (25 bp):
TTTTAAGGGTGATATTCGGGTCGGG
Found at i:1095445 original size:16 final size:18
Alignment explanation
Indices: 1095419--1095462 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
1095409 TCAGATTCAG
*
1095419 ATTCTAATTCC-T-ACAT
1 ATTCCAATTCCTTCACAT
*
1095435 ATTTCAATTCCTTCACAT
1 ATTCCAATTCCTTCACAT
1095453 ATTCCAATTC
1 ATTCCAATTC
1095463 TCTCAAAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 9 0.39
17 1 0.04
18 13 0.57
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTCCAATTCCTTCACAT
Found at i:1100274 original size:7 final size:7
Alignment explanation
Indices: 1100262--1100286 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1100252 ATGCATCTTT
1100262 TTTTTTC
1 TTTTTTC
1100269 TTTTTTC
1 TTTTTTC
1100276 TTTTTTC
1 TTTTTTC
1100283 TTTT
1 TTTT
1100287 CGGTAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:1105747 original size:15 final size:16
Alignment explanation
Indices: 1105727--1105756 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1105717 AAAATGAATT
1105727 ATATTTTCTA-AAAAA
1 ATATTTTCTATAAAAA
1105742 ATATTTTCTATAAAA
1 ATATTTTCTATAAAA
1105757 CCAATTACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTTTCTATAAAAA
Found at i:1119940 original size:21 final size:21
Alignment explanation
Indices: 1119916--1119967 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1119906 AACAATCTTC
1119916 TGTTAATTTAACTATTTTTTA
1 TGTTAATTTAACTATTTTTTA
1119937 TGTTAATTTAACTATTTTTTA
1 TGTTAATTTAACTATTTTTTA
*
1119958 TATTAATTTA
1 TGTTAATTTA
1119968 TCAAATTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (21 bp):
TGTTAATTTAACTATTTTTTA
Found at i:1119975 original size:22 final size:21
Alignment explanation
Indices: 1119918--1119983 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
1119908 CAATCTTCTG
* *
1119918 TTAATTTAACTATTTTTTATG
1 TTAATTTAACAATTTTTTATA
*
1119939 TTAATTTAACTATTTTTTATA
1 TTAATTTAACAATTTTTTATA
* * *
1119960 TTAATTTATCAAATTTTAATA
1 TTAATTTAACAATTTTTTATA
1119981 TTA
1 TTA
1119984 TTCGTTAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.59
Consensus pattern (21 bp):
TTAATTTAACAATTTTTTATA
Found at i:1121912 original size:26 final size:26
Alignment explanation
Indices: 1121877--1121943 Score: 134
Period size: 26 Copynumber: 2.6 Consensus size: 26
1121867 GGAGGTCAAT
1121877 ACGACGCCGTTTTGGAACTAAACGGG
1 ACGACGCCGTTTTGGAACTAAACGGG
1121903 ACGACGCCGTTTTGGAACTAAACGGG
1 ACGACGCCGTTTTGGAACTAAACGGG
1121929 ACGACGCCGTTTTGG
1 ACGACGCCGTTTTGG
1121944 CGTACGAGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.24, C:0.24, G:0.31, T:0.21
Consensus pattern (26 bp):
ACGACGCCGTTTTGGAACTAAACGGG
Found at i:1123454 original size:55 final size:55
Alignment explanation
Indices: 1123321--1123744 Score: 565
Period size: 55 Copynumber: 7.7 Consensus size: 55
1123311 TGGTTTTATC
* * * **
1123321 CCCTATTGCTTCAGGGAGTA--AAACTCGAA-AATCTTCGTCAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* ** ** * * * *
1123373 CCCCATTT-TTCCAGAGAGTACAAGACTAAAACGAT-TCTCGATAATCATGTCTGCT
1 CCCTATTTCTT-CAGAGAGTATGAGACTCGAACAATCT-TCAACAATCGTGTCTGCT
*
1123428 CCCTATTTTTTCAGAGAGTATGAGACTCGAACAAT-TCTCAACGAA-CGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCT-TCAAC-AATCGTGTCTGCT
1123483 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
*
1123538 CCCTATTTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAAACGTGTCTGCT
1 CCCTATTT-CTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
*
1123594 CTCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* *
1123649 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* *
1123704 CCCTATTTCTTCAGAGAGTATAAGACTCGATCAATCTTCAA
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
1123745 TTATCGTTGG
Statistics
Matches: 335, Mismatches: 27, Indels: 17
0.88 0.07 0.04
Matches are distributed among these distances:
51 2 0.01
52 14 0.04
54 9 0.03
55 252 0.75
56 58 0.17
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.30
Consensus pattern (55 bp):
CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
Found at i:1123623 original size:166 final size:164
Alignment explanation
Indices: 1123321--1123744 Score: 572
Period size: 166 Copynumber: 2.6 Consensus size: 164
1123311 TGGTTTTATC
* * * ** *
1123321 CCCTATTGCTTCAGGGAGTA-AAACTCGAA-AATCTTCGTCAATCGTGTCTGCTCCCCATTT-TT
1 CCCTATTTCTTCAGAGAGTATAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTT
* ** * * * * *
