Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007711.1 Hibiscus syriacus cultivar Beakdansim tig00109926_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: 1768490
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 6 of 8
Found at i:1352796 original size:17 final size:16
Alignment explanation
Indices: 1352773--1352808 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
1352763 TAATTTCCGT
1352773 TTTAAAAAATATTGTG
1 TTTAAAAAATATTGTG
*
1352789 TTT-AAAAATATTTTG
1 TTTAAAAAATATTGTG
1352804 TTTAA
1 TTTAA
1352809 TTTACATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (16 bp):
TTTAAAAAATATTGTG
Found at i:1353099 original size:26 final size:25
Alignment explanation
Indices: 1353070--1353128 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
1353060 AAATCATATT
*
1353070 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
1353096 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
1353122 ATTATTA
1 ATTATTA
1353129 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:1356167 original size:124 final size:124
Alignment explanation
Indices: 1355947--1356341 Score: 781
Period size: 124 Copynumber: 3.2 Consensus size: 124
1355937 ATGTATTTAT
1355947 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1356012 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
1356071 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1356136 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
1356195 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1356260 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
1356319 TAATCATTATAAAAATGAGTTTA
1 TAATCATTATAAAAATGA-TTTA
1356342 CAATTGTTGT
Statistics
Matches: 270, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
124 266 0.99
125 4 0.01
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (124 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
Found at i:1356330 original size:26 final size:26
Alignment explanation
Indices: 1356005--1356336 Score: 316
Period size: 26 Copynumber: 13.2 Consensus size: 26
1355995 GATGATTTAG
*
1356005 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
1356031 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
1356057 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
1356083 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
1356106 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
*
1356129 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
1356155 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
1356181 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
1356207 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
1356230 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
*
1356253 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
1356279 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
1356305 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
*
1356331 AAATGA
1 TAATGA
1356337 GTTTACAATT
Statistics
Matches: 255, Mismatches: 34, Indels: 34
0.79 0.11 0.11
Matches are distributed among these distances:
21 8 0.03
22 6 0.02
23 24 0.09
24 14 0.05
25 15 0.06
26 186 0.73
27 2 0.01
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:1357406 original size:20 final size:21
Alignment explanation
Indices: 1357381--1357421 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1357371 TGTTCAATAA
1357381 TTTTAATCAAAATTTT-TATT
1 TTTTAATCAAAATTTTATATT
* *
1357401 TTTTAATTAATATTTTATATT
1 TTTTAATCAAAATTTTATATT
1357422 AAAATAGAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTAATCAAAATTTTATATT
Found at i:1358445 original size:15 final size:14
Alignment explanation
Indices: 1358422--1358452 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1358412 TACAACACTA
1358422 AACTTTAATATAAT
1 AACTTTAATATAAT
1358436 AACTTATAATATAAT
1 AACTT-TAATATAAT
1358451 AA
1 AA
1358453 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:1358460 original size:16 final size:16
Alignment explanation
Indices: 1358427--1358473 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1358417 CACTAAACTT
*
1358427 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
1358442 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
1358458 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
1358474 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:1358706 original size:46 final size:48
Alignment explanation
Indices: 1358629--1358720 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 48
1358619 CAACAAACAA
*
1358629 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTTT
1 ATATAACTTAACTATTTAACTAAAACAAACTAATT-AATAATTTTTTTT
*
1358678 ATATAAC-TAACTA-TTAAC-AAAACAAACTAATTAATTATTTTTT
1 ATATAACTTAACTATTTAACTAAAACAAACTAATTAATAATTTTTT
1358721 AACTATATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 10 0.24
46 13 0.32
47 5 0.12
48 6 0.15
49 7 0.17
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (48 bp):
ATATAACTTAACTATTTAACTAAAACAAACTAATTAATAATTTTTTTT
Found at i:1358731 original size:47 final size:48
Alignment explanation
Indices: 1358629--1358733 Score: 135
Period size: 47 Copynumber: 2.2 Consensus size: 48
1358619 CAACAAACAA
* *
1358629 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTTT
1 ATATAAC-TAACTATTTAACTAAAACAAACTAATTAAATAATTTTTTCT
*
1358678 ATATAACTAACTA-TTAAC-AAAACAAACTAATT-AATTATTTTTTAACT
1 ATATAACTAACTATTTAACTAAAACAAACTAATTAAATAATTTTTT--CT
1358725 ATATAACTA
1 ATATAACTA
1358734 TCAAACATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
45 10 0.20
46 13 0.25
47 15 0.29
48 6 0.12
49 7 0.14
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (48 bp):
ATATAACTAACTATTTAACTAAAACAAACTAATTAAATAATTTTTTCT
Found at i:1358789 original size:41 final size:40
Alignment explanation
Indices: 1358701--1358789 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
1358691 TTAACAAAAC
* *
1358701 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
1358742 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
1358783 AAACTAA
1 AAACTAA
1358790 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:1358954 original size:21 final size:21
Alignment explanation
Indices: 1358924--1358976 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1358914 CCCTTTCTTC
*
1358924 TTCTTACTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
1358945 TTCTTTCTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
1358966 TTCTTTCTTTC
1 TTCTTTCTTTC
1358977 TCGGCTGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (21 bp):
TTCTTTCTTTCCTTTCTCCCT
Found at i:1358967 original size:17 final size:16
Alignment explanation
Indices: 1358947--1358978 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1358937 TTCTCCCTTT
1358947 CTTTCTTTCCTTTCTCC
1 CTTTCTTT-CTTTCTCC
1358964 CTTTCTTTCTTTCTC
1 CTTTCTTTCTTTCTC
1358979 GGCTGCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTTCTTTCTTTCTCC
Found at i:1359011 original size:23 final size:23
Alignment explanation
Indices: 1358981--1359026 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1358971 TCTTTCTCGG
1358981 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
1359004 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
1359027 TCTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.39, G:0.04, T:0.48
Consensus pattern (23 bp):
CTGCAATCTCTTCTCCCTTTCTT
Found at i:1359173 original size:27 final size:27
Alignment explanation
Indices: 1359143--1359198 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
1359133 AATAATTCAC
1359143 GGCTCAAACGGTTCACATGCATGCATT
1 GGCTCAAACGGTTCACATGCATGCATT
*
1359170 GGCTCAAATGGTTCACATGCATGCATT
1 GGCTCAAACGGTTCACATGCATGCATT
1359197 GG
1 GG
1359199 GAGCTGTAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (27 bp):
GGCTCAAACGGTTCACATGCATGCATT
Found at i:1359299 original size:29 final size:29
Alignment explanation
Indices: 1359267--1359346 Score: 99
Period size: 29 Copynumber: 2.8 Consensus size: 29
1359257 ATGGGAATGG
* *
1359267 CGCCGGGACTACATGGCGACCTAGAGGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
*
1359296 CGCCGGGAATACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
* *
1359325 CGCCTAGG-CTGCATGGCGACCT
1 CGCC-GGGACTACATGGCGACCT
1359347 CTCTATTCCT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
29 42 0.95
30 2 0.05
ACGTcount: A:0.21, C:0.30, G:0.34, T:0.15
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTACAAGGT
Found at i:1359396 original size:13 final size:13
Alignment explanation
Indices: 1359378--1359404 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1359368 TCGTATATGG
1359378 CTCGTATGTCACC
1 CTCGTATGTCACC
1359391 CTCGTATGTCACC
1 CTCGTATGTCACC
1359404 C
1 C
1359405 CATATGGCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.41, G:0.15, T:0.30
Consensus pattern (13 bp):
CTCGTATGTCACC
Found at i:1359431 original size:45 final size:46
Alignment explanation
