Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008228.1 Hibiscus syriacus cultivar Beakdansim tig00110864_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: 3739947
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 20
Found at i:1653019 original size:64 final size:64
Alignment explanation
Indices: 1652935--1653092 Score: 282
Period size: 64 Copynumber: 2.5 Consensus size: 64
1652925 TTAATTGAAT
1652935 TTTACATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGT-AATAAGAATTATTTTTTGCTT
1 TTTA-ATTGATTTGTAAAAGTTGATTTGTTTAATTGATG-GGTAAATAAGAATTATTTTTTGCTT
1652999 G
64 G
*
1653000 TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAAGAATTATTTTTTGCTTG
1 TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGGGTAAATAAGAATTATTTTTTGCTTG
1653064 TTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTAATTGATTTGTAAAAGTTGATTTGTT
1653093 GTTTATTCAA
Statistics
Matches: 91, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
63 2 0.02
64 85 0.93
65 4 0.04
ACGTcount: A:0.29, C:0.02, G:0.18, T:0.51
Consensus pattern (64 bp):
TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGGGTAAATAAGAATTATTTTTTGCTTG
Found at i:1653198 original size:20 final size:20
Alignment explanation
Indices: 1653147--1653192 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1653137 AAGGTACACT
1653147 TTCGCAACGCGAAAATCAAA
1 TTCGCAACGCGAAAATCAAA
*
1653167 TTCGCAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAATCAAA
1653187 TTCGCA
1 TTCGCA
1653193 TTGCGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.17
Consensus pattern (20 bp):
TTCGCAACGCGAAAATCAAA
Found at i:1653245 original size:34 final size:34
Alignment explanation
Indices: 1653175--1653247 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
1653165 AATTCGCAAC
* **
1653175 GCGAAAGTCAAATTCGCATTGCGATTTTTTTGTT
1 GCGATAGTCAAATTCGCATTGCGATTTTAATGTT
* *
1653209 GCGATAGTCAAATTCGCGTTTCGATTTTCAAT-TT
1 GCGATAGTCAAATTCGCATTGCGATTTT-AATGTT
1653243 GCGAT
1 GCGAT
1653248 TTCGCGTTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
34 32 0.97
35 1 0.03
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (34 bp):
GCGATAGTCAAATTCGCATTGCGATTTTAATGTT
Found at i:1653327 original size:34 final size:34
Alignment explanation
Indices: 1653257--1653331 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 34
1653247 TTTCGCGTTT
* * * * **
1653257 CGAATTTGACTTTCGCAACGCGATAATCGCGTTG
1 CGAATTTGACTATCACAACGCAAAAATCGCAATG
*
1653291 CGAATTTGACTATCACAACGCAAAAATCTCAATG
1 CGAATTTGACTATCACAACGCAAAAATCGCAATG
1653325 CGAATTT
1 CGAATTT
1653332 AACTTTTGCA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (34 bp):
CGAATTTGACTATCACAACGCAAAAATCGCAATG
Found at i:1656676 original size:16 final size:16
Alignment explanation
Indices: 1656655--1656693 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1656645 AAATCATTGA
*
1656655 AAAATTATATAGAAAT
1 AAAATTATATAAAAAT
*
1656671 AAAATTATGTAAAAAT
1 AAAATTATATAAAAAT
1656687 AAAATTA
1 AAAATTA
1656694 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (16 bp):
AAAATTATATAAAAAT
Found at i:1656933 original size:21 final size:19
Alignment explanation
Indices: 1656880--1656938 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
1656870 TTGTGATTCA
*
1656880 AAAATCGAGTTGCGAATTT
1 AAAATCCAGTTGCGAATTT
* *
1656899 GAAATTCAGTTGCGAATTT
1 AAAATCCAGTTGCGAATTT
1656918 AAAATCCAGTGTTGCGAATTT
1 AAAATCCA--GTTGCGAATTT
1656939 GACTTATTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 22 0.67
21 11 0.33
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (19 bp):
AAAATCCAGTTGCGAATTT
Found at i:1659385 original size:6 final size:6
Alignment explanation
Indices: 1659376--1659467 Score: 73
Period size: 6 Copynumber: 15.0 Consensus size: 6
1659366 AAAAGGATAT
1659376 ATAATA ATAATA ATAATA ATAATA ATAA-A ATATATA CAT-ATA TATAA-A
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATA-ATA -ATAATA -ATAATA
* * * * *
1659424 CGTTAAAA ATAATA ACAATA ATAACA ATAATA ATAACA ATAATA
1 --ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
1659468 TATATATATA
Statistics
Matches: 69, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
5 4 0.06
6 57 0.83
7 5 0.07
8 3 0.04
ACGTcount: A:0.64, C:0.05, G:0.01, T:0.29
Consensus pattern (6 bp):
ATAATA
Found at i:1659390 original size:9 final size:9
Alignment explanation
Indices: 1659376--1659467 Score: 73
Period size: 9 Copynumber: 10.0 Consensus size: 9
1659366 AAAAGGATAT
1659376 ATAATAATA
1 ATAATAATA
1659385 ATAATAATA
1 ATAATAATA
1659394 ATAATAATA
1 ATAATAATA
1659403 A-AATATATA
1 ATAATA-ATA
1659412 CAT-ATATATA
1 -ATAATA-ATA
* *
1659422 A-ACGTTAAAA
1 ATA--ATAATA
*
1659432 ATAATAACA
1 ATAATAATA
*
1659441 ATAATAACA
1 ATAATAATA
1659450 ATAATAATA
1 ATAATAATA
*
1659459 ACAATAATA
1 ATAATAATA
1659468 TATATATATA
Statistics
Matches: 70, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
8 4 0.06
9 52 0.74
10 11 0.16
11 3 0.04
ACGTcount: A:0.64, C:0.05, G:0.01, T:0.29
Consensus pattern (9 bp):
ATAATAATA
Found at i:1660402 original size:21 final size:21
Alignment explanation
Indices: 1660378--1660420 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1660368 AAACTAAAAT
*
1660378 ATAAGTAATAAAA-CAATAATA
1 ATAA-TAAAAAAATCAATAATA
*
1660399 ATAATAAAAAAATGAATAATA
1 ATAATAAAAAAATCAATAATA
1660420 A
1 A
1660421 AAAAATACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (21 bp):
ATAATAAAAAAATCAATAATA
Found at i:1660408 original size:18 final size:18
Alignment explanation
Indices: 1660378--1660435 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
1660368 AAACTAAAAT
1660378 ATAAGTAAT-AAAACAATA
1 ATAA-TAATAAAAACAATA
1660396 ATAATAATAAAAA-AATGA
1 ATAATAATAAAAACAAT-A
*
1660414 ATAATAAAAAAATACAA-A
1 ATAATAATAAAA-ACAATA
1660432 ATAA
1 ATAA
1660436 GAAAATATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
17 7 0.20
18 25 0.71
19 1 0.03
20 2 0.06
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.21
Consensus pattern (18 bp):
ATAATAATAAAAACAATA
Found at i:1660418 original size:15 final size:15
Alignment explanation
Indices: 1660398--1660426 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1660388 AAACAATAAT
1660398 AATAATAAAAAAATG
1 AATAATAAAAAAATG
1660413 AATAATAAAAAAAT
1 AATAATAAAAAAAT
1660427 ACAAAATAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AATAATAAAAAAATG
Found at i:1660434 original size:15 final size:14
Alignment explanation
Indices: 1660395--1660442 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
1660385 ATAAAACAAT
*
1660395 AATAATAATAAAAA
1 AATAAAAATAAAAA
*
1660409 AATGAATAATAAAAA
1 AAT-AAAAATAAAAA
*
1660424 AATACAAAATAAGAA
1 AATA-AAAATAAAAA
1660439 AATA
1 AATA
1660443 TTTTTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 4 0.13
15 26 0.87
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (14 bp):
AATAAAAATAAAAA
Found at i:1660451 original size:26 final size:26
Alignment explanation
Indices: 1660421--1660477 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
1660411 TGAATAATAA
1660421 AAAAATACAAAATAAGA-AAATATTTTT
1 AAAAA-ACAAAATAAGACAAAT-TTTTT
* * *
1660448 AAAAAACTATATAATACAAATTTTTT
1 AAAAAACAAAATAAGACAAATTTTTT
1660474 AAAA
1 AAAA
1660478 CGTTCTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 17 0.65
27 9 0.35
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (26 bp):
AAAAAACAAAATAAGACAAATTTTTT
Found at i:1660528 original size:41 final size:38
Alignment explanation
Indices: 1660437--1660541 Score: 104
Period size: 39 Copynumber: 2.7 Consensus size: 38
1660427 ACAAAATAAG
**
1660437 AAAATATTTTTAAAAAACTATATAATACAAATTTTTTAA
1 AAAAT-TTTTTAAAAAACTATATAATACAAATTTTCAAA
** *
1660476 AACGTTCTTTTAAAAAACTATATTATATATAAATTTTCAAA
1 AAAATT-TTTTAAAAAACTATA-TA-ATACAAATTTTCAAA
*
1660517 AATAATTTTTT-AAAAAGTATATAAT
1 AA-AATTTTTTAAAAAACTATATAAT
1660542 TTTCAAAAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
38 3 0.06
39 20 0.37
40 11 0.20
41 18 0.33
42 2 0.04
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (38 bp):
AAAATTTTTTAAAAAACTATATAATACAAATTTTCAAA
Found at i:1660585 original size:38 final size:38
Alignment explanation
Indices: 1660534--1660952 Score: 454
Period size: 38 Copynumber: 11.1 Consensus size: 38
1660524 TTTTAAAAAG
* *
1660534 TATATAA-TTTTCAAAAATGTTTT-AAAATTATATATTA
1 TATATAAGTTTTC-AAAATGTTTTAAAAACTATATAATA
1660571 TATATAAGTTTTCAAAAATGTTTTAAAAGACTATAT-AT-
1 TATATAAGTTTTC-AAAATGTTTTAAAA-ACTATATAATA
*
1660609 TATATAAGTTTTCAAAAATGTTTTCAAAGACTATAT-AT-
1 TATATAAGTTTTC-AAAATGTTTT-AAAAACTATATAATA
* *
1660647 TATCTAAGTTTTCAAAATGATTTTAAAAATTATATAATA
1 TATATAAGTTTTCAAAATG-TTTTAAAAACTATATAATA
* *
1660686 TATATATGTTTTCAAAATGTTTTAAAAACTATATATTA
1 TATATAAGTTTTCAAAATGTTTTAAAAACTATATAATA
*
1660724 TATAT-ACTTTT-AAAATGTTTTAAAAACTATATAATA
1 TATATAAGTTTTCAAAATGTTTTAAAAACTATATAATA
1660760 TATA-AATGTTTTCGAAAATGTTTTAAAAACTATATAATA
1 TATATAA-GTTTTC-AAAATGTTTTAAAAACTATATAATA
* *
1660799 TATATATGTTTTCAAAATGTTTTAAAAACTATATTATA
1 TATATAAGTTTTCAAAATGTTTTAAAAACTATATAATA
* *
1660837 TATAT-A-TATTCAAAACGTTTTAAAAACTATATAATA
1 TATATAAGTTTTCAAAATGTTTTAAAAACTATATAATA
* * *
1660873 TATA-AATGTTTTCAAAAATGCTTTTCAAAACCATATTATA
1 TATATAA-GTTTTC-AAAATG-TTTTAAAAACTATATAATA
* *
1660913 TATAT-A-TATAT-ATAAATGCTTTCAAAAACTATATAATA
1 TATATAAGT-TTTCA-AAATG-TTTTAAAAACTATATAATA
1660951 TA
1 TA
1660953 CTTGTTTTCA
Statistics
Matches: 332, Mismatches: 30, Indels: 39
0.83 0.07 0.10
Matches are distributed among these distances:
36 61 0.18
37 31 0.09
38 146 0.44
39 66 0.20
40 28 0.08
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.43
Consensus pattern (38 bp):
TATATAAGTTTTCAAAATGTTTTAAAAACTATATAATA
Found at i:1660786 original size:113 final size:113
Alignment explanation
Indices: 1660541--1660919 Score: 495
Period size: 113 Copynumber: 3.3 Consensus size: 113
1660531 AAGTATATAA
* * *
1660541 TTTTCAAAAATG-TTTT-AAAATTATATATTATATATAAGTTTTCAAAAATGTTTTAAAAGACTA
1 TTTTCAAAAATGATTTTAAAAACTATATAATATATATATGTTTTC-AAAATGTTTTAAAA-ACTA
* * *
1660604 TATATTATATA-AGTTTTCAAAAATGTTTTCAAAGACTATATATTATCT-AA-G
64 TATATTATATATA-TTTT--AAAATGTTTT-AAAAACTATATAATATATAAATG
*
1660655 TTTTC-AAAATGATTTTAAAAATTATATAATATATATATGTTTTCAAAATGTTTTAAAAACTATA
1 TTTTCAAAAATGATTTTAAAAACTATATAATATATATATGTTTTCAAAATGTTTTAAAAACTATA
1660719 TATTATATATACTTTTAAAATGTTTTAAAAACTATATAATATATAAATG
66 TATTATATATA-TTTTAAAATGTTTTAAAAACTATATAATATATAAATG
*
1660768 TTTTCGAAAATG-TTTTAAAAACTATATAATATATATATGTTTTCAAAATGTTTTAAAAACTATA
1 TTTTCAAAAATGATTTTAAAAACTATATAATATATATATGTTTTCAAAATGTTTTAAAAACTATA
* *
1660832 T-TATATATATATATTCAAAACGTTTTAAAAACTATATAATATATAAATG
66 TAT-TATATATAT-TTTAAAATGTTTTAAAAACTATATAATATATAAATG
* * * *
1660881 TTTTCAAAAATGCTTTTCAAAACCATATTATATATATAT
1 TTTTCAAAAATGATTTTAAAAACTATATAATATATATAT
1660920 ATATATAAAT
Statistics
Matches: 243, Mismatches: 13, Indels: 18
0.89 0.05 0.07
Matches are distributed among these distances:
111 15 0.06
112 14 0.06
113 132 0.54
114 57 0.23
115 25 0.10
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (113 bp):
TTTTCAAAAATGATTTTAAAAACTATATAATATATATATGTTTTCAAAATGTTTTAAAAACTATA
TATTATATATATTTTAAAATGTTTTAAAAACTATATAATATATAAATG
Found at i:1661494 original size:168 final size:168
Alignment explanation
Indices: 1661207--1661691 Score: 731
Period size: 168 Copynumber: 2.9 Consensus size: 168
1661197 TGGTGCCCAT
* * *
1661207 AAAGCTGAGTGTAGTCGAACTTGAGGGTATTTGGTTGGCAGATAACCCTTCTCCACTTAAGCTAT
1 AAAGCTGAGTGTAGTCGAACTCGAGGGTATTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
* * *
1661272 GCTGCAAATGATGTGTCGTTGAGCTGAGCGTAGTCGAAATCAAAGGCCTTTGTTGACAGATAACC
66 GCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGTTGACAGATAACC
* * *
1661337 CTTCTAGCCTTTATTTATGCTACAAATGATGTGCCCTC
131 CTTCTAGCCTTGAGTTATGCTACAAATGATATGCCCTC
* *
1661375 GAAA-CTGAGTGTAGTCGAACTCGAGGGTCTTTGGTTGACAGATAGCCCTTCTCGACTTAAGCTA
1 -AAAGCTGAGTGTAGTCGAACTCGAGGGTATTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTA
*
1661439 TGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTATTTGTTGACAGATAAC
65 TGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGTTGACAGATAAC
* **
1661504 CCTTTTAGCCTTGAGTTATGCTGTAAATGATATGCCCTC
130 CCTTCTAGCCTTGAGTTATGCTACAAATGATATGCCCTC