1123383 CCAGAGAGTACAAGACTAAAACGAT-TCTCGATAATCATGTCTGCTCCCTATTTTTTCAGAGAGT
66 -CAGAGAGTATAAGACTCGAACAATCT-TCAACAAACATGTCTGCTCCCTATTTCTTCAGAGAGT
1123447 ATGAGACTCGAACAAT-TCTCAACGAA-CGTGTCTGCT
129 ATGAGACTCGAACAATCT-TCAAC-AATCGTGTCTGCT
1123483 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCC
1 CCCTATTTCTTCAGAGAGTAT-AGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTT-C
* * *
1123548 TTCAGAGAGTATGAGACTCGAACAATCTTCAACAAACGTGTCTGCTCTCTATTTCTTCAGAGAGT
64 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACATGTCTGCTCCCTATTTCTTCAGAGAGT
1123613 ATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
129 ATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
*
1123649 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTAT-AGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCT
*
1123714 TCAGAGAGTATAAGACTCGATCAATCTTCAA
65 TCAGAGAGTATAAGACTCGAACAATCTTCAA
1123745 TTATCGTTGG
Statistics
Matches: 233, Mismatches: 21, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
162 18 0.08
164 8 0.03
165 61 0.26
166 142 0.61
167 4 0.02
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.30
Consensus pattern (164 bp):
CCCTATTTCTTCAGAGAGTATAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTT
CAGAGAGTATAAGACTCGAACAATCTTCAACAAACATGTCTGCTCCCTATTTCTTCAGAGAGTAT
GAGACTCGAACAATCTTCAACAATCGTGTCTGCT
Found at i:1124768 original size:11 final size:11
Alignment explanation
Indices: 1124754--1124826 Score: 60
Period size: 11 Copynumber: 6.6 Consensus size: 11
1124744 CTTTTTTCCA
1124754 TTTTTTCATTT
1 TTTTTTCATTT
1124765 TTTTATT-ATTT
1 TTTT-TTCATTT
*
1124776 TTTTTTTATTTT
1 TTTTTTCA-TTT
1124788 TTTTTTCA-TT
1 TTTTTTCATTT
***
1124798 TTCACTCATTT
1 TTTTTTCATTT
* *
1124809 TTTCTTCTTTT
1 TTTTTTCATTT
1124820 TTTTTTC
1 TTTTTTC
1124827 TTCAAGCAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
10 9 0.18
11 28 0.57
12 12 0.24
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTCATTT
Found at i:1124781 original size:14 final size:13
Alignment explanation
Indices: 1124762--1124793 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
1124752 CATTTTTTCA
1124762 TTTTTTTATTATTT
1 TTTTTTTATT-TTT
1124776 TTTTTTTATTTTT
1 TTTTTTTATTTTT
1124789 TTTTT
1 TTTTT
1124794 CATTTTCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (13 bp):
TTTTTTTATTTTT
Found at i:1124786 original size:22 final size:23
Alignment explanation
Indices: 1124754--1124799 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
1124744 CTTTTTTCCA
1124754 TTTTTTCATTTTTTTATT-ATTT
1 TTTTTTCATTTTTTTATTCATTT
* *
1124776 TTTTTTTATTTTTTTTTTCATTT
1 TTTTTTCATTTTTTTATTCATTT
1124799 T
1 T
1124800 CACTCATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.11, C:0.04, G:0.00, T:0.85
Consensus pattern (23 bp):
TTTTTTCATTTTTTTATTCATTT
Found at i:1124792 original size:12 final size:12
Alignment explanation
Indices: 1124762--1124799 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1124752 CATTTTTTCA
*
1124762 TTTTTTTATTA-
1 TTTTTTTTTTAT
1124773 TTTTTTTTTTAT
1 TTTTTTTTTTAT
*
1124785 TTTTTTTTTCAT
1 TTTTTTTTTTAT
1124797 TTT
1 TTT
1124800 CACTCATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTTTTTTTAT
Found at i:1136791 original size:26 final size:26
Alignment explanation
Indices: 1136756--1136822 Score: 134
Period size: 26 Copynumber: 2.6 Consensus size: 26
1136746 GGAGGTCAAT
1136756 ACGACGCCGTTTTGGAACTAAACGGG
1 ACGACGCCGTTTTGGAACTAAACGGG
1136782 ACGACGCCGTTTTGGAACTAAACGGG
1 ACGACGCCGTTTTGGAACTAAACGGG
1136808 ACGACGCCGTTTTGG
1 ACGACGCCGTTTTGG
1136823 CGTACGAGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.24, C:0.24, G:0.31, T:0.21
Consensus pattern (26 bp):
ACGACGCCGTTTTGGAACTAAACGGG
Found at i:1139237 original size:108 final size:107
Alignment explanation
Indices: 1139050--1139270 Score: 257
Period size: 108 Copynumber: 2.1 Consensus size: 107
1139040 TAAAATTTTC
* * *
1139050 AAATCATTTTCTTCTTTATCTCATCATCTCCTTCCCCAATCTTAAAGCATCAAATCTCCATGTTT
1 AAATCATTTTCTTCTTTATCCCATCATCTCCTTCCCCAATCTTAAAGCATCAAACCTACATGTTT
* * *
1139115 TGCTCTACTCTTTCTTTAATCCACCATTATAATCTAA-ATTAA
66 TACTATACTCTTTCTTTAATCCACCAATATAATC-AAGATTAA
* * * * *
1139157 AAATCACTTCTTCTTCTTTATCCCATCCTTTTCTTCCCCAATCTT-AAGCATTAGACCTACATGT
1 AAATCA-TT-TTCTTCTTTATCCCATCATCTCCTTCCCCAATCTTAAAGCATCAAACCTACATGT
* ** * *
1139221 TTTACTATGCTCTTTCTTTGGTTCACCAATATAATCAAGATTTA
64 TTTACTATACTCTTTCTTTAATCCACCAATATAATCAAGATTAA
1139265 AAATCA
1 AAATCA