Indices: 1359367--1359456 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 46
1359357 GCATGCTCCC
1359367 CTCGTATATGGCTCGTATGTCACCCTCGTA-TGTCACCCCATATGG
1 CTCGTATATGGCTCGTATGTCACCCTCGTATTGTCACCCCATATGG
*
1359412 CTCGTATATGGCTCGTATGTCACCCTCGTATTGTCACCCCGTATG
1 CTCGTATATGGCTCGTATGTCACCCTCGTATTGTCACCCCATATG
1359457 TCGCCTGGAT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 30 0.70
46 13 0.30
ACGTcount: A:0.17, C:0.31, G:0.20, T:0.32
Consensus pattern (46 bp):
CTCGTATATGGCTCGTATGTCACCCTCGTATTGTCACCCCATATGG
Found at i:1359441 original size:13 final size:13
Alignment explanation
Indices: 1359423--1359458 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1359413 TCGTATATGG
1359423 CTCGTATGTCACC
1 CTCGTATGTCACC
1359436 CTCGTATTGTCACC
1 CTCGTA-TGTCACC
1359450 C-CGTATGTC
1 CTCGTATGTC
1359459 GCCTGGATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 10 0.45
14 8 0.36
ACGTcount: A:0.14, C:0.36, G:0.17, T:0.33
Consensus pattern (13 bp):
CTCGTATGTCACC
Found at i:1360659 original size:31 final size:31
Alignment explanation
Indices: 1360588--1360675 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 31
1360578 TCATTTTACG
* *
1360588 TGACATGA-ATTATTTTATTAGTATTTTCCTG
1 TGACATGACA-TATTTTATTAATATTTTCCTA
* ** *
1360619 TAATGTGACATATTTTATTAATATTTTCTTA
1 TGACATGACATATTTTATTAATATTTTCCTA
1360650 TGACATGACATGA-TTTATTAATATTT
1 TGACATGACAT-ATTTTATTAATATTT
1360676 AATGTCATGT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
31 44 0.96
32 2 0.04
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (31 bp):
TGACATGACATATTTTATTAATATTTTCCTA
Found at i:1361210 original size:14 final size:14
Alignment explanation
Indices: 1361191--1361246 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
1361181 TCCATAATCT
1361191 GTTCATTTATGTTC
1 GTTCATTTATGTTC
*
1361205 GTTCATTTATATTC
1 GTTCATTTATGTTC
**
1361219 GTTCGGTTATG-T-
1 GTTCATTTATGTTC
1361231 -TT-ATTTATGTTC
1 GTTCATTTATGTTC
1361243 GTTC
1 GTTC
1361247 GTTAATGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
10 5 0.16
11 3 0.09
13 3 0.09
14 21 0.66
ACGTcount: A:0.14, C:0.12, G:0.16, T:0.57
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:1361243 original size:24 final size:24
Alignment explanation
Indices: 1361209--1361266 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
1361199 ATGTTCGTTC
*
1361209 ATTTATATTCGTTCGGTT-ATGTTT
1 ATTTATGTTCGTTC-GTTAATGTTT
1361233 ATTTATGTTCGTTCGTTAATGTTT
1 ATTTATGTTCGTTCGTTAATGTTT
*
1361257 GTTTATGTTC
1 ATTTATGTTC
1361267 TCCATACCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 3 0.10
24 28 0.90
ACGTcount: A:0.16, C:0.09, G:0.17, T:0.59
Consensus pattern (24 bp):
ATTTATGTTCGTTCGTTAATGTTT
Found at i:1361849 original size:24 final size:24
Alignment explanation
Indices: 1361818--1361889 Score: 135
Period size: 24 Copynumber: 3.0 Consensus size: 24
1361808 TCATTTCGTT
*
1361818 TATGTTCACGAACAAGCTCGTTTA
1 TATGTTCATGAACAAGCTCGTTTA
1361842 TATGTTCATGAACAAGCTCGTTTA
1 TATGTTCATGAACAAGCTCGTTTA
1361866 TATGTTCATGAACAAGCTCGTTTA
1 TATGTTCATGAACAAGCTCGTTTA
1361890 AAAGCTTGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (24 bp):
TATGTTCATGAACAAGCTCGTTTA
Found at i:1363788 original size:20 final size:20
Alignment explanation
Indices: 1363765--1363923 Score: 183
Period size: 20 Copynumber: 7.8 Consensus size: 20
1363755 GAACACCAGT
* *
1363765 TTCGCAACACAATTTTCAAA
1 TTCGCAACGCGATTTTCAAA
*
1363785 TTCGCAACGCGATTTTTAAA
1 TTCGCAACGCGATTTTCAAA
* *
1363805 TTCGCAACACGATTCTCTAAA
1 TTCGCAACGCGATTTTC-AAA
* *
1363826 ATCGCAACGCGGTTTTCAAA
1 TTCGCAACGCGATTTTCAAA
*
1363846 TTCGCAACGCGATTCTCCAAA
1 TTCGCAACGCGATT-TTCAAA
* *
1363867 ATCGCAATGCGATTTTCAAA
1 TTCGCAACGCGATTTTCAAA
* **
1363887 TTAGCAACGTAATTTTCAAA
1 TTCGCAACGCGATTTTCAAA
1363907 TTCGCAACGCGATTTTC
1 TTCGCAACGCGATTTTC
1363924 GTTTTCGCAA
Statistics
Matches: 113, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
20 80 0.71
21 33 0.29
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (20 bp):
TTCGCAACGCGATTTTCAAA
Found at i:1363836 original size:41 final size:40
Alignment explanation
Indices: 1363765--1363923 Score: 183
Period size: 41 Copynumber: 3.9 Consensus size: 40
1363755 GAACACCAGT
* * *
1363765 TTCGCAACACAATTTTCAAATTCGCAACGCGATTTTTAAA
1 TTCGCAACACAATTCTCAAAATCGCAACGCGATTTTCAAA
* *
1363805 TTCGCAACACGATTCTCTAAAATCGCAACGCGGTTTTCAAA
1 TTCGCAACACAATTCTC-AAAATCGCAACGCGATTTTCAAA
* * *
1363846 TTCGCAACGCGATTCTCCAAAATCGCAATGCGATTTTCAAA
1 TTCGCAACACAATTCT-CAAAATCGCAACGCGATTTTCAAA
* ** * *
1363887 TTAGCAACGTAATTTTCAAATTCGCAACGCGATTTTC
1 TTCGCAACACAATTCTCAAAATCGCAACGCGATTTTC
1363924 GTTTTCGCAA
Statistics
Matches: 103, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
40 34 0.33
41 68 0.66
42 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (40 bp):
TTCGCAACACAATTCTCAAAATCGCAACGCGATTTTCAAA
Found at i:1363842 original size:61 final size:60
Alignment explanation
Indices: 1363768--1363923 Score: 186
Period size: 61 Copynumber: 2.6 Consensus size: 60
1363758 CACCAGTTTC
* * * *
1363768 GCAACACAATTTTCAAATTCGCAACGCGATTTTTAAATTCGCAACACGATTCTCTAAAATC
1 GCAACGCAATTTTCAAATTCGCAACGCGATTTTCAAAATCGCAACACGATTCTC-AAAATA
** * ** * *
1363829 GCAACGCGGTTTTCAAATTCGCAACGCGATTCTCCAAAATCGCAATGCGATTTTCAAATTA
1 GCAACGCAATTTTCAAATTCGCAACGCGATT-TTCAAAATCGCAACACGATTCTCAAAATA
*
1363890 GCAACGTAATTTTCAAATTCGCAACGCGATTTTC
1 GCAACGCAATTTTCAAATTCGCAACGCGATTTTC
1363924 GTTTTCGCAA
Statistics
Matches: 79, Mismatches: 15, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
60 2 0.03
61 60 0.76
62 17 0.22
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.29
Consensus pattern (60 bp):
GCAACGCAATTTTCAAATTCGCAACGCGATTTTCAAAATCGCAACACGATTCTCAAAATA
Found at i:1364121 original size:20 final size:20
Alignment explanation
Indices: 1364098--1364157 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
1364088 AAACAAAATT
1364098 CGCGTTGCGAATTTGAAAAC
1 CGCGTTGCGAATTTGAAAAC
* * *
1364118 CGCGTTGCGATTTTGGAGAAT
1 CGCGTTGCGAATTT-GAAAAC
1364139 CGCGTTGCGAATTTGAAAA
1 CGCGTTGCGAATTTGAAAA
1364158 ATGAGTTGCG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
CGCGTTGCGAATTTGAAAAC
Found at i:1364144 original size:21 final size:21
Alignment explanation
Indices: 1364092--1364167 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
1364082 TTGCGAAAAC
1364092 AAAATTCGCGTTGCGAATTT-G
1 AAAA-TCGCGTTGCGAATTTGG
* *
1364113 AAAACCGCGTTGCGATTTTGG
1 AAAATCGCGTTGCGAATTTGG
* *
1364134 AGAATCGCGTTGCGAATTTGA
1 AAAATCGCGTTGCGAATTTGG
*
1364155 AAAAT-GAGTTGCG
1 AAAATCGCGTTGCG
1364168 TGTTTACCTA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
20 20 0.43
21 26 0.57
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (21 bp):
AAAATCGCGTTGCGAATTTGG
Found at i:1364167 original size:20 final size:20
Alignment explanation
Indices: 1364099--1364167 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
1364089 AACAAAATTC
**
1364099 GCGTTGCGAATTTGAAAACC
1 GCGTTGCGAATTTGAAAAAT
* * *
1364119 GCGTTGCGATTTTGGAGAAT
1 GCGTTGCGAATTTGAAAAAT
1364139 CGCGTTGCGAATTTGAAAAAT
1 -GCGTTGCGAATTTGAAAAAT
*
1364160 GAGTTGCG
1 GCGTTGCG
1364168 TGTTTACCTA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 22 0.56
21 17 0.44
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.29
Consensus pattern (20 bp):
GCGTTGCGAATTTGAAAAAT
Found at i:1364248 original size:21 final size:20
Alignment explanation
Indices: 1364224--1364279 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
1364214 TGCGATCTTA
1364224 GAGAACCGCGTTGC-AATTTT
1 GAGAACCGCGTTGCGAA-TTT
*
1364244 GGAGAATCGCGTTGCGAATTT
1 -GAGAACCGCGTTGCGAATTT
*
1364265 GAAAACCGCGTTGCG
1 GAGAACCGCGTTGCG
1364280 TGTTTACCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.42
21 16 0.52
22 2 0.06
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (20 bp):
GAGAACCGCGTTGCGAATTT
Found at i:1364276 original size:20 final size:22
Alignment explanation
Indices: 1364227--1364279 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
1364217 GATCTTAGAG
*
1364227 AACCGCGTTGC-AATTTTGGAG
1 AACCGCGTTGCGAATTTTGGAA
*
1364248 AATCGCGTTGCGAA-TTT-GAA
1 AACCGCGTTGCGAATTTTGGAA
1364268 AACCGCGTTGCG
1 AACCGCGTTGCG
1364280 TGTTTACCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 13 0.46
21 13 0.46
22 2 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (22 bp):
AACCGCGTTGCGAATTTTGGAA
Found at i:1364278 original size:112 final size:111
Alignment explanation
Indices: 1364035--1364497 Score: 705
Period size: 111 Copynumber: 4.2 Consensus size: 111
1364025 TTTCGCAACA
*
1364035 CGAATTTGAAAACCGCGTTGC-TGGTTTACATATATCGGTAATTAGCGTTGCGAAAACAAAATTC
1 CGAATTTGAAAACCGCGTTGCGT-GTTTACCTATATCGGTAATTAGCGTTGCGAAAACAAAATTC
*
1364099 GCGTTGCGAATTTGAAAACCGCGTTGCGATTTTGGAGAATCGCGTTG
65 GCATTGCGAATTTGAAAACCGCGTTGCGATTTTGGAGAATCGCGTTG
** * *
1364146 CGAATTTGAAAAATGAGTTGCGTGTTTACCTATATCGGTAATTAGAGTTGCGAAAACAAAATTCG
1 CGAATTTGAAAACCGCGTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACAAAATTCG
* *
1364211 CATTGCG-ATCTTAGAGAACCGCGTTGCAATTTTGGAGAATCGCGTTG
66 CATTGCGAAT-TT-GAAAACCGCGTTGCGATTTTGGAGAATCGCGTTG
*
1364258 CGAATTTGAAAACCGCGTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACGAAATTCG
1 CGAATTTGAAAACCGCGTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACAAAATTCG
* **
1364323 CATTGCGAATTTAAAAACCGCGTTTTGATTTTGGAGAATCGCGTTG
66 CATTGCGAATTTGAAAACCGCGTTGCGATTTTGGAGAATCGCGTTG
* * * * *
1364369 CTAATTTGAAAACTGAGTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACGAAATTCA
1 CGAATTTGAAAACCGCGTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACAAAATTCG
* **
1364434 CGTTGCGAATTTGAAAACCGCGTTGCGATTTTGGAGAATCATGTTG
66 CATTGCGAATTTGAAAACCGCGTTGCGATTTTGGAGAATCGCGTTG
1364480 CGAATTTGAAAACCGCGT
1 CGAATTTGAAAACCGCGT
1364498 CGCGAATTTG
Statistics
Matches: 317, Mismatches: 31, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
110 2 0.01
111 211 0.67
112 102 0.32
113 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (111 bp):
CGAATTTGAAAACCGCGTTGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACAAAATTCG
CATTGCGAATTTGAAAACCGCGTTGCGATTTTGGAGAATCGCGTTG
Found at i:1364423 original size:223 final size:222
Alignment explanation
Indices: 1364035--1364497 Score: 741
Period size: 223 Copynumber: 2.1 Consensus size: 222
1364025 TTTCGCAACA
1364035 CGAATTTGAAAACCGCGTTGCTGGTTTACATATATCGGTAATTAGCGTTGCGAAAACAAAATTCG
1 CGAATTTGAAAACCGCGTTGCTGGTTTACATATATCGGTAATTAGCGTTGCGAAAACAAAATTCG
* *
1364100 CGTTGCGAATTTGAAAACCGCGTTGCGATTTTGGAGAATCGCGTTGCGAATTTGAAAAATGAGTT
66 CATTGCGAATTTAAAAACCGCGTTGCGATTTTGGAGAATCGCGTTGCGAATTTGAAAAATGAGTT
* *
1364165 GCGTGTTTACCTATATCGGTAATTAGAGTTGCGAAAACAAAATTCGCATTGCG-ATCTTAGAGAA
131 GCGTGTTTACCTATATCGGTAATTAGAGTTGCGAAAACAAAATTCACATTGCGAAT-TT-GAAAA
*
1364229 CCGCGTTGCAATTTTGGAGAATCGCGTTG
194 CCGCGTTGCAATTTTGGAGAATCACGTTG
* *
1364258 CGAATTTGAAAACCGCGTTGC-GTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACGAAATTC
1 CGAATTTGAAAACCGCGTTGCTG-GTTTACATATATCGGTAATTAGCGTTGCGAAAACAAAATTC
** * *
1364322 GCATTGCGAATTTAAAAACCGCGTTTTGATTTTGGAGAATCGCGTTGCTAATTTGAAAACTGAGT
65 GCATTGCGAATTTAAAAACCGCGTTGCGATTTTGGAGAATCGCGTTGCGAATTTGAAAAATGAGT
* * *
1364387 TGCGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACGAAATTCACGTTGCGAATTTGAAAAC
130 TGCGTGTTTACCTATATCGGTAATTAGAGTTGCGAAAACAAAATTCACATTGCGAATTTGAAAAC
* *
1364452 CGCGTTGCGATTTTGGAGAATCATGTTG
195 CGCGTTGCAATTTTGGAGAATCACGTTG
1364480 CGAATTTGAAAACCGCGT
1 CGAATTTGAAAACCGCGT
1364498 CGCGAATTTG
Statistics
Matches: 222, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
222 49 0.22
223 171 0.77
224 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (222 bp):
CGAATTTGAAAACCGCGTTGCTGGTTTACATATATCGGTAATTAGCGTTGCGAAAACAAAATTCG
CATTGCGAATTTAAAAACCGCGTTGCGATTTTGGAGAATCGCGTTGCGAATTTGAAAAATGAGTT
GCGTGTTTACCTATATCGGTAATTAGAGTTGCGAAAACAAAATTCACATTGCGAATTTGAAAACC
GCGTTGCAATTTTGGAGAATCACGTTG
Found at i:1364522 original size:20 final size:20
Alignment explanation
Indices: 1364434--1364523 Score: 99
Period size: 20 Copynumber: 4.5 Consensus size: 20
1364424 ACGAAATTCA
1364434 CGTTGCGAATTTGAAAACCG
1 CGTTGCGAATTTGAAAACCG
* * * *
1364454 CGTTGCGATTTTGGAGAATCA
1 CGTTGCGAATTT-GAAAACCG
*
1364475 TGTTGCGAATTTGAAAACCG
1 CGTTGCGAATTTGAAAACCG
* *
1364495 CGTCGCGAATTTGAAAACTG
1 CGTTGCGAATTTGAAAACCG
*
1364515 TGTTGCGAA
1 CGTTGCGAA
1364524 ACTGGTATTC
Statistics
Matches: 55, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 40 0.73
21 15 0.27
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.29
Consensus pattern (20 bp):
CGTTGCGAATTTGAAAACCG
Found at i:1368463 original size:33 final size:33
Alignment explanation
Indices: 1368426--1368494 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
1368416 TGTTCCGTGA
*
1368426 ACGGAGGGTGGGCGAAAAATAAGGGGTCAATGG
1 ACGGAGGGTGGACGAAAAATAAGGGGTCAATGG
* *
1368459 ACGGAGGGTGGACGGATAATAAGGGGTCAATGG
1 ACGGAGGGTGGACGAAAAATAAGGGGTCAATGG
1368492 ACG
1 ACG
1368495 AAATATGATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.32, C:0.10, G:0.45, T:0.13
Consensus pattern (33 bp):
ACGGAGGGTGGACGAAAAATAAGGGGTCAATGG
Found at i:1368632 original size:21 final size:20
Alignment explanation
Indices: 1368603--1368641 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1368593 TTGAACTAGG
1368603 GTTTAAAATTTAGATTTTAGT
1 GTTTAAAATTTA-ATTTTAGT
*
1368624 GTTTTAAATTTAATTTTA
1 GTTTAAAATTTAATTTTA
1368642 AATCTTACAT
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:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (20 bp):
GTTTAAAATTTAATTTTAGT
Found at i:1374850 original size:18 final size:19
Alignment explanation
Indices: 1374808--1374858 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 19
1374798 TTTAGTTCAC
1374808 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAG-G
* *
1374828 GGAATGTGAGATTATCA-G
1 GGAATGTAAGATTACCAGG
1374846 GGAA--TAAGATTAC
1 GGAATGTAAGATTAC
1374859 TGGAAATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 7 0.26
18 5 0.19
20 15 0.56
ACGTcount: A:0.37, C:0.08, G:0.29, T:0.25
Consensus pattern (19 bp):
GGAATGTAAGATTACCAGG
Found at i:1374959 original size:14 final size:14
Alignment explanation
Indices: 1374940--1374968 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1374930 AAAGATTATT
1374940 AGAATGTATATTTG
1 AGAATGTATATTTG
1374954 AGAATGTATATTTG
1 AGAATGTATATTTG
1374968 A
1 A
1374969 CCAAATTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (14 bp):
AGAATGTATATTTG
Found at i:1375020 original size:22 final size:22
Alignment explanation
Indices: 1374995--1375051 Score: 114
Period size: 22 Copynumber: 2.6 Consensus size: 22
1374985 ATATATTTGT
1374995 TTTTTTTTTACAAGGAATATAA
1 TTTTTTTTTACAAGGAATATAA
1375017 TTTTTTTTTACAAGGAATATAA
1 TTTTTTTTTACAAGGAATATAA
1375039 TTTTTTTTTACAA
1 TTTTTTTTTACAA
1375052 AATTGAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.54
Consensus pattern (22 bp):
TTTTTTTTTACAAGGAATATAA
Found at i:1377013 original size:23 final size:24
Alignment explanation
Indices: 1376969--1377013 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
1376959 TGGTTCATGT
* * *
1376969 TCGAGTTTGAGTTTGAGGTTTTAA
1 TCGAGTTTAAGTTTAAGATTTTAA
1376993 TCGAG-TTAAGTTTAAGATTTT
1 TCGAGTTTAAGTTTAAGATTTT
1377014 TTTTTCATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.47
Consensus pattern (24 bp):
TCGAGTTTAAGTTTAAGATTTTAA
Found at i:1378408 original size:19 final size:18
Alignment explanation
Indices: 1378386--1378429 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
1378376 TTTTTATATA
1378386 TTTTA-TAGTATTATTAGTT
1 TTTTACTAGTATT-TTA-TT
1378405 TTTTATCTAGTATTTTATT
1 TTTTA-CTAGTATTTTATT
1378424 TTTTAC
1 TTTTAC
1378430 ATATATGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 1 0.04
19 12 0.52
20 3 0.13
21 7 0.30
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.66
Consensus pattern (18 bp):
TTTTACTAGTATTTTATT
Found at i:1378636 original size:24 final size:23
Alignment explanation
Indices: 1378591--1378641 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
1378581 TTACCTTTTT
1378591 TTTATTTCTTGTTATTTAATTTA
1 TTTATTTCTTGTTATTTAATTTA
*
1378614 TTTATTT-TTGTCGTATTTTATTTA
1 TTTATTTCTTGT--TATTTAATTTA
1378638 TTTA
1 TTTA
1378642 CATTTGTTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 4 0.16
23 7 0.28
24 14 0.56
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.71
Consensus pattern (23 bp):
TTTATTTCTTGTTATTTAATTTA
Found at i:1378647 original size:24 final size:24
Alignment explanation
Indices: 1378603--1378648 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1378593 TATTTCTTGT
**
1378603 TATTTAATTTATTTATTTTTGTCG
1 TATTTAATTTATTTACATTTGTCG
*
1378627 TATTTTATTTATTTACATTTGT
1 TATTTAATTTATTTACATTTGT
1378649 TCCTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (24 bp):
TATTTAATTTATTTACATTTGTCG
Found at i:1384404 original size:22 final size:22
Alignment explanation
Indices: 1384376--1384440 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
1384366 AATATTAATA
1384376 GGTACCGATACCCCTATGAATT
1 GGTACCGATACCCCTATGAATT
1384398 GGTACCGATACCCCTATGAATT
1 GGTACCGATACCCCTATGAATT
*
1384420 GGTACCGATACTCCTATGAAT
1 GGTACCGATACCCCTATGAAT
1384441 GCTCAAACAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (22 bp):
GGTACCGATACCCCTATGAATT
Found at i:1386128 original size:22 final size:21
Alignment explanation
Indices: 1386094--1386134 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1386084 ATAATTATTT
1386094 AAAAAATTAAATAAAAATATC
1 AAAAAATTAAATAAAAATATC
*
1386115 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
1386135 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATATC
Found at i:1386310 original size:19 final size:19
Alignment explanation
Indices: 1386286--1386361 Score: 80
Period size: 19 Copynumber: 3.8 Consensus size: 19
1386276 ATTCGCGTTG
1386286 CATTTCGCGTTGCGATTTC
1 CATTTCGCGTTGCGATTTC
*