* * *
1661543 AAAGATGAGTGTAGTCGAACTGGAGGGTTTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
1 AAAGCTGAGTGTAGTCGAACTCGAGGGTATTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
* * * *
1661608 GCTGCAAATGATGTACC-TCGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAA
66 GCTGCAAATGATGTGCCGT-TGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT-GTTGACAGATAA
1661672 CCCTTCTAGCCTTGAGTTAT
129 CCCTTCTAGCCTTGAGTTAT
1661692 ACTGAAAATA
Statistics
Matches: 288, Mismatches: 25, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
167 4 0.01
168 251 0.87
169 33 0.11
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (168 bp):
AAAGCTGAGTGTAGTCGAACTCGAGGGTATTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
GCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGTTGACAGATAACC
CTTCTAGCCTTGAGTTATGCTACAAATGATATGCCCTC
Found at i:1663044 original size:100 final size:98
Alignment explanation
Indices: 1662816--1663075 Score: 373
Period size: 100 Copynumber: 2.6 Consensus size: 98
1662806 GGCTAGCTAA
* * * *
1662816 ATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGAACAACTCAA--TGATATTATATAGG
1 ATCCATAAAGCCG-GGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCT-TTATTGTATAGA
1662879 TATTATAACCACCTTTATCAGGCTAGCTGAATATT
64 TATTATAACCACCTTTATCAGGCTAGCTGAATATT
*
1662914 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCCAGAGGGACAACTCAAGCTTTATTGTATAGAT
1 ATCCATAAAGCC-GGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAGAT
* *
1662979 ATTATAATCACCTTTATCAGGCTTAG-TCGAATCTT
65 ATTATAACCACCTTTATCAGGC-TAGCT-GAATATT
*
1663014 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATA
1 ATCCATAAAGCC-GGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATA
1663076 TATAATATTA
Statistics
Matches: 147, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
98 45 0.31
99 33 0.22
100 69 0.47
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (98 bp):
ATCCATAAAGCCGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAGATA
TTATAACCACCTTTATCAGGCTAGCTGAATATT
Found at i:1663189 original size:30 final size:30
Alignment explanation
Indices: 1663150--1663224 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 30
1663140 AAAATTGAAT
1663150 TAAACGGGGACGGGGAAAAACCATTTATGC
1 TAAACGGGGACGGGGAAAAACCATTTATGC
* * ** *
1663180 TAAATGGGGACGGAG-AAAACTGTTTATGT
1 TAAACGGGGACGGGGAAAAACCATTTATGC
1663209 TAAACGGGGACGGGGA
1 TAAACGGGGACGGGGA
1663225 CGGGTTTAGT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
29 24 0.65
30 13 0.35
ACGTcount: A:0.35, C:0.12, G:0.35, T:0.19
Consensus pattern (30 bp):
TAAACGGGGACGGGGAAAAACCATTTATGC
Found at i:1667422 original size:16 final size:16
Alignment explanation
Indices: 1667401--1667433 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1667391 AGCACATGAA
*
1667401 ATAAATAAGGTAAAAT
1 ATAAATAAGATAAAAT
1667417 ATAAATAAGATAAAAT
1 ATAAATAAGATAAAAT
1667433 A
1 A
1667434 AAGAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (16 bp):
ATAAATAAGATAAAAT
Found at i:1667434 original size:14 final size:14
Alignment explanation
Indices: 1667399--1667507 Score: 50
Period size: 14 Copynumber: 7.7 Consensus size: 14
1667389 CAAGCACATG
*
1667399 AAATAAATAAGGTAA
1 AAATAAATAAGAT-A
1667414 AATATAAATAAGATA
1 AA-ATAAATAAGATA
* *
1667429 AAATAAAGAAAATA
1 AAATAAATAAGATA
*
1667443 AAA-AACA-CA-ATA
1 AAATAA-ATAAGATA
*
1667455 AAGATAAATAGGATA
1 AA-ATAAATAAGATA
* *
1667470 AGATAAAGGAA-ATA
1 AAATAAA-TAAGATA
1667484 AAAT--ATAATGATA
1 AAATAAATAA-GATA
1667497 ATAATAAATAA
1 A-AATAAATAA
1667508 AGAAGAAGAA
Statistics
Matches: 71, Mismatches: 11, Indels: 23
0.68 0.10 0.22
Matches are distributed among these distances:
11 2 0.03
12 6 0.08
13 9 0.13
14 30 0.42
15 10 0.14
16 14 0.20
ACGTcount: A:0.68, C:0.02, G:0.10, T:0.20
Consensus pattern (14 bp):
AAATAAATAAGATA
Found at i:1667605 original size:9 final size:9
Alignment explanation
Indices: 1667579--1667616 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
1667569 AACTAGGGAA
1667579 AAAT-AAAT
1 AAATAAAAT
* *
1667587 AAGTACAAT
1 AAATAAAAT
1667596 AAATAAAAT
1 AAATAAAAT
1667605 AAATAAAAT
1 AAATAAAAT
1667614 AAA
1 AAA
1667617 AAAGGGATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
8 3 0.12
9 22 0.88
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:1667635 original size:3 final size:3
Alignment explanation
Indices: 1667627--1667704 Score: 54
Period size: 3 Copynumber: 25.0 Consensus size: 3
1667617 AAAGGGATAT
* *
1667627 ATA ATA ATA ATA ATA A-A ATA TATA CAT- ATA TATA TATA CGTTA AAA
1 ATA ATA ATA ATA ATA ATA ATA -ATA -ATA ATA -ATA -ATA --ATA ATA
*
1667673 ATA ATA ACA ATA ATA AT- ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1667705 TTAGATATAT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
2 6 0.10
3 41 0.67
4 12 0.20
5 2 0.03
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1667698 original size:14 final size:14
Alignment explanation
Indices: 1667625--1667705 Score: 63
Period size: 14 Copynumber: 5.3 Consensus size: 14
1667615 AAAAAGGGAT
1667625 ATATAATAATAATA
1 ATATAATAATAATA
*
1667639 ATAAAATATATACATA
1 ATATAATA-ATA-ATA
* *
1667655 TATATATATACGTTAAAA
1 -ATATA-ATA--ATAATA
*
1667673 ATAATAACAATAATA
1 AT-ATAATAATAATA
1667688 ATATAATAATAATA
1 ATATAATAATAATA
1667702 ATAT
1 ATAT
1667706 TAGATATATA
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
14 22 0.42
15 9 0.17
16 3 0.06
17 8 0.15
18 8 0.15
19 2 0.04
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (14 bp):
ATATAATAATAATA
Found at i:1668323 original size:3 final size:3
Alignment explanation
Indices: 1668317--1668366 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
1668307 AAAGGGATAT
1668317 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1668364 ATA
1 ATA
1668367 TATACATATA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1668323 original size:37 final size:35
Alignment explanation
Indices: 1668240--1668323 Score: 82
Period size: 37 Copynumber: 2.3 Consensus size: 35
1668230 AAAGGAATAT
**
1668240 ATATATATATAAGAAATAAATAAATGAAAACTAGGG
1 ATATATA-ATAAGAAATAAATAAATGAAAAAAAGGG
*
1668276 A-AAATAAATAAGTACAATAAATAAAAT-AAAAAAAGGG
1 ATATAT-AATAAG-A-AATAAAT-AAATGAAAAAAAGGG
1668313 ATATATAATAA
1 ATATATAATAA
1668324 TAATAATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
35 8 0.21
36 3 0.08
37 21 0.54
38 7 0.18
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.23
Consensus pattern (35 bp):
ATATATAATAAGAAATAAATAAATGAAAAAAAGGG
Found at i:1669343 original size:3 final size:3
Alignment explanation
Indices: 1669324--1669377 Score: 62
Period size: 3 Copynumber: 18.7 Consensus size: 3
1669314 GAAACAAAAA
1669324 AAT AA- AAT -AT AAGT AAT AAT AA- AAT AAT AAT AAT AAT AAT AA-
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1669366 AAT GAAT AAT AA
1 AAT -AAT AAT AA
1669378 AAAAAATACA
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
2 8 0.18
3 31 0.69
4 6 0.13
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:1669346 original size:17 final size:17
Alignment explanation
Indices: 1669324--1669385 Score: 69
Period size: 17 Copynumber: 3.7 Consensus size: 17
1669314 GAAACAAAAA
1669324 AATAAAAT-ATAAGTAAT
1 AATAAAATAATAA-TAAT
1669341 AATAAAATAATAATAAT
1 AATAAAATAATAATAAT
1669358 AATAATAA-AATGAATAAT
1 AATAA-AATAAT-AATAAT
1669376 AA-AAAA-AATA
1 AATAAAATAATA
1669386 CAAAGTAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.02
16 5 0.12
17 22 0.52
18 14 0.33
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
AATAAAATAATAATAAT
Found at i:1669385 original size:9 final size:11
Alignment explanation
Indices: 1669322--1669379 Score: 68
Period size: 11 Copynumber: 5.4 Consensus size: 11
1669312 CTGAAACAAA
1669322 AAAATAA-AAT
1 AAAATAATAAT
*
1669332 ATAAGTAATAAT
1 A-AAATAATAAT
1669344 AAAATAATAAT
1 AAAATAATAAT
1669355 --AATAATAAT
1 AAAATAATAAT
1669364 AAAATGAATAAT
1 AAAAT-AATAAT
1669376 AAAA
1 AAAA
1669380 AAAATACAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 9 0.22
10 1 0.02
11 17 0.41
12 14 0.34
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:1669514 original size:38 final size:38
Alignment explanation
Indices: 1669472--1669782 Score: 191
Period size: 38 Copynumber: 8.1 Consensus size: 38
1669462 AATTTTCAAA
*
1669472 AAAAAATTTAAAAACTATATAA-TTTTCAAAAATGTTTT
1 AAAAAATTTAAATA-TATATAAGTTTTCAAAAATGTTTT
*
1669510 -AAAAATTATATATTATATATAAGTTTTCAAAAATGTTTT
1 AAAAAATT-TA-AATATATATAAGTTTTCAAAAATGTTTT
* * *
1669549 CAAAAA-CTATATATTATATAAGTTTTC-AAAATGATTTT
1 AAAAAATTTAAATA-TATATAAGTTTTCAAAAATG-TTTT
* *
1669587 AAAAACTATAATATATATATATATATGTTTTC-AAAATGTTTT
1 AAAAA--AT--T-TAAATATATATAAGTTTTCAAAAATGTTTT
* * * * *
1669629 TAAAAA-CTATATATTATATTTACTTTT---AAATGTTTT
1 AAAAAATTTAAATA-TATA-TAAGTTTTCAAAAATGTTTT
* * *
1669665 AAAAACTATATAATATATA-AATGTTTTCGAAAATGTTTT
1 AAAAAATTTA-AATATATATAA-GTTTTCAAAAATGTTTT
* * *
1669704 AAAAACTATATAATATATATATGTTTTC-AAAATGTTTT
1 AAAAAATTTA-AATATATATAAGTTTTCAAAAATGTTTT
* * *
1669742 AAAATATATATAT-TATATATA-TTTTC-AAAATGTTTT
1 AAAAAATTTAAATATATATA-AGTTTTCAAAAATGTTTT
1669778 AAAAA
1 AAAAA
1669783 CTATATAATA
Statistics
Matches: 226, Mismatches: 25, Indels: 46
0.76 0.08 0.15
Matches are distributed among these distances:
35 1 0.00
36 48 0.21
37 27 0.12
38 58 0.26
39 52 0.23
40 8 0.04
42 8 0.04
43 18 0.08
44 6 0.03
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (38 bp):
AAAAAATTTAAATATATATAAGTTTTCAAAAATGTTTT
Found at i:1669641 original size:36 final size:35
Alignment explanation
Indices: 1669600--1669794 Score: 227
Period size: 36 Copynumber: 5.3 Consensus size: 35
1669590 AACTATAATA
1669600 TATATATATATATGTTTTCAAAATGTTTTTAAAAAC
1 TATATATATATATGTTTTCAAAATG-TTTTAAAAAC
**
1669636 TATATAT-TATAT-TTACTTTTAAATGTTTTAAAAAC
1 TATATATATATATGTT--TTCAAAATGTTTTAAAAAC
1669671 TATATAATATATAAATGTTTTCGAAAATGTTTTAAAAAC
1 TATAT-ATATAT--ATGTTTTC-AAAATGTTTTAAAAAC
1669710 TATATAATATATATATGTTTTCAAAATGTTTTAAAATA-
1 --TAT-ATATATATATGTTTTCAAAATGTTTTAAAA-AC
*
1669748 TATATATTATATATATTTTCAAAATGTTTTAAAAAC
1 TATATA-TATATATGTTTTCAAAATGTTTTAAAAAC
1669784 TATATA-ATATA
1 TATATATATATA
1669795 CTTATTTTCG
Statistics
Matches: 140, Mismatches: 5, Indels: 30
0.80 0.03 0.17
Matches are distributed among these distances:
34 7 0.05
35 24 0.17
36 51 0.36
37 3 0.02
38 16 0.11
39 26 0.19
40 2 0.01
41 9 0.06
42 2 0.01
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (35 bp):
TATATATATATATGTTTTCAAAATGTTTTAAAAAC
Found at i:1669803 original size:36 final size:37
Alignment explanation
Indices: 1669487--1669794 Score: 365
Period size: 39 Copynumber: 8.1 Consensus size: 37
1669477 ATTTAAAAAC
* * *
1669487 TATATAATTTTCAAAAATGTTTTAAAAATTATATATTA
1 TATATAGTTTTC-AAAATGTTTTAAAAACTATATAATA
*
1669525 TATATAAGTTTTCAAAAATGTTTTCAAAAACTATATATTA
1 TATAT-AGTTTTC-AAAATGTTTT-AAAAACTATATAATA
1669565 TATA-AGTTTTCAAAATGATTTTAAAAACTATAATATATATA
1 TATATAGTTTTCAAAATG-TTTTAAAAAC--T-ATATA-ATA
*
1669606 TATATATGTTTTCAAAATGTTTTTAAAAACTATATATTA
1 TATATA-GTTTTCAAAATG-TTTTAAAAACTATATAATA
* *
1669645 TATTTACTTTT--AAATGTTTTAAAAACTATATAATA
1 TATATAGTTTTCAAAATGTTTTAAAAACTATATAATA
*
1669680 TATAAATGTTTTCGAAAATGTTTTAAAAACTATATAATA
1 TATATA-GTTTTC-AAAATGTTTTAAAAACTATATAATA
*
1669719 TATATATGTTTTCAAAATGTTTTAAAATA-TATATATTA
1 TATATA-GTTTTCAAAATGTTTTAAAA-ACTATATAATA
1669757 TATATA-TTTTCAAAATGTTTTAAAAACTATATAATA
1 TATATAGTTTTCAAAATGTTTTAAAAACTATATAATA
1669793 TA
1 TA
1669795 CTTATTTTCG
Statistics
Matches: 241, Mismatches: 14, Indels: 32
0.84 0.05 0.11
Matches are distributed among these distances:
35 23 0.10
36 38 0.16
37 12 0.05
38 48 0.20
39 62 0.26
40 28 0.12
41 7 0.03
42 1 0.00
43 22 0.09
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (37 bp):
TATATAGTTTTCAAAATGTTTTAAAAACTATATAATA
Found at i:1669835 original size:74 final size:72
Alignment explanation
Indices: 1669596--1669845 Score: 228
Period size: 74 Copynumber: 3.4 Consensus size: 72
1669586 TAAAAACTAT
* * * *
1669596 AATATATATA-TATATATGTTTTCAAAATGTTTTTAAAAACTATATATTATATTTACTTTT--AA
1 AATATATACATTATATAT-TTTTCAAAATG-TTTTAAAAACTATATAATATATATAGTTTTCAAA
*
1669658 ATGTTTTAAA
64 ATATTTT-AA
*