1139271 ATACAAAAAA
Statistics
Matches: 95, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
107 8 0.08
108 56 0.59
109 31 0.33
ACGTcount: A:0.28, C:0.26, G:0.05, T:0.42
Consensus pattern (107 bp):
AAATCATTTTCTTCTTTATCCCATCATCTCCTTCCCCAATCTTAAAGCATCAAACCTACATGTTT
TACTATACTCTTTCTTTAATCCACCAATATAATCAAGATTAA
Found at i:1139943 original size:2 final size:2
Alignment explanation
Indices: 1139936--1139997 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
1139926 GACCTGGATC
1139936 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
1139978 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
1139998 GAGTTAGGAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1141245 original size:26 final size:26
Alignment explanation
Indices: 1141216--1141267 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
1141206 ATGTTAATTG
1141216 GTGTCTAATGGCATTCACAATTATGA
1 GTGTCTAATGGCATTCACAATTATGA
*
1141242 GTGTCTAATGGCATTCATAATTATGA
1 GTGTCTAATGGCATTCACAATTATGA
1141268 TGTTTATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (26 bp):
GTGTCTAATGGCATTCACAATTATGA
Found at i:1144544 original size:26 final size:26
Alignment explanation
Indices: 1144501--1144559 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
1144491 AACATTTAAA
* * *
1144501 TTTTAAAATGTGCTTTTATTA-AATAT
1 TTTTAAAAAGTGCATTTA-TACAACAT
*
1144527 TTTTAAAAAGTTCATTTATACAACAT
1 TTTTAAAAAGTGCATTTATACAACAT
1144553 TTTTAAA
1 TTTTAAA
1144560 TACCACTCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 2 0.07
26 26 0.93
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (26 bp):
TTTTAAAAAGTGCATTTATACAACAT
Found at i:1144861 original size:37 final size:37
Alignment explanation
Indices: 1144788--1144862 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 37
1144778 GTTGGAAAAT
*
1144788 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTTAAAATCATAAA
* *
1144825 ATTTATATAATTTTTTTTACAAAATTTAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTTAAAATCATAAA
1144862 A
1 A
1144863 AGGTTTAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 14 0.41
38 20 0.59
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTTAAAATCATAAA
Found at i:1154274 original size:29 final size:30
Alignment explanation
Indices: 1154220--1154287 Score: 104
Period size: 29 Copynumber: 2.3 Consensus size: 30
1154210 GTCAACTCAC
1154220 TGACTTTGATCGAGTCAACCCGTTGACCGT
1 TGACTTTGATCGAGTCAACCCGTTGACCGT
*
1154250 TGACTTTGATC-AGTCTGA-CCGTTGACCGT
1 TGACTTTGATCGAGTC-AACCCGTTGACCGT
1154279 TGACTTTGA
1 TGACTTTGA
1154288 CCGAAAAAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
29 24 0.67
30 12 0.33
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.34
Consensus pattern (30 bp):
TGACTTTGATCGAGTCAACCCGTTGACCGT
Found at i:1155855 original size:2 final size:2
Alignment explanation
Indices: 1155848--1155910 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
1155838 ATTTTGTTTA
1155848 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
1155890 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
1155911 ACATGGTTGA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1156149 original size:22 final size:23
Alignment explanation
Indices: 1156107--1156149 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1156097 AAACTCTAAA
*
1156107 ATATTTTTAAATAATTTAAATAT
1 ATATTTTTAAATAATTAAAATAT
*
1156130 ATATTTTT-AATCATTAAAAT
1 ATATTTTTAAATAATTAAAAT
1156150 CAACTTAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
ATATTTTTAAATAATTAAAATAT
Found at i:1157806 original size:15 final size:15
Alignment explanation
Indices: 1157786--1157822 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1157776 GAATAGAAAT
1157786 TGTTAATTAACAAAC
1 TGTTAATTAACAAAC
*
1157801 TGTTAATTAATAAAC
1 TGTTAATTAACAAAC
1157816 TGTTAAT
1 TGTTAAT
1157823 GTTCTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (15 bp):
TGTTAATTAACAAAC
Found at i:1158935 original size:2 final size:2
Alignment explanation
Indices: 1158928--1158994 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
1158918 TTTTTAAAAC
1158928 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
1158970 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1158995 CCCCCATCCC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1159181 original size:12 final size:12
Alignment explanation
Indices: 1159156--1159225 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
