Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014432.1 Kokia drynarioides strain JFW-HI SEQ_129470, 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: 130003
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:1736 original size:65 final size:65
Alignment explanation
Indices: 1636--1757 Score: 181
Period size: 65 Copynumber: 1.9 Consensus size: 65
1626 TTCAACGCCA
** * *
1636 GAAAGCAATCAAATTAAAGCAAAAGGCAATTTAAAGGGACCAAAGATGAAGTTAAACCAACGCTG
1 GAAAGCAATCAAATTAAAGCAAAAAACAATATAAAGGGACCAAAGATGAAATTAAACCAACGCTG
* * *
1701 GAAAGCAATTAAGTTGAAGCAAAAAACAATATAAAGGGACCAAAGATGAAATTAAAC
1 GAAAGCAATCAAATTAAAGCAAAAAACAATATAAAGGGACCAAAGATGAAATTAAAC
1758 AAAAAGTAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 50 1.00
ACGTcount: A:0.52, C:0.13, G:0.19, T:0.16
Consensus pattern (65 bp):
GAAAGCAATCAAATTAAAGCAAAAAACAATATAAAGGGACCAAAGATGAAATTAAACCAACGCTG
Found at i:4079 original size:10 final size:10
Alignment explanation
Indices: 4064--4292 Score: 79
Period size: 9 Copynumber: 24.5 Consensus size: 10
4054 TATTTTTATT
4064 AAAATATATA
1 AAAATATATA
4074 AAAATATATA
1 AAAATATATA
* *
4084 AAAA-AAATT
1 AAAATATATA
4093 AAAATCA-AT-
1 AAAAT-ATATA
4102 -AAATGATATA
1 AAAAT-ATATA
* *
4112 AATAT-TATT
1 AAAATATATA
* *
4121 AAATTTTA-A
1 AAAATATATA
4130 AAAATAT-TA
1 AAAATATATA
**
4139 AAAAT-CGTA
1 AAAATATATA
4148 AAAA-ATAT-
1 AAAATATATA
*
4156 AAAA-A-GTA
1 AAAATATATA
* *
4164 AAATTTTATA
1 AAAATATATA
**
4174 AAAA-ACGTA
1 AAAATATATA
4183 AAAAT-TAT-
1 AAAATATATA
4191 AAAATATATA
1 AAAATATATA
*
4201 AAAATATAAA
1 AAAATATATA
4211 AAAAT-TATA
1 AAAATATATA
* *
4220 AAATTTTAT-
1 AAAATATATA
*
4229 AAAATCGTA-A
1 AAAAT-ATATA
4239 GAAAAT-TATA
1 -AAAATATATA
4249 CAAAATATA-A
1 -AAAATATATA
*
4259 AGAA-ATATA
1 AAAATATATA
*
4268 AAATTCATA-A
1 AAAAT-ATATA
4278 AAAATATATA
1 AAAATATATA
4288 AAAAT
1 AAAAT
4293 TTTCGTACCA
Statistics
Matches: 161, Mismatches: 33, Indels: 50
0.66 0.14 0.20
Matches are distributed among these distances:
7 1 0.01
8 21 0.13
9 65 0.40
10 60 0.37
11 14 0.09
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (10 bp):
AAAATATATA
Found at i:4194 original size:28 final size:29
Alignment explanation
Indices: 4162--4232 Score: 92
Period size: 28 Copynumber: 2.5 Consensus size: 29
4152 ATATAAAAAG
**
4162 TAAAATTTTATAAAAA-ACGTAAAAATTA
1 TAAAATTTTATAAAAATACAAAAAAATTA
* *
4190 TAAAA-TATATAAAAATATAAAAAAATTA
1 TAAAATTTTATAAAAATACAAAAAAATTA
4218 TAAAATTTTATAAAA
1 TAAAATTTTATAAAA
4233 TCGTAAGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 9 0.25
28 19 0.53
29 8 0.22
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (29 bp):
TAAAATTTTATAAAAATACAAAAAAATTA
Found at i:4194 original size:44 final size:43
Alignment explanation
Indices: 4121--4204 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 43
4111 AAATATTATT
* *
4121 AAATTTTAAAAAATATTAAAAATCGTAAAAAATATAAAAAGTA
1 AAATTTTAAAAAATAGTAAAAATCATAAAAAATATAAAAAGTA
* *
4164 AAATTTTATAAAAA-ACGTAAAAATTATAAAATATATAAAAA
1 AAATTTTA-AAAAATA-GTAAAAATCATAAAAAATATAAAAA
4205 TATAAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 9 0.26
44 26 0.74
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (43 bp):
AAATTTTAAAAAATAGTAAAAATCATAAAAAATATAAAAAGTA
Found at i:4209 original size:35 final size:34
Alignment explanation
Indices: 4127--4213 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 34
4117 TATTAAATTT
*
4127 TAAAAAATATTAAAAATCGTAAAAAATATAAAAAG
1 TAAAAAATA-TAAAAAACGTAAAAAATATAAAAAG
** *
4162 TAAAATTTTATAAAAAACGTAAAAATTATAAAATA-
1 TAAAA-AATATAAAAAACGTAAAAAATATAAAA-AG
4197 TATAAAAATATAAAAAA
1 TA-AAAAATATAAAAAA
4214 ATTATAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
35 37 0.86
36 6 0.14
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.26
Consensus pattern (34 bp):
TAAAAAATATAAAAAACGTAAAAAATATAAAAAG
Found at i:4233 original size:28 final size:28
Alignment explanation
Indices: 4162--4248 Score: 86
Period size: 28 Copynumber: 3.1 Consensus size: 28
4152 ATATAAAAAG
* ***
4162 TAAAATTTTATAAAAAACGTAAAAATTA
1 TAAAATTTTATAAAATATAAAAAAATTA
*
4190 TAAAA-TATATAAAAATATAAAAAAATTA
1 TAAAATTTTAT-AAAATATAAAAAAATTA
* *
4218 TAAAATTTTATAAAATCGTAAGAAAATTA
1 TAAAATTTTATAAAAT-ATAAAAAAATTA
4247 TA
1 TA
4249 CAAAATATAA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
27 4 0.08
28 28 0.58
29 16 0.33
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.32
Consensus pattern (28 bp):
TAAAATTTTATAAAATATAAAAAAATTA
Found at i:4257 original size:28 final size:27
Alignment explanation
Indices: 4182--4270 Score: 88
Period size: 28 Copynumber: 3.1 Consensus size: 27
4172 TAAAAAACGT
4182 AAAAATTATAAAATATATAAAAATATAA
1 AAAAATTATAAAATATAT-AAAATATAA
* *
4210 AAAAATTATAAAATTTTATAAAATCGTAA
1 AAAAATTATAAAA-TATATAAAAT-ATAA
* *
4239 GAAAATTATACAAAATATAAAGAAATATAA
1 AAAAATTAT--AAAATATATA-AAATATAA
4269 AA
1 AA
4271 TTCATAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
28 18 0.37
29 15 0.31
30 8 0.16
31 8 0.16
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.28
Consensus pattern (27 bp):
AAAAATTATAAAATATATAAAATATAA
Found at i:4279 original size:57 final size:56
Alignment explanation
Indices: 4162--4270 Score: 150
Period size: 57 Copynumber: 1.9 Consensus size: 56
4152 ATATAAAAAG
4162 TAAAATTTTATAAAAAACGTAAAAATTATAAAATATATAAAAATATAAAAAAATTA
1 TAAAATTTTATAAAAAACGTAAAAATTATAAAATATATAAAAATATAAAAAAATTA
*
4218 TAAAATTTTAT-AAAATCGTAAGAAAATTATACAAA-ATATAAAGAAATATAAAA
1 TAAAATTTTATAAAAAACGT-A-AAAATTATA-AAATATAT-AA-AAATATAAAA
4271 TTCATAAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
55 7 0.15
56 12 0.26
57 13 0.28
58 5 0.11
59 10 0.21
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (56 bp):
TAAAATTTTATAAAAAACGTAAAAATTATAAAATATATAAAAATATAAAAAAATTA
Found at i:4293 original size:21 final size:20
Alignment explanation
Indices: 4182--4293 Score: 71
Period size: 19 Copynumber: 5.8 Consensus size: 20
4172 TAAAAAACGT
4182 AAAAAT-TAT-AAAA-TATA
1 AAAAATATATAAAAATTATA
*
4199 TAAAAATATAAAAAAATTAT-
1 -AAAAATATATAAAAATTATA
* * **
4219 AAAATTTTAT-AAAATCGTA
1 AAAAATATATAAAAATTATA
4238 AGAAAAT-TATACAAAA-TATA
1 A-AAAATATATA-AAAATTATA
*
4258 AAGAA-ATAT-AAAATTCATA
1 AAAAATATATAAAAATT-ATA
4277 AAAAATATATAAAAATT
1 AAAAATATATAAAAATT