1669668 AACTATATA-ATATATAAATGTTTTCGAAAATGTTTTAAAAACTATATAATATATATATGTTTTC
1 AA-TATATACAT-TATATAT-TTTTC-AAAATGTTTTAAAAACTATATAATATATATA-GTTTTC
*
1669732 AAAATGTTTTAA
61 AAAATATTTTAA
*
1669744 AATATATATATTATATATATTTTCAAAATGTTTTAAAAACTATATAATATACT-TA-TTTTCGAA
1 AATATATACATTATATAT-TTTTCAAAATGTTTTAAAAACTATATAATATA-TATAGTTTTC-AA
1669807 AATCATTTTCCGAA
63 AAT-ATTTT---AA
*
1669821 AAT-TATACATTATAT-TTTGTCAAAA
1 AATATATACATTATATATTTTTCAAAA
1669846 ACTATATTAC
Statistics
Matches: 155, Mismatches: 9, Indels: 26
0.82 0.05 0.14
Matches are distributed among these distances:
72 8 0.05
73 11 0.07
74 76 0.49
75 29 0.19
76 17 0.11
77 14 0.09
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (72 bp):
AATATATACATTATATATTTTTCAAAATGTTTTAAAAACTATATAATATATATAGTTTTCAAAAT
ATTTTAA
Found at i:1670263 original size:13 final size:13
Alignment explanation
Indices: 1670245--1670270 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1670235 CCAATAAGTG
1670245 TTTGAAAGTGTAT
1 TTTGAAAGTGTAT
1670258 TTTGAAAGTGTAT
1 TTTGAAAGTGTAT
1670271 ATGTGTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (13 bp):
TTTGAAAGTGTAT
Found at i:1675504 original size:3 final size:3
Alignment explanation
Indices: 1675496--1676083 Score: 586
Period size: 3 Copynumber: 194.7 Consensus size: 3
1675486 TCTTTTCTTC
* * * *
1675496 AAG AAG AAG AAG GAG AAG AAG AAG AAG GAG GAG AAG GAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * * * *
1675544 AAG GAG AAG GAG AAG AAG GAG AAG AAG AA- AGAG AAG GAG AAG GAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A-AG AAG AAG AAG AAG
* * * * * * *
1675589 AAG GAG AAG GAG AAG AAG AAG AAG GAG GAG AAG GAG AAG GAG AAG GAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * *
1675637 AAG GAG AAG GAG AAG GAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * *
1675685 AAG AAG AAG GAG AAGG AAG AAG GAG AAG AA- AAG AAG AAG AAG GAG
1 AAG AAG AAG AAG AA-G AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
1675730 AAG AAGG AGG AAG AAG AAG AAG AGAG AGAG AAG AAG AAG -AG AGAG AAG
1 AAG AA-G AAG AAG AAG AAG AAG A-AG A-AG AAG AAG AAG AAG A-AG AAG
*
1675778 AAG AAG -AG AAG -AG AAG AAG AAG AAG GAG -AG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * * * * *
1675823 AAG AGAG GAG GAG GAG AAG AAG AGG AGG AGG AGAG AAG -AG AGAG AGAG
1 AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG A-AG AAG AAG A-AG A-AG
* *
1675871 AGAG GAG AAG AAG AAG AAG AAG AAG -AG AAG AAG AAG AAG GAG AGAG
1 A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A-AG
* *
1675917 AGG AGAG AAG AAG AGAG GAG AAG AAG AAG AATG -AG AAG AAG AAG AAG
1 AAG A-AG AAG AAG A-AG AAG AAG AAG AAG AA-G AAG AAG AAG AAG AAG
* *
1675964 AAG AAG AAG AAG AAG AAG -AG AAG AAG AAG AAG GAG AAG AAG AAG GAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * *
1676011 AAG AAG AAG AAG GAG AAG AAG AAG AAG AAG AAG GAG AAG AAG AAG GAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * *
1676059 GAG AAG AAG GAG GAG -AG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
1676084 TTGGGTGACC
Statistics
Matches: 496, Mismatches: 66, Indels: 46
0.82 0.11 0.08
Matches are distributed among these distances:
2 20 0.04
3 438 0.88
4 38 0.08
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1686133 original size:5 final size:5
Alignment explanation
Indices: 1686125--1686197 Score: 119
Period size: 5 Copynumber: 14.6 Consensus size: 5
1686115 AGCATAATAA
1686125 ACAAT ACAAT ACAAT ACAAT ACAAT ACAAT ACAAT ACAAT ACAAT ACAAT
1 ACAAT ACAAT ACAAT ACAAT ACAAT ACAAT ACAAT ACAAT ACAAT ACAAT
* * *
1686175 ATAAT ATAAT ATAAT ACAAT ACA
1 ACAAT ACAAT ACAAT ACAAT ACA
1686198 TTTGTTGAGA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 66 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.23
Consensus pattern (5 bp):
ACAAT
Found at i:1687886 original size:17 final size:17
Alignment explanation
Indices: 1687864--1687898 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1687854 ATCGAAGGGG
1687864 AAAAAATA-AAATGAAAT
1 AAAAAATAGAAAT-AAAT
1687881 AAAAAATAGAAATAAAT
1 AAAAAATAGAAATAAAT
1687898 A
1 A
1687899 GAAATAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (17 bp):
AAAAAATAGAAATAAAT
Found at i:1688149 original size:30 final size:30
Alignment explanation
Indices: 1688090--1688151 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
1688080 CCGGAAGAAT
*
1688090 CGGCTGAAAACCGAGAAAATCGGGGTGAAC
1 CGGCTGAAAACCGAGAAAACCGGGGTGAAC
**
1688120 CGGCTGAAAACCG-GCAAAACCGGTTTGAAC
1 CGGCTGAAAACCGAG-AAAACCGGGGTGAAC
1688150 CG
1 CG
1688152 TCGGTTCACT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 1 0.04
30 27 0.96
ACGTcount: A:0.34, C:0.24, G:0.31, T:0.11
Consensus pattern (30 bp):
CGGCTGAAAACCGAGAAAACCGGGGTGAAC
Found at i:1689714 original size:3 final size:3
Alignment explanation
Indices: 1689708--1689750 Score: 50
Period size: 3 Copynumber: 13.3 Consensus size: 3
1689698 TTATTATTAT
*
1689708 TAA TAA TAA TAAA TAA TAA TAA AAA TAAA TAA TAAA TAA TAA T
1 TAA TAA TAA T-AA TAA TAA TAA TAA T-AA TAA T-AA TAA TAA T
1689751 TTTTTTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
3 26 0.74
4 9 0.26
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:1689722 original size:10 final size:10
Alignment explanation
Indices: 1689709--1689750 Score: 57
Period size: 10 Copynumber: 3.9 Consensus size: 10
1689699 TATTATTATT
1689709 AATAATAATA
1 AATAATAATA
1689719 AATAATAATAAA
1 AATAATAAT--A
1689731 AATAAATAATA
1 AAT-AATAATA
1689742 AATAATAAT
1 AATAATAAT
1689751 TTTTTTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 15 0.52
11 4 0.14
12 4 0.14
13 6 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AATAATAATA
Found at i:1689724 original size:7 final size:7
Alignment explanation
Indices: 1689709--1689749 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
1689699 TATTATTATT
1689709 AATAAT-
1 AATAATA
1689715 AATAA-A
1 AATAATA
1689721 TAATAATA
1 -AATAATA
1689729 AA-AATA
1 AATAATA
1689735 AATAATA
1 AATAATA
1689742 AATAATA
1 AATAATA
1689749 A
1 A
1689750 TTTTTTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 11 0.35
7 19 0.61
8 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AATAATA
Found at i:1689724 original size:13 final size:13
Alignment explanation
Indices: 1689708--1689750 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
1689698 TTATTATTAT
1689708 TAATAATAATAAA
1 TAATAATAATAAA
1689721 TAATAATAA-AAA
1 TAATAATAATAAA
1689733 T-A-AATAATAAA
1 TAATAATAATAAA
1689744 TAATAAT
1 TAATAAT
1689751 TTTTTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 5 0.19
11 5 0.19
12 5 0.19
13 12 0.44
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
TAATAATAATAAA
Found at i:1690236 original size:36 final size:36
Alignment explanation
Indices: 1690185--1690508 Score: 249
Period size: 36 Copynumber: 9.1 Consensus size: 36
1690175 CAAAGATTGG
* *
1690185 TGTTTCAAGATAAACTGTCTTAAGAGAGGCAAAATT
1 TGTTTCAAGAGAAACTGTCTTAAGAGAGACAAAATT
*
1690221 TGTTTCAAGGGAAACTGTCTTAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTTAAGAGAGACAAAATT
* * *
1690257 TGTTTCAAGAGAACCTCTCTTAAGAGAGAC--AACT
1 TGTTTCAAGAGAAACTGTCTTAAGAGAGACAAAATT
*
1690291 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAGACAAAATT
1 TGTTTCAAGAGAAACTGTCT-TA-AGAG----AGACAAAATT
* *
1690333 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTTAAGAGAGACAAAA-TT
* * * * * * *
1690370 AGTTCCAAAAGAAGCTGTCTCAAGGGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTTAAGAGAGACAAAATT
* * * * * *
1690406 T-TTTTAATGTA-CAAC-ATATTCA-A-AG----ATTT
1 TGTTTCAA-G-AGAAACTGTCTTAAGAGAGACAAAATT
*
1690435 TGTTTCAAG-GAAAACTATCTTAAGAGAGACAAAATT
1 TGTTTCAAGAG-AAACTGTCTTAAGAGAGACAAAATT
* *
1690471 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTTAAGAGAGACAAAATT
1690507 TG
1 TG
1690509 CTTGAAGGGA
Statistics
Matches: 227, Mismatches: 39, Indels: 44
0.73 0.13 0.14
Matches are distributed among these distances:
29 8 0.04
30 10 0.04
31 1 0.00
32 2 0.01
33 2 0.01
34 21 0.09
35 8 0.04
36 113 0.50
37 31 0.14
40 8 0.04
41 1 0.00
42 22 0.10
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTTAAGAGAGACAAAATT
Found at i:1690315 original size:15 final size:17
Alignment explanation
Indices: 1690281--1690317 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
1690271 CTCTCTTAAG
*
1690281 AGAGACAACTTGTTTCA
1 AGAGACAACTTGTCTCA
1690298 AGAGA-AAC-TGTCTCA
1 AGAGACAACTTGTCTCA
1690313 AGAGA
1 AGAGA
1690318 GACAAAGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 11 0.58
16 3 0.16
17 5 0.26
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.22
Consensus pattern (17 bp):
AGAGACAACTTGTCTCA
Found at i:1690530 original size:36 final size:36
Alignment explanation
Indices: 1690433--1690519 Score: 120
Period size: 36 Copynumber: 2.4 Consensus size: 36
1690423 ATTCAAAGAT
* * * *
1690433 TTTGTTTCAAGGAAAACTATCTTAAGAGAGACAAAA
1 TTTGCTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
1690469 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGCTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
1690505 TTTGCTTGAAGGGAA
1 TTTGCTTCAAGGGAA
1690520 TTAGTCTCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (36 bp):
TTTGCTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:1690819 original size:124 final size:124
Alignment explanation
Indices: 1690594--1690834 Score: 394
Period size: 124 Copynumber: 1.9 Consensus size: 124
1690584 CTTGTTCCTG
* * *
1690594 AAGATGAATGTTGCTGGTGGGTACAATTCCATTCGTCGTGAAGTTGAAACCGCGGATGGACCCTT
1 AAGATGAATGCTGCTGGTGAGCACAATTCCATTCGTCGTGAAGTTGAAACCGCGGATGGACCCTT
* *
1690659 CGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTA
66 CGTTGTGAAGTTGAGCCTTGAATTGGATATCATTCGTCGTAAAGTTGAAATCCAATCTA
* * *
1690718 AAGATGAATGCTGCTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGG-CCCAT
1 AAGATGAATGCTGCTGGTGAGCACAATTCCATTCGTCGTGAAGTTGAAACCGCGGATGGACCC-T
1690782 TCGTTGTGAAGTTGAGCCTTGAATTGGATATCATTCGTCGTAAAGTTGAAATC
65 TCGTTGTGAAGTTGAGCCTTGAATTGGATATCATTCGTCGTAAAGTTGAAATC
1690835 TAATGTAAGT
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
123 3 0.03
124 105 0.97
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (124 bp):
AAGATGAATGCTGCTGGTGAGCACAATTCCATTCGTCGTGAAGTTGAAACCGCGGATGGACCCTT
CGTTGTGAAGTTGAGCCTTGAATTGGATATCATTCGTCGTAAAGTTGAAATCCAATCTA
Found at i:1695216 original size:17 final size:17
Alignment explanation
Indices: 1695190--1695225 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1695180 AAATCAAAGG
1695190 AAAAAAATAAAAAAAAT
1 AAAAAAATAAAAAAAAT
* *
1695207 AAAAACATAAAAAAGAT
1 AAAAAAATAAAAAAAAT
1695224 AA
1 AA
1695226 TAAATTGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.83, C:0.03, G:0.03, T:0.11
Consensus pattern (17 bp):
AAAAAAATAAAAAAAAT
Found at i:1695265 original size:23 final size:23
Alignment explanation
Indices: 1695239--1695292 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
1695229 ATTGAAGAGG
1695239 AAAAATAAAAT-GAAATAAAAAAT
1 AAAAATAAAATAGAAAT-AAAAAT
*
1695262 AAAAAT-AAATAGAAATAGAAAT
1 AAAAATAAAATAGAAATAAAAAT
*
1695284 AGAAATAAA
1 AAAAATAAA
1695293 TCAAAGAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (23 bp):
AAAAATAAAATAGAAATAAAAAT
Found at i:1696115 original size:3 final size:3
Alignment explanation
Indices: 1696109--1696147 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
1696099 TTATTATTAT
*
1696109 TAA TAA TAA TAAA TAA TAA AAA TAA TAA TAAA TAA TAA T
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA T-AA TAA TAA T
1696148 TTTTTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 26 0.81
4 6 0.19
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1696123 original size:10 final size:10
Alignment explanation
Indices: 1696110--1696147 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
1696100 TATTATTATT
1696110 AATAATAATA
1 AATAATAATA
1696120 AATAATAA-A
1 AATAATAATA
1696129 AATAATAATA
1 AATAATAATA
1696139 AATAATAAT
1 AATAATAAT
1696148 TTTTTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.33
10 18 0.67
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AATAATAATA
Found at i:1696134 original size:19 final size:19
Alignment explanation
Indices: 1696110--1696146 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1696100 TATTATTATT