1159146 ACGGAGATAT
* *
1159156 CAGAAATCAAAA
1 CAGAATTCAGAA
1159168 CAGAATTCAGAA
1 CAGAATTCAGAA
1159180 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
1159192 CAGAATCCAGAT
1 CAGAATTCAGAA
*
1159204 CAGAAATCAGAA
1 CAGAATTCAGAA
1159216 CAGAATTCAG
1 CAGAATTCAG
1159226 GTCATATATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1159183 original size:24 final size:24
Alignment explanation
Indices: 1159156--1159248 Score: 105
Period size: 24 Copynumber: 3.9 Consensus size: 24
1159146 ACGGAGATAT
*
1159156 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* * *
1159180 CAGATATCAGAACAGAATCCAGAT
1 CAGAAATCAGAACAGAATTCAGAA
**
1159204 CAGAAATCAGAACAGAATTCAGGT
1 CAGAAATCAGAACAGAATTCAGAA
* * *
1159228 CATATATCAGAACAAAATTCA
1 CAGAAATCAGAACAGAATTCA
1159249 AGTCGGAAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.51, C:0.18, G:0.14, T:0.17
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:1159258 original size:48 final size:48
Alignment explanation
Indices: 1159154--1159262 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 48
1159144 AAACGGAGAT
* * *
1159154 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAAAATCAAG
** *
1159202 ATCAGAAATCAGAACAGAATTCAGGTCATATATCAGAACAAAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAAAA-TCAAG
*
1159251 -TCGGAAATCAGA
1 ATCAGAAATCAGA
1159263 TAAAATATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
48 49 0.92
49 4 0.08
ACGTcount: A:0.50, C:0.17, G:0.16, T:0.17
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAAAATCAAG
Found at i:1159260 original size:24 final size:24
Alignment explanation
Indices: 1159155--1159262 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
1159145 AACGGAGATA
* *
1159155 TCAGAAATCAAAACAGAATTC-AG
1 TCAGAAATCAGAACAAAATTCAAG
* * * *
1159178 AACAGATATCAGAACAGAA-TCCAG
1 -TCAGAAATCAGAACAAAATTCAAG
* *
1159202 ATCAGAAATCAGAACAGAATTCAGG
1 -TCAGAAATCAGAACAAAATTCAAG
* *
1159227 TCATATATCAGAACAAAATTCAAG
1 TCAGAAATCAGAACAAAATTCAAG
*
1159251 TCGGAAATCAGA
1 TCAGAAATCAGA
1159263 TAAAATATTT
Statistics
Matches: 68, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
23 2 0.03
24 63 0.93
25 3 0.04
ACGTcount: A:0.49, C:0.18, G:0.16, T:0.18
Consensus pattern (24 bp):
TCAGAAATCAGAACAAAATTCAAG
Found at i:1161801 original size:13 final size:13
Alignment explanation
Indices: 1161768--1161804 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1161758 GTCAACGGGT
*
1161768 CGGGTCGAGTCAA
1 CGGGTCGGGTCAA
1161781 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
1161794 CGGGTCGGGTC
1 CGGGTCGGGTC
1161805 GGTTTGTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.14, C:0.24, G:0.46, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:1163964 original size:12 final size:12
Alignment explanation
Indices: 1163939--1164008 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
1163929 ACGGAGATAT
* *
1163939 CAGAAATCAAAA
1 CAGAATTCAGAA
1163951 CAGAATTCAGAA
1 CAGAATTCAGAA
1163963 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
1163975 CAGAATCCAGAT
1 CAGAATTCAGAA
*
1163987 CAGAAATCAGAA
1 CAGAATTCAGAA
1163999 CAGAATTCAG
1 CAGAATTCAG
1164009 GTCATATATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1163966 original size:24 final size:24
Alignment explanation
Indices: 1163939--1164031 Score: 105
Period size: 24 Copynumber: 3.9 Consensus size: 24
1163929 ACGGAGATAT
*
1163939 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* * *
1163963 CAGATATCAGAACAGAATCCAGAT
1 CAGAAATCAGAACAGAATTCAGAA
**
1163987 CAGAAATCAGAACAGAATTCAGGT
1 CAGAAATCAGAACAGAATTCAGAA
* * *
1164011 CATATATCAGAACAAAATTCA
1 CAGAAATCAGAACAGAATTCA
1164032 AGTCGGAAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.51, C:0.18, G:0.14, T:0.17
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:1164041 original size:48 final size:48
Alignment explanation
Indices: 1163937--1164045 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 48
1163927 AAACGGAGAT
* * *
1163937 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAAAATCAAG
** *
1163985 ATCAGAAATCAGAACAGAATTCAGGTCATATATCAGAACAAAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAAAA-TCAAG
*
1164034 -TCGGAAATCAGA
1 ATCAGAAATCAGA
1164046 TAAATTATAT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
48 49 0.92
49 4 0.08
ACGTcount: A:0.50, C:0.17, G:0.16, T:0.17
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAAAATCAAG
Found at i:1164043 original size:24 final size:24
Alignment explanation
Indices: 1163938--1164045 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
1163928 AACGGAGATA
* *
1163938 TCAGAAATCAAAACAGAATTC-AG
1 TCAGAAATCAGAACAAAATTCAAG
* * * *
1163961 AACAGATATCAGAACAGAA-TCCAG
1 -TCAGAAATCAGAACAAAATTCAAG
* *
1163985 ATCAGAAATCAGAACAGAATTCAGG
1 -TCAGAAATCAGAACAAAATTCAAG
* *
1164010 TCATATATCAGAACAAAATTCAAG
1 TCAGAAATCAGAACAAAATTCAAG
*
1164034 TCGGAAATCAGA
1 TCAGAAATCAGA
1164046 TAAATTATAT
Statistics
Matches: 68, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
23 2 0.03
24 63 0.93
25 3 0.04
ACGTcount: A:0.49, C:0.18, G:0.16, T:0.18
Consensus pattern (24 bp):
TCAGAAATCAGAACAAAATTCAAG
Found at i:1166513 original size:7 final size:7
Alignment explanation
Indices: 1166501--1166530 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1166491 TGGTCAACGC
1166501 CGGTCAA
1 CGGTCAA
1166508 CGGTCAA
1 CGGTCAA
1166515 CGGTCAA
1 CGGTCAA
1166522 CGGTCAA
1 CGGTCAA
1166529 CG
1 CG
1166531 ATTAATGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.30, G:0.30, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:1166555 original size:13 final size:13
Alignment explanation
Indices: 1166537--1166567 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1166527 AACGATTAAT
1166537 GGGTCAACGGGTC
1 GGGTCAACGGGTC
1166550 GGGTCAACGGGTC
1 GGGTCAACGGGTC
1166563 GGGTC
1 GGGTC
1166568 GGTTTGTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.48, T:0.16
Consensus pattern (13 bp):
GGGTCAACGGGTC
Found at i:1168729 original size:12 final size:12
Alignment explanation
Indices: 1168704--1168796 Score: 73
Period size: 12 Copynumber: 7.8 Consensus size: 12
1168694 ACGGAGATAT
* *
1168704 CAGAAATCAAAA
1 CAGAATTCAGAA
1168716 CAGAATTCAGAA
1 CAGAATTCAGAA
1168728 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* * *
1168740 CAGAATCCATAT
1 CAGAATTCAGAA
*
1168752 CAGAAATCAGAA
1 CAGAATTCAGAA
**
1168764 CAGAATTCAGGT
1 CAGAATTCAGAA
*
1168776 CA-TATATCAGAA
1 CAGAAT-TCAGAA
1168788 CAGAATTCA
1 CAGAATTCA
1168797 AGTCGGAAAT
Statistics
Matches: 61, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
11 4 0.07
12 53 0.87
13 4 0.07
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.18
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1168731 original size:24 final size:24
Alignment explanation
Indices: 1168702--1168810 Score: 121
Period size: 24 Copynumber: 4.5 Consensus size: 24
1168692 AAACGGAGAT
*
1168702 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * * *
1168726 AACAGATATCAGAACAGAATCCAT
1 ATCAGAAATCAGAACAGAATTCAG
1168750 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
1168774 GTCATATATCAGAACAGAATTCA-
1 ATCAGAAATCAGAACAGAATTCAG
*
1168797 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
1168811 TAAAATATTT
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
24 68 1.00
ACGTcount: A:0.49, C:0.17, G:0.16, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:1168771 original size:48 final size:48
Alignment explanation
Indices: 1168700--1168810 Score: 152
Period size: 48 Copynumber: 2.3 Consensus size: 48
1168690 TTAAACGGAG
*
1168700 ATATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCC
** * *
1168748 ATATCAGAAATCAGAACAGAATTCAGGTCATATATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCC
*
1168796 A-AGTCGGAAATCAGA
1 ATA-TCAGAAATCAGA
1168811 TAAAATATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
47 1 0.02
48 55 0.98
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.19
Consensus pattern (48 bp):
ATATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCC
Found at i:1178567 original size:6 final size:6
Alignment explanation
Indices: 1178558--1178588 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1178548 GAGAGATCGA
1178558 CACCTT CACCTT CACCTT CACCTT CACCTT C
1 CACCTT CACCTT CACCTT CACCTT CACCTT C
1178589 CTCTTTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.52, G:0.00, T:0.32
Consensus pattern (6 bp):
CACCTT
Found at i:1187337 original size:15 final size:15
Alignment explanation
Indices: 1187317--1187348 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1187307 ATGAATTTAA
1187317 TATGATAAATAAATG
1 TATGATAAATAAATG
1187332 TATGATAAATAAATG
1 TATGATAAATAAATG
1187347 TA
1 TA
1187349 CTCTAATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.34
Consensus pattern (15 bp):
TATGATAAATAAATG
Found at i:1187832 original size:10 final size:10