1386305 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGAT--TTC
* ** *
1386326 AAAATCGCGTTGGGATTTTC
1 CATTTCGCGTTGCGA-TTTC
1386346 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1386362 AGTCTGCAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
19 17 0.39
20 13 0.30
21 13 0.30
22 1 0.02
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (19 bp):
CATTTCGCGTTGCGATTTC
Found at i:1386378 original size:41 final size:42
Alignment explanation
Indices: 1386290--1386406 Score: 147
Period size: 41 Copynumber: 2.9 Consensus size: 42
1386280 GCGTTGCATT
1386290 TCGCGTTGCGA-TTTCCATTTCGCGTTGCGATAGT-TGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTGAAAA
* *
1386330 TCGCGTTGGGATTTTCCATTTCGCGTTGCGATAGTCTG-CAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTGAAAA
*
1386371 T-GTCGTTGCGATTTTCCAAATT--CGTTGCGATAGTCT
1 TCG-CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCT
1386407 ACAGTTGTTG
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
40 25 0.36
41 39 0.57
42 5 0.07
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.38
Consensus pattern (42 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTGAAAA
Found at i:1386421 original size:22 final size:22
Alignment explanation
Indices: 1386392--1386445 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
1386382 TTTTCCAAAT
1386392 TCGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
* *
1386414 TTGTTGCGAAAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
1386436 TCGTTGCGAT
1 TCGTTGCGAT
1386446 TTTCCAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.37
Consensus pattern (22 bp):
TCGTTGCGATAGTCTACAGTTG
Found at i:1386555 original size:6 final size:6
Alignment explanation
Indices: 1386544--1386568 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1386534 GAAGACACGT
1386544 ATTACC ATTACC ATTACC ATTACC A
1 ATTACC ATTACC ATTACC ATTACC A
1386569 CGACCACGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (6 bp):
ATTACC
Found at i:1386574 original size:6 final size:6
Alignment explanation
Indices: 1386565--1386614 Score: 93
Period size: 6 Copynumber: 8.5 Consensus size: 6
1386555 CATTACCATT
1386565 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1386612 ACC
1 ACC
1386615 CGAGACGGAC
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.11
6 39 0.89
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1387115 original size:6 final size:6
Alignment explanation
Indices: 1387104--1387142 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
1387094 TCTCGTCTCG
1387104 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1387143 AATACGTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.15, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1387245 original size:19 final size:19
Alignment explanation
Indices: 1387221--1387287 Score: 134
Period size: 19 Copynumber: 3.5 Consensus size: 19
1387211 TTTTTTAACT
1387221 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
1387240 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
1387259 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
1387278 ATCGCAACGA
1 ATCGCAACGA
1387288 CAACTGTAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.19
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:1387399 original size:19 final size:20
Alignment explanation
Indices: 1387343--1387443 Score: 60
Period size: 22 Copynumber: 4.9 Consensus size: 20
1387333 TTTCGTAACG
1387343 AATTTGGAAAATCGCAACGAC
1 AATTTGGAAAATCGCAAC-AC
* * **
1387364 AACTGTAGACTATCGCAAC-C
1 AA-TTTGGAAAATCGCAACAC
1387384 AATTTGGAAAATCGCAACGAC
1 AATTTGGAAAATCGCAAC-AC
* * ** *
1387405 AACTGTAGACTATCGCAACGC
1 AA-TTTGGAAAATCGCAACAC
**
1387426 AAACTGGAAAATCGCAAC
1 AATTTGGAAAATCGCAAC
1387444 GCGATTTTCA
Statistics
Matches: 58, Mismatches: 18, Indels: 9
0.68 0.21 0.11
Matches are distributed among these distances:
19 12 0.21
20 14 0.24
21 8 0.14
22 24 0.41
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (20 bp):
AATTTGGAAAATCGCAACAC
Found at i:1387400 original size:41 final size:42
Alignment explanation
Indices: 1387218--1387444 Score: 234
Period size: 41 Copynumber: 5.8 Consensus size: 42
1387208 TCTTTTTTTA
* *
1387218 ACTATCGCAACG-AATTTGGAAAATCGCAACG--AA-TTTGG
1 ACTATCGCAACGCAATTTGGAAAATCGCAACGACAACTGTAG
**
1387256 AAAATCGCAACG-AATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGCAATTTGGAAAATCGCAACGACAACTGTAG
* * * *
1387297 ACTATCGCAACGTGAA-CTGGAAAATCGCAATG-CGA-T-T--
1 ACTATCGCAACG-CAATTTGGAAAATCGCAACGACAACTGTAG
*
1387334 --T-TCGTAACG-AATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGCAATTTGGAAAATCGCAACGACAACTGTAG
1387372 ACTATCGCAAC-CAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGCAATTTGGAAAATCGCAACGACAACTGTAG
**
1387413 ACTATCGCAACGCAAACTGGAAAATCGCAACG
1 ACTATCGCAACGCAATTTGGAAAATCGCAACG
1387445 CGATTTTCAA
Statistics
Matches: 157, Mismatches: 16, Indels: 28
0.78 0.08 0.14
Matches are distributed among these distances:
32 2 0.01
33 14 0.09
34 9 0.06
35 2 0.01
36 1 0.01
38 29 0.18
39 1 0.01
40 4 0.03
41 61 0.39
42 32 0.20
43 2 0.01
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.20
Consensus pattern (42 bp):
ACTATCGCAACGCAATTTGGAAAATCGCAACGACAACTGTAG
Found at i:1387405 original size:116 final size:113
Alignment explanation
Indices: 1387226--1387452 Score: 355
Period size: 116 Copynumber: 2.0 Consensus size: 113
1387216 TAACTATCGC
* * *
1387226 AACGAATTTGGAAAATCGCAACGAATTTGGAAAATCGCAACGAATTTGGAAAATCGCAACGACAA
1 AACGAATTTGGAAAATCGCAACGAATGTAGAAAATCGCAACCAATTTGGAAAATCGCAACGACAA
** *
1387291 CTGTAGACTATCGCAACGTGAACTGGAAAATCGCAATGCGATTTTCGT
66 CTGTAGACTATCGCAACGCAAACTGGAAAATCGCAACGCGATTTTCGT
**
1387339 AACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACCAATTTGGAAAATCGCAACGA
1 AACGAATTTGGAAAATCGCAACG--AA-TGTAGAAAATCGCAACCAATTTGGAAAATCGCAACGA
1387404 CAACTGTAGACTATCGCAACGCAAACTGGAAAATCGCAACGCGATTTTC
63 CAACTGTAGACTATCGCAACGCAAACTGGAAAATCGCAACGCGATTTTC
1387453 AATTATCGCA
Statistics
Matches: 103, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
113 23 0.22
115 2 0.02
116 78 0.76
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (113 bp):
AACGAATTTGGAAAATCGCAACGAATGTAGAAAATCGCAACCAATTTGGAAAATCGCAACGACAA
CTGTAGACTATCGCAACGCAAACTGGAAAATCGCAACGCGATTTTCGT
Found at i:1387431 original size:22 final size:22
Alignment explanation
Indices: 1387353--1387424 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
1387343 AATTTGGAAA
1387353 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
1387375 ATCGCAAC--CAA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
1387394 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
1387416 ATCGCAACG
1 ATCGCAACG
1387425 CAAACTGGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 12 0.31
20 3 0.08
21 3 0.08
22 21 0.54
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:1389486 original size:27 final size:26
Alignment explanation
Indices: 1389419--1389490 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 26
1389409 TTCATATATA
1389419 TTAATTTAAAAAATACTTTTAGATTAAC
1 TTAATTT-AAAAATA-TTTTAGATTAAC
* **
1389447 TT-A-TTAAATATATTTTCTTATTAAC
1 TTAATTTAAAAATATTTT-AGATTAAC
1389472 TTAATTTAAAAATATTTTA
1 TTAATTTAAAAATATTTTA
1389491 TTTTTATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
24 4 0.11
25 14 0.39
26 3 0.08
27 13 0.36
28 2 0.06
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (26 bp):
TTAATTTAAAAATATTTTAGATTAAC
Found at i:1396656 original size:21 final size:21
Alignment explanation
Indices: 1396539--1396656 Score: 80
Period size: 21 Copynumber: 5.7 Consensus size: 21
1396529 ACGCGAAATA
**
1396539 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
1396559 ATAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
*
1396579 AAAATCGCAACGCGATTCTT-A
1 AAAATCGCAACGCGATT-TTCC
* ** *
1396600 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
1396621 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
1396642 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
1396657 ATATGAAAAT
Statistics
Matches: 72, Mismatches: 22, Indels: 7
0.71 0.22 0.07
Matches are distributed among these distances:
19 1 0.01
20 24 0.33
21 45 0.62
22 2 0.03
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.22
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:1396705 original size:20 final size:20
Alignment explanation
Indices: 1396682--1396872 Score: 215
Period size: 20 Copynumber: 9.6 Consensus size: 20
1396672 CACGAACACA
1396682 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* *
1396702 TAAATCGCAACGTGTATCTG
1 TAAATCGCAACGCGTATCCG
**
1396722 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACGCGTATCCG
*
1396742 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
1396762 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
1396782 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* * *
1396802 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