1696110 AATAATAATAAATAATAAA
1 AATAATAATAAATAATAAA
1696129 AATAATAATAAATAATAA
1 AATAATAATAAATAATAA
1696147 TTTTTTTAAA
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AATAATAATAAATAATAAA
Found at i:1696987 original size:19 final size:18
Alignment explanation
Indices: 1696963--1697000 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
1696953 AATAATTTTT
1696963 AAAAAAATATTAAATATTC
1 AAAAAAATATTAAA-ATTC
1696982 AAAAAAATATTAAAATTC
1 AAAAAAATATTAAAATTC
1697000 A
1 A
1697001 CTAGAAGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAAAATATTAAAATTC
Found at i:1705018 original size:20 final size:20
Alignment explanation
Indices: 1704983--1705030 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1704973 CCATTTTTGG
* *
1704983 TATCGATA-CTCAGGGTGAA
1 TATCGATACCCCAGGGTCAA
1705002 TATCGATACCCCAGGGTCAA
1 TATCGATACCCCAGGGTCAA
1705022 TATCGATAC
1 TATCGATAC
1705031 TATTGGGGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (20 bp):
TATCGATACCCCAGGGTCAA
Found at i:1708693 original size:10 final size:10
Alignment explanation
Indices: 1708678--1708715 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1708668 AAATAAGAAC
1708678 TCATATAGGA
1 TCATATAGGA
1708688 TCATATA-GA
1 TCATATAGGA
*
1708697 TGCATTTAGGA
1 T-CATATAGGA
1708708 TCATATAG
1 TCATATAG
1708716 TTGCATGTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 3 0.12
10 18 0.75
11 3 0.12
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (10 bp):
TCATATAGGA
Found at i:1708708 original size:20 final size:20
Alignment explanation
Indices: 1708683--1708721 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1708673 AGAACTCATA
1708683 TAGGATCATATAGATGCATT
1 TAGGATCATATAGATGCATT
*
1708703 TAGGATCATATAGTTGCAT
1 TAGGATCATATAGATGCAT
1708722 GTGGTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (20 bp):
TAGGATCATATAGATGCATT
Found at i:1714762 original size:101 final size:101
Alignment explanation
Indices: 1714466--1715047 Score: 347
Period size: 101 Copynumber: 5.8 Consensus size: 101
1714456 GAAACCAACT
* * * * * *
1714466 TCATTA-ATGACATGTAAGACAAAA-AGAGTTT-TATTTATAACAAT-ATTGGTAGCGCATTTTT
1 TCATTATA-GACATGTAAGACAAAACATAGTTTAAATTTATAACAATAAAT-GTAACACCTTTTT
* *
1714527 ATTGTGTCAACCGTTTACGTGATATGA-TTGAAACCTTTA
64 ATAGTGTCAACCATTTACGTGATAT-ATTTGAAA-CTTTA
* * * * * * * * *
1714566 TTATTA-CGAAACTATAAGAGATAACA-AGTTTAAATTT-TAACAATACATGTAGCGCCTTTTTT
1 TCATTATAGACA-TGTAAGACAAAACATAGTTTAAATTTATAACAATAAATGTAACACC-TTTTT
* * * ** * * ** *
1714628 ATATTGTCAACCGTGTAATTTATATGTACGAAACTTGTG
64 ATAGTGTCAACCATTTACGTGATATATTTGAAACTT-TA
* *
1714667 TCATTATGGACATGTAAGACAAAACATAGTTT-TATTTATAACAATAAATGTAACACCTTTTTAT
1 TCATTATAGACATGTAAGACAAAACATAGTTTAAATTTATAACAATAAATGTAACACCTTTTTAT
1714731 AGTGTCAACCATTTACGTGATATATTTGAAACATTTA
66 AGTGTCAACCATTTACGTGATATATTTGAAAC-TTTA
* * * * * * **
1714768 TTATTA-AAAAACTGTAATAGAAAACAT-GTTTAAATTTATAACAATTCAA-GTTGCACCTTTTT
1 TCATTATAGACA-TGTAAGACAAAACATAGTTTAAATTTATAACAA-TAAATGTAACACCTTTTT
* ** * * * *
1714830 ATATTGGAAACCATGTGA-GTTATATCTGTGAAACCTATT-
64 ATAGTGTCAACCAT-TTACGTGATATATTTGAAA-CT-TTA
* * * * *
1714869 TCATTAT-GAACATGTAGGACAAAACAT-GGTTATATTTATGACAATACATGTAACACCTTTTTA
1 TCATTATAG-ACATGTAAGACAAAACATAGTTTAAATTTATAACAATAAATGTAACACCTTTTTA
* * * *
1714932 TAGTGTCAATCGTTTACGTGATATGTTTGAAATCTTTT
65 TAGTGTCAACCATTTACGTGATATATTTGAAA-CTTTA
* * * * *
1714970 TTATTAATAGAC-TATAAGA-AAAA-AAAGTTTAAATTTATAACAATATAGGTAACACCTTTTTA
1 TCATT-ATAGACATGTAAGACAAAACATAGTTTAAATTTATAACAATAAATGTAACACCTTTTTA
* *
1715032 TATTGTCAATCATTTA
65 TAGTGTCAACCATTTA
1715048 AGTTATAAGT
Statistics
Matches: 366, Mismatches: 91, Indels: 50
0.72 0.18 0.10
Matches are distributed among these distances:
99 4 0.01
100 97 0.27
101 224 0.61
102 40 0.11
103 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (101 bp):
TCATTATAGACATGTAAGACAAAACATAGTTTAAATTTATAACAATAAATGTAACACCTTTTTAT
AGTGTCAACCATTTACGTGATATATTTGAAACTTTA
Found at i:1714770 original size:202 final size:198
Alignment explanation
Indices: 1714401--1715260 Score: 692
Period size: 202 Copynumber: 4.3 Consensus size: 198
1714391 CGCAGTTTTA
** *
1714401 TATAACAATACAAGTAGCGTCTTTTTATATTGTCAACAGTGTAAGTTATATATGTGAAACCA-AC
1 TATAACAATACAAGTAGCACCTTTTTATATTGTCAACCGTGTAA-TT-TATATGTGAAA-CATA-
* * * * *
1714465 TTCATTAAT-GACATGTAAGACAAAA-AGAGTTTTATTTATAACAAT-ATTGGTAGCGCATTTTT
62 TTCATT-ATGGACATGTAAGACAAAACATAGTTTTATTTATAACAATAAAT-GTAACACCTTTTT
* ** *
1714527 ATTGTGTCAACCGTTTACGTGATATGA-TTGAAACCTTTATTATTACGAAACTATAAGAGATAAC
125 ATAGTGTCAACCGTTTACGTGATAT-ATTTGAAA-CTTTATTATTAAAAAACTATAAGAGAAAAC
1714591 AAGTTTAAATT
188 AAGTTTAAATT
* * * *
1714602 T-TAACAATACATGTAGCGCCTTTTTTATATTGTCAACCGTGTAATTTATATGTACGAAACTTGT
1 TATAACAATACAAGTAGCACC-TTTTTATATTGTCAACCGTGTAATTTATATGT--GAAACATAT
1714666 GTCATTATGGACATGTAAGACAAAACATAGTTTTATTTATAACAATAAATGTAACACCTTTTTAT
63 -TCATTATGGACATGTAAGACAAAACATAGTTTTATTTATAACAATAAATGTAACACCTTTTTAT
* * * *
1714731 AGTGTCAACCATTTACGTGATATATTTGAAACATTTATTATTAAAAAACTGTAATAGAAAACATG
127 AGTGTCAACCGTTTACGTGATATATTTGAAAC-TTTATTATTAAAAAACTATAAGAGAAAACAAG
1714796 TTTAAATT
191 TTTAAATT
* * ** * * * *
1714804 TATAACAATTCAAGTTGCACCTTTTTATATTGGAAACCATGTGAGTTATATCTGTGAAACCTATT
1 TATAACAATACAAGTAGCACCTTTTTATATTGTCAACCGTGT-AATT-TATATGTGAAACATA-T
* * * * * *
1714869 TCATTATGAACATGTAGGACAAAACATGGTTATATTTATGACAATACATGTAACACCTTTTTATA
63 TCATTATGGACATGTAAGACAAAACATAGTTTTATTTATAACAATAAATGTAACACCTTTTTATA
* * * * * *
1714934 GTGTCAATCGTTTACGTGATATGTTTGAAATCTTTTTTATTAATAGACTATAAGA-AAAAAAAGT
128 GTGTCAACCGTTTACGTGATATATTTGAAA-CTTTATTATTAAAAAACTATAAGAGAAAACAAGT
1714998 TTAAATT
192 TTAAATT
* * * * * * * * *
1715005 TATAACAATATAGGTAACACCTTTTTATATTGTCAATCATTTAAGTTATAAGTGTGAAACCTTTT
1 TATAACAATACAAGTAGCACCTTTTTATATTGTCAACCGTGTAATTTAT-A-TGTGAAA-CATAT
* * * * ** ** * * * * *** * *
1715070 TTATTATGAACATATAAGACCAAGTAGGGTTATATTTATAGCAATATAGGTAGGGCATTTTTTTA
63 TCATTATGGACATGTAAGACAAAACATAGTTTTATTTATAACAATAAATGTAACACCTTTTTATA
* * * * * * * * * *
1715135 CTATCAATCGTTTACATGATA-AGTTTGAAACCTTTTTTATTAAGAAACTGTAAGATAAAGCATG
128 GTGTCAACCGTTTACGTGATATA-TTTGAAA-CTTTATTATTAAAAAACTATAAGAGAAAACAAG
**
1715199 AGTAAATT
191 TTTAAATT
*** * * * * *
1715207 TATAACAATACAAGTAGCGTATTCTTGTATTGTCAACCGTTTAAGTTATGTGTG
1 TATAACAATACAAGTAGCACCTTTTTATATTGTCAACCGTGTAATTTATATGTG
1715261 TGAAACCTTT
Statistics
Matches: 540, Mismatches: 99, Indels: 41
0.79 0.15 0.06
Matches are distributed among these distances:
199 10 0.02
200 29 0.05
201 200 0.37
202 273 0.51
203 22 0.04
204 6 0.01
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.38
Consensus pattern (198 bp):
TATAACAATACAAGTAGCACCTTTTTATATTGTCAACCGTGTAATTTATATGTGAAACATATTCA
TTATGGACATGTAAGACAAAACATAGTTTTATTTATAACAATAAATGTAACACCTTTTTATAGTG
TCAACCGTTTACGTGATATATTTGAAACTTTATTATTAAAAAACTATAAGAGAAAACAAGTTTAA
ATT
Found at i:1715189 original size:101 final size:100
Alignment explanation
Indices: 1714896--1715216 Score: 270
Period size: 101 Copynumber: 3.2 Consensus size: 100
1714886 GACAAAACAT
* * * * * * * * *
1714896 GGTTATATTTATGACAATACATGTAACACCTTTTTATAGTGTCAATCGTTTACGTGATATGTTTG
1 GGTTAAATTTATAACAATATAGGTAACACATTTTTATACTATCAATCGTTTACATGATAAGTTTG
* * *
1714961 AAATCTTTTTTATTAATAGACTATAAGAAAAAAAA
66 AAACCTTTTTTATTAAGAAACTATAAGAAAAAAAA
* * * * * * *
1714996 GTTTAAATTTATAACAATATAGGTAACACCTTTTTATATTGTCAATCATTTA-AGTTATAAGTGT
1 GGTTAAATTTATAACAATATAGGTAACACATTTTTATACTATCAATCGTTTACA-TGATAAGTTT
* * ** *
1715060 GAAACCTTTTTTATTATG-AACATATAAGACCAAGTAG
65 GAAACCTTTTTTATTAAGAAAC-TATAAGA-AAAAAAA
* * *** *
1715097 GGTTATATTTATAGCAATATAGGTAGGGCATTTTTTTACTATCAATCGTTTACATGATAAGTTTG
1 GGTTAAATTTATAACAATATAGGTAACACATTTTTATACTATCAATCGTTTACATGATAAGTTTG
* ** *
1715162 AAACCTTTTTTATTAAGAAACTGTAAGATAAAGCAT
66 AAACCTTTTTTATTAAGAAACTATAAGA-AAAAAAA
1715198 GAG-TAAATTTATAACAATA
1 G-GTTAAATTTATAACAATA
1715217 CAAGTAGCGT
Statistics
Matches: 175, Mismatches: 40, Indels: 11
0.77 0.18 0.05
Matches are distributed among these distances:
99 2 0.01
100 74 0.42
101 94 0.54
102 5 0.03
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.39
Consensus pattern (100 bp):
GGTTAAATTTATAACAATATAGGTAACACATTTTTATACTATCAATCGTTTACATGATAAGTTTG
AAACCTTTTTTATTAAGAAACTATAAGAAAAAAAA
Found at i:1715265 original size:403 final size:403
Alignment explanation
Indices: 1714401--1715268 Score: 931
Period size: 403 Copynumber: 2.2 Consensus size: 403
1714391 CGCAGTTTTA
* *
1714401 TATAACAATACAAGTAGCGTCTTTTTATATTGTCAACAGTGTAAGTTATATATGTGAAACCAACT
1 TATAACAATACAAGTAGCGTCTTTTTATATTGTCAACCGTGTAAGTTATATATGTGAAACCTACT
* * * * *
1714466 TCATTAATGACATGTAAGACAAAAAGAGTTTTATTTATAACAATATTGGTAGCGCATTTTTATTG
66 TCATTAATGACATGTAAGACAAAAAGAGTTATATTTATAACAATAATGGTAACACATTTTTATAG
* * *
1714531 TGTCAACCGTTTACGTGATATGATTGAAACCTTTATTATTACGAAACTATAAGAGATAACAAGTT
131 TGTCAACCGTTTACGTGATATGATTGAAACCTTTATTATTAAGAAACTATAAGAGAAAAAAAGTT
* * * * * *
1714596 TAAATTTTAACAATACATGTAGCGCCTTTTTTATATTGTCAACCGTGTAATTTATATGTACGAAA
196 TAAATTTTAACAATACAGGTAACACCTTTTTTATATTGTCAACCATGTAAGTTATAAGTACGAAA
* * * * * *
1714661 CTTGTGTCATTATGGACATGTAAGACAAAACATAGTTTTATTTATAACAATAAATGTAACACCTT
261 CTTGTGTCATTATGAACATATAAGACAAAACAGAGTTATATTTATAACAATAAAGGTAACACATT
* * * *
1714726 TTTATAGTGTCAACCATTTACGTGATATATTTGAAACATTTATTATTAAAAAACTGTAATAGAAA
326 TTTATACTATCAACCATTTACATGATATATTTGAAACATTTATTATTAAAAAACTGTAAGAGAAA
**
1714791 ACATGTTTAAATT
391 ACATGAGTAAATT
* * ** ** * * * *
1714804 TATAACAATTCAAGTTGCACCTTTTTATATTGGAAACCATGTGAGTTATATCTGTGAAACCTATT
1 TATAACAATACAAGTAGCGTCTTTTTATATTGTCAACCGTGTAAGTTATATATGTGAAACCTACT
* * *
1714869 TCATT-ATGAACATGTAGGACAAAACATG-GTTATATTTATGACAATACAT-GTAACACCTTTTT
66 TCATTAATG-ACATGTAAGACAAAA-A-GAGTTATATTTATAACAATA-ATGGTAACACATTTTT
* * * * * *
1714931 ATAGTGTCAATCGTTTACGTGATATGTTTGAAATCTTTTTTATTAATAGACTATAAGA-AAAAAA
127 ATAGTGTCAACCGTTTACGTGATATGATTGAAACCTTTATTATTAAGAAACTATAAGAGAAAAAA
* * * *
1714995 AGTTTAAATTTATAACAATATAGGTAACACC-TTTTTATATTGTCAATCATTTAAGTTATAAGTG
192 AGTTTAAATTT-TAACAATACAGGTAACACCTTTTTTATATTGTCAACCATGTAAGTTATAAGTA
* * * * ** * * * *
1715059 TGAAACCTT-TTTTATTATGAACATATAAGACCAAGTAGGGTTATATTTATAGCAATATAGGTAG
256 CGAAA-CTTGTGTCATTATGAACATATAAGACAAAACAGAGTTATATTTATAACAATAAAGGTAA
** * * * * * *
1715123 GGCATTTTTTTACTATCAATCGTTTACATGATA-AGTTTGAAACCTTTTTTATTAAGAAACTGTA
320 CACATTTTTATACTATCAACCATTTACATGATATA-TTTGAAACATTTATTATTAAAAAACTGTA
* *
1715187 AGATAAAGCATGAGTAAATT
384 AGAGAAAACATGAGTAAATT
* * * * * *
1715207 TATAACAATACAAGTAGCGTATTCTTGTATTGTCAACCGTTTAAGTTATGTGTGTGAAACCT
1 TATAACAATACAAGTAGCGTCTTTTTATATTGTCAACCGTGTAAGTTATATATGTGAAACCT
1715269 TTATGATTAT
Statistics
Matches: 373, Mismatches: 85, Indels: 14
0.79 0.18 0.03
Matches are distributed among these distances:
402 4 0.01
403 272 0.73
404 95 0.25
405 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.38
Consensus pattern (403 bp):
TATAACAATACAAGTAGCGTCTTTTTATATTGTCAACCGTGTAAGTTATATATGTGAAACCTACT
TCATTAATGACATGTAAGACAAAAAGAGTTATATTTATAACAATAATGGTAACACATTTTTATAG
TGTCAACCGTTTACGTGATATGATTGAAACCTTTATTATTAAGAAACTATAAGAGAAAAAAAGTT
TAAATTTTAACAATACAGGTAACACCTTTTTTATATTGTCAACCATGTAAGTTATAAGTACGAAA
CTTGTGTCATTATGAACATATAAGACAAAACAGAGTTATATTTATAACAATAAAGGTAACACATT
TTTATACTATCAACCATTTACATGATATATTTGAAACATTTATTATTAAAAAACTGTAAGAGAAA
ACATGAGTAAATT
Found at i:1719180 original size:19 final size:19
Alignment explanation
Indices: 1719156--1719194 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1719146 TTGATTGGTG
1719156 AGGCTTTTCAAATGATTTA
1 AGGCTTTTCAAATGATTTA
1719175 AGGCTTTTCAAATGATTTA
1 AGGCTTTTCAAATGATTTA
1719194 A
1 A
1719195 TTTTAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.41
Consensus pattern (19 bp):
AGGCTTTTCAAATGATTTA
Found at i:1720073 original size:186 final size:187
Alignment explanation
Indices: 1719563--1720275 Score: 856
Period size: 186 Copynumber: 3.8 Consensus size: 187
1719553 ACATTCATGG
* * *
1719563 GCGCAACCGTATTTCTTATATATGTTCATAATATTTTTAGTTTTAAACTTATTTTCTTATACTCG
1 GCGCAACCGTATTTCTTATATATGTTCATAACATTTTTAATTTTAAACTTATTTTCTTATACTTG
* * * ** *
1719628 GATAATCGAAGGCCCCATCTGCTTAAACTCTAATAATATTTTCGATGCAACCTATTTTAATATTA