4294 TTCGTACCAA
Statistics
Matches: 71, Mismatches: 11, Indels: 21
0.69 0.11 0.20
Matches are distributed among these distances:
17 4 0.06
18 13 0.18
19 26 0.37
20 15 0.21
21 13 0.18
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (20 bp):
AAAAATATATAAAAATTATA
Found at i:4600 original size:19 final size:18
Alignment explanation
Indices: 4571--4611 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
4561 TTTTAAAGTT
4571 TTTAAAATTTTAT-TAAAA
1 TTTAAAATTTT-TCTAAAA
4589 TTTAATAATTTTTCTAAAA
1 TTTAA-AATTTTTCTAAAA
4608 TTTA
1 TTTA
4612 TTTTTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTAAAATTTTTCTAAAA
Found at i:15917 original size:25 final size:23
Alignment explanation
Indices: 15877--15922 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
15867 CCAATTAGGG
15877 AATTATTGTTTAAATTTAATTCA
1 AATTATTGTTTAAATTTAATTCA
*
15900 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTA-AATTTAATT
15923 TGGATCAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 5 0.25
25 9 0.45
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
AATTATTGTTTAAATTTAATTCA
Found at i:18424 original size:68 final size:69
Alignment explanation
Indices: 18301--18435 Score: 193
Period size: 68 Copynumber: 2.0 Consensus size: 69
18291 TGATTAAACT
* * * *
18301 TAATCACTTTAATATTAAATTAACATAATATTTATCAAAATAATTATTAGATTAAATTTAATATT
1 TAATCACTTTAATATTAAATTAACAAAATATCTATCAAAATAAGTATTAAATTAAATTTAATATT
18366 AAGA
66 AAGA
* *
18370 TAATCACTTTAATATTAATTTAATAAAATA-CTAGT-AAAATAAGTATTAAATTAAATTTAATAT
1 TAATCACTTTAATATTAAATTAACAAAATATCTA-TCAAAATAAGTATTAAATTAAATTTAATAT
18433 TAA
65 TAA
18436 ACTATTAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
68 31 0.53
69 28 0.47
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.41
Consensus pattern (69 bp):
TAATCACTTTAATATTAAATTAACAAAATATCTATCAAAATAAGTATTAAATTAAATTTAATATT
AAGA
Found at i:18445 original size:37 final size:36
Alignment explanation
Indices: 18378--18453 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
18368 GATAATCACT
18378 TTAATATTAATTTAATAAAATACTAGTAAAATAAGTA
1 TTAATATTAATTTAATAAAATACTAGTAAAATAA-TA
* *
18415 TTAA-ATTAAATTTAATATTAA-ACTATTAAAATAATA
1 TTAATATT-AATTTAATA-AAATACTAGTAAAATAATA
18451 TTA
1 TTA
18454 TTTTTGGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 8 0.23
37 25 0.71
38 2 0.06
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (36 bp):
TTAATATTAATTTAATAAAATACTAGTAAAATAATA
Found at i:20531 original size:17 final size:17
Alignment explanation
Indices: 20506--20587 Score: 92
Period size: 17 Copynumber: 4.8 Consensus size: 17
20496 TTGGGCCCAA
*
20506 TAAACTTAAATTTATTT
1 TAAATTTAAATTTATTT
* * *
20523 TAAAATTAAGTTTATTC
1 TAAATTTAAATTTATTT
**
20540 TAAATTTAAATTTAGCT
1 TAAATTTAAATTTATTT
* *
20557 GAAATTTAAATTTATTA
1 TAAATTTAAATTTATTT
20574 TAAATTTAAATTTA
1 TAAATTTAAATTTA
20588 AAATTTATTT
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 52 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (17 bp):
TAAATTTAAATTTATTT
Found at i:22853 original size:29 final size:29
Alignment explanation
Indices: 22328--22869 Score: 456
Period size: 29 Copynumber: 18.4 Consensus size: 29
22318 GTCCTCGAAT
* * * * * *
22328 CTTCTAAAAATTTCGTTTTTATCTTCGAA
1 CTTCCAAAAATTCCATTTTTACCCTCAAA
* *
22357 CTTCTAAAAATCCCATTTTTAACCC-CAAAA
1 CTTCCAAAAATTCCATTTTT-ACCCTC-AAA
* * * *
22387 TTTCTAAAAATTCTATTTTTACCCAT-GAA
1 CTTCCAAAAATTCCATTTTTACCC-TCAAA
* *
22416 CTTCCAAAAATCCCATTTTAACCC-CAAAA
1 CTTCCAAAAATTCCATTTTTACCCTC-AAA
*
22445 CTTCTAAAAATTCCATTTTTACCCTCAAA
1 CTTCCAAAAATTCCATTTTTACCCTCAAA
* *
22474 CTTCTAAAAA-TCTCATTTTTAACCCTAAAA
1 CTTCCAAAAATTC-CATTTTT-ACCCTCAAA
*
22504 CTTCCAAAAATTCAATTTTTACCCTCAAA
1 CTTCCAAAAATTCCATTTTTACCCTCAAA
*
22533 CTTCCAAAAA-TCCAATTTTTAACCTCAAAA
1 CTTCCAAAAATTCC-ATTTTTACCCTC-AAA
* * * * *
22563 TTTCTAAAAAGTCTATTTTTACCCCCAAA
1 CTTCCAAAAATTCCATTTTTACCCTCAAA
*
22592 CTTCCAAAAATCCCATTTTTAACCC-CGAAA
1 CTTCCAAAAATTCCATTTTT-ACCCTC-AAA
** * *
22622 CTTTTAAAAATTCAATTTTTACCCTCGAA
1 CTTCCAAAAATTCCATTTTTACCCTCAAA
* *
22651 CTTCCAAAAATCCCATTCTTAACCC-CACAA
1 CTTCCAAAAATTCCATT-TTTACCCTCA-AA
* * * *
22681 CTTCAAAAAATTCAAATTTTACCCTTAAA
1 CTTCCAAAAATTCCATTTTTACCCTCAAA
* *
22710 CTTTCAAAAATCCCATTTTTGACCC-CAAAA
1 CTTCCAAAAATTCCATTTTT-ACCCTC-AAA
* * *
22740 CTTCTAAAAACTCCTTTTTTACCCTCAAA
1 CTTCCAAAAATTCCATTTTTACCCTCAAA
*
22769 CTTCCAAAAATCCCATTTTTGACCC-CAAAA
1 CTTCCAAAAATTCCATTTTT-ACCCTC-AAA
* *
22799 CTTCCAAAAATTCCATTTTTAGCCTCGAA
1 CTTCCAAAAATTCCATTTTTACCCTCAAA
22828 CTTCCAAAAATTCCATTTTTGA-CCTCGAAA
1 CTTCCAAAAATTCCATTTTT-ACCCTC-AAA
*
22858 CCTCCAAAAATT
1 CTTCCAAAAATT
22870 ACCGTTTTAC
Statistics
Matches: 414, Mismatches: 72, Indels: 53
0.77 0.13 0.10
Matches are distributed among these distances:
28 4 0.01
29 230 0.56
30 176 0.43
31 4 0.01
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (29 bp):
CTTCCAAAAATTCCATTTTTACCCTCAAA
Found at i:22869 original size:59 final size:59
Alignment explanation
Indices: 22328--22847 Score: 666
Period size: 59 Copynumber: 8.8 Consensus size: 59
22318 GTCCTCGAAT
* * * * * *
22328 CTTCTAAAAATTTCGTTTTTATCTTCGAACTTCTAAAAATCCCATTTTTAACCCCAAAA
1 CTTCTAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCAAAA
* * *
22387 TTTCTAAAAATTCTATTTTTACCCAT-GAACTTCCAAAAATCCCA-TTTTAACCCCAAAA
1 CTTCTAAAAATTCCATTTTTACCC-TCAAACTTCCAAAAATCCCATTTTTAACCCCAAAA
* * *
22445 CTTCTAAAAATTCCATTTTTACCCTCAAACTTCTAAAAATCTCATTTTTAACCCTAAAA
1 CTTCTAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCAAAA
* * * *
22504 CTTCCAAAAATTCAATTTTTACCCTCAAACTTCCAAAAATCCAATTTTTAACCTCAAAA
1 CTTCTAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCAAAA
* * * * *
22563 TTTCTAAAAAGTCTATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCGAAA
1 CTTCTAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCAAAA
* * * * *
22622 CTTTTAAAAATTCAATTTTTACCCTCGAACTTCCAAAAATCCCATTCTTAACCCCACAA
1 CTTCTAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCAAAA
* * * * * *
22681 CTTCAAAAAATTCAAATTTTACCCTTAAACTTTCAAAAATCCCATTTTTGACCCCAAAA
1 CTTCTAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCAAAA
* * *
22740 CTTCTAAAAACTCCTTTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAA
1 CTTCTAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCAAAA
* * * *
22799 CTTCCAAAAATTCCATTTTTAGCCTCGAACTTCCAAAAATTCCATTTTT
1 CTTCTAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTT
22848 GACCTCGAAA
Statistics
Matches: 399, Mismatches: 59, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
57 1 0.00
58 51 0.13
59 346 0.87
60 1 0.00
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.34
Consensus pattern (59 bp):
CTTCTAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCAAAA
Found at i:35388 original size:17 final size:17
Alignment explanation
Indices: 35363--35456 Score: 56
Period size: 17 Copynumber: 5.8 Consensus size: 17
35353 CTAGGCTCAA
* *
35363 TAAACTTAAATTTATTT
1 TAAAATTAAATTTATTC
*
35380 TAAAATTAAGTTTATTC
1 TAAAATTAAATTTATTC
*
35397 T-AAATTTAA---A-TC
1 TAAAATTAAATTTATTC
* *
35409 TAAATTTAAATTTA-GC
1 TAAAATTAAATTTATTC
* *
35425 TGAAATTTAAATTTATTA
1 T-AAAATTAAATTTATTC
*
35443 TAAATTTAAATTTA
1 TAAAATTAAATTTA
35457 AAATTTATTT
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
12 3 0.05
13 7 0.11
16 9 0.15
17 41 0.67
18 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (17 bp):
TAAAATTAAATTTATTC
Found at i:35406 original size:6 final size:6
Alignment explanation
Indices: 35363--35463 Score: 61
Period size: 6 Copynumber: 17.3 Consensus size: 6
35353 CTAGGCTCAA
* * * * *
35363 TAAACT TAAATT T-ATTT TAAAAT TAAGTT T--ATT CTAAATT TAAATC
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT -TAAATT TAAATT
** *
35409 TAAATT TAAATT T-AGCT GAAATT TAAATT T--ATT ATAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT -TAAATT TAAATT
35455 TAAAATT TA
1 T-AAATT TA
35464 TTTTAAATGT
Statistics
Matches: 71, Mismatches: 15, Indels: 18
0.68 0.14 0.17
Matches are distributed among these distances:
4 5 0.07
5 8 0.11
6 46 0.65
7 12 0.17
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.48
Consensus pattern (6 bp):
TAAATT
Found at i:35422 original size:29 final size:29
Alignment explanation
Indices: 35380--35436 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
35370 AAATTTATTT
* *
35380 TAAAATTAAGTTTATTCT-AAATTTAAATC
1 TAAAATTAAATTTA-GCTGAAATTTAAATC
*
35409 TAAATTTAAATTTAGCTGAAATTTAAAT
1 TAAAATTAAATTTAGCTGAAATTTAAAT
35437 TTATTATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (29 bp):
TAAAATTAAATTTAGCTGAAATTTAAATC
Found at i:35465 original size:24 final size:23
Alignment explanation
Indices: 35378--35471 Score: 75
Period size: 23 Copynumber: 4.0 Consensus size: 23
35368 TTAAATTTAT
* * *
35378 TTTAAAATTAAGTTTATTCTAAA
1 TTTAAATTTAAATTTATTATAAA
* *
35401 TTTAAATCTAAATTTAAATT-T-AG
1 TTTAAATTTAAATTT--ATTATAAA
* *
35424 CTGAAATTTAAATTTATTATAAA
1 TTTAAATTTAAATTTATTATAAA
*
35447 TTTAAATTTAAAATTTATTTTAAA
1 TTTAAATTT-AAATTTATTATAAA
35471 T
1 T
35472 GTCCAAATTC
Statistics
Matches: 55, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
21 3 0.05
22 1 0.02
23 33 0.60
24 15 0.27
25 3 0.05
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (23 bp):
TTTAAATTTAAATTTATTATAAA
Found at i:37341 original size:29 final size:28
Alignment explanation
Indices: 37288--37862 Score: 326
Period size: 29 Copynumber: 20.0 Consensus size: 28
37278 CCCTGGAGGT
*
37288 CCCCGAAACTTCTAAAAATTTCATTTTTA
1 CCCCG-AACTTCTAAAAATTCCATTTTTA
* * *
37317 TCCTCGAACTTCTAAAAATCCCATTTTAA
1 -CCCCGAACTTCTAAAAATTCCATTTTTA
* **
37346 CCCCAAAACTTCTAAAAATTTTATTTTTA
1 CCCC-GAACTTCTAAAAATTCCATTTTTA
* * *
37375 CCCCTGAACTTCCAAGAATCCCATTTTTGA
1 CCCC-GAACTTCTAAAAATTCCATTTTT-A
* *
37405 CCCCGAAACTTCTTAAAATTCTATTTTTA
1 CCCCG-AACTTCTAAAAATTCCATTTTTA
* *
37434 CCCCCGTACTTCTAAAAATCCCATTTTT-
1 -CCCCGAACTTCTAAAAATTCCATTTTTA
** * *
37462 CCCAAAAATTCCAAAAATTCCATTTTTA
1 CCCCGAACTTCTAAAAATTCCATTTTTA
* * *
37490 CCCCCAAACTTCCAAAAATCCCATTTTTGA
1 -CCCCGAACTTCTAAAAATTCCATTTTT-A
* * * *
37520 CCCCAAAATTTTTGAAAATTCCATTTTTA
1 CCCC-GAACTTCTAAAAATTCCATTTTTA
* *
37549 CACCCGAACTTCCAAAAA-TCCTATTCTTGA
1 C-CCCGAACTTCTAAAAATTCC-ATT-TTTA
* *
37579 CCTCGAAACTTCTAAAATTTCCATTTTT-
1 CCCCG-AACTTCTAAAAATTCCATTTTTA
* * ** * *
37607 -TCCAAAAATCT---CATT--A--TTGA
1 CCCCGAACTTCTAAAAATTCCATTTTTA
** *
37627 CCCTAAAACTTCTAAAAATTCTATTTTTA
1 CCC-CGAACTTCTAAAAATTCCATTTTTA
* * *
37656 CCCCCGAACTTCCAAAAATCCCATTTTTGGG
1 -CCCCGAACTTCTAAAAATTCCATTTTT--A
**
37687 CCCAAAACTTCTAAAAATTCCATTTTTA
1 CCCCGAACTTCTAAAAATTCCATTTTTA
* *
37715 CCCCCAAACTTCTAAAAATCCCATTTTTAA
1 -CCCCGAACTTCTAAAAATTCCATTTTT-A
** * *
37745 CCCTAAAACTTCCAAAAATTCCCTTTTTTA
1 CCC-CGAACTTCTAAAAATT-CCATTTTTA
* * *
37775 CCCTCAAACTTTTAAAAATCCCATTTTTGA
1 CCC-CGAACTTCTAAAAATTCCATTTTT-A
* *
37805 CCCCGAAACTTCCAAAAATTCTATTTTTA
1 CCCCG-AACTTCTAAAAATTCCATTTTTA
* * *
37834 GCCACGAACTTCCAAAAATTCTATTTTTA
1 -CCCCGAACTTCTAAAAATTCCATTTTTA
37863 ACCTCGAAAC
Statistics
Matches: 420, Mismatches: 92, Indels: 67
0.73 0.16 0.12
Matches are distributed among these distances:
19 2 0.00
21 2 0.00
22 6 0.01
23 2 0.00
25 3 0.01
26 5 0.01
27 23 0.05
28 6 0.01
29 208 0.50
30 153 0.36
31 10 0.02
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.35
Consensus pattern (28 bp):
CCCCGAACTTCTAAAAATTCCATTTTTA
Found at i:37431 original size:59 final size:59
Alignment explanation
Indices: 37288--37861 Score: 570
Period size: 59 Copynumber: 10.0 Consensus size: 59
37278 CCCTGGAGGT
* * * * *
37288 CCCCGAAACTTCTAAAAATT-TCATTTTTATCCTCGAACTTCTAAAAATCCCA-TTTTAA
1 CCCCAAAACTTCTAAAAATTCT-ATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * *
37346 CCCCAAAACTTCTAAAAATTTTATTTTTACCCCTGAACTTCCAAGAATCCCATTTTTGA
1 CCCCAAAACTTCTAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * * *
37405 CCCCGAAACTTCTTAAAATTCTATTTTTACCCCCGTACTTCTAAAAATCCCATTTTT--
1 CCCCAAAACTTCTAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * * *
37462 -CCCAAAAATTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA
1 CCCCAAAACTTCTAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * * * * * *
37520 CCCCAAAATTTTTGAAAATTCCATTTTTACACCCGAACTTCCAAAAATCCTATTCTTGA
1 CCCCAAAACTTCTAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * * * * *
37579 CCTCGAAACTTCTAAAATTTCCA-TTTT----------TTCCAAAAATCTCATTATTGA
1 CCCCAAAACTTCTAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* *
37627 CCCTAAAACTTCTAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGG
1 CCCCAAAACTTCTAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * * * *
37686 GCCCAAAACTTCTAAAAATTCCATTTTTACCCCCAAACTTCTAAAAATCCCATTTTTAA
1 CCCCAAAACTTCTAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * * * **
37745 CCCTAAAACTTCCAAAAATTCCCT-TTTTTACCCTCAAACTTTTAAAAATCCCATTTTTGA
1 CCCCAAAACTTCTAAAAATT--CTATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * * * * *
37805 CCCCGAAACTTCCAAAAATTCTATTTTTAGCCACGAACTTCCAAAAATTCTATTTTT
1 CCCCAAAACTTCTAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCCCATTTTT
37862 AACCTCGAAA
Statistics
Matches: 427, Mismatches: 70, Indels: 37
0.80 0.13 0.07
Matches are distributed among these distances:
48 36 0.08
49 4 0.01
56 48 0.11
58 50 0.12
59 237 0.56
60 51 0.12
61 1 0.00
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.35
Consensus pattern (59 bp):
CCCCAAAACTTCTAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
Found at i:37636 original size:48 final size:48
Alignment explanation
Indices: 37558--37654 Score: 126
Period size: 48 Copynumber: 2.0 Consensus size: 48
37548 ACACCCGAAC
* * *
37558 TTCCAAAAATCCTATTCTTGACCTCGAAACTTCTAAAATTTCCATTTT
1 TTCCAAAAATCCTATTATTGACCTCAAAACTTCTAAAAATTCCATTTT
*
37606 TTCCAAAAAT-CTCATTATTGACC-CTAAAACTTCTAAAAATTCTATTTT
1 TTCCAAAAATCCT-ATTATTGACCTC-AAAACTTCTAAAAATTCCATTTT
37654 T
1 T
37655 ACCCCCGAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
47 3 0.07
48 40 0.93
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (48 bp):
TTCCAAAAATCCTATTATTGACCTCAAAACTTCTAAAAATTCCATTTT
Found at i:37695 original size:107 final size:107
Alignment explanation
Indices: 37499--37713 Score: 297
Period size: 107 Copynumber: 2.0 Consensus size: 107
37489 ACCCCCAAAC
* * * *
37499 TTCCAAAAATCCCATTTTTGACCCCAAAATTTTTGAAAATTCCATTTTTACACCCGAACTTCCAA
1 TTCCAAAAATCCCATTATTGACCCCAAAACTTCTAAAAATTCCATTTTTACACCCGAACTTCCAA
* * *
37564 AAATCCTATTCTTGACCTCGAAACTTCTAAAATTTCCATTTT
66 AAATCCCATTCTTGACCTCAAAACTTCTAAAAATTCCATTTT
* * * *
37606 TTCCAAAAATCTCATTATTGACCCTAAAACTTCTAAAAATTCTATTTTTACCCCCGAACTTCCAA
1 TTCCAAAAATCCCATTATTGACCCCAAAACTTCTAAAAATTCCATTTTTACACCCGAACTTCCAA
* *
37671 AAATCCCATTTTTGGGCC-CAAAACTTCTAAAAATTCCATTTT
66 AAATCCCATTCTT-GACCTCAAAACTTCTAAAAATTCCATTTT
37713 T
1 T
37714 ACCCCCAAAC
Statistics
Matches: 94, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
107 91 0.97
108 3 0.03
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (107 bp):
TTCCAAAAATCCCATTATTGACCCCAAAACTTCTAAAAATTCCATTTTTACACCCGAACTTCCAA
AAATCCCATTCTTGACCTCAAAACTTCTAAAAATTCCATTTT
Found at i:37756 original size:166 final size:166
Alignment explanation
Indices: 37465--37773 Score: 431
Period size: 166 Copynumber: 1.9 Consensus size: 166
37455 CATTTTTCCC
*
37465 AAAAATTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAAATT
1 AAAAATTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACT
* * * * * * *
37530 TTTGAAAATTCCATTTTTACACCCGAACTTCCAAAAATCCTATTCTTGACCTCGAAACTTCTAAA
66 TCTAAAAATTCCATTTTTACACCCAAACTTCCAAAAATCCCATTCTTAACCTCAAAACTTCCAAA
*
37595 ATTTCCATTTTTTCCAAAAATCTCATTATTGACCCT
131 AATTCCATTTTTTCCAAAAATCTCATTATTGACCCT
* * * * **
37631 AAAACTTCTAAAAATTCTATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGGGCCCAAAACT
1 AAAAATTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACT
* * *
37696 TCTAAAAATTCCATTTTTACCCCCAAACTTCTAAAAATCCCATTTTTAACC-CTAAAACTTCCAA
66 TCTAAAAATTCCATTTTTACACCCAAACTTCCAAAAATCCCATTCTTAACCTC-AAAACTTCCAA
*
37760 AAATTCCCTTTTTT
130 AAATTCCATTTTTT
37774 ACCCTCAAAC
Statistics
Matches: 123, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
165 1 0.01
166 122 0.99
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (166 bp):
AAAAATTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACT
TCTAAAAATTCCATTTTTACACCCAAACTTCCAAAAATCCCATTCTTAACCTCAAAACTTCCAAA
AATTCCATTTTTTCCAAAAATCTCATTATTGACCCT
Found at i:37880 original size:30 final size:30
Alignment explanation
Indices: 37606--37883 Score: 233
Period size: 30 Copynumber: 9.4 Consensus size: 30
37596 TTTCCATTTT
* * **
37606 TTCCAAAAA-TCTCATTATTGACCCTAAAAC
1 TTCCAAAAATTC-CATTTTTAACCCCGAAAC
* * *
37636 TTCTAAAAATTCTATTTTTACCCCCG-AAC
1 TTCCAAAAATTCCATTTTTAACCCCGAAAC
* *** *
37665 TTCCAAAAATCCCATTTTTGGGCCCAAAAC
1 TTCCAAAAATTCCATTTTTAACCCCGAAAC
* *
37695 TTCTAAAAATTCCATTTTT-ACCCCCAAAC
1 TTCCAAAAATTCCATTTTTAACCCCGAAAC
* * **
37724 TTCTAAAAATCCCATTTTTAACCCTAAAAC
1 TTCCAAAAATTCCATTTTTAACCCCGAAAC
* *
37754 TTCCAAAAATTCCCTTTTTTACCCTC-AAAC
1 TTCCAAAAATTCCATTTTTAACCC-CGAAAC
** * *
37784 TTTTAAAAATCCCATTTTTGACCCCGAAAC
1 TTCCAAAAATTCCATTTTTAACCCCGAAAC
* * *
37814 TTCCAAAAATTCTATTTTTAGCCACG-AAC
1 TTCCAAAAATTCCATTTTTAACCCCGAAAC
* *
37843 TTCCAAAAATTCTATTTTTAACCTCGAAAC
1 TTCCAAAAATTCCATTTTTAACCCCGAAAC
*
37873 CTCCAAAAATT
1 TTCCAAAAATT
37884 ACCGTTTTAC
Statistics
Matches: 200, Mismatches: 42, Indels: 12
0.79 0.17 0.05
Matches are distributed among these distances:
29 75 0.38
30 123 0.62
31 2 0.01
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (30 bp):
TTCCAAAAATTCCATTTTTAACCCCGAAAC
Found at i:40330 original size:22 final size:23
Alignment explanation
Indices: 40305--40348 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
40295 AATATTTGTT
40305 AATTTAATTTG-A-TAATTTTTTG
1 AATTT-ATTTGTATTAATTTTTTG
40327 AATTTATTTGTATTAATTTTTT
1 AATTTATTTGTATTAATTTTTT
40349 AGTGTATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 6 0.30
23 9 0.45
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (23 bp):
AATTTATTTGTATTAATTTTTTG
Found at i:43385 original size:23 final size:24
Alignment explanation
Indices: 43359--43405 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
43349 TCATGTTCCA
*
43359 TTATTAA-ATAATAATAATGACGT
1 TTATTAATATAAAAATAATGACGT
*
43382 TTATTAATATAAAAATATTGACGT
1 TTATTAATATAAAAATAATGACGT
43406 GGTAATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (24 bp):
TTATTAATATAAAAATAATGACGT
Found at i:43649 original size:18 final size:19
Alignment explanation
Indices: 43623--43658 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
43613 CCGTTTAACC
*
43623 AAATTAAGTC-TCAAATAA
1 AAATCAAGTCTTCAAATAA
43641 AAATCAAGTCTTCAAATA
1 AAATCAAGTCTTCAAATA
43659 CTTGAGGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.53, C:0.14, G:0.06, T:0.28