1396822 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* * *
1396842 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
1396862 TAAATCACAAC
1 TAAATCGCAAC
1396873 ACTGAAATTT
Statistics
Matches: 145, Mismatches: 22, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
19 1 0.01
20 144 0.99
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:1396707 original size:40 final size:40
Alignment explanation
Indices: 1396643--1396874 Score: 186
Period size: 40 Copynumber: 5.8 Consensus size: 40
1396633 CGATTTTCCA
* ** * *
1396643 AAATCGCAACGCGAATATGAAAATCGCAACACG-AACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACACGTAAC-CGT
** * *
1396683 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCTGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACACGTAACCGT
** ** *
1396723 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACACGTAACCGT
*
1396763 ATATCGCAACGCGTATCCGTAAATCGC-A-ACGATAATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACACG-TAA-CCGT
* * *
1396803 AAATCGCAACGAGAATCTGTAAATCGC-A-ACGATAATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACACG-TAA-CCGT
* * * *
1396843 AAATCGCAACGAGAATCTGTAAATCACAACAC
1 AAATCGCAACGCGTATCCGTAAATCGCAACAC
1396875 TGAAATTTTG
Statistics
Matches: 163, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
38 2 0.01
39 3 0.02
40 153 0.94
41 3 0.02
42 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACACGTAACCGT
Found at i:1396727 original size:60 final size:59
Alignment explanation
Indices: 1396643--1396852 Score: 197
Period size: 60 Copynumber: 3.5 Consensus size: 59
1396633 CGATTTTCCA
** * *
1396643 AAATCGCAACGCGAATATGAAAATCGCAACACGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACACGAAC-CGTAAATCGCAACGCGTATCCGT
* * * * *** *
1396703 AAATCGCAACGTGTATCTGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACACG-AACCGTAAATCGCAACGCGTATCCGT
* * * * * *
1396763 ATATCGCAACGCGTATCCGTAAATCGCAACGA-TAATCCGTAAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGTAAATCGCAAC-ACGAA-CCGTAAATCGCAACGCGTATCCGT
**
1396823 AAATCGCAACGATAATCCGTAAATCGCAAC
1 AAATCGCAACGCGAATCCGTAAATCGCAAC
1396853 GAGAATCTGT
Statistics
Matches: 121, Mismatches: 26, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
59 1 0.01
60 119 0.98
61 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (59 bp):
AAATCGCAACGCGAATCCGTAAATCGCAACACGAACCGTAAATCGCAACGCGTATCCGT
Found at i:1397594 original size:24 final size:24
Alignment explanation
Indices: 1397555--1397601 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1397545 AAATTTGGTC
1397555 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1397579 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1397602 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1400131 original size:33 final size:33
Alignment explanation
Indices: 1400080--1400257 Score: 241
Period size: 33 Copynumber: 5.2 Consensus size: 33
1400070 CGGAAATTAC
*
1400080 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
*
1400113 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGA-GAAAATCGCAATGC-GAAATGAA
*
1400147 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
1400180 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAA
* *
1400218 AATCGCAACGAGAGAATCGCAATGCGAAATTAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
1400251 AATCGCA
1 AATCGCA
1400258 TTGCGATTCT
Statistics
Matches: 130, Mismatches: 7, Indels: 16
0.85 0.05 0.10
Matches are distributed among these distances:
32 1 0.01
33 64 0.49
34 30 0.23
35 3 0.02
36 2 0.02
37 1 0.01
38 29 0.22
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCGCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:1400185 original size:19 final size:19
Alignment explanation
Indices: 1400094--1400263 Score: 181
Period size: 19 Copynumber: 9.7 Consensus size: 19
1400084 GCAACGAGAG
1400094 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1400113 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1400127 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1400147 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1400161 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1400180 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1400199 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1400218 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
1400232 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
1400251 AATCGCATTGCGA
1 AATCGCAATGCGA
1400264 TTCTCTCGTT
Statistics
Matches: 127, Mismatches: 8, Indels: 32
0.76 0.05 0.19
Matches are distributed among these distances:
14 32 0.25
15 2 0.02
16 5 0.04
17 4 0.03
18 3 0.02
19 68 0.54
20 13 0.10
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1400246 original size:71 final size:71
Alignment explanation
Indices: 1400061--1400263 Score: 299
Period size: 67 Copynumber: 2.9 Consensus size: 71
1400051 GCATTTGACT
** * * *
1400061 ATCGCAACACGGAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C--
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
1400122 ATGAAA
66 ATGAAA
1400128 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCG-
1400193 AATGAAA
65 AATGAAA
* *
1400200 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCATTGCGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
1400264 TTCTCTCGTT
Statistics
Matches: 124, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
67 55 0.44
69 1 0.01
70 1 0.01
71 51 0.41
72 16 0.13
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (71 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
ATGAAA
Found at i:1400366 original size:52 final size:53
Alignment explanation
Indices: 1400253--1400369 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
1400243 GAAATTAAAA
1400253 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1400306 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1400358 TCGCATTGCGAT
1 TCGCATTGCGAT
1400370 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:1400377 original size:19 final size:19
Alignment explanation
Indices: 1400272--1400369 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1400262 GATTCTCTCG
1400272 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1400292 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1400311 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1400325 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1400344 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1400363 TTGCGAT
1 TTGCGAT
1400370 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1400495 original size:14 final size:14
Alignment explanation
Indices: 1400476--1400512 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1400466 CATCAATTAC
1400476 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1400490 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1400504 ACAAATCAA
1 ACAAATCAA
1400513 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1404413 original size:28 final size:29
Alignment explanation
Indices: 1404353--1404413 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
1404343 GTTGAACATT
* * *
1404353 TTACACAAATAGCACCCTTTTTAAAATAT
1 TTACACAAATAGCACCCATTTCAAAATAA
* *
1404382 TTACA-AAATAGCACCCATTTCGAATTAA
1 TTACACAAATAGCACCCATTTCAAAATAA
1404410 TTAC
1 TTAC
1404414 TAGAATAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (29 bp):
TTACACAAATAGCACCCATTTCAAAATAA
Found at i:1404442 original size:29 final size:29
Alignment explanation
Indices: 1404402--1404510 Score: 164
Period size: 29 Copynumber: 3.8 Consensus size: 29
1404392 GCACCCATTT
* *
1404402 CGAATTAATTACTAGAATAGAACCAAAAC
1 CGAATTATTTACCAGAATAGAACCAAAAC
* * *
1404431 CAAAATATTTACCAGAATAGCACCAAAAC
1 CGAATTATTTACCAGAATAGAACCAAAAC
*
1404460 CGAATTATTTACCAGAATAGCACCAAAAC
1 CGAATTATTTACCAGAATAGAACCAAAAC
1404489 CGAATTATTTACCAGAATAGAA
1 CGAATTATTTACCAGAATAGAA
1404511 TCGATCAACG
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 72 1.00
ACGTcount: A:0.49, C:0.20, G:0.10, T:0.21
Consensus pattern (29 bp):
CGAATTATTTACCAGAATAGAACCAAAAC
Found at i:1404466 original size:58 final size:58
Alignment explanation
Indices: 1404375--1404508 Score: 171
Period size: 58 Copynumber: 2.3 Consensus size: 58
1404365 CACCCTTTTT
* * *** *
1404375 AAAATATTTA-CAAAATAGCACCCATTTCGAATTAATTACTAGAATAGAACCAAAACC
1 AAAATATTTACCAGAATAGCACCAAAACCGAATTAATTACCAGAATAGAACCAAAACC
* *
1404432 AAAATATTTACCAGAATAGCACCAAAACCGAATTATTTACCAGAATAGCACCAAAACC
1 AAAATATTTACCAGAATAGCACCAAAACCGAATTAATTACCAGAATAGAACCAAAACC
* *
1404490 GAATTATTTACCAGAATAG
1 AAAATATTTACCAGAATAG
1404509 AATCGATCAA
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
57 10 0.15
58 56 0.85
ACGTcount: A:0.48, C:0.20, G:0.09, T:0.23
Consensus pattern (58 bp):
AAAATATTTACCAGAATAGCACCAAAACCGAATTAATTACCAGAATAGAACCAAAACC
Found at i:1411829 original size:28 final size:28
Alignment explanation