66 GATAATCCAAGGCCCCATCAGCTTAAACTCTAATAACATTTTCGGCGCAACCTATTTTATTATTA
* * * * * * *
1719693 AAAATATTTACATTCCAAATTAAAATCTATTTTATTTTTTAACCATTACATTTTTTA
131 AAAATATTAACATTCCAAATTAAAACCTCTTTTATTATTGAACCATCACATTATTTA
* * * * * * * *
1719750 ACACAATCGTATTTATTATATATGTTCATAATATTTTAAAGTTTTAAAACTTATTTTCTTAAACA
1 GCGCAACCGTATTTCTTATATATGTTCATAACATTTTTAA-TTTT-AAACTTATTTTCTTATACT
* * * **
1719815 GGGATAATCTAAGTCCCCATCAGCTTAAA-TCTAATAACATTTTCGGTACAACCCTATTTTATTA
64 TGGATAATCCAAGGCCCCATCAGCTTAAACTCTAATAACATTTTCGGCGCAA-CCTATTTTATTA
* * * * *
1719879 TTAAAAGTATTAACATTACATATTATAACCTCTTTTATTATTGAATCATCACATTATTTA
128 TTAAAAATATTAACATTCCAAATTAAAACCTCTTTTATTATTGAACCATCACATTATTTA
*
1719939 GCGCAACCGTATTTCTTATATATGTTCATAACATTTTTAACTTTAAACTTATTTTCTTATA-TTG
1 GCGCAACCGTATTTCTTATATATGTTCATAACATTTTTAATTTTAAACTTATTTTCTTATACTTG
** * *
1720003 GATAATCCAATACACCATCAGCATAAACTCTAATAACATTTTCGGCGCAACCTATTTTATTATTA
66 GATAATCCAAGGCCCCATCAGCTTAAACTCTAATAACATTTTCGGCGCAACCTATTTTATTATTA
* * * * **
1720068 AAAGTATTAACATTCCAGATTACAACCTCTTTTATTATTGAACCATGACATTATTGG
131 AAAATATTAACATTCCAAATTAAAACCTCTTTTATTATTGAACCATCACATTATTTA
* * * *
1720125 GCGTAACCGTATTTCTTATATATATTCATAACATTTTCAATTCTAAACTTATTTTCTTATA-TTG
1 GCGCAACCGTATTTCTTATATATGTTCATAACATTTTTAATTTTAAACTTATTTTCTTATACTTG
* * ** * * * *
1720189 GGTAAACCAAGGCTTCATCAGCTTAAACTCTAAAAATATTTTCGGCGCAACTTACTTTATTATTA
66 GATAATCCAAGGCCCCATCAGCTTAAACTCTAATAACATTTTCGGCGCAACCTATTTTATTATTA
*
1720254 AAAATATTAACATTCCACATTA
131 AAAATATTAACATTCCAAATTA
1720276 CATGTAACAC
Statistics
Matches: 452, Mismatches: 70, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
186 221 0.49
187 70 0.15
188 26 0.06
189 135 0.30
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (187 bp):
GCGCAACCGTATTTCTTATATATGTTCATAACATTTTTAATTTTAAACTTATTTTCTTATACTTG
GATAATCCAAGGCCCCATCAGCTTAAACTCTAATAACATTTTCGGCGCAACCTATTTTATTATTA
AAAATATTAACATTCCAAATTAAAACCTCTTTTATTATTGAACCATCACATTATTTA
Found at i:1720924 original size:26 final size:26
Alignment explanation
Indices: 1720855--1721193 Score: 248
Period size: 26 Copynumber: 14.4 Consensus size: 26
1720845 TTATTTGTTA
1720855 ATTTCATTTATGGCATCCTTT--T--
1 ATTTCATTTATGGCATCCTTTCATGC
* *
1720877 A-TTCCTTAAT-GCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGC
1720901 ATTTCATTTATGGCAT-CTTATCATGC
1 ATTTCATTTATGGCATCCTT-TCATGC
* * *
1720927 ----C-TTAAT-GCATCATTTCATGT
1 ATTTCATTTATGGCATCCTTTCATGC
1720947 ATTTCATTTATGGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGC
* *
1720973 ----C-TTAAT-GCATCATTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGC
*
1720993 ATTTTATTTATGGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGC
1721019 ATTTCATTTATGGCATCCTTTCATG-
1 ATTTCATTTATGGCATCCTTTCATGC
* * *
1721044 ---TC-TTAAT-GCATCATTCCATGC
1 ATTTCATTTATGGCATCCTTTCATGC
* *
1721065 TTTTCATTTATGACATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGC
*
1721091 ----C-TTAAT-GCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGC
* *
1721111 ATTTCATCTATGTCATCCTTTCATG-
1 ATTTCATTTATGGCATCCTTTCATGC
* *
1721136 ---TC-TTAAT-GCATCCTTTTATGC
1 ATTTCATTTATGGCATCCTTTCATGC
1721157 ATTTCATTTATGGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGC
1721183 ATTTCATTTAT
1 ATTTCATTTAT
1721194 AGATTCATTT
Statistics
Matches: 245, Mismatches: 34, Indels: 72
0.70 0.10 0.21
Matches are distributed among these distances:
20 66 0.27
21 28 0.11
22 9 0.04
24 7 0.03
25 29 0.12
26 106 0.43
ACGTcount: A:0.21, C:0.23, G:0.10, T:0.47
Consensus pattern (26 bp):
ATTTCATTTATGGCATCCTTTCATGC
Found at i:1720930 original size:46 final size:46
Alignment explanation
Indices: 1720855--1721018 Score: 267
Period size: 46 Copynumber: 3.6 Consensus size: 46
1720845 TTATTTGTTA
* * *
1720855 ATTTCATTTATGGCATCCTTTTATTCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
*
1720901 ATTTCATTTATGGCAT-CTTATCATGCCTTAATGCATCATTTCATGT
1 ATTTCATTTATGGCATCCTT-TCATGCCTTAATGCATCATTTCATGC
1720947 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
*
1720993 ATTTTATTTATGGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGC
1721019 ATTTCATTTA
Statistics
Matches: 110, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
45 3 0.03
46 104 0.95
47 3 0.03
ACGTcount: A:0.21, C:0.22, G:0.10, T:0.46
Consensus pattern (46 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
Found at i:1720944 original size:20 final size:20
Alignment explanation
Indices: 1720921--1720992 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 20
1720911 TGGCATCTTA
1720921 TCATGCCTTAATGCATCATT
1 TCATGCCTTAATGCATCATT
* * *
1720941 TCATGTATTTCATTTATGGCATCCTT
1 TCATG-----CCTTAAT-GCATCATT
1720967 TCATGCCTTAATGCATCATT
1 TCATGCCTTAATGCATCATT
1720987 TCATGC
1 TCATGC
1720993 ATTTTATTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
20 18 0.45
21 5 0.12
25 5 0.12
26 12 0.30
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (20 bp):
TCATGCCTTAATGCATCATT
Found at i:1721018 original size:118 final size:118
Alignment explanation
Indices: 1720887--1721135 Score: 403
Period size: 118 Copynumber: 2.1 Consensus size: 118
1720877 ATTCCTTAAT
*
1720887 GCATCCTTTCATGCATTTCATTTATGGCAT-CTTATCATGCCTTAATGCATCATTTCATG-TATT
1 GCATCCTTTCATGCATTTCATTTATGGCATCCTT-TCATGCCTTAATGCATCATTCCATGCT-TT
* * *
1720950 TCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTATG
64 TCATTTATGACATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATCTATG
*
1721005 GCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGTCTTAATGCATCATTCCATGCTTTTC
1 GCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTCCATGCTTTTC
*
1721070 ATTTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCATCTATG
66 ATTTATGACATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATCTATG
*
1721123 TCATCCTTTCATG
1 GCATCCTTTCATG
1721136 TCTTAATGCA
Statistics
Matches: 122, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
118 118 0.97
119 4 0.03
ACGTcount: A:0.21, C:0.24, G:0.10, T:0.45
Consensus pattern (118 bp):
GCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTCCATGCTTTTC
ATTTATGACATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATCTATG
Found at i:1721055 original size:46 final size:46
Alignment explanation
Indices: 1721005--1721181 Score: 282
Period size: 46 Copynumber: 3.8 Consensus size: 46
1720995 TTTATTTATG
1721005 GCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGTCTTAAT
1 GCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGTCTTAAT
* * * * *
1721051 GCATCATTCCATGCTTTTCATTTATGACATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGTCTTAAT
* *
1721097 GCATCCTTTCATGCATTTCATCTATGTCATCCTTTCATGTCTTAAT
1 GCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGTCTTAAT
*
1721143 GCATCCTTTTATGCATTTCATTTATGGCATCCTTTCATG
1 GCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATG
1721182 CATTTCATTT
Statistics
Matches: 117, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 117 1.00
ACGTcount: A:0.20, C:0.25, G:0.10, T:0.45
Consensus pattern (46 bp):
GCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGTCTTAAT
Found at i:1721055 original size:92 final size:92
Alignment explanation
Indices: 1720867--1721193 Score: 248
Period size: 92 Copynumber: 3.5 Consensus size: 92
1720857 TTCATTTATG
* * *
1720867 GCATCCTTTTATTCCTTAATGCATCCTTTCATGCATTTCATTTATGGCAT-CTTATCATGC----
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCCTT-TCATGCATTT
* * *
1720927 C-TTAAT-GCATCATTTCATGTATTTCATTTAT
65 CATTTATGGCATCCTTTCATG----TC-TTAAT
*
1720958 GGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGGCATCCTTTCATGCATTT
1 -GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCATTT
1721023 CATTTATGGCATCCTTTCATGTCTTAAT
65 CATTTATGGCATCCTTTCATGTCTTAAT
* * * *
1721051 GCATCATTCCATGCTTTTCATTTATGACATCCTTTCATGC--CTTA---AT-GCATCCTTTCATG
1 GCATCCTTTCATGC----C-TTAATG-CATCCTTTCATGCATTTTATTTATGGCATCCTTTCATG
* *
1721110 CATTTCATCTATGTCATCCTTTCATGTCTTAAT
60 CATTTCATTTATGGCATCCTTTCATGTCTTAAT
* * *
1721143 GCATCCTTTTATGCATTTCATTTATGGCATCCTTTCATGCATTTCATTTAT
1 GCATCCTTTCATGC----C-TTAAT-GCATCCTTTCATGCATTTTATTTAT
1721194 AGATTCATTT
Statistics
Matches: 196, Mismatches: 20, Indels: 33
0.79 0.08 0.13
Matches are distributed among these distances:
92 142 0.72
93 10 0.05
94 4 0.02
96 5 0.03
97 11 0.06
98 24 0.12
ACGTcount: A:0.21, C:0.23, G:0.10, T:0.46
Consensus pattern (92 bp):
GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCATTTC
ATTTATGGCATCCTTTCATGTCTTAAT
Found at i:1721130 original size:164 final size:164
Alignment explanation
Indices: 1720855--1721193 Score: 529
Period size: 164 Copynumber: 2.1 Consensus size: 164
1720845 TTATTTGTTA
* * * *
1720855 ATTTCATTTATGGCATCCTTTTATTCCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCTT
1 ATTTCATTTATGGCATCCTTTCATTCCTTAATGCATCATTCCATGCATTTCATTTATGACATCTT
* *
1720920 ATCATGCCTTAATGCATCATTTCATGTATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCA
66 ATCATGCCTTAATGCATCATTTCATGCATTTCATCTATGGCATCCTTTCATGCCTTAATGCATCA
*
1720985 TTTCATGCATTTTATTTATGGCATCCTTTCATGC
131 TTTCATGCATTTCATTTATGGCATCCTTTCATGC
*
1721019 ATTTCATTTATGGCATCCTTTCATGT-CTTAATGCATCATTCCATGCTTTTCATTTATGACATCC
1 ATTTCATTTATGGCATCCTTTCAT-TCCTTAATGCATCATTCCATGCATTTCATTTATGACAT-C
* * *
1721083 TT-TCATGCCTTAATGCATCCTTTCATGCATTTCATCTATGTCATCCTTTCATGTCTTAATGCAT
64 TTATCATGCCTTAATGCATCATTTCATGCATTTCATCTATGGCATCCTTTCATGCCTTAATGCAT
* *
1721147 CCTTTTATGCATTTCATTTATGGCATCCTTTCATGC
129 CATTTCATGCATTTCATTTATGGCATCCTTTCATGC
1721183 ATTTCATTTAT
1 ATTTCATTTAT
1721194 AGATTCATTT
Statistics
Matches: 160, Mismatches: 13, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
164 156 0.98
165 4 0.03
ACGTcount: A:0.21, C:0.23, G:0.10, T:0.47
Consensus pattern (164 bp):
ATTTCATTTATGGCATCCTTTCATTCCTTAATGCATCATTCCATGCATTTCATTTATGACATCTT
ATCATGCCTTAATGCATCATTTCATGCATTTCATCTATGGCATCCTTTCATGCCTTAATGCATCA
TTTCATGCATTTCATTTATGGCATCCTTTCATGC
Found at i:1721188 original size:118 final size:115
Alignment explanation
Indices: 1720887--1721193 Score: 343
Period size: 118 Copynumber: 2.6 Consensus size: 115
1720877 ATTCCTTAAT
* * *
1720887 GCATCCTTTCATGCATTTCATTTATGGCAT-CTTATCATGCCTTAATGCATCATTTCATGTATTT
1 GCATCCTTTCATG---TTCATTAATGGCATCCTT-TCATGTCTTAATGCATCATTTCATGCATTT
* * *
1720951 CATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTATG
62 CATTTATGACATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATCTATG
* * *
1721005 GCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGTCTTAATGCATCATTCCATGCTTTTC
1 GCATCCTTTCATG---TTCATTAATGGCATCCTTTCATGTCTTAATGCATCATTTCATGCATTTC
*
1721070 ATTTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCATCTATG
63 ATTTATGACATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATCTATG
* * * *
1721123 TCATCCTTTCATG-TC-TTAAT-GCATCCTTTTATGCATTTCATTTATGGCATCCTTTCATGCAT
1 GCATCCTTTCATGTTCATTAATGGCATCC--TT-T-CATGTC-TTAAT-GCATCATTTCATGCAT
1721185 TTCATTTAT
60 TTCATTTAT
1721194 AGATTCATTT
Statistics
Matches: 167, Mismatches: 15, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
112 6 0.04
113 4 0.02
114 4 0.02
115 1 0.01
116 5 0.03
117 4 0.02
118 140 0.84
119 3 0.02
ACGTcount: A:0.21, C:0.23, G:0.10, T:0.46
Consensus pattern (115 bp):
GCATCCTTTCATGTTCATTAATGGCATCCTTTCATGTCTTAATGCATCATTTCATGCATTTCATT
TATGACATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATCTATG
Found at i:1721647 original size:22 final size:22
Alignment explanation
Indices: 1721619--1721692 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 22
1721609 CCTACCATGA
1721619 TATCGATACTTCTATACTATGG
1 TATCGATACTTCTATACTATGG
* *
1721641 TATCGATACTT-T-T-CTCTCAG
1 TATCGATACTTCTATACTAT-GG
* *
1721661 TATCGATACTACTACACTATGG
1 TATCGATACTTCTATACTATGG
*
1721683 TATTGATACT
1 TATCGATACT
1721693 CCCTTTCGAT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
19 3 0.07
20 12 0.29
21 2 0.05
22 21 0.51
23 3 0.07
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (22 bp):
TATCGATACTTCTATACTATGG
Found at i:1727967 original size:46 final size:46
Alignment explanation
Indices: 1727845--1728125 Score: 412
Period size: 46 Copynumber: 6.2 Consensus size: 46
1727835 TTATTTGTTA
* *
1727845 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* **