Consensus pattern (19 bp):
AAATCAAGTCTTCAAATAA
Found at i:44763 original size:9 final size:9
Alignment explanation
Indices: 44749--44775 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
44739 ATTATAAACA
44749 CTTTGAGTG
1 CTTTGAGTG
44758 CTTTGAGTG
1 CTTTGAGTG
44767 CTTTGAGTG
1 CTTTGAGTG
44776 ATCTTTAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.33, T:0.44
Consensus pattern (9 bp):
CTTTGAGTG
Found at i:45098 original size:20 final size:20
Alignment explanation
Indices: 45049--45088 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
45039 CATTAAATTT
45049 AATTTAATATTAAGATAATA
1 AATTTAATATTAAGATAATA
*
45069 AATTTAATATTAATATAATA
1 AATTTAATATTAAGATAATA
45089 CTATTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
AATTTAATATTAAGATAATA
Found at i:60049 original size:19 final size:19
Alignment explanation
Indices: 60027--60065 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
60017 CGATATATTG
* *
60027 TACTGGCACGTAAGAGCGA
1 TACTAGCACGTAAAAGCGA
*
60046 TACTAGCTCGTAAAAGCGA
1 TACTAGCACGTAAAAGCGA
60065 T
1 T
60066 TCACTGACTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.21
Consensus pattern (19 bp):
TACTAGCACGTAAAAGCGA
Found at i:60138 original size:36 final size:36
Alignment explanation
Indices: 60075--60255 Score: 197
Period size: 36 Copynumber: 5.0 Consensus size: 36
60065 TTCACTGACT
* *
60075 GGGCTCGTATGAGCTAAAATTTACTGGGAGGCTTGGA
1 GGGCTCGTATGAGCT-AAATTTACTGGGAGACTTGAA
60112 GGGCTCGTATGAGCTAAATTTACTGGG-GACTTGAA
1 GGGCTCGTATGAGCTAAATTTACTGGGAGACTTGAA
** * * *
60147 GATCTCATATGAGCTAAAATTTACTAGAAGACTTGAA
1 GGGCTCGTATGAGCT-AAATTTACTGGGAGACTTGAA
* * *
60184 GAGATCGTATGAGCTAAATTTACTAGGAGACTTG-A
1 GGGCTCGTATGAGCTAAATTTACTGGGAGACTTGAA
* * *
60219 GGAGATCGTATGAGCTAAA-TTACTGGGAAAATTGAA
1 GG-GCTCGTATGAGCTAAATTTACTGGGAGACTTGAA
60255 G
1 G
60256 AGATCGTTTG
Statistics
Matches: 125, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
35 32 0.26
36 58 0.46
37 35 0.28
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.28
Consensus pattern (36 bp):
GGGCTCGTATGAGCTAAATTTACTGGGAGACTTGAA
Found at i:60199 original size:72 final size:73
Alignment explanation
Indices: 60082--60267 Score: 218
Period size: 72 Copynumber: 2.6 Consensus size: 73
60072 ACTGGGCTCG
* * * * * *
60082 TATGAGCTAAAATTTACTGGGAGGCTTGGAGGGCTCGTATGAGCTAAATTTACT-GGGGACTTGA
1 TATGAGCTAAAATTTACTGGAAGACTTGAAGAGATCGTATGAGCTAAATTTACTAGGAGACTTGA
**
60146 AGATCTCA
66 AGAGATCA
*
60154 TATGAGCTAAAATTTACTAGAAGACTTGAAGAGATCGTATGAGCTAAATTTACTAGGAGACTTGA
1 TATGAGCTAAAATTTACTGGAAGACTTGAAGAGATCGTATGAGCTAAATTTACTAGGAGACTTGA
* *
60219 GGAGATCG
66 AGAGATCA
* *
60227 TATGAGCT-AAA-TTACTGGGAA-AATTGAAGAGATCGTTTGAG
1 TATGAGCTAAAATTTACT-GGAAGACTTGAAGAGATCGTATGAG
60268 ACACGAATGT
Statistics
Matches: 98, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
71 23 0.23
72 54 0.55
73 21 0.21
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.28
Consensus pattern (73 bp):
TATGAGCTAAAATTTACTGGAAGACTTGAAGAGATCGTATGAGCTAAATTTACTAGGAGACTTGA
AGAGATCA
Found at i:64599 original size:21 final size:24
Alignment explanation
Indices: 64575--64626 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 24
64565 TATTGATAAG
64575 ATATAATCTA-TTTTCGAAA-A-A
1 ATATAATCTAGTTTTCGAAATATA
*
64596 ATAT-ATTTAGGTTTTCGAAATATA
1 ATATAATCTA-GTTTTCGAAATATA
64620 ATATAAT
1 ATATAAT
64627 AAAATTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 4 0.16
21 4 0.16
22 9 0.36
23 1 0.04
24 5 0.20
25 2 0.08
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (24 bp):
ATATAATCTAGTTTTCGAAATATA
Found at i:67253 original size:19 final size:19
Alignment explanation
Indices: 67231--67280 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
67221 ATGATTTACA
67231 AATATAAATAATAAAAAAC
1 AATATAAATAATAAAAAAC
* *
67250 AATATACATAA-AAAAAGC
1 AATATAAATAATAAAAAAC
67268 AA-ATAAAATAATA
1 AATAT-AAATAATA
67281 TACATACATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 2 0.08
18 13 0.50
19 11 0.42
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.20
Consensus pattern (19 bp):
AATATAAATAATAAAAAAC
Found at i:67419 original size:30 final size:30
Alignment explanation
Indices: 67385--67719 Score: 103
Period size: 30 Copynumber: 11.2 Consensus size: 30
67375 TTAAAATTTA
*
67385 GTCAAATTTGAATTTTTGG-AAACTTCAGTG
1 GTCAAATTCGAATTTTTGGAAAACTTCAG-G
* * *
67415 GTCAAA-TCAAATTTTTTGGAAAATTTGAGG
1 GTCAAATTCGAA-TTTTTGGAAAACTTCAGG
* * **
67445 GTCAAATTGGAATTTTT-G-TATGTTCGAGG
1 GTCAAATTCGAATTTTTGGAAAACTTC-AGG
* * * *
67474 GTTAAATTCAAATTTTTGG-AAAGTTTAGG
1 GTCAAATTCGAATTTTTGGAAAACTTCAGG
* * * **
67503 AGTCAAATTTGATTTTTTTTGAAAA-TTTGGG
1 -GTCAAATTCGA-ATTTTTGGAAAACTTCAGG
* * * ** **
67534 GTTCAAATTCAAATTTCTAGAAAGTTTGGGG
1 G-TCAAATTCGAATTTTTGGAAAACTTCAGG
* * **
67565 GTCAAATTCAAATTTTTGG-AAAGTTTGGG
1 GTCAAATTCGAATTTTTGGAAAACTTCAGG
* * ** * *
67594 GTCAAAATCAAATTTTTGGAAAGTTTAATG
1 GTCAAATTCGAATTTTTGGAAAACTTCAGG
* * **
67624 GTCAAATTCAAATTTTT-GAAAAGTTTGGAG
1 GTCAAATTCGAATTTTTGGAAAACTTCAG-G
* * * * **
67654 GTAAAATTTGAATTTTTAG-AAAGTTTGGG
1 GTCAAATTCGAATTTTTGGAAAACTTCAGG
* * * *
67683 AGTCAAATTTGAATTTTTTGAAAATTTGAGG
1 -GTCAAATTCGAATTTTTGGAAAACTTCAGG
67714 GTCAAA
1 GTCAAA
67720 AAACAATTTT
Statistics
Matches: 236, Mismatches: 54, Indels: 30
0.74 0.17 0.09
Matches are distributed among these distances:
28 3 0.01
29 56 0.24
30 131 0.56
31 43 0.18
32 3 0.01
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.39
Consensus pattern (30 bp):
GTCAAATTCGAATTTTTGGAAAACTTCAGG
Found at i:67661 original size:89 final size:88
Alignment explanation
Indices: 67395--67719 Score: 271
Period size: 89 Copynumber: 3.6 Consensus size: 88
67385 GTCAAATTTG
* * * **
67395 AATTTTTGGAAACTTCAGTGGTC-AAATCAAATTTTTTGGAAAATTTGAGGGTCAAATTGGAATT
1 AATTTTTGGAAAGTT-TGGGGTCAAAATCAAA-TTTTTGGAAAATTT-AGGGTCAAATTCAAATT
* * * *
67459 TTTG-TATG-TTCGAGGGTTAAATTCA
63 TTTGAAAAGTTTGGA-GGTAAAATTCA
* * * ** * *
67484 AATTTTTGGAAAGTTTAGGAGTCAAATTTGATTTTTTTTGAAAATTTGGGGTTCAAATTCAAATT
1 AATTTTTGGAAAGTTT-GGGGTCAAA-ATCAAATTTTTGGAAAATTTAGGG-TCAAATTCAAATT
* * *
67549 TCT-AGAAAGTTTGGGGGTCAAATTCA
63 TTTGA-AAAGTTTGGAGGTAAAATTCA
* *
67575 AATTTTTGGAAAGTTTGGGGTCAAAATCAAATTTTTGGAAAGTTTAATGGTCAAATTCAAATTTT