Alignment explanation
Indices: 1187817--1187842 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1187807 CTCTGGCTAA
1187817 TATTTTCAAC
1 TATTTTCAAC
1187827 TATTTTCAAC
1 TATTTTCAAC
1187837 TATTTT
1 TATTTT
1187843 ATCGGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.15, G:0.00, T:0.58
Consensus pattern (10 bp):
TATTTTCAAC
Found at i:1188409 original size:14 final size:14
Alignment explanation
Indices: 1188385--1188419 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1188375 TTAAAAAATC
1188385 ATAAC-ATAATTAT
1 ATAACTATAATTAT
1188398 ATAACTATAATTAT
1 ATAACTATAATTAT
1188412 ATAACTAT
1 ATAACTAT
1188420 TCTTTCACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAACTATAATTAT
Found at i:1191720 original size:26 final size:26
Alignment explanation
Indices: 1191690--1191749 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
1191680 CGACTTGCCT
*
1191690 TAGCTCGCTAGCTCCTCTCGGACGCC
1 TAGCTCGCTAACTCCTCTCGGACGCC
1191716 TAGCTCGCTAACTCCTCTCGGACGCC
1 TAGCTCGCTAACTCCTCTCGGACGCC
1191742 TAGCTCGC
1 TAGCTCGC
1191750 CACTCCTTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.13, C:0.42, G:0.22, T:0.23
Consensus pattern (26 bp):
TAGCTCGCTAACTCCTCTCGGACGCC
Found at i:1192754 original size:103 final size:103
Alignment explanation
Indices: 1192516--1192758 Score: 269
Period size: 104 Copynumber: 2.3 Consensus size: 103
1192506 TTCCAATATC
*
1192516 CAATTTTGGTATCGATACTCATAGGAGTATCAATACAGAGGGTAGTGTATTGATACTCCCAGTAA
1 CAATTTTGGTATCGATACTCATAGGAGTATCAATACAGAGGGTAGTCTATTGATACTCCCAGTAA
*
1192581 GGATATTGATATTGGGATAATTTTCCTAAACATCGAATG
66 GGATATTGATATTGGGAT-ATTTTCCAAAACATCGAATG
* * * * * ** *
1192620 CAATTTTGGTATCAATACTCATTGGTGTATCAATACTGCGGGTA-TACTATTGATACTCTTAG-G
1 CAATTTTGGTATCGATACTCATAGGAGTATCAATACAGAGGGTAGT-CTATTGATACTCCCAGTA
* *
1192683 AGGAGTATTGATATTGAGGCT-TTTTCCAAAACATTGAATG
65 AGGA-TATTGATATTG-GGATATTTTCCAAAACATCGAATG
* * * *
1192723 TAATTTTGATACCGATACTCA-GGGCAGTATCAATAC
1 CAATTTTGGTATCGATACTCATAGG-AGTATCAATAC
1192759 CCTAGGAGGG
Statistics
Matches: 117, Mismatches: 18, Indels: 9
0.81 0.12 0.06
Matches are distributed among these distances:
102 2 0.02
103 49 0.42
104 63 0.54
105 3 0.03
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34
Consensus pattern (103 bp):
CAATTTTGGTATCGATACTCATAGGAGTATCAATACAGAGGGTAGTCTATTGATACTCCCAGTAA
GGATATTGATATTGGGATATTTTCCAAAACATCGAATG
Found at i:1196383 original size:15 final size:16
Alignment explanation
Indices: 1196363--1196392 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1196353 TGTCGATGCA
1196363 ATCATA-TATGTTTGT
1 ATCATACTATGTTTGT
1196378 ATCATACTATGTTTG
1 ATCATACTATGTTTG
1196393 AGTTTATTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.10, G:0.13, T:0.50
Consensus pattern (16 bp):
ATCATACTATGTTTGT
Found at i:1198520 original size:39 final size:39
Alignment explanation
Indices: 1198465--1198539 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
1198455 ATAACAAATA
* *
1198465 GTGGCATATTATGACAAAAGGCCAACGGGAGTTTGATCG
1 GTGGCATATTACGACAAAAGACCAACGGGAGTTTGATCG
1198504 GTGGCATATTACGACAAAAGACCAACGGGAGTTTGA
1 GTGGCATATTACGACAAAAGACCAACGGGAGTTTGA
1198540 GTATGTGCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.21
Consensus pattern (39 bp):
GTGGCATATTACGACAAAAGACCAACGGGAGTTTGATCG
Found at i:1201692 original size:20 final size:20
Alignment explanation
Indices: 1201667--1201704 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1201657 TTTGGTTCAC
1201667 GGAATGTAAGATTACCAGTA
1 GGAATGTAAGATTACCAGTA
1201687 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
1201705 GGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTA
Found at i:1205397 original size:18 final size:18
Alignment explanation
Indices: 1205374--1205422 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1205364 CCCATCCCTA
1205374 GGTCTAACCCCCTAAACT
1 GGTCTAACCCCCTAAACT
**
1205392 GGTCTAACCTTCTAAACT
1 GGTCTAACCCCCTAAACT
* *
1205410 GGTTTGACCCCCT
1 GGTCTAACCCCCT
1205423 GAATCGGTCT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.22, C:0.35, G:0.14, T:0.29
Consensus pattern (18 bp):
GGTCTAACCCCCTAAACT
Found at i:1207938 original size:27 final size:25
Alignment explanation
Indices: 1207890--1207940 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
1207880 TATGATTCTG
1207890 TAAAAATAAAATGTAGATATTAAAA
1 TAAAAATAAAATGTAGATATTAAAA
* *
1207915 TAAATAATAATAATTTAGGTATTAAA