1727891 ATTTCATTTATGACATCCTTTCATG-C-----GCATCCTTTCATAT
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1727931 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
1727977 ATTTCATTTATGGCATCCTTTAATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* **
1728023 ATTTCATCTATGGCATCCTTTCACACCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
1728069 ATTTCATCTATGGCATCCTTTCATGCCTTAATGAATCATTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1728115 ATTTCATTTAT
1 ATTTCATTTAT
1728126 ATATTCATTT
Statistics
Matches: 211, Mismatches: 18, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
40 35 0.17
41 1 0.00
45 1 0.00
46 174 0.82
ACGTcount: A:0.22, C:0.25, G:0.10, T:0.43
Consensus pattern (46 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:1727968 original size:20 final size:20
Alignment explanation
Indices: 1727943--1728114 Score: 110
Period size: 20 Copynumber: 7.7 Consensus size: 20
1727933 TTCATTTATG
1727943 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
1727963 GCATCCTTTCATGCATTTCATTTAT
1 GCATCCTTTCATGC----C-TTAAT
*
1727988 GGCATCCTTTAATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
1728009 GCATCCTTTCATGCATTTCATCTAT
1 GCATCCTTTCATGC-CTT-A---AT
**
1728034 GGCATCCTTTCACACCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
1728055 GCATCCTTTCATGCATTTCATCTAT
1 GCATCCTTTCATGC-CTT-A---AT
1728080 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* *
1728101 GAATCATTTCATGC
1 GCATCCTTTCATGC
1728115 ATTTCATTTA
Statistics
Matches: 120, Mismatches: 14, Indels: 36
0.71 0.08 0.21
Matches are distributed among these distances:
20 51 0.43
21 12 0.10
22 3 0.03
24 3 0.03
25 12 0.10
26 39 0.32
ACGTcount: A:0.22, C:0.27, G:0.10, T:0.41
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:1727994 original size:26 final size:26
Alignment explanation
Indices: 1727917--1728094 Score: 149
Period size: 26 Copynumber: 7.5 Consensus size: 26
1727907 CCTTTCATGC
**
1727917 GCATCCTTTCATATATTTCATTTATG
1 GCATCCTTTCATGCATTTCATTTATG
*
1727943 GCATCCTTTCATGC----C-TTAAT-
1 GCATCCTTTCATGCATTTCATTTATG
1727963 GCATCCTTTCATGCATTTCATTTATG
1 GCATCCTTTCATGCATTTCATTTATG
* *
1727989 GCATCCTTTAATGC----C-TTAAT-
1 GCATCCTTTCATGCATTTCATTTATG
*
1728009 GCATCCTTTCATGCATTTCATCTATG
1 GCATCCTTTCATGCATTTCATTTATG
* *
1728035 GCATCCTTTCA--CA---CCTTAAT-
1 GCATCCTTTCATGCATTTCATTTATG
*
1728055 GCATCCTTTCATGCATTTCATCTATG
1 GCATCCTTTCATGCATTTCATTTATG
1728081 GCATCCTTTCATGC
1 GCATCCTTTCATGC
1728095 CTTAATGAAT
Statistics
Matches: 119, Mismatches: 15, Indels: 36
0.70 0.09 0.21
Matches are distributed among these distances:
20 38 0.32
21 12 0.10
22 4 0.03
24 4 0.03
25 11 0.09
26 50 0.42
ACGTcount: A:0.21, C:0.27, G:0.10, T:0.42
Consensus pattern (26 bp):
GCATCCTTTCATGCATTTCATTTATG
Found at i:1729887 original size:188 final size:186
Alignment explanation
Indices: 1729525--1729865 Score: 468
Period size: 188 Copynumber: 1.8 Consensus size: 186
1729515 CATTACAACA
* *
1729525 TTTTTTATTATTGAATCATGACATTATTGGGCGCAACCATATTTCTTATATATGTTCATAACATT
1 TTTTTTATTATTGAATCATCACATTATTGGGCGCAACCATATTTCTTATATATGATCATAACATT
* * * * * *
1729590 TTCAGTTTTAAATTTATTTTCTTATACCGGGATAATTCAAGGCTCCATCAGCTTAAACTCTGGTA
66 TTCAATTTTAAACTTATTTTCTTATACCGAGATAATCCAACGCTCCATCAGCTTAAACTCTGATA
* ** * * * ** *
1729655 ATATTTTTGGTGTAACTTGTTTTATTATTAAAAGTATTAACATTTTAGATTCAATATT
131 ACATTTTCAGCGCAAC-T-CTAAAATATTAAAAGTATTAACATTTTAGATTCAATATT
*
1729713 TTTTTTATTATTGAATCATCACATTATTGGGCGCAACTATATTTCTTATATATGATCATAACATT
1 TTTTTTATTATTGAATCATCACATTATTGGGCGCAACCATATTTCTTATATATGATCATAACATT
* * *
1729778 TTTAATTTTAAACTTATTTTCTTATACTGAGATAATCCAACGCTCTATCAGCTTAAACTCTGATA
66 TTCAATTTTAAACTTATTTTCTTATACCGAGATAATCCAACGCTCCATCAGCTTAAACTCTGATA
1729843 ACATTTTCAGCGCAAC-CTAAAAT
131 ACATTTTCAGCGCAACTCTAAAAT
1729866 GTTCATAGTA
Statistics
Matches: 132, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
185 3 0.02
188 129 0.98
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (186 bp):
TTTTTTATTATTGAATCATCACATTATTGGGCGCAACCATATTTCTTATATATGATCATAACATT
TTCAATTTTAAACTTATTTTCTTATACCGAGATAATCCAACGCTCCATCAGCTTAAACTCTGATA
ACATTTTCAGCGCAACTCTAAAATATTAAAAGTATTAACATTTTAGATTCAATATT
Found at i:1735858 original size:21 final size:21
Alignment explanation
Indices: 1735829--1735869 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1735819 GACTATCGCA
1735829 TTGCAATTTTCCAAATTCGTG
1 TTGCAATTTTCCAAATTCGTG
* *
1735850 TTGCGATTTTCCTAATTCGT
1 TTGCAATTTTCCAAATTCGT
1735870 AACGCGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.46
Consensus pattern (21 bp):
TTGCAATTTTCCAAATTCGTG
Found at i:1735876 original size:21 final size:21
Alignment explanation
Indices: 1735834--1735876 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1735824 TCGCATTGCA
***
1735834 ATTTTCCAAATTCGTGTTGCG
1 ATTTTCCAAATTCGTAACGCG
*
1735855 ATTTTCCTAATTCGTAACGCG
1 ATTTTCCAAATTCGTAACGCG
1735876 A
1 A
1735877 ATACGTAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (21 bp):
ATTTTCCAAATTCGTAACGCG
Found at i:1736122 original size:22 final size:22
Alignment explanation
Indices: 1736097--1736162 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
1736087 GGCGACATCC
1736097 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
1736119 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* * *
1736141 GTCTCCATCTCTGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
1736163 TTCACGGTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.24, C:0.38, G:0.15, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:1736614 original size:20 final size:20
Alignment explanation
Indices: 1736499--1736605 Score: 119
Period size: 20 Copynumber: 5.5 Consensus size: 20
1736489 CAATTCTGTC
* *
1736499 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTGTCATTTTCGT
* ** **
1736518 GTTGCGATAGTCAAATTCAC
1 GTTGCGATTGTCATTTTCGT
1736538 GTTGCGATTGTCATTTTCGT
1 GTTGCGATTGTCATTTTCGT
*
1736558 GTTGCGATTTTCA-TTTCGT
1 GTTGCGATTGTCATTTTCGT
*
1736577 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTGTCATTTTCGT
1736597 GTTGCGATT
1 GTTGCGATT
1736606 TTAAGTTTCA
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
19 28 0.38
20 45 0.62
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.45
Consensus pattern (20 bp):
GTTGCGATTGTCATTTTCGT
Found at i:1738221 original size:13 final size:13
Alignment explanation
Indices: 1738203--1738234 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1738193 TTTACTTGAA
*
1738203 GAATCAACTACAG
1 GAATCAACGACAG
1738216 GAATCAACGACAG
1 GAATCAACGACAG
1738229 GAATCA
1 GAATCA
1738235 TATATGTTGG
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:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (13 bp):
GAATCAACGACAG
Found at i:1739266 original size:33 final size:34
Alignment explanation
Indices: 1739209--1739304 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
1739199 AAAACAGACT
* **
1739209 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
1739243 ATCGCAATGCG-AAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
*
1739276 ATTGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCGAAAATGAAAATCGCAACG
1739305 CGAAACTAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 30 0.53
34 27 0.47
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.14
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:1739340 original size:20 final size:19
Alignment explanation
Indices: 1739315--1739381 Score: 81
Period size: 20 Copynumber: 3.7 Consensus size: 19
1739305 CGAAACTAAA
1739315 TTCGCATTGCGATTTTCATT
1 TTCGCATTGCGATTTTCA-T
1739335 TTCGCATTGCGA--TT-AT
1 TTCGCATTGCGATTTTCAT
*
1739351 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1739368 TTCGCATTGCGATT
1 TTCGCATTGCGATT
1739382 CTCTCGTTGC
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
14 6 0.15
16 6 0.15
17 6 0.15
18 2 0.05
19 8 0.20
20 12 0.30
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:1739364 original size:34 final size:34
Alignment explanation
Indices: 1739321--1739414 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 34
1739311 TAAATTCGCA
1739321 TTGCGATTTTCATTTTCGCATTGCGATTATCTCG
1 TTGCGATTTTCATTTTCGCATTGCGATTATCTCG
*
1739355 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTTCGCATTGCGATTATCTCG
** * *
1739388 TTGCGATAGTCATTTCCGCGTTGCGAT
1 TTGCGATTTTCATTTTCGCATTGCGAT
1739415 AGTCATTTCC
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.56
34 24 0.44
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (34 bp):
TTGCGATTTTCATTTTCGCATTGCGATTATCTCG
Found at i:1739411 original size:20 final size:20
Alignment explanation
Indices: 1739386--1739479 Score: 136
Period size: 20 Copynumber: 4.7 Consensus size: 20
1739376 GCGATTCTCT
1739386 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
1739406 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1739426 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
* * *
1739446 TGTTGCGATAGCCATATT-CA
1 CGTTGCGATAGTCAT-TTCCG
1739466 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
1739480 AATGAATGTC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 65 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1742815 original size:20 final size:20
Alignment explanation
Indices: 1742790--1742873 Score: 159
Period size: 20 Copynumber: 4.2 Consensus size: 20
1742780 TTCAGTATTA
1742790 CGATAGTCAGAATCGCGTTG
1 CGATAGTCAGAATCGCGTTG
1742810 CGATAGTCAGAATCGCGTTG
1 CGATAGTCAGAATCGCGTTG
1742830 CGATAGTCAGAATCGCGTTG
1 CGATAGTCAGAATCGCGTTG
*
1742850 CGATAGTCAGATTCGCGTTG
1 CGATAGTCAGAATCGCGTTG
1742870 CGAT
1 CGAT
1742874 TTACGTATTC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (20 bp):
CGATAGTCAGAATCGCGTTG
Found at i:1742883 original size:20 final size:20
Alignment explanation
Indices: 1742860--1742912 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1742850 CGATAGTCAG
*
1742860 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1742880 ATTCGCAATGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1742900 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1742913 ATTAGGAAAA
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:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1742927 original size:21 final size:21
Alignment explanation
Indices: 1742909--1742949 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1742899 TATTCGCATT
1742909 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
*
1742930 GCGAATTTGGAAAATCGCAA
1 GCGAATTAGGAAAATCGCAA
1742950 TGTGATAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1744335 original size:42 final size:42
Alignment explanation
Indices: 1744061--1744319 Score: 455
Period size: 42 Copynumber: 6.2 Consensus size: 42
1744051 AAGTAAATAA
* *
1744061 ATAACATCATTAAGTCTCAATAAGTCTAAAATAAATAACACC
1 ATAACACCATTAAGTCTCAATAAGTTTAAAATAAATAACACC
*
1744103 AGAACACCATTAAGTCTCAATAAGTTTAAAATAAATAACACC
1 ATAACACCATTAAGTCTCAATAAGTTTAAAATAAATAACACC
1744145 ATAACACCATTAAGTCTCAATAAGTTTAAAATAAATAACACC
1 ATAACACCATTAAGTCTCAATAAGTTTAAAATAAATAACACC
*
1744187 ATAACACCATTAAGTCTCAATAAGTTTAAAATAAATAACATC
1 ATAACACCATTAAGTCTCAATAAGTTTAAAATAAATAACACC
* *
1744229 ATAACACCATTAAGTCTCAATAAGTCTAAAATAAATAATACC
1 ATAACACCATTAAGTCTCAATAAGTTTAAAATAAATAACACC
*
1744271 ATAACACCATTAAATCTCAATAAGTTTAAAATAAATAACACC
1 ATAACACCATTAAGTCTCAATAAGTTTAAAATAAATAACACC
1744313 ATAACAC
1 ATAACAC
1744320 TAATAAATTT
Statistics
Matches: 206, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 206 1.00
ACGTcount: A:0.51, C:0.19, G:0.05, T:0.26
Consensus pattern (42 bp):
ATAACACCATTAAGTCTCAATAAGTTTAAAATAAATAACACC
Found at i:1744337 original size:31 final size:34
Alignment explanation
Indices: 1744271--1744338 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
1744261 AAATAATACC
*
1744271 ATAACACCATTAAATCTCAATAAGTTTAAAATAA
1 ATAACACCATTAAATCTCAATAAATTTAAAATAA
1744305 ATAACACCA-TAACA-CT-AATAAATTT-AAATAA
1 ATAACACCATTAA-ATCTCAATAAATTTAAAATAA
1744336 ATA
1 ATA
1744339 TTAATTTTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
31 9 0.28
32 8 0.25
33 5 0.16
34 10 0.31
ACGTcount: A:0.56, C:0.15, G:0.01, T:0.28
Consensus pattern (34 bp):
ATAACACCATTAAATCTCAATAAATTTAAAATAA