1 AATTTTTGGAAAGTTTGGGGTCAAAATCAAATTTTTGGAAAATTT-AGGGTCAAATTCAAATTTT
**
67640 TGAAAAGTTTGGAGGTAAAATTTG
65 TGAAAAGTTTGGAGGTAAAATTCA
* * ** *
67664 AATTTTTAGAAAGTTTGGGAGTCAAATTTGAATTTTTTGAAAATTTGAGGGTCAAA
1 AATTTTTGGAAAGTTTGGG-GTCAAAATCAAATTTTTGGAAAATTT-AGGGTCAAA
67720 AAACAATTTT
Statistics
Matches: 186, Mismatches: 40, Indels: 19
0.76 0.16 0.08
Matches are distributed among these distances:
89 85 0.46
90 68 0.37
91 30 0.16
92 3 0.02
ACGTcount: A:0.34, C:0.06, G:0.21, T:0.39
Consensus pattern (88 bp):
AATTTTTGGAAAGTTTGGGGTCAAAATCAAATTTTTGGAAAATTTAGGGTCAAATTCAAATTTTT
GAAAAGTTTGGAGGTAAAATTCA
Found at i:67698 original size:60 final size:58
Alignment explanation
Indices: 67472--67720 Score: 232
Period size: 60 Copynumber: 4.1 Consensus size: 58
67462 GTATGTTCGA
* * * **
67472 GGGTTAAATTCAAATTTTTGGAAAGTTTAGGAGTCAAATTTGATTTTTTTTGAAAATTTG
1 GGGTAAAATTCAAATTTTTAGAAAGTTTAGGAGTCAAA-TTCA-AATTTTTGAAAATTTG
* * * * *
67532 GGGTTCAAATTCAAATTTCTAGAAAGTTTGGGGGTCAAATTCAAATTTTTGGAAAGTTTG
1 GGG-TAAAATTCAAATTTTTAGAAAGTTTAGGAGTCAAATTCAAATTTTT-GAAAATTTG
* *
67592 GGGTCAAAA-TCAAATTTTTGGAAAGTTTAATG-GTCAAATTCAAATTTTTGAAAAGTTTG
1 GGGT-AAAATTCAAATTTTTAGAAAGTTT-AGGAGTCAAATTCAAATTTTTGAAAA-TTTG
** * * *
67651 GAGGTAAAATTTGAATTTTTAGAAAGTTTGGGAGTCAAATTTGAATTTTTTGAAAATTTG
1 G-GGTAAAATTCAAATTTTTAGAAAGTTTAGGAGTCAAA-TTCAAATTTTTGAAAATTTG
67711 AGGGTCAAAA
1 -GGGT-AAAA
67721 AACAATTTTA
Statistics
Matches: 156, Mismatches: 22, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
58 4 0.03
59 50 0.32
60 53 0.34
61 49 0.31
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.39
Consensus pattern (58 bp):
GGGTAAAATTCAAATTTTTAGAAAGTTTAGGAGTCAAATTCAAATTTTTGAAAATTTG
Found at i:67720 original size:120 final size:120
Alignment explanation
Indices: 67421--67720 Score: 315
Period size: 120 Copynumber: 2.5 Consensus size: 120
67411 AGTGGTCAAA
* * * * * * * *
67421 TCAAATTTTTTGGAAAATTTGAGGGTCAAATTGGAA-TTTTTGTATGTTCGAGGGTTAAATTCAA
1 TCAAA-TTTTTAGAAAGTTTG-GGGTCAAATTCGAATTTTTTGAAAGTTTGAGGGTCAAAATCAA
* ** *
67485 ATTTTTGGAAAGTTTAGGAGTCAAATTTGATTTTTTTTGAAAATTTGGGGTTCAAAT
64 ATTTTTGGAAAGTTTAGGAGTCAAATTTCATAATTTTTGAAAATTTGGGGTTAAAAT
* * *
67542 TCAAATTTCTAGAAAGTTTGGGGGTCAAATTCAAATTTTTGGAAAGTTTG-GGGTCAAAATCAAA
1 TCAAATTTTTAGAAAGTTT-GGGGTCAAATTCGAATTTTTTGAAAGTTTGAGGGTCAAAATCAAA
*
67606 TTTTTGGAAAGTTTAATG-GTCAAA-TTCA-AATTTTTGAAAAGTTTGGAGG-TAAAAT
65 TTTTTGGAAAGTTT-AGGAGTCAAATTTCATAATTTTTGAAAA-TTTGG-GGTTAAAAT
** * *
67661 TTGAATTTTTAGAAAGTTTGGGAGTCAAATTTGAATTTTTTGAAAATTTGAGGGTCAAAA
1 TCAAATTTTTAGAAAGTTTGGG-GTCAAATTCGAATTTTTTGAAAGTTTGAGGGTCAAAA
67721 AACAATTTTA
Statistics
Matches: 149, Mismatches: 23, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
118 13 0.09
119 52 0.35
120 66 0.44
121 18 0.12
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (120 bp):
TCAAATTTTTAGAAAGTTTGGGGTCAAATTCGAATTTTTTGAAAGTTTGAGGGTCAAAATCAAAT
TTTTGGAAAGTTTAGGAGTCAAATTTCATAATTTTTGAAAATTTGGGGTTAAAAT
Found at i:67729 original size:60 final size:59
Alignment explanation
Indices: 67384--67720 Score: 263
Period size: 59 Copynumber: 5.6 Consensus size: 59
67374 ATTAAAATTT
* * * * * *
67384 AGTCAAATTTGAATTTTTGGAAACTTCAGTGGTC-AAATCAAATTTTTTGGAAAATTTGAGG
1 AGTCAAATTTGAATTTTTTGAAAATT-TGGGGTCAAAATCAAA-TTTTTAGAAAGTTT-AGG
* * ** * * * *
67445 -GTCAAATTGGAA-TTTTTGTATGTTCGAGGGTTAAATTCAAATTTTTGGAAAGTTTAGG
1 AGTCAAATTTGAATTTTTTGAAAATTTG-GGGTCAAAATCAAATTTTTAGAAAGTTTAGG
* * * *
67503 AGTCAAATTTGATTTTTTTTGAAAATTTGGGGTTCAAATTCAAATTTCTAGAAAGTTTGGG
1 AGTCAAATTTGA-ATTTTTTGAAAATTTGGGG-TCAAAATCAAATTTTTAGAAAGTTTAGG
* ** * * * *
67564 GGTCAAATTCAAATTTTTGGAAAGTTTGGGGTCAAAATCAAATTTTTGGAAAGTTTAATG
1 AGTCAAATTTGAATTTTTTGAAAATTTGGGGTCAAAATCAAATTTTTAGAAAGTTT-AGG
* * ** *
67624 -GTCAAA-TTCAAATTTTTGAAAAGTTTGGAGGT-AAAATTTGAATTTTTAGAAAGTTTGGG
1 AGTCAAATTTGAATTTTTTGAAAA-TTTGG-GGTCAAAA-TCAAATTTTTAGAAAGTTTAGG
67683 AGTCAAATTTGAATTTTTTGAAAATTTGAGGGTCAAAA
1 AGTCAAATTTGAATTTTTTGAAAATTTG-GGGTCAAAA
67721 AACAATTTTA
Statistics
Matches: 219, Mismatches: 43, Indels: 28
0.76 0.15 0.10
Matches are distributed among these distances:
58 15 0.07
59 72 0.33
60 70 0.32
61 62 0.28
ACGTcount: A:0.34, C:0.06, G:0.21, T:0.39
Consensus pattern (59 bp):
AGTCAAATTTGAATTTTTTGAAAATTTGGGGTCAAAATCAAATTTTTAGAAAGTTTAGG
Found at i:68899 original size:8 final size:9
Alignment explanation
Indices: 68885--68916 Score: 50
Period size: 8 Copynumber: 3.8 Consensus size: 9
68875 AAAATAATAG
68885 TTTATTTTA
1 TTTATTTTA
68894 -TTATTTTA
1 TTTATTTTA
68902 TTTA-TTTA
1 TTTATTTTA
68910 TTTATTT
1 TTTATTT
68917 ACATTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTATTTTA
Found at i:69705 original size:40 final size:41
Alignment explanation
Indices: 69645--69774 Score: 158
Period size: 39 Copynumber: 3.2 Consensus size: 41
69635 GGACTGCCTC
* * *
69645 AATCTGCCCCATGGTTGGGGTTAGATATCGGATGAT-CTTT
1 AATCTGCCCCATGGTCGGGGTAAGAGATCGGATGATGCTTT
* * *
69685 AATCCGCCCCATGGTCGGGGTAAAAGATTGGAT--TGCTTT
1 AATCTGCCCCATGGTCGGGGTAAGAGATCGGATGATGCTTT
* *
69724 AATCTGCCTCATGGTCGGGGTAAGAGATCGGATGATGTTTT
1 AATCTGCCCCATGGTCGGGGTAAGAGATCGGATGATGCTTT
69765 CAATCTGCCC
1 -AATCTGCCC
69775 TCTGATTAAG
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
38 1 0.01
39 33 0.45
40 27 0.36
41 5 0.07
42 8 0.11
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.31
Consensus pattern (41 bp):
AATCTGCCCCATGGTCGGGGTAAGAGATCGGATGATGCTTT
Found at i:69737 original size:39 final size:39
Alignment explanation
Indices: 69625--69774 Score: 131
Period size: 39 Copynumber: 3.7 Consensus size: 39
69615 AACTTTAGGT
* * * * *
69625 GTAAAAGATTGGACTGCCTCAATCTGCCCCATGGTTGGG
1 GTAAAAGATCGGATTGCTTTAATCTGCCCCATGGTCGGG
* * * *
69664 GTTAGATATCGGA-TGATCTTTAATCCGCCCCATGGTCGGG
1 GTAAAAGATCGGATTG--CTTTAATCTGCCCCATGGTCGGG
* *
69704 GTAAAAGATTGGATTGCTTTAATCTGCCTCATGGTCGGG
1 GTAAAAGATCGGATTGCTTTAATCTGCCCCATGGTCGGG
* *
69743 GTAAGAGATCGGATGATGTTTTCAATCTGCCC
1 GTAAAAGATCGGAT--TGCTTT-AATCTGCCC
69775 TCTGATTAAG
Statistics
Matches: 87, Mismatches: 18, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
38 2 0.02
39 42 0.48
40 28 0.32
41 7 0.08
42 8 0.09
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (39 bp):
GTAAAAGATCGGATTGCTTTAATCTGCCCCATGGTCGGG
