Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012429.1 Corchorus olitorius cultivar O-4 contig12462, 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: 41930
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:128 original size:16 final size:15
Alignment explanation
Indices: 94--131 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
84 AAGACCTTGC
94 AAAAAG-AGGAAAAT
1 AAAAAGAAGGAAAAT
*
108 AAAAAGAAGTAAAAGT
1 AAAAAGAAGGAAAA-T
124 AAAAAGAA
1 AAAAAGAA
132 AACCTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 6 0.29
16 9 0.43
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (15 bp):
AAAAAGAAGGAAAAT
Found at i:4530 original size:11 final size:11
Alignment explanation
Indices: 4510--4544 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
4500 TTGATAGCGC
4510 AACAAAAACAA
1 AACAAAAACAA
*
4521 AACGAAAACAA
1 AACAAAAACAA
4532 AACAAAAACAA
1 AACAAAAACAA
4543 AA
1 AA
4545 AACAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:18229 original size:22 final size:23
Alignment explanation
Indices: 18187--18290 Score: 107
Period size: 22 Copynumber: 4.9 Consensus size: 23
18177 TAATTTTGGA
*
18187 GGTTA-TCAAAA-TTCATAGTGT
1 GGTTACTCAAAATTTTATAGTGT
18208 GGTTACT-AAAATTTTATAGTGT
1 GGTTACTCAAAATTTTATAGTGT
* *
18230 GGTT-CTCAAAAGTTTATAGTCT
1 GGTTACTCAAAATTTTATAGTGT
*
18252 --TTA-TCAAAATTTTATAGTGA
1 GGTTACTCAAAATTTTATAGTGT
*
18272 GGTTAC-CAAAATTTCATAG
1 GGTTACTCAAAATTTTATAG
18291 ACAGGATATT
Statistics
Matches: 69, Mismatches: 7, Indels: 13
0.78 0.08 0.15
Matches are distributed among these distances:
20 16 0.23
21 11 0.16
22 42 0.61
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (23 bp):
GGTTACTCAAAATTTTATAGTGT
Found at i:18363 original size:22 final size:22
Alignment explanation
Indices: 18317--18557 Score: 84
Period size: 22 Copynumber: 10.8 Consensus size: 22
18307 TTATATTGTA
* *
18317 GTTATCACAATTTCATGA-GAT
1 GTTATCAAAATTTCATAAGGAT
18338 GTTATCAAAATTTCATAAGGAT
1 GTTATCAAAATTTCATAAGGAT
* * *
18360 GTTATTAAAATAAAATTTCAAAAGTAT
1 GTTA-T----CAAAATTTCATAAGGAT
* * * *
18387 TTTATCAAAAGTTCATATGGAG
1 GTTATCAAAATTTCATAAGGAT
* * *
18409 GTTATCGAAA-TTCAT-GGGAAG
1 GTTATCAAAATTTCATAAGG-AT
* * * *
18430 GTTATCAAACTTTCACAGGGAG
1 GTTATCAAAATTTCATAAGGAT
***
18452 GTTA-CTAAAATTTCAT-ACTCT
1 GTTATC-AAAATTTCATAAGGAT
*
18473 GGTTATCAAAATTTCATACGGA-
1 -GTTATCAAAATTTCATAAGGAT
* * **
18495 GATTAACAAAATCTCAT-AGGGC
1 G-TTATCAAAATTTCATAAGGAT
* *
18517 GATTATCAAAATTTTATATGGA-
1 G-TTATCAAAATTTCATAAGGAT
*
18539 GATTATCAAAATTTGATAA
1 G-TTATCAAAATTTCATAA
18558 TGTGATTATA
Statistics
Matches: 164, Mismatches: 40, Indels: 31
0.70 0.17 0.13
Matches are distributed among these distances:
20 2 0.01
21 35 0.21
22 102 0.62
23 7 0.04
26 1 0.01
27 17 0.10
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.34
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAGGAT
Found at i:18391 original size:27 final size:27
Alignment explanation
Indices: 18344--18396 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
18334 AGATGTTATC
* *
18344 AAAATTTCATAAGGATGTTATTAAAAT
1 AAAATTTCAAAAGGATGTTATCAAAAT
* *
18371 AAAATTTCAAAAGTATTTTATCAAAA
1 AAAATTTCAAAAGGATGTTATCAAAA
18397 GTTCATATGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.36
Consensus pattern (27 bp):
AAAATTTCAAAAGGATGTTATCAAAAT
Found at i:18506 original size:44 final size:44
Alignment explanation
Indices: 18429--18552 Score: 117
Period size: 44 Copynumber: 2.8 Consensus size: 44
18419 TTCATGGGAA
* * * * *
18429 GGTTATCAAACTTTCACAGGGAGGTT-ACTAAAATTTCATA-CTC
1 GGTTATCAAAATTTCATACGGAGATTAAC-AAAATTTCATAGCGC
* *
18472 TGGTTATCAAAATTTCATACGGAGATTAACAAAATCTCATAGGGC
1 -GGTTATCAAAATTTCATACGGAGATTAACAAAATTTCATAGCGC
* * * *
18517 GATTATCAAAATTTTATATGGAGATTATCAAAATTT
1 GGTTATCAAAATTTCATACGGAGATTAACAAAATTT
18553 GATAATGTGA
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
44 63 0.95
45 3 0.05
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (44 bp):
GGTTATCAAAATTTCATACGGAGATTAACAAAATTTCATAGCGC
Found at i:18564 original size:22 final size:22
Alignment explanation
Indices: 18475--18573 Score: 92
Period size: 22 Copynumber: 4.5 Consensus size: 22
18465 CATACTCTGG
* *
18475 TTATCAAAATTTCATACGGAGA
1 TTATCAAAATTTGATATGGAGA
* * * * *
18497 TTAACAAAATCTCATAGGGCGA
1 TTATCAAAATTTGATATGGAGA
*
18519 TTATCAAAATTTTATATGGAGA
1 TTATCAAAATTTGATATGGAGA
*
18541 TTATCAAAATTTGATAAT-GTGA
1 TTATCAAAATTTGAT-ATGGAGA
*
18563 TTATAAAAATT
1 TTATCAAAATT
18574 ACATAGTGAG
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
22 62 0.97
23 2 0.03
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTGATATGGAGA
Found at i:18565 original size:44 final size:44
Alignment explanation
Indices: 18475--18578 Score: 118
Period size: 44 Copynumber: 2.4 Consensus size: 44
18465 CATACTCTGG
*
18475 TTATCAAAATTTCATACGGAGATTAACAAAATCTCATAGGGCGA
1 TTATCAAAATTTCATACGGAGATTAACAAAATCTCATAAGGCGA
* * * * * * *
18519 TTATCAAAATTTTATATGGAGATTATCAAAATTTGATAATGTGA
1 TTATCAAAATTTCATACGGAGATTAACAAAATCTCATAAGGCGA
* *
18563 TTATAAAAATTACATA
1 TTATCAAAATTTCATA
18579 GTGAGATAGA
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (44 bp):
TTATCAAAATTTCATACGGAGATTAACAAAATCTCATAAGGCGA
Found at i:18683 original size:22 final size:23
Alignment explanation
Indices: 18655--18717 Score: 85
Period size: 22 Copynumber: 2.8 Consensus