Indices: 1411769--1411841 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
1411759 GTTGAACATT
* * *
1411769 TTACACAAATAGCACCCTTTTTAAAATAT
1 TTACA-AAATAGCACCCATTTCAAAATAA
* *
1411798 TTACAAAATAGCACCCATTTCGAATTAA
1 TTACAAAATAGCACCCATTTCAAAATAA
*
1411826 TTACTAGAATAGCACC
1 TTAC-AAAATAGCACC
1411842 AAAACCAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
28 22 0.59
29 15 0.41
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (28 bp):
TTACAAAATAGCACCCATTTCAAAATAA
Found at i:1411858 original size:29 final size:29
Alignment explanation
Indices: 1411818--1411923 Score: 142
Period size: 29 Copynumber: 3.7 Consensus size: 29
1411808 GCACCCATTT
* *
1411818 CGAATTAATTACTAGAATAGCACCAAAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
* * *
1411847 CAAAATATTTACCAGTATAGCACCAAAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
* *
1411876 TGAATTATTTACCAGAATAACACCAAAA-
1 CGAATTATTTACCAGAATAGCACCAAAAC
1411904 CGAATTATTTACCAGAATAG
1 CGAATTATTTACCAGAATAG
1411924 TACCGATCAA
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
28 18 0.28
29 47 0.72
ACGTcount: A:0.47, C:0.20, G:0.09, T:0.24
Consensus pattern (29 bp):
CGAATTATTTACCAGAATAGCACCAAAAC
Found at i:1411970 original size:18 final size:18
Alignment explanation
Indices: 1411947--1411987 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1411937 TCAACGATCG
*
1411947 GGTCGGGTCAACGGGTCA
1 GGTCGGGTAAACGGGTCA
1411965 GGTCGGGTAAACGGGTCA
1 GGTCGGGTAAACGGGTCA
1411983 GGTCG
1 GGTCG
1411988 TGACCGGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.20, G:0.46, T:0.17
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCA
Found at i:1413466 original size:13 final size:13
Alignment explanation
Indices: 1413448--1413474 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1413438 TTTTTAATGA
1413448 GAAAGCTGGCTAT
1 GAAAGCTGGCTAT
1413461 GAAAGCTGGCTAT
1 GAAAGCTGGCTAT
1413474 G
1 G
1413475 GAAGATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.33, T:0.22
Consensus pattern (13 bp):
GAAAGCTGGCTAT
Found at i:1420532 original size:2 final size:2
Alignment explanation
Indices: 1420527--1420552 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1420517 TGTGTGTGTG
1420527 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1420553 ACCTGAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1427654 original size:36 final size:36
Alignment explanation
Indices: 1427607--1427677 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
1427597 GCTTATTTTT
1427607 TGGGAACCGGAACCTGTTGC-ACCGATTCCTAAAAAA
1 TGGGAACCGGAACCTGTT-CAACCGATTCCTAAAAAA
*
1427643 TGGGAACCGGAACCTGTTCAACCGGTTCCTAAAAA
1 TGGGAACCGGAACCTGTTCAACCGATTCCTAAAAA
1427678 TTGAGATCCT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
35 1 0.03
36 32 0.97
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.20
Consensus pattern (36 bp):
TGGGAACCGGAACCTGTTCAACCGATTCCTAAAAAA
Found at i:1427692 original size:36 final size:36
Alignment explanation
Indices: 1427610--1427692 Score: 105
Period size: 36 Copynumber: 2.3 Consensus size: 36
1427600 TATTTTTTGG
*
1427610 GAACCGGAACCTGTTGCACCGATTCCTAAAAAATGG
1 GAACCGGAACCTGTTGCACCGATTCCTAAAAAATGA
* *
1427646 GAACCGGAACCTGTT-CAACCGGTTCCTAAAAATTGA
1 GAACCGGAACCTGTTGC-ACCGATTCCTAAAAAATGA
* *
1427682 GATCCTGAACC
1 GAACCGGAACC
1427693 GGAACTTGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
35 1 0.02
36 40 0.98
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (36 bp):
GAACCGGAACCTGTTGCACCGATTCCTAAAAAATGA
Found at i:1429790 original size:22 final size:21
Alignment explanation
Indices: 1429765--1429807 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
1429755 AAAAATCAAT
*
1429765 TTAAAATTTATCTGATAAATAA
1 TTAAAAGTTATCT-ATAAATAA
* *
1429787 TTAATAGTTATCTATTAATAA
1 TTAAAAGTTATCTATAAATAA
1429808 CTTATTTGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (21 bp):
TTAAAAGTTATCTATAAATAA
Found at i:1431341 original size:22 final size:22
Alignment explanation
Indices: 1431311--1431354 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1431301 TTTAAACATA
1431311 TAAACGAACGA-TAAACAAACAC
1 TAAACGAAC-ATTAAACAAACAC
* *
1431333 TAAATGAACATTAAACGAACAC
1 TAAACGAACATTAAACAAACAC
1431355 ATTCATGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.57, C:0.20, G:0.09, T:0.14
Consensus pattern (22 bp):
TAAACGAACATTAAACAAACAC
Found at i:1431411 original size:24 final size:24
Alignment explanation
Indices: 1431384--1431429 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1431374 ACATATAAAT
*
1431384 GAATATATTCACGAACATTAAAAC
1 GAATATATTCACGAACAATAAAAC
* *
1431408 GAATATGTTCGCGAACAATAAA
1 GAATATATTCACGAACAATAAA
1431430 TAAACGAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.24
Consensus pattern (24 bp):
GAATATATTCACGAACAATAAAAC
Found at i:1435848 original size:23 final size:22
Alignment explanation
Indices: 1435820--1435878 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
1435810 TGTTTTAATT
1435820 TAATATTATTTTAAATAAATAAA
1 TAATATTATTTTAAA-AAATAAA
* *
1435843 TAATATAATTTTAAAAAATAAC
1 TAATATTATTTTAAAAAATAAA
1435865 TAA-A-TATTTTAAAA
1 TAATATTATTTTAAAA
1435879 TATTTTCATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.27
21 1 0.03
22 9 0.27
23 14 0.42
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TAATATTATTTTAAAAAATAAA
Found at i:1435863 original size:18 final size:20
Alignment explanation
Indices: 1435826--1435878 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 20
1435816 AATTTAATAT
*
1435826 TATTTTAAATAAATAAATAATA
1 TATTTTAAA-AAATAACTAA-A
1435848 TAATTTTAAAAAATAACTAAA
1 T-ATTTTAAAAAATAACTAAA
1435869 TATTTTAAAA
1 TATTTTAAAA
1435879 TATTTTCATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 9 0.31
21 2 0.07
22 10 0.34
23 8 0.28
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TATTTTAAAAAATAACTAAA
Found at i:1436666 original size:19 final size:18
Alignment explanation
Indices: 1436642--1436700 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
1436632 AGAATTGCTC
1436642 TTATTTTAATAACTCAAAT
1 TTATTTTAATAACT-AAAT
*
1436661 TTATTTTATTAA-T--AT
1 TTATTTTAATAACTAAAT
*
1436676 TT-TATTAATAACTAAAAT
1 TTATTTTAATAACT-AAAT
1436694 TTATTTT
1 TTATTTT
1436701 GTTAATATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 7 0.23
15 5 0.16
18 5 0.16
19 14 0.45
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (18 bp):
TTATTTTAATAACTAAAT
Found at i:1436678 original size:11 final size:11
Alignment explanation
Indices: 1436662--1436745 Score: 50
Period size: 11 Copynumber: 7.6 Consensus size: 11
1436652 AACTCAAATT
1436662 TATTTTATTAA
1 TATTTTATTAA
1436673 TATTTTATTAA
1 TATTTTATTAA
** *
1436684 TA-ACTA-AAA
1 TATTTTATTAA
*
1436693 TTTATTTTGTTAA
1 --TATTTTATTAA
1436706 TATTTTATTAA
1 TATTTTATTAA
**
1436717 TAACTCATATT--
1 T-A-TTTTATTAA
1436728 TATTTTATTAA
1 TATTTTATTAA
1436739 TATTTTA
1 TATTTTA
1436746 ATAACTCAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 16
0.65 0.15 0.20
Matches are distributed among these distances:
9 7 0.13
10 3 0.06
11 34 0.64
12 2 0.04
13 7 0.13
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:1436686 original size:33 final size:33
Alignment explanation
Indices: 1436647--1436760 Score: 171
Period size: 33 Copynumber: 3.5 Consensus size: 33
1436637 TGCTCTTATT
1436647 TTAATAACTCAAATTTATTTTATTAATATTTTA
1 TTAATAACTCAAATTTATTTTATTAATATTTTA
* *
1436680 TTAATAACTAAAATTTATTTTGTTAATATTTTA
1 TTAATAACTCAAATTTATTTTATTAATATTTTA
*
1436713 TTAATAACTCATATTTATTTTATTAATA--TT-
1 TTAATAACTCAAATTTATTTTATTAATATTTTA
1436743 TTAATAACTCAAAGTTTA
1 TTAATAACTCAAA-TTTA
1436761 AATTACTTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
30 12 0.16
31 6 0.08
33 56 0.76
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (33 bp):
TTAATAACTCAAATTTATTTTATTAATATTTTA
Found at i:1438143 original size:34 final size:30
Alignment explanation
Indices: 1438105--1438173 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
1438095 TTGATATAAC
1438105 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
1438139 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
1438168 AATTTA
1 AATTTA
1438174 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:1438184 original size:29 final size:30
Alignment explanation
Indices: 1438114--1438173 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1438104 CAATTTAAGG
1438114 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1438145 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1438174 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1438280 original size:21 final size:20
Alignment explanation
Indices: 1438254--1438369 Score: 144
Period size: 21 Copynumber: 5.5 Consensus size: 20
1438244 AGGGTGTCAA
1438254 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
1438275 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
*
1438296 AGTACATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