Found at i:72866 original size:19 final size:19
Alignment explanation
Indices: 72842--72880 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
72832 TACATTTATG
*
72842 AAATAATAAAT-AAATAAAT
1 AAATAA-AAATGAAAAAAAT
72861 AAATAAAAATGAAAAAAAT
1 AAATAAAAATGAAAAAAAT
72880 A
1 A
72881 GTTTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (19 bp):
AAATAAAAATGAAAAAAAT
Found at i:74999 original size:30 final size:30
Alignment explanation
Indices: 74937--75139 Score: 130
Period size: 30 Copynumber: 6.8 Consensus size: 30
74927 CTATTTTCAT
* * *
74937 ATTTTTGGAAAGTTTAGGG-CCAAATTTGA
1 ATTTTTGGAAAGTTTAGGGATCAAATCTAA
*
74966 ATTTTTGGGAAGTTTAGGGATCAAATCTAA
1 ATTTTTGGAAAGTTTAGGGATCAAATCTAA
* * *
74996 ATTTTTGGAAAGTTTAAGGATCAAAACTTA
1 ATTTTTGGAAAGTTTAGGGATCAAATCTAA
** * * * *
75026 ATTTTTTTAAAGTTTGGGGGTTAAAAC-ATA
1 ATTTTTGGAAAGTTTAGGGATCAAATCTA-A
* * * *
75056 TTTTTTGGAAA-TTTAGGGGTTAAAT-AATA
1 ATTTTTGGAAAGTTTAGGGATCAAATCTA-A
** *
75085 ATTTTTTAAAAGTTTAAGGG-TCAAACCTAA
1 ATTTTTGGAAAGTTT-AGGGATCAAATCTAA
* *
75115 ATTTTTAGATAGTTTAGAGG-TCAAA
1 ATTTTTGGAAAGTTTAG-GGATCAAA
75140 AAATAATTTC
Statistics
Matches: 138, Mismatches: 29, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
29 43 0.31
30 90 0.65
31 5 0.04
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.39
Consensus pattern (30 bp):
ATTTTTGGAAAGTTTAGGGATCAAATCTAA
Found at i:75145 original size:60 final size:58
Alignment explanation
Indices: 74975--75148 Score: 154
Period size: 59 Copynumber: 2.9 Consensus size: 58
74965 AATTTTTGGG
* ** *
74975 AAGTTTAGGGATCAAATCTAAATTTTTGGAAAGTTTA-AGGATCAAAACTTAATTTTTTTA
1 AAGTTTAGGG-TCAAAACTAAATTTTTGG-AAGTTTAGAGG-TCAAAAAATAATTTTTTAA
* * * * * * *
75035 AAGTTTGGGGGTTAAAAC-ATATTTTTTGGAAATTTAGGGGTTAAATAATAATTTTTTAA
1 AAGTTT-AGGGTCAAAACTA-AATTTTTGGAAGTTTAGAGGTCAAAAAATAATTTTTTAA
* *
75094 AAGTTTAAGGGTCAAACCTAAATTTTTAGATAGTTTAGAGGTCAAAAAATAATTT
1 AAGTTT-AGGGTCAAAACTAAATTTTTGGA-AGTTTAGAGGTCAAAAAATAATTT
75149 CTAAATAAAA
Statistics
Matches: 88, Mismatches: 21, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
59 43 0.49
60 42 0.48
61 3 0.03
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.39
Consensus pattern (58 bp):
AAGTTTAGGGTCAAAACTAAATTTTTGGAAGTTTAGAGGTCAAAAAATAATTTTTTAA
Found at i:76144 original size:22 final size:21
Alignment explanation
Indices: 76108--76155 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
76098 TTTGAATACA
* * *
76108 TTTTGTTTCTTTTTCTTTTCAT
1 TTTTGTCTCTGTTTCTCTTC-T
76130 TTTTGTCTCTGTTTCTCTTCT
1 TTTTGTCTCTGTTTCTCTTCT
76151 TTTTG
1 TTTTG
76156 CAGGCCTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.02, C:0.17, G:0.08, T:0.73
Consensus pattern (21 bp):
TTTTGTCTCTGTTTCTCTTCT
Found at i:79170 original size:22 final size:22
Alignment explanation
Indices: 79145--79186 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
79135 TATTTGTTAC
*
79145 TAATTTGTTTT-ATTTCTTTTGT
1 TAATTT-TTTTCAATTCTTTTGT
79167 TAATTTTTTTCAATTCTTTT
1 TAATTTTTTTCAATTCTTTT
79187 TATGTGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.71
Consensus pattern (22 bp):
TAATTTTTTTCAATTCTTTTGT
Found at i:89238 original size:3 final size:3
Alignment explanation
Indices: 89230--89267 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
89220 GAGGAAGAGA
*
89230 AAG AAG AAG AAT AAG AAG AAG -AG AAAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG AA
89268 CCTGCCGAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.87
4 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:89245 original size:12 final size:11
Alignment explanation
Indices: 89223--89264 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 11
89213 TCAAGATGAG
89223 GAAGAGAAAGAA
1 GAAGA-AAAGAA
89235 GAAGAATAAGAA
1 GAAGAA-AAGAA
89247 GAAGAGAAAGAA
1 GAAGA-AAAGAA
89259 GAAGAA
1 GAAGAA
89265 GAACCTGCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 2 0.07
12 25 0.89
13 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (11 bp):
GAAGAAAAGAA
Found at i:97405 original size:15 final size:14
Alignment explanation
Indices: 97385--97429 Score: 58
Period size: 12 Copynumber: 3.3 Consensus size: 14
97375 AACAAAAGAA
97385 AAGAGAAGAAGAAGG
1 AAGAGAAGAA-AAGG
97400 AAGAGAAGAAAAGG
1 AAGAGAAGAAAAGG
*
97414 AA-A-AAGAAAATG
1 AAGAGAAGAAAAGG
97426 AAGA
1 AAGA
97430 AGATTTTGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 10 0.36
13 2 0.07
14 6 0.21
15 10 0.36
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (14 bp):
AAGAGAAGAAAAGG
Found at i:99352 original size:29 final size:29
Alignment explanation
Indices: 99310--99367 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
99300 CTCGTGAAGA
99310 AATTAATTCCACATTTTTCGGTTCTCTTT
1 AATTAATTCCACATTTTTCGGTTCTCTTT
99339 AATTAATTCCACATTTTTCGGTTCTCTTT
1 AATTAATTCCACATTTTTCGGTTCTCTTT
99368 TAAAGTGAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.52
Consensus pattern (29 bp):
AATTAATTCCACATTTTTCGGTTCTCTTT
Found at i:104296 original size:19 final size:19
Alignment explanation
Indices: 104254--104372 Score: 105
Period size: 19 Copynumber: 6.3 Consensus size: 19
104244 CAGTACAGTA
* * *
104254 TATTGCTCTCACGAGCAAG
1 TATTGCTCTTACAAGCCAG
*
104273 AATTGCTCTTACAAGCCAG
1 TATTGCTCTTACAAGCCAG
* * *
104292 TATTGTTCTTACGAGCCAA
1 TATTGCTCTTACAAGCCAG
* * *
104311 TACTGCTCTTATGAA-TCAG
1 TATTGCTCTTA-CAAGCCAG
* *
104330 TATTGCTCTTACAAACCAA
1 TATTGCTCTTACAAGCCAG
*
104349 TATTGCTCTTACAAGTCAG
1 TATTGCTCTTACAAGCCAG
104368 TATTG
1 TATTG
104373 TTGATTTCTT
Statistics
Matches: 77, Mismatches: 21, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
18 2 0.03
19 74 0.96
20 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.34
Consensus pattern (19 bp):
TATTGCTCTTACAAGCCAG
Found at i:104306 original size:38 final size:37
Alignment explanation
Indices: 104254--104372 Score: 123
Period size: 38 Copynumber: 3.1 Consensus size: 37
104244 CAGTACAGTA
* * *
104254 TATTGCTCTCACGAGCAAGAATTGCTCTTACAAGCCAG
1 TATTGCTCTTACGAGCAA-TATTGCTCTTACAAGTCAG
* * *
104292 TATTGTTCTTACGAGCCAATACTGCTCTTATGAA-TCAG
1 TATTGCTCTTACGAG-CAATATTGCTCTTA-CAAGTCAG
* *
104330 TATTGCTCTTACAAACCAATATTGCTCTTACAAGTCAG
1 TATTGCTCTTAC-GAGCAATATTGCTCTTACAAGTCAG
104368 TATTG
1 TATTG
104373 TTGATTTCTT