Found at i:1747454 original size:21 final size:20
Alignment explanation
Indices: 1747430--1747468 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1747420 TATAAAAGTC
*
1747430 AATTTTAAATTTCTCAAAAAA
1 AATTTAAAATTT-TCAAAAAA
1747451 AATTTAAAATTTTCAAAA
1 AATTTAAAATTTTCAAAA
1747469 TTTGAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTTAAAATTTTCAAAAAA
Found at i:1753428 original size:13 final size:13
Alignment explanation
Indices: 1753410--1753434 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1753400 ATTTTTTTAA
1753410 AAAAAATATTTTT
1 AAAAAATATTTTT
1753423 AAAAAATATTTT
1 AAAAAATATTTT
1753435 ATTTAAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAAAATATTTTT
Found at i:1753870 original size:19 final size:19
Alignment explanation
Indices: 1753818--1753875 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
1753808 AATTCGTGAT
* *
1753818 ATATTAAATAATTATATGAT
1 ATATTAAA-AATTATATAAA
* *
1753838 ATAAATATAAATTATATAAA
1 AT-ATTAAAAATTATATAAA
1753858 ATATTAAAAATTATATAA
1 ATATTAAAAATTATATAA
1753876 TATAATCATA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 14 0.45
20 13 0.42
21 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
ATATTAAAAATTATATAAA
Found at i:1755287 original size:22 final size:23
Alignment explanation
Indices: 1755239--1755286 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
1755229 TTATGACACA
1755239 TTTTCATCTGTATTTATGGTACT
1 TTTTCATCTGTATTTATGGTACT
* *
1755262 TTTTC-TCTGTCTTTA-GGTATT
1 TTTTCATCTGTATTTATGGTACT
1755283 TTTT
1 TTTT
1755287 TGTTCATCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 9 0.39
22 9 0.39
23 5 0.22
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.62
Consensus pattern (23 bp):
TTTTCATCTGTATTTATGGTACT
Found at i:1757569 original size:2 final size:2
Alignment explanation
Indices: 1757562--1757600 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1757552 CTTTTAAAAC
1757562 AT AT AT AT AT AT AT AT AT AT -T 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
1757601 TTAAAACATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1757587 original size:17 final size:17
Alignment explanation
Indices: 1757565--1757598 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1757555 TTAAAACATA
1757565 TATATATATATATATAT
1 TATATATATATATATAT
1757582 TATATATATATATATAT
1 TATATATATATATATAT
1757599 ATTTAAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:1757587 original size:19 final size:19
Alignment explanation
Indices: 1757563--1757601 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1757553 TTTTAAAACA
1757563 TATATATATATATATATAT
1 TATATATATATATATATAT
1757582 TATATATATATATATATAT
1 TATATATATATATATATAT
1757601 T
1 T
1757602 TAAAACATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATATATATATATATATAT
Found at i:1762856 original size:75 final size:76
Alignment explanation
Indices: 1762677--1762871 Score: 225
Period size: 75 Copynumber: 2.5 Consensus size: 76
1762667 ATTACATTTC
* * *
1762677 TGTTCTTCAATTATG-CTGGATTTAC-GTTTAAGAAGTTGCTGTGTTTGTTGTTATGGTTCTTCA
1 TGTTCTTCAATTATGATTGGATTTACTG-TTAAGAAG-T--TGAGTTTGTTGTTATGATTCTTCA
*
1762740 GTGACAATTTGTTGTTCG
62 GTGACAA--T-TAGTTCG
* * *
1762758 TGTTCTTCAATTACGATTGGATTTGCTGTTAAGAAGTTGAGTTTGTTGTTATGATTCTTCAGTGG
1 TGTTCTTCAATTATGATTGGATTTACTGTTAAGAAGTTGAGTTTGTTGTTATGATTCTTCAGTGA
*
1762823 CAA-TAGTTCT
66 CAATTAGTTCG
*
1762833 TGTTCTTCAATTATGATTGGATTTTCTGTTAAGAAGTTG
1 TGTTCTTCAATTATGATTGGATTTACTGTTAAGAAGTTG
1762872 CTGAGATTGC
Statistics
Matches: 102, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
75 42 0.41
79 28 0.27
81 15 0.15
82 16 0.16
83 1 0.01
ACGTcount: A:0.20, C:0.10, G:0.23, T:0.47
Consensus pattern (76 bp):
TGTTCTTCAATTATGATTGGATTTACTGTTAAGAAGTTGAGTTTGTTGTTATGATTCTTCAGTGA
CAATTAGTTCG
Found at i:1762937 original size:65 final size:66
Alignment explanation
Indices: 1762833--1762957 Score: 182
Period size: 65 Copynumber: 1.9 Consensus size: 66
1762823 CAATAGTTCT
* **
1762833 TGTTCTTCAATTATGATTGGATTTTCTGTTAAGAAGTTGCTGAGATTGCTG-TTATAATTGCTTT
1 TGTTCTTCAATTATGATTGGATTTACCATTAAGAAGTTGCTGAGATTGCTGTTTATAATTGCTTT
1762897 C
66 C
* *
1762898 TGTTCTTCAATTATGCTTGGATTTACCATCTAA-AAGTTGCTGAGATTGTTGTTTATAATT
1 TGTTCTTCAATTATGATTGGATTTACCAT-TAAGAAGTTGCTGAGATTGCTGTTTATAATT
1762958 TTTTCAGTGA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
65 42 0.79
66 11 0.21
ACGTcount: A:0.23, C:0.11, G:0.18, T:0.47
Consensus pattern (66 bp):
TGTTCTTCAATTATGATTGGATTTACCATTAAGAAGTTGCTGAGATTGCTGTTTATAATTGCTTT
C
Found at i:1765182 original size:30 final size:30
Alignment explanation
Indices: 1765141--1765218 Score: 147
Period size: 30 Copynumber: 2.6 Consensus size: 30
1765131 TTGCTTATGT
*
1765141 TATTTGAATTGAATTCAAATTCAATCCACA
1 TATTGGAATTGAATTCAAATTCAATCCACA
1765171 TATTGGAATTGAATTCAAATTCAATCCACA
1 TATTGGAATTGAATTCAAATTCAATCCACA
1765201 TATTGGAATTGAATTCAA
1 TATTGGAATTGAATTCAA
1765219 TATGTTAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (30 bp):
TATTGGAATTGAATTCAAATTCAATCCACA
Found at i:1766962 original size:38 final size:38
Alignment explanation
Indices: 1766920--1766994 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
1766910 TATTTGAATT
*
1766920 AATATTTAGTTAACTTGTGACACTTATTAAAAAGAAGC
1 AATATTTAATTAACTTGTGACACTTATTAAAAAGAAGC
* *
1766958 AATATTTAATTAACTTGTGAGACTTGTTAAAAAGAAG
1 AATATTTAATTAACTTGTGACACTTATTAAAAAGAAG
1766995 TTAAATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.35
Consensus pattern (38 bp):
AATATTTAATTAACTTGTGACACTTATTAAAAAGAAGC
Found at i:1768137 original size:77 final size:76
Alignment explanation
Indices: 1768010--1768160 Score: 266
Period size: 77 Copynumber: 2.0 Consensus size: 76
1768000 GATCTTCGTG
*
1768010 AATCAGGGCATTAAGCCCAATCAAAATCACTGAAAACCTTAAGTTTTAGATCATTTTTTACTAAA
1 AATCAGGGAATTAAGCCCAATCAAAATCACTGAAAACCTTAAGTTTTAGATCATTTTTTACTAAA
1768075 ACAAACAAGCGC
66 A-AAACAAGCGC
* *
1768087 AATCAGGGAATTAAGCCCAATCAAAATCATTGAAAACCTTAAGTTTTAGATCATTTTTTGCTAAA
1 AATCAGGGAATTAAGCCCAATCAAAATCACTGAAAACCTTAAGTTTTAGATCATTTTTTACTAAA
1768152 AAAACAAGC
66 AAAACAAGC
1768161 TTACCCTGGA
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
76 8 0.11
77 63 0.89
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (76 bp):
AATCAGGGAATTAAGCCCAATCAAAATCACTGAAAACCTTAAGTTTTAGATCATTTTTTACTAAA
AAAACAAGCGC
Found at i:1769690 original size:21 final size:20
Alignment explanation
Indices: 1769653--1769692 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1769643 CCTCGATATT
1769653 AAAAAATAAATAAATAATTA
1 AAAAAATAAATAAATAATTA
* *
1769673 AAAACAATTAATATATAATT
1 AAAA-AATAAATAAATAATT
1769693 TATAAAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAAAATAAATAAATAATTA
Found at i:1769695 original size:120 final size:120
Alignment explanation
Indices: 1769558--1769794 Score: 300
Period size: 121 Copynumber: 2.0 Consensus size: 120
1769548 AAAAATATAT
* * * * *
1769558 ATTAATTTATATATTTAT-AAATAAAATATTTATTTATTTAGAAATATCAGAAAA-GGACTTCTA
1 ATTAATATATATATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAATAGACATCCA
*
1769621 GGTGCTTTAAGACAGCTCTTTTCCTCGATATTAAAAAATAAATAAATAATTAAAAACA
66 GGTGCTTTAAGACAGC-CTTTT-CTCAATATTAAAAAATAAATAAAT-ATTAAAAACA
** *
1769679 ATTAATATATA-ATTTATAAAATAGGATATTTATTTATTTAAAAATATTAGAAAATAGACATCCA
1 ATTAATATATATATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAATAGACATCCA
* * * * *
1769743 GTTGTTTTAAGACTGCCTTTTCTTAATATTGAAAAATAAATAAATATTAAAA
66 GGTGCTTTAAGACAGCCTTTTCTCAATATTAAAAAATAAATAAATATTAAAA
1769795 CAAGATTAAA
Statistics
Matches: 100, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
119 7 0.07
120 27 0.27
121 47 0.47
122 19 0.19
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (120 bp):
ATTAATATATATATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAATAGACATCCA
GGTGCTTTAAGACAGCCTTTTCTCAATATTAAAAAATAAATAAATATTAAAAACA
Found at i:1769843 original size:20 final size:18
Alignment explanation
Indices: 1769818--1769859 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
1769808 AGTTAAAAGT
*
1769818 AATAAAATAAGATTTTAATA
1 AATAAAATAA-ATATT-ATA
1769838 AATAAAATAAATATTATA
1 AATAAAATAAATATTATA
1769856 AATA
1 AATA
1769860 TATATATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 4 0.19
20 10 0.48
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
AATAAAATAAATATTATA
Found at i:1771316 original size:3 final size:3
Alignment explanation
Indices: 1771308--1771388 Score: 103
Period size: 3 Copynumber: 26.7 Consensus size: 3
1771298 GGCCTGTTTG
**
1771308 TAA TAA TAA TAA TTT TAA TAA TAA TAAA TAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
1771353 TATA TAA -AA TAA TAA TAA TAA TAAA TAA TAA TAA TA
1 TA-A TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TA
1771389 GAAAATGGAG
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
2 4 0.06
3 56 0.81
4 9 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1771334 original size:21 final size:21
Alignment explanation
Indices: 1771323--1771388 Score: 114
Period size: 21 Copynumber: 3.1 Consensus size: 21
1771313 ATAATAATTT
1771323 TAATAATAATAAATAAAATAA
1 TAATAATAATAAATAAAATAA
*
1771344 TAATAATAATATATAAAATAA
1 TAATAATAATAAATAAAATAA
1771365 TAATAATAATAAATAATAATAA
1 TAATAATAATAAATAA-AATAA
1771387 TA
1 TA
1771389 GAAAATGGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
21 35 0.83
22 7 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
TAATAATAATAAATAAAATAA
Found at i:1771939 original size:113 final size:113
Alignment explanation
Indices: 1771798--1772263 Score: 765
Period size: 113 Copynumber: 4.1 Consensus size: 113
1771788 ATGAGTTATT
* * * *
1771798 CTCTATCTGGCAATGTTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTC
1 CTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTAAACAAGTTCTTCTC
*
1771863 ATTATGAACTTCTTCTTCCTTATTCAGATGAGTTCTTCTCATTATGAA
66 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
1771911 CTCTACCTGGAAATGATGATCCATCGAATGATGAATTCAAGAAAAAAGTTGAACAAGTTCTTCTC
1 CTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTAAACAAGTTCTTCTC
1771976 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
66 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * *
1772024 CTCTACCTGGAAATGCTGATCCATC-AAGTGATGGATTTGAA-CAAAAGGTTAAATAAGCTCTTC
1 CTCTACCTGGAAATGCTGATCCATCGAA-TGAT-GAATTCAAGCAAAAAGTTAAACAAGTTCTTC
* *
1772087 TCATTATGAACTTCATATTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
64 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1772137 CTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTAAACAAGTTCTTCTC
1 CTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTAAACAAGTTCTTCTC
1772202 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
66 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1772250 CTCTACCTGGAAAT
1 CTCTACCTGGAAAT
1772264 TTTTTAAGAA
Statistics
Matches: 327, Mismatches: 22, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
112 8 0.02
113 311 0.95
114 8 0.02
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (113 bp):
CTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTAAACAAGTTCTTCTC
ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
Found at i:1772239 original size:339 final size:332
Alignment explanation
Indices: 1771619--1772263 Score: 915
Period size: 339 Copynumber: 1.9 Consensus size: 332
1771609 TTGGAAAAGG
* *
1771619 GTTGAACAAGTTCTTATCATTATGAACTTTTTTTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTATCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * *
1771684 ACTCTACCTGGAAATGTTGATGATGATCTATCTATTTCTGTGATAGAGTCATGCAAAAGGTTGAA
66 ACTCTACCTGGAAA---T-ATGATGATCCATCTA--T-AGTGATAGAGTCATGCAAAAGGTTAAA
* * * * *
1771749 CAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCTATCTGGCAATGT
124 CAAGCTCTTCTCATTATGAACTTCATATTCCTTCTTCAGATGAGTTATTCTCTACCTGGAAATGC
*
1771814 TGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
189 TGATCCATCGAATGATGAATTCAAGCAAAAAGTTAAACAAGTTCTTCTCATTATGAACTTCTTCT
1771879 TCCTTATTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGATGATCCATCGAATGATG
254 TCCTTATTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGATGATCCATCGAATGATG
1771944 AATTCAAGAAAAAA
319 AATTCAAGAAAAAA