1438317 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
* *
1438338 TAGTGCATCGATGCACCATGC
1 -AGTGCATCCATGCACCCTGC
1438359 AGTGCATCCAT
1 AGTGCATCCAT
1438370 ACACTCAAAC
Statistics
Matches: 85, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
19 4 0.05
20 10 0.12
21 55 0.65
22 13 0.15
23 3 0.04
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:1438461 original size:20 final size:20
Alignment explanation
Indices: 1438394--1438461 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
1438384 AATGCAATCA
*
1438394 GTGCATCGATGCATCGT-TCT
1 GTGCATCGATGCATCATGT-T
*
1438414 GTGCATCGATGCATCAAGGTT
1 GTGCATCGATGCATC-ATGTT
* *
1438435 ATGCATCGATGCATCCTGTT
1 GTGCATCGATGCATCATGTT
1438455 GTGCATC
1 GTGCATC
1438462 CATGTACGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 24 0.60
21 15 0.38
22 1 0.03
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (20 bp):
GTGCATCGATGCATCATGTT
Found at i:1441700 original size:34 final size:30
Alignment explanation
Indices: 1441662--1441730 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
1441652 TTGATATAAC
1441662 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
1441696 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
1441725 AATTTA
1 AATTTA
1441731 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:1441741 original size:29 final size:30
Alignment explanation
Indices: 1441671--1441730 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1441661 CAATTTAAGG
1441671 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1441702 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1441731 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1441836 original size:21 final size:20
Alignment explanation
Indices: 1441810--1441908 Score: 101
Period size: 21 Copynumber: 4.8 Consensus size: 20
1441800 AGGGTGTCAA
*
1441810 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCATGC
1441831 AGTGCATCCATGCATCCATGC
1 AGTGCATCCATGCA-CCATGC
* * *
1441852 AATGCATCCCTGCA-CTTGCAC
1 AGTGCATCCATGCACCATG--C
*
1441873 TAGTGCATCGATGCACCATGC
1 -AGTGCATCCATGCACCATGC
1441894 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
1441909 TCAAACACCG
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
19 3 0.05
20 14 0.22
21 33 0.52
22 11 0.17
23 3 0.05
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACCATGC
Found at i:1441955 original size:21 final size:21
Alignment explanation
Indices: 1441929--1442012 Score: 109
Period size: 21 Copynumber: 4.0 Consensus size: 21
1441919 AATGCAATCA
*
1441929 GTGCATCGATGCATCAAGGTT
1 GTGCATCGATGCATCAAGGCT
1441950 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCT
**
1441971 GTGCATCGATGCATC-CTGCT
1 GTGCATCGATGCATCAAGGCT
*
1441991 GTGCATCCATGCA-CGAAGGCT
1 GTGCATCGATGCATC-AAGGCT
1442012 G
1 G
1442013 CAACGGCTAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.02
20 15 0.27
21 39 0.71
ACGTcount: A:0.21, C:0.25, G:0.29, T:0.25
Consensus pattern (21 bp):
GTGCATCGATGCATCAAGGCT
Found at i:1442010 original size:41 final size:42
Alignment explanation
Indices: 1441929--1442012 Score: 109
Period size: 41 Copynumber: 2.0 Consensus size: 42
1441919 AATGCAATCA
* *
1441929 GTGCATCGATGCATCAAGGTTGTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCTGTGCATCCATGCATCAAGGCT
**
1441971 GTGCATCGATGCATC-CTGCTGTGCATCCATGCA-CGAAGGCT
1 GTGCATCGATGCATCAAGGCTGTGCATCCATGCATC-AAGGCT
1442012 G
1 G
1442013 CAACGGCTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
40 1 0.03
41 21 0.57
42 15 0.41
ACGTcount: A:0.21, C:0.25, G:0.29, T:0.25
Consensus pattern (42 bp):
GTGCATCGATGCATCAAGGCTGTGCATCCATGCATCAAGGCT
Found at i:1442154 original size:20 final size:22
Alignment explanation
Indices: 1442116--1442155 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1442106 TTTTAGTAGA
1442116 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
1442138 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
1442156 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:1443718 original size:19 final size:19
Alignment explanation
Indices: 1443694--1443763 Score: 122
Period size: 19 Copynumber: 3.7 Consensus size: 19
1443684 GGCAGACTTA
* *
1443694 GTGTATTGGTATATCCCAG
1 GTGTATCGGTACATCCCAG
1443713 GTGTATCGGTACATCCCAG
1 GTGTATCGGTACATCCCAG
1443732 GTGTATCGGTACATCCCAG
1 GTGTATCGGTACATCCCAG
1443751 GTGTATCGGTACA
1 GTGTATCGGTACA
1443764 CTAATTACAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (19 bp):
GTGTATCGGTACATCCCAG
Found at i:1444015 original size:15 final size:15
Alignment explanation
Indices: 1443991--1444027 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
1443981 AGTAAGGTTT
1443991 AAAA-TTGACATTTG
1 AAAACTTGACATTTG
1444005 AAAACTTGACATTTG
1 AAAACTTGACATTTG
1444020 AAAACTTG
1 AAAACTTG
1444028 GAGTAACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (15 bp):
AAAACTTGACATTTG
Found at i:1444814 original size:20 final size:20
Alignment explanation
Indices: 1444789--1444826 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1444779 GTACTGCTCA
*
1444789 TTACTGTTCATACAATATCG
1 TTACTGTTCACACAATATCG
1444809 TTACTGTTCACACAATAT
1 TTACTGTTCACACAATAT
1444827 ATGCACTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (20 bp):
TTACTGTTCACACAATATCG
Found at i:1451055 original size:31 final size:31
Alignment explanation
Indices: 1451020--1451125 Score: 142
Period size: 31 Copynumber: 3.4 Consensus size: 31
1451010 AGTTTTGAAA
*
1451020 ATAAC-AAATCGATCACTAATGTTATCAATTT
1 ATAACAAAAT-GATCACTAACGTTATCAATTT
*
1451051 ATAACAAAATAATCACTAACGTTATCAATTT
1 ATAACAAAATGATCACTAACGTTATCAATTT
* * * *
1451082 ATAACAAAATGATCGCCAACATTATCGATTT
1 ATAACAAAATGATCACTAACGTTATCAATTT
1451113 ATAACAAAATGAT
1 ATAACAAAATGAT
1451126 GATTTCACTA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 63 0.94
32 4 0.06
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (31 bp):
ATAACAAAATGATCACTAACGTTATCAATTT
Found at i:1451703 original size:16 final size:17
Alignment explanation
Indices: 1451674--1451720 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 17
1451664 AAAATATTTT
1451674 ATATATAATTAATATAAA
1 ATATATAA-TAATATAAA
*
1451692 ATATATAA-AATATAAT
1 ATATATAATAATATAAA
1451708 ATATATATATAAT
1 ATATATA-ATAAT
1451721 CGGGGAGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 14 0.54
17 1 0.04
18 11 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATATAATAATATAAA
Found at i:1455445 original size:31 final size:29
Alignment explanation
Indices: 1455382--1455455 Score: 87
Period size: 31 Copynumber: 2.5 Consensus size: 29
1455372 GTTGTATCGT
1455382 TTATACCACTGAACTTTTAATTTTGTCAA
1 TTATACCACTGAACTTTTAATTTTGTCAA
* *
1455411 TTATAGCACTGAAC-TTTGATTTTCGTTTCAA
1 TTATACCACTGAACTTTTAATTTT-G--TCAA
*
1455442 TTATACCATTGAAC
1 TTATACCACTGAAC
1455456 CGTTAAATCC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 8 0.21
29 14 0.37
31 16 0.42
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (29 bp):
TTATACCACTGAACTTTTAATTTTGTCAA
Found at i:1458733 original size:38 final size:37
Alignment explanation
Indices: 1458671--1458745 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
1458661 GTAGGGTCGG
* *
1458671 GTGGAGGTTGTATAATTCTCGGGTC-AGGTCAGGGTTGA
1 GTGGAGGGTATATAATTCTCGGGTCGA-GTC-GGGTTGA
* *
1458709 GTGGAGGGTATATAATTTTTGGGTCGAGTCGGGTTGA
1 GTGGAGGGTATATAATTCTCGGGTCGAGTCGGGTTGA
1458746 CCGGAGTCCG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 7 0.22
38 24 0.75
39 1 0.03
ACGTcount: A:0.19, C:0.08, G:0.40, T:0.33
Consensus pattern (37 bp):
GTGGAGGGTATATAATTCTCGGGTCGAGTCGGGTTGA
Found at i:1461035 original size:14 final size:15
Alignment explanation
Indices: 1461005--1461041 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1460995 ATAAATTAGT
1461005 TAAAA-ATTTAAATA
1 TAAAATATTTAAATA
*
1461019 TAAATTATTTAAA-A
1 TAAAATATTTAAATA
1461033 TAAAATATT
1 TAAAATATT
1461042 AATTACATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAAATATTTAAATA
Found at i:1461040 original size:21 final size:23
Alignment explanation
Indices: 1460994--1461046 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
1460984 AATGTGTAAT
*
1460994 TATAAATTAGTTAAAAATTTAAA
1 TATAAATTAGTTAAAAATTAAAA
*
1461017 TATAAATTA-TTTAAAA-TAAAA
1 TATAAATTAGTTAAAAATTAAAA
*
1461038 TATTAATTA
1 TATAAATTA
1461047 CATTATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 12 0.44
22 6 0.22
23 9 0.33
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
TATAAATTAGTTAAAAATTAAAA
Found at i:1461488 original size:16 final size:16
Alignment explanation
Indices: 1461467--1461498 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1461457 TTAAATTAAA
1461467 TTAATAGTGTTCATCG
1 TTAATAGTGTTCATCG
1461483 TTAATAGTGTTCATCG
1 TTAATAGTGTTCATCG
1461499 GTACTCGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (16 bp):
TTAATAGTGTTCATCG
Found at i:1482421 original size:22 final size:23
Alignment explanation
Indices: 1482390--1482479 Score: 67
Period size: 27 Copynumber: 3.7 Consensus size: 23