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
37 2 0.03
38 58 0.88
39 6 0.09
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.34
Consensus pattern (37 bp):
TATTGCTCTTACGAGCAATATTGCTCTTACAAGTCAG
Found at i:107215 original size:15 final size:15
Alignment explanation
Indices: 107195--107226 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
107185 TGTGCAAGTG
107195 AACACTTGTCGATGC
1 AACACTTGTCGATGC
*
107210 AACACTTTTCGATGC
1 AACACTTGTCGATGC
107225 AA
1 AA
107227 GTATAATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (15 bp):
AACACTTGTCGATGC
Found at i:115680 original size:22 final size:20
Alignment explanation
Indices: 115662--115700 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
115652 TTTTATTAAT
115662 TTTTTTATATTTTTATATTTC
1 TTTTTTA-ATTTTTATATTTC
115683 TTTTTTAATTTTTA-ATTT
1 TTTTTTAATTTTTATATTT
115701 TATAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 7 0.39
21 7 0.39
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTTAATTTTTATATTTC
Found at i:115686 original size:19 final size:19
Alignment explanation
Indices: 115650--115701 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
115640 TTTAAAAGTC
115650 ATTTTTATTAATTTTTTTAT-
1 ATTTTTA-T-ATTTTTTTATA
*
115670 ATTTTTATATTTCTTTTTTA
1 ATTTTTATATTT-TTTTATA
115690 ATTTTTA-ATTTT
1 ATTTTTATATTTT
115702 ATAATTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 5 0.17
19 10 0.34
20 14 0.48
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (19 bp):
ATTTTTATATTTTTTTATA
Found at i:115698 original size:37 final size:36
Alignment explanation
Indices: 115657--115757 Score: 109
Period size: 37 Copynumber: 2.8 Consensus size: 36
115647 GTCATTTTTA
* * *
115657 TTAATTTTTTTATATTTTTATAT-TTCTTTTTTAATTT
1 TTAATTTTTTTA-ATTTTTAAATGAT-TTTTTCAATTT
* *
115694 TTAA-TTTTATAATTTTTAAATGATTTTTTCCATTT
1 TTAATTTTTTTAATTTTTAAATGATTTTTTCAATTT
115729 TATAATTTTTTTAATTTTTAAAT-ATTTTT
1 T-TAATTTTTTTAATTTTTAAATGATTTTT
115758 CAAATGATGA
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
35 19 0.35
36 16 0.29
37 20 0.36
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (36 bp):
TTAATTTTTTTAATTTTTAAATGATTTTTTCAATTT
Found at i:115701 original size:6 final size:7
Alignment explanation
Indices: 115663--115712 Score: 50
Period size: 8 Copynumber: 7.0 Consensus size: 7
115653 TTTATTAATT
115663 TTTTTATA
1 TTTTTA-A
115671 TTTTTATA
1 TTTTTA-A
*
115679 TTTCT--
1 TTTTTAA
115684 TTTTTAA
1 TTTTTAA
115691 TTTTTAA
1 TTTTTAA
115698 TTTTATAA
1 TTTT-TAA
115706 TTTTTAA
1 TTTTTAA
115713 ATGATTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
5 4 0.11
7 14 0.38
8 19 0.51
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTTAA
Found at i:115706 original size:15 final size:15
Alignment explanation
Indices: 115683--115712 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
115673 TTTATATTTC
*
115683 TTTTTTAATTTTTAA
1 TTTTATAATTTTTAA
115698 TTTTATAATTTTTAA
1 TTTTATAATTTTTAA
115713 ATGATTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTATAATTTTTAA
Found at i:116221 original size:11 final size:11
Alignment explanation
Indices: 116205--116234 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
116195 AATAAGGTCG
116205 AAGTTATAATT
1 AAGTTATAATT
116216 AAGTTATAATT
1 AAGTTATAATT
*
116227 AAATTATA
1 AAGTTATA
116235 TATTTTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (11 bp):
AAGTTATAATT
Found at i:117850 original size:188 final size:188
Alignment explanation
Indices: 117533--117907 Score: 696
Period size: 188 Copynumber: 2.0 Consensus size: 188
117523 TCAGTCAATT
117533 CATTACTCTTTTAAATTATTCAAATAATGTTGAGGTTCAAATTAACGAGAAAGATCGTTCTATGC
1 CATTACTCTTTTAAATTATTCAAATAATGTTGAGGTTCAAATTAACGAGAAAGATCGTTCTATGC
*
117598 TATTGTTATGCTCTTTATCCCATTCATTAAAGCCTTTTAAGGAAACCATGATTTATGGGAGAGAT
66 TATTGTTATGCTCTTTATCCCATTCATAAAAGCCTTTTAAGGAAACCATGATTTATGGGAGAGAT
117663 AATTTCTCATTTGAGGATGTGAAGGGTCATTTGTTAAGCAAAGACAAACTCGATAATC
131 AATTTCTCATTTGAGGATGTGAAGGGTCATTTGTTAAGCAAAGACAAACTCGATAATC
* *
117721 CATTACTCTTTTAAATTATTTAAATAATGTTGAGGTTCAAATTAATGAGAAAGATCGTTCTATGC
1 CATTACTCTTTTAAATTATTCAAATAATGTTGAGGTTCAAATTAACGAGAAAGATCGTTCTATGC
* *
117786 TATTGTTGTGCTCTTTATCCCATTCATAAAAGTCTTTTAAGGAAACCATGATTTATGGGAGAGAT
66 TATTGTTATGCTCTTTATCCCATTCATAAAAGCCTTTTAAGGAAACCATGATTTATGGGAGAGAT
*
117851 AATTTCTCATTTGAGGATGTGAAGGGTCATTTGTTGAGCAAAGACAAACTCGATAAT
131 AATTTCTCATTTGAGGATGTGAAGGGTCATTTGTTAAGCAAAGACAAACTCGATAAT
117908 GAGTTTGATC
Statistics
Matches: 181, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
188 181 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (188 bp):
CATTACTCTTTTAAATTATTCAAATAATGTTGAGGTTCAAATTAACGAGAAAGATCGTTCTATGC
TATTGTTATGCTCTTTATCCCATTCATAAAAGCCTTTTAAGGAAACCATGATTTATGGGAGAGAT
AATTTCTCATTTGAGGATGTGAAGGGTCATTTGTTAAGCAAAGACAAACTCGATAATC
Found at i:124718 original size:20 final size:20
Alignment explanation
Indices: 124681--124717 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
124671 TAAATTAGAA
124681 AAAAAAGAAAGAGAAAAAGT
1 AAAAAAGAAAGAGAAAAAGT
124701 AAAAAAGAAA-AGAAAAA
1 AAAAAAGAAAGAGAAAAA
124718 ATAACTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (20 bp):
AAAAAAGAAAGAGAAAAAGT
Found at i:124753 original size:22 final size:21
Alignment explanation
Indices: 124715--124755 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
124705 AAGAAAAGAA
124715 AAAATAACTTATATATTAATT
1 AAAATAACTTATATATTAATT
* *
124736 AAAATTACTATATTTATTAA
1 AAAATAACT-TATATATTAA
124756 ATATTTTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAATAACTTATATATTAATT
Found at i:128376 original size:65 final size:65
Alignment explanation
Indices: 128247--128368 Score: 172
Period size: 65 Copynumber: 1.9 Consensus size: 65
128237 TTTACATTTT
* * **
128247 GTTTAATTTAATCTTTGGTCCCTTTATATTGTTTTTTGCTTCAACTTAATTGCTTTCCAGCGTTG
1 GTTTAACTTAATCTTTGGTCCCTTTAAATTGCCTTTTGCTTCAACTTAATTGCTTTCCAGCGTTG
* * * *
128312 GTTTAACTTCATCTTTGGTCCCTTTAAATTGCCTTTTGCTTTAATTTGATTGCTTTC
1 GTTTAACTTAATCTTTGGTCCCTTTAAATTGCCTTTTGCTTCAACTTAATTGCTTTC
128369 TGGCGTTGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
65 49 1.00
ACGTcount: A:0.16, C:0.18, G:0.13, T:0.52
Consensus pattern (65 bp):
GTTTAACTTAATCTTTGGTCCCTTTAAATTGCCTTTTGCTTCAACTTAATTGCTTTCCAGCGTTG
Done.