1 TAAA-AATAA-AATGTAGATATTAAA
1207941 CATATAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.18
26 5 0.23
27 13 0.59
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (25 bp):
TAAAAATAAAATGTAGATATTAAAA
Found at i:1207990 original size:2 final size:2
Alignment explanation
Indices: 1207967--1208012 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
1207957 AAATAAAATG
* * *
1207967 TA TA TA TT TG TA TA CA TA -A 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
1208008 TA TA T
1 TA TA T
1208013 TAAATTTGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1209220 original size:13 final size:13
Alignment explanation
Indices: 1209172--1209232 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
1209162 ATTTTGTTAG
1209172 TATTTTATTTAAT
1 TATTTTATTTAAT
* *
1209185 TATTTGA-TTATT
1 TATTTTATTTAAT
1209197 TGATTTT-TTTAAT
1 T-ATTTTATTTAAT
*
1209210 TATTTTATTTAAA
1 TATTTTATTTAAT
1209223 TATTTTATTT
1 TATTTTATTT
1209233 TTTTTGCAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
12 10 0.25
13 30 0.75
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:1211447 original size:5 final size:5
Alignment explanation
Indices: 1211437--1211571 Score: 270
Period size: 5 Copynumber: 27.0 Consensus size: 5
1211427 CAAAGCGAAA
1211437 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1211487 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1211537 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1211572 CATGTATTTG
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 130 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:1211956 original size:9 final size:9
Alignment explanation
Indices: 1211942--1211994 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
1211932 TTCTTCTGGG
*
1211942 TCCACCATC
1 TCCACCACC
1211951 TCCACCACC
1 TCCACCACC
*
1211960 ACCACCACC
1 TCCACCACC
*
1211969 TCCACCTCC
1 TCCACCACC
1211978 ATCTCTACCACC
1 -TC-C-ACCACC
1211990 TCCAC
1 TCCAC
1211995 TGTCATTATC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
9 25 0.69
10 3 0.08
11 3 0.08
12 5 0.14
ACGTcount: A:0.23, C:0.60, G:0.00, T:0.17
Consensus pattern (9 bp):
TCCACCACC
Found at i:1211960 original size:12 final size:12
Alignment explanation
Indices: 1211943--1211994 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
1211933 TCTTCTGGGT
*
1211943 CCACCATCTCCA
1 CCACCACCTCCA
*
1211955 CCACCACCACCA
1 CCACCACCTCCA
*
1211967 CCTCCACCTCCA
1 CCACCACCTCCA
1211979 TCTCTACCACCTCCA
1 -C-C-ACCACCTCCA
1211994 C
1 C
1211995 TGTCATTATC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
12 20 0.62
13 1 0.03
14 2 0.06
15 9 0.28
ACGTcount: A:0.23, C:0.62, G:0.00, T:0.15
Consensus pattern (12 bp):
CCACCACCTCCA
Found at i:1212773 original size:34 final size:35
Alignment explanation
Indices: 1212727--1212801 Score: 116
Period size: 34 Copynumber: 2.2 Consensus size: 35
1212717 AAAACAGTCC
* *
1212727 TCAATTTTATTCTAAACCCCAATTTCC-AAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
1212761 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
1212796 TCAATT
1 TCAATT
1212802 AAATTCAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
34 24 0.65
35 13 0.35
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:1213344 original size:130 final size:130
Alignment explanation
Indices: 1213198--1213445 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
1213188 TATTTATATA
* **
1213198 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
1213263 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
1213328 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
1213393 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
1213446 GAAGAAAATT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:1213476 original size:130 final size:129
Alignment explanation
Indices: 1213212--1213476 Score: 309
Period size: 130 Copynumber: 2.0 Consensus size: 129
1213202 ATTTGGTCCT
* ** *
1213212 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
1213277 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
1213342 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * *
1213407 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
1213471 -A
128 CA
1213472 AAATT
1 AAATT
1213477 TGGGTCTTGG
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
130 100 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:1213938 original size:16 final size:18
Alignment explanation