1482380 AAGTTTTAAG
*
1482390 TTTAAGTATTTTAAAATAT-TAT
1 TTTAATTATTTTAAAATATATAT
*
1482412 TTTAATTA-TTTATAAATTTATAT
1 TTTAATTATTTTA-AAATATATAT
*
1482435 TTTATATTTATTTTCAAAATTTTAATATT
1 TTTA-A-TTATTTT-AAAA-TAT-ATA-T
1482464 TTTAATTATTTATAAA
1 TTTAATTATTT-TAAA
1482480 TTTAAATATT
Statistics
Matches: 56, Mismatches: 2, Indels: 15
0.77 0.03 0.21
Matches are distributed among these distances:
21 4 0.07
22 12 0.21
23 7 0.12
24 1 0.02
25 3 0.05
26 6 0.11
27 13 0.23
28 5 0.09
29 5 0.09
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (23 bp):
TTTAATTATTTTAAAATATATAT
Found at i:1482432 original size:21 final size:23
Alignment explanation
Indices: 1482390--1482445 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 23
1482380 AAGTTTTAAG
1482390 TTTAAGTATTT-TAAAATATTAT-
1 TTTAA-TATTTATAAAATATTATA
1482412 TTTAATTATTTAT-AAAT-TTATA
1 TTTAA-TATTTATAAAATATTATA
*
1482434 TTTTATATTTAT
1 TTTAATATTTAT
1482446 TTTCAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 11 0.37
22 18 0.60
23 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTAATATTTATAAAATATTATA
Found at i:1482480 original size:26 final size:26
Alignment explanation
Indices: 1482411--1482490 Score: 94
Period size: 26 Copynumber: 3.1 Consensus size: 26
1482401 TAAAATATTA
1482411 TTTTAATTATTTATAAA-TTT-ATAT
1 TTTTAATTATTTATAAATTTTAATAT
*
1482435 TTTATATTTATTT-TCAAAATTTTAATAT
1 TTT-TAATTATTTAT--AAATTTTAATAT
*
1482463 TTTTAATTATTTATAAATTTAAATAT
1 TTTTAATTATTTATAAATTTTAATAT
1482489 TT
1 TT
1482491 ATTTATAAGT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
24 4 0.09
25 8 0.17
26 16 0.34
27 11 0.23
28 8 0.17
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTTAATTATTTATAAATTTTAATAT
Found at i:1482510 original size:46 final size:48
Alignment explanation
Indices: 1482411--1482537 Score: 120
Period size: 52 Copynumber: 2.6 Consensus size: 48
1482401 TAAAATATTA
1482411 TTTTAATTATTTATAAATTTATATTTTATATTTATTTTCAAAATTTTAATAT
1 TTTTAATTATTTATAAATTTATA---TATATTTATTTT-AAAATTTTAATAT
* *
1482463 TTTTAATTATTTATAAATTTA-A-ATATTTA-TTTATAAGTTTTAGTA-
1 TTTTAATTATTTATAAATTTATATATATTTATTTTA-AAATTTTAATAT
* * *
1482508 TTTTAA-TATATATATATATATATATCATTT
1 TTTTAATTATTTATAAATTTATATAT-ATTT
1482538 TTATATGTGT
Statistics
Matches: 66, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
44 11 0.17
45 8 0.12
46 14 0.21
47 11 0.17
51 1 0.02
52 21 0.32
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTTAATTATTTATAAATTTATATATATTTATTTTAAAATTTTAATAT
Found at i:1483648 original size:21 final size:21
Alignment explanation
Indices: 1483624--1483665 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1483614 TCGTTTAATT
1483624 AAATGAACGAACGA-GAACATA
1 AAATGAACGAAC-ATGAACATA
1483645 AAATGAACGAACATGAACATA
1 AAATGAACGAACATGAACATA
1483666 GGTCTCGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.57, C:0.14, G:0.17, T:0.12
Consensus pattern (21 bp):
AAATGAACGAACATGAACATA
Found at i:1483702 original size:14 final size:14
Alignment explanation
Indices: 1483685--1483737 Score: 69
Period size: 14 Copynumber: 4.1 Consensus size: 14
1483675 CGTTCATTTA
1483685 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1483699 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1483713 CG-T---TTATGTT
1 CGTTCGGTTATGTT
*
1483723 CGTTCGTTTATGTT
1 CGTTCGGTTATGTT
1483737 C
1 C
1483738 ATTCATTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 24 0.69
ACGTcount: A:0.08, C:0.15, G:0.25, T:0.53
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:1483713 original size:24 final size:24
Alignment explanation
Indices: 1483672--1483737 Score: 96
Period size: 24 Copynumber: 2.8 Consensus size: 24
1483662 CATAGGTCTC
* *
1483672 GTTCGTTCATTTACGTTCGGTTAT
1 GTTCGTTCGTTTATGTTCGGTTAT
* *
1483696 GTTCGTTCGGTTATGTTCGTTTAT
1 GTTCGTTCGTTTATGTTCGGTTAT
1483720 GTTCGTTCGTTTATGTTC
1 GTTCGTTCGTTTATGTTC
1483738 ATTCATTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.09, C:0.15, G:0.23, T:0.53
Consensus pattern (24 bp):
GTTCGTTCGTTTATGTTCGGTTAT
Found at i:1483746 original size:14 final size:14
Alignment explanation
Indices: 1483715--1483750 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1483705 GTTATGTTCG
* *
1483715 TTTATGTTCGTTCG
1 TTTATGTTCATTCA
1483729 TTTATGTTCATTCA
1 TTTATGTTCATTCA
1483743 TTTATGTT
1 TTTATGTT
1483751 TAACCCAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.14, C:0.11, G:0.14, T:0.61
Consensus pattern (14 bp):
TTTATGTTCATTCA
Found at i:1483748 original size:38 final size:38
Alignment explanation
Indices: 1483672--1483750 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
1483662 CATAGGTCTC
* *
1483672 GTTCGTTCATTTACGTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTCATTTACGTTCGGTTATGTTCATTCAGTTAT
* * *
1483710 GTTCGTTTATGTT-CGTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTCAT-TTACGTTCGGTTATGTTCATTCAGTTAT
1483748 GTT
1 GTT
1483751 TAACCCAATC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 33 0.94
39 2 0.06
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.54
Consensus pattern (38 bp):
GTTCGTTCATTTACGTTCGGTTATGTTCATTCAGTTAT
Found at i:1483931 original size:7 final size:7
Alignment explanation
Indices: 1483919--1484019 Score: 67
Period size: 7 Copynumber: 14.4 Consensus size: 7
1483909 TAATTATTAA
1483919 AAACCCT
1 AAACCCT
1483926 AAACCCT
1 AAACCCT
*
1483933 AAATCCT
1 AAACCCT
*
1483940 AAACCTT
1 AAACCCT
* *
1483947 AAATCTT
1 AAACCCT
* *
1483954 AAATCAT
1 AAACCCT
* *
1483961 AATCCAT
1 AAACCCT
*
1483968 AAAACCT
1 AAACCCT
* *
1483975 AAAACTT
1 AAACCCT
1483982 AAACCCT
1 AAACCCT
*
1483989 AACCCCT
1 AAACCCT
* *
1483996 AAAACTT
1 AAACCCT
1484003 AAACCCT
1 AAACCCT
*
1484010 AACCCCT
1 AAACCCT
1484017 AAA
1 AAA
1484020 ATCTAAACCT
Statistics
Matches: 73, Mismatches: 21, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 73 1.00
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.22
Consensus pattern (7 bp):
AAACCCT
Found at i:1483949 original size:21 final size:21
Alignment explanation
Indices: 1483919--1484028 Score: 87
Period size: 21 Copynumber: 5.2 Consensus size: 21
1483909 TAATTATTAA
1483919 AAACCCTAAACCCTAAATCCT
1 AAACCCTAAACCCTAAATCCT
* * * *
1483940 AAACCTTAAATCTTAAATCAT
1 AAACCCTAAACCCTAAATCCT
* * * * *
1483961 AATCCATAAAACCTAAAACTT
1 AAACCCTAAACCCTAAATCCT
* * *
1483982 AAACCCTAACCCCTAAAACTT
1 AAACCCTAAACCCTAAATCCT
*
1484003 AAACCCTAACCCCTAAAAT-CT
1 AAACCCTAAACCCT-AAATCCT
1484024 AAACC
1 AAACC
1484029 TTTAATCTGA
Statistics
Matches: 72, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
21 69 0.96
22 3 0.04
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (21 bp):
AAACCCTAAACCCTAAATCCT
Found at i:1485289 original size:23 final size:23
Alignment explanation
Indices: 1485257--1485314 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
1485247 CTGGACTGGG
1485257 TCAATCGAGCTCAAAATTGAGCT
1 TCAATCGAGCTCAAAATTGAGCT
*
1485280 TGAATCGAGCTCAAAATTGAGCT
1 TCAATCGAGCTCAAAATTGAGCT
1485303 TCAATCGAGCTC
1 TCAATCGAGCTC
1485315 GAGTCGAGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (23 bp):
TCAATCGAGCTCAAAATTGAGCT
Found at i:1485591 original size:16 final size:16
Alignment explanation
Indices: 1485551--1485623 Score: 69
Period size: 16 Copynumber: 4.7 Consensus size: 16
1485541 CTAACATTTA
* *
1485551 TGTTCGTTTATGTTCA
1 TGTTCATTTATGTTCG
*
1485567 TATTCATTTATGTTCG
1 TGTTCATTTATGTTCG
* * *
1485583 TGTTTATTTATATTTG
1 TGTTCATTTATGTTCG
*
1485599 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
1485615 T-TT-ATTTAT
1 TGTTCATTTAT
1485624 TAAATGAACG
Statistics
Matches: 45, Mismatches: 12, Indels: 2
0.76 0.20 0.03
Matches are distributed among these distances:
14 5 0.11
15 2 0.04
16 38 0.84
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:1486683 original size:14 final size:14
Alignment explanation
Indices: 1486659--1486692 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1486649 AAATAATAAT
1486659 AAATGAAATAAAGAA
1 AAAT-AAATAAAGAA
1486674 AAATAAATAAAGAA
1 AAATAAATAAAGAA
1486688 AAATA
1 AAATA
1486693 TTTTTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (14 bp):
AAATAAATAAAGAA
Found at i:1486821 original size:13 final size:13
Alignment explanation
Indices: 1486800--1486900 Score: 52
Period size: 13 Copynumber: 7.9 Consensus size: 13
1486790 AATATATAAT
1486800 TTTTAAAAACTAA
1 TTTTAAAAACTAA
*
1486813 TTTTCAAAACT-A
1 TTTTAAAAACTAA
* *
1486825 -TATAATATA-TATA
1 TTTTAA-AAACTA-A
1486838 TTTTAAAAACTAA
1 TTTTAAAAACTAA
* *
1486851 TTTTCAAAA-TTA
1 TTTTAAAAACTAA
* *
1486863 -TATAATATA-TATA
1 TTTTAA-AAACTA-A
1486876 TTTTAAAAACTAA
1 TTTTAAAAACTAA
*
1486889 TTTTCAAAACTA
1 TTTTAAAAACTA
1486901 TATAATATAT
Statistics
Matches: 64, Mismatches: 15, Indels: 18
0.66 0.15 0.19
Matches are distributed among these distances:
11 7 0.11
12 8 0.12
13 37 0.58
14 12 0.19
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTTAAAAACTAA
Done.