*
1771958 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTATCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * * *
1772023 ACTCTACCTGG-AA-ATGCTGATCCATC-A-AGTGATGGA-T-TTGAACAAAAGGTTAAATAAGC
66 ACTCTACCTGGAAATATGATGATCCATCTATAGTGATAGAGTCATG--CAAAAGGTTAAACAAGC
1772082 TCTTCTCATTATGAACTTCATATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGG
129 TCTTCTCATTATGAACTTCATATTCCTTCTTCAGATGAG----T-T-A-T-T---CTCTACCTGG
1772147 AAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTAAACAAGTTCTTCTCATTATGAACT
183 AAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTAAACAAGTTCTTCTCATTATGAACT
*
1772212 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAAT
248 TCTTCTTCCTTATTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAAT
1772264 TTTTTAAGAA
Statistics
Matches: 276, Mismatches: 17, Indels: 26
0.87 0.05 0.08
Matches are distributed among these distances:
326 2 0.01
327 1 0.00
328 59 0.21
332 2 0.01
333 12 0.04
334 1 0.00
335 1 0.00
336 1 0.00
338 2 0.01
339 195 0.71
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (332 bp):
GTTGAACAAGTTCTTATCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACTCTACCTGGAAATATGATGATCCATCTATAGTGATAGAGTCATGCAAAAGGTTAAACAAGCTC
TTCTCATTATGAACTTCATATTCCTTCTTCAGATGAGTTATTCTCTACCTGGAAATGCTGATCCA
TCGAATGATGAATTCAAGCAAAAAGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTAT
TCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGATGATCCATCGAATGATGAATTCAA
GAAAAAA
Found at i:1772416 original size:76 final size:76
Alignment explanation
Indices: 1772284--1772463 Score: 288
Period size: 76 Copynumber: 2.4 Consensus size: 76
1772274 AGAAAAAAAA
* * * * * * *
1772284 ACATTATGCACTGTAGGGCTTACAGCTGACTCAAAGGTTTTGAAAACATCAAAAAGCTCCCGAAG
1 ACATCATGCACTGTAGGACTTATAGATGACCCAAAGGCTTTAAAAACATCAAAAAGCTCCCGAAG
1772349 GCTTTTTGGAC
66 GCTTTTTGGAC
*
1772360 ACATCATGCACTGTAGGACTTATAGATGACCCTAAGGCTTTAAAAACATCAAAAAGCTCCCGAAG
1 ACATCATGCACTGTAGGACTTATAGATGACCCAAAGGCTTTAAAAACATCAAAAAGCTCCCGAAG
1772425 GCTTTTTGGAC
66 GCTTTTTGGAC
1772436 ACATCATGCACTGTAGGACTTATAGATG
1 ACATCATGCACTGTAGGACTTATAGATG
1772464 TGGGAAATAA
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 96 1.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (76 bp):
ACATCATGCACTGTAGGACTTATAGATGACCCAAAGGCTTTAAAAACATCAAAAAGCTCCCGAAG
GCTTTTTGGAC
Found at i:1772859 original size:113 final size:113
Alignment explanation
Indices: 1772728--1773420 Score: 1025
Period size: 113 Copynumber: 6.1 Consensus size: 113
1772718 ATGAGTTCTT
* * * *
1772728 CTCTATCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTC
1 CTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAGGTTGAACAAGCTCTTCTC
*
1772793 ATTATGAACTTCTTCTTCCGTCTTCAGATGAGTTCTTCTCATTATGAA
66 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
1772841 CTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTC
1 CTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAGGTTGAACAAGCTCTTCTC
1772906 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
66 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * *
1772954 CTCTACCTGGAAATGCTGATCCATC-AAGTGATGGATTTAAACAAAAGGTTAAACAAGCTCTTCT
1 CTCTACCTGGAAATGCTGATCCATCGAA-TGATGAATTCAAGCAAAAGGTTGAACAAGCTCTTCT
1773018 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
65 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * ** *
1773067 CT-TTCTCTGGAAATGCTGATCCATC-AAGTAATGAATTTTAGCCAAAGGTTGAACAAGCTCTTC
1 CTCTAC-CTGGAAATGCTGATCCATCGAA-TGATGAATTCAAGCAAAAGGTTGAACAAGCTCTTC
* * *
1773130 TTATTATGAACTTCTTCTTCCTTCTTAAGATGAGTTCTTCTCATTATAAA
64 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * **
1773180 CTCTACCTGGTAATGATGATCTATCGAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTC
1 CTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAGGTTGAACAAGCTCTTCTC
*
1773245 ATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAA
66 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * * **
1773293 CTAT-CTCTAGAAAAGCTGATCCATCGAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCT
1 CTCTAC-CTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAGGTTGAACAAGCTCTTCT
1773357 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
65 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1773406 CTCTACCTGGAAATG
1 CTCTACCTGGAAATG
1773421 TTTTAAGAAA
Statistics
Matches: 524, Mismatches: 50, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
112 5 0.01
113 514 0.98
114 5 0.01
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (113 bp):
CTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAGGTTGAACAAGCTCTTCTC
ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
Found at i:1773276 original size:339 final size:338
Alignment explanation
Indices: 1772667--1773420 Score: 1147
Period size: 339 Copynumber: 2.3 Consensus size: 338
1772657 TAGAGTCATG
1772667 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC-
1 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
1772731 ---T--A----TCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTT
66 TTATGAACTTCTCTGGAAATGCTGATCCATCGAATAATGAATTCAAGCAAAAAGTTGAACAAGCT
* *
1772787 CTTCTCATTATGAACTTCTTCTTCCGTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGA
131 CTTCTCATTATGAACTTCTTCTTCCGTCTTAAGATGAGTTCTTCTCATTATAAACTCTACCTGGA
* * *
1772852 AATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
196 AATGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTT
* * *
1772917 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGGAAATGCTGATCCATCAA
261 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTAT-CTCTAGAAAAGCTGATCCATCAA
1772981 GTGATGGATTTAAA
325 GTGATGGATTTAAA
*
1772995 CAAAAGGTTAAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
** * *
1773060 TTATGAACTTTCTCTGGAAATGCTGATCCATC-AAGTAATGAATTTTAGCCAAAGGTTGAACAAG
66 TTATGAAC-TTCTCTGGAAATGCTGATCCATCGAA-TAATGAATTCAAGCAAAAAGTTGAACAAG
* *
1773124 CTCTTCTTATTATGAACTTCTTCTTCCTTCTTAAGATGAGTTCTTCTCATTATAAACTCTACCTG
129 CTCTTCTCATTATGAACTTCTTCTTCCGTCTTAAGATGAGTTCTTCTCATTATAAACTCTACCTG
* * *
1773189 GTAATGATGATCTATCGAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
194 GAAATGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAAC
* *
1773254 TTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTATCTCTAGAAAAGCTGATCCATCG
259 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTATCTCTAGAAAAGCTGATCCATCA
* *
1773319 AGTGATGGATTTGAG
324 AGTGATGGATTTAAA
1773334 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1773399 TTATGAAC-TCTACCTGGAAATG
66 TTATGAACTTCT--CTGGAAATG
1773421 TTTTAAGAAA
Statistics
Matches: 385, Mismatches: 26, Indels: 19
0.90 0.06 0.04
Matches are distributed among these distances:
328 63 0.16
332 1 0.00
334 1 0.00
337 3 0.01
338 3 0.01
339 314 0.82
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.36
Consensus pattern (338 bp):
CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTCTCTGGAAATGCTGATCCATCGAATAATGAATTCAAGCAAAAAGTTGAACAAGCT
CTTCTCATTATGAACTTCTTCTTCCGTCTTAAGATGAGTTCTTCTCATTATAAACTCTACCTGGA
AATGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTT
CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTATCTCTAGAAAAGCTGATCCATCAAG
TGATGGATTTAAA
Found at i:1774200 original size:22 final size:22
Alignment explanation
Indices: 1774175--1774227 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1774165 TAAAGCTTTT
1774175 ATCTTTGAAAAGAGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
*
1774197 ATCTTTAAAAAGAGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
1774219 ATCTTTGAA
1 ATCTTTGAA
1774228 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCTTTGAAAAGAGAATCTATC
Found at i:1778970 original size:7 final size:7
Alignment explanation
Indices: 1778958--1779013 Score: 55
Period size: 7 Copynumber: 8.4 Consensus size: 7
1778948 TTCTCCCTCT
1778958 TTTTTTC
1 TTTTTTC
1778965 TTTTTT-
1 TTTTTTC
1778971 TTTTTTC
1 TTTTTTC
*
1778978 ATTTTTC
1 TTTTTTC
*
1778985 CTTTTTC
1 TTTTTTC
* *
1778992 -ATCTT-
1 TTTTTTC
1778997 TTTTTTC
1 TTTTTTC
1779004 TTTTTTC
1 TTTTTTC
1779011 TTT
1 TTT
1779014 CTTTGTTGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
6 12 0.30
7 28 0.70
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTTC
Found at i:1778971 original size:9 final size:9
Alignment explanation
Indices: 1778957--1779009 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
1778947 TTTCTCCCTC
1778957 TTTTTTTCT
1 TTTTTTTCT
*
1778966 TTTTTTTTT
1 TTTTTTTCT
1778975 TTCATTTTTCCT
1 TT--TTTTT-CT
**
1778987 TTTTCATCT
1 TTTTTTTCT
1778996 TTTTTTTCT
1 TTTTTTTCT
1779005 TTTTT
1 TTTTT
1779010 CTTTCTTTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
9 24 0.69
10 3 0.09
11 5 0.14
12 3 0.09
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:1779027 original size:26 final size:26
Alignment explanation
Indices: 1778998--1779050 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
1778988 TTTCATCTTT
* *
1778998 TTTTTCTTTTTTCTTTCTTTGTTGGA
1 TTTTTCCTTTTTCTTTCTTTCTTGGA
1779024 TTTTTCCTTTTTCTTTCTTTCTTGGA
1 TTTTTCCTTTTTCTTTCTTTCTTGGA
1779050 T
1 T
1779051 GAGTATAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.04, C:0.15, G:0.09, T:0.72
Consensus pattern (26 bp):
TTTTTCCTTTTTCTTTCTTTCTTGGA
Found at i:1782677 original size:14 final size:14
Alignment explanation
Indices: 1782639--1782692 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
1782629 CATAAAAATA
* *
1782639 CAAATGCAAAGATG
1 CAAATGTAAATATG
1782653 CCAAATGTAAATATG
1 -CAAATGTAAATATG
* *
1782668 CAATTGTAAAAATG
1 CAAATGTAAATATG
*
1782682 TAAATGTAAAT
1 CAAATGTAAAT
1782693 TATTTAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:1784299 original size:14 final size:13
Alignment explanation
Indices: 1784278--1784328 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
1784268 ACCTGAATAA
1784278 AATA-AATAAAAT
1 AATATAATAAAAT
1784290 AATATTAATAAAAT
1 AATA-TAATAAAAT
1784304 AATAT-A-AAAAT
1 AATATAATAAAAT
1784315 AATAAGTAATAAAA
1 AAT-A-TAATAAAA
1784329 AATTTGAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 8 0.24
12 6 0.18
13 2 0.06
14 13 0.39
15 4 0.12
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (13 bp):
AATATAATAAAAT
Found at i:1784303 original size:23 final size:26
Alignment explanation
Indices: 1784273--1784328 Score: 82
Period size: 23 Copynumber: 2.3 Consensus size: 26
1784263 TTAATACCTG
*
1784273 AATAAAATAA-AT-AAAATAAT-ATT
1 AATAAAATAATATAAAAATAATAAGT
1784296 AATAAAATAATATAAAAATAATAAGT
1 AATAAAATAATATAAAAATAATAAGT
1784322 AATAAAA
1 AATAAAA
1784329 AATTTGAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 10 0.34
24 2 0.07
25 8 0.28
26 9 0.31
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (26 bp):
AATAAAATAATATAAAAATAATAAGT
Found at i:1784317 original size:19 final size:18
Alignment explanation
Indices: 1784278--1784331 Score: 56
Period size: 19 Copynumber: 3.0 Consensus size: 18
1784268 ACCTGAATAA
* * *
1784278 AATAAATAAAATAATATT
1 AATAAATAATATAAAAAT
1784296 AATAAAATAATATAAAAAT
1 AAT-AAATAATATAAAAAT
*
1784315 AATAAGTAATA-AAAAAT
1 AATAAATAATATAAAAAT
1784332 TTGAAAGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 6 0.19
18 10 0.32
19 15 0.48
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (18 bp):
AATAAATAATATAAAAAT
Found at i:1784330 original size:28 final size:28
Alignment explanation
Indices: 1784273--1784331 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
1784263 TTAATACCTG
*
1784273 AATAAAATAAATAAAATAATATTAATAA
1 AATAAAATAAATAAAATAATAATAATAA
*
1784301 AATAATATAAA-AATAATAAGTAATAA-AA
1 AATAAAATAAATAA-AATAA-TAATAATAA
1784329 AAT
1 AAT
1784332 TTGAAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 2 0.07
28 20 0.74
29 5 0.19
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (28 bp):
AATAAAATAAATAAAATAATAATAATAA
Found at i:1784958 original size:20 final size:19
Alignment explanation
Indices: 1784919--1784960 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1784909 TTTCCTCGAT
1784919 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1784938 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
1784958 ATT
1 ATT
1784961 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Done.