Indices: 1213917--1213950 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1213907 ATTTCTTATT
1213917 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
1213933 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
1213951 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:1216047 original size:28 final size:29
Alignment explanation
Indices: 1216007--1216063 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
1215997 TTTAAAATTC
*
1216007 AACAATTGTTGGCCACTGTTTG-CTTTAA
1 AACAATTGTTGGCCACCGTTTGACTTTAA
*
1216035 AACAATTTTTGGCCACCGTTTGACTTTAA
1 AACAATTGTTGGCCACCGTTTGACTTTAA
1216064 CAATCTCCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (29 bp):
AACAATTGTTGGCCACCGTTTGACTTTAA
Found at i:1220645 original size:28 final size:29
Alignment explanation
Indices: 1220596--1220650 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
1220586 TTTAAAATTC
* * *
1220596 AACAATTGTTGGCCACCGTTTG-CTTTTA
1 AACAATTGTTGGACAACATTTGACTTTTA
1220624 AACAATTGTTGGACAACATTTGACTTT
1 AACAATTGTTGGACAACATTTGACTTT
1220651 AACAAAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.38
Consensus pattern (29 bp):
AACAATTGTTGGACAACATTTGACTTTTA
Found at i:1234019 original size:19 final size:16
Alignment explanation
Indices: 1233953--1234020 Score: 70
Period size: 16 Copynumber: 4.2 Consensus size: 16
1233943 TAATAATAAT
*
1233953 AAAAATGAG-AAGAAG
1 AAAAATGAGAAAAAAG
*
1233968 AAAAA-GA-AGAAAAG
1 AAAAATGAGAAAAAAG
1233982 AAAAATGAGAAAAAAG
1 AAAAATGAGAAAAAAG
1233998 AAAAATGATGGAAAAAACG
1 AAAAATGA--GAAAAAA-G
1234017 AAAA
1 AAAA
1234021 GAAAAAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
14 11 0.25
15 7 0.16
16 14 0.32
18 7 0.16
19 5 0.11
ACGTcount: A:0.72, C:0.01, G:0.21, T:0.06
Consensus pattern (16 bp):
AAAAATGAGAAAAAAG
Found at i:1234037 original size:18 final size:17
Alignment explanation
Indices: 1234009--1234068 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 17
1233999 AAAATGATGG
*
1234009 AAAAAACGAAAAGAAAA
1 AAAAAATGAAAAGAAAA
*
1234026 AAAAAATGGAAAATG-GAA
1 AAAAAAT-GAAAA-GAAAA
*
1234044 GAAAAATGAAAGAGAAAA
1 AAAAAATGAAA-AGAAAA
1234062 ACAAAAA
1 A-AAAAA
1234069 GAGAAAAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
17 11 0.33
18 16 0.48
19 6 0.18
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.05
Consensus pattern (17 bp):
AAAAAATGAAAAGAAAA
Found at i:1234069 original size:48 final size:45
Alignment explanation
Indices: 1233953--1234076 Score: 126
Period size: 45 Copynumber: 2.7 Consensus size: 45
1233943 TAATAATAAT
* * *
1233953 AAAAATGAGAAGAAGAAA-AAGAAGAAAAGAAAAATGAGAAAAAAG
1 AAAAATGA-AAGAAAAAACAAAAAGAAAAAAAAAATGAGAAAAAAG
** *
1233998 AAAAATGATGGAAAAAACGAAAAGAAAAAAAAAATG-GAAAATGGAAG
1 AAAAATGAAAGAAAAAACAAAAAGAAAAAAAAAATGAGAAAA---AAG
*
1234045 AAAAATGAAAGAGAAAAACAAAAAGAGAAAAA
1 AAAAATGAAAGA-AAAAACAAAAAGAAAAAAA
1234077 TGAAAAAAAG
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
44 11 0.17
45 23 0.36
47 13 0.20
48 17 0.27
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.06
Consensus pattern (45 bp):
AAAAATGAAAGAAAAAACAAAAAGAAAAAAAAAATGAGAAAAAAG
Found at i:1234076 original size:47 final size:45
Alignment explanation
Indices: 1233915--1234076 Score: 122
Period size: 47 Copynumber: 3.6 Consensus size: 45
1233905 AGAAGAACTA
* * *
1233915 AAAGAGAAAAAGAAAAAAATGAAAAAAAT--AATAATAATAAAAATG
1 AAAGAGAAAAACAAAAAGA-GAAAAAAATGGAA-AATAAGAAAAATG
*
1233960 AGAAGAAGAAAAAGAAGAAA-AG--AAAAATGAGAAAA-AAGAAAAATG
1 A-AAG-AGAAAAACAA-AAAGAGAAAAAAATG-GAAAATAAGAAAAATG
** * *
1234005 ATGGA-AAAAACGAAAAGAAAAAAAAAATGGAAAATGGAAGAAAAATG
1 AAAGAGAAAAACAAAAAG-AGAAAAAAATGGAAAAT--AAGAAAAATG
1234052 AAAGAGAAAAACAAAAAGAGAAAAA
1 AAAGAGAAAAACAAAAAGAGAAAAA
1234077 TGAAAAAAAG
Statistics
Matches: 93, Mismatches: 10, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
41 3 0.03
42 6 0.06
43 2 0.02
44 12 0.13
45 18 0.19
46 6 0.06
47 32 0.34
48 14 0.15
ACGTcount: A:0.73, C:0.01, G:0.18, T:0.07
Consensus pattern (45 bp):
AAAGAGAAAAACAAAAAGAGAAAAAAATGGAAAATAAGAAAAATG
Found at i:1234082 original size:14 final size:14
Alignment explanation
Indices: 1234043--1234082 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1234033 GGAAAATGGA
1234043 AGAAAAATG-AAAG
1 AGAAAAATGAAAAG
**
1234056 AGAAAAACAAAAAG
1 AGAAAAATGAAAAG
1234070 AGAAAAATGAAAA
1 AGAAAAATGAAAA
1234083 AAAGAGAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.05
Consensus pattern (14 bp):
AGAAAAATGAAAAG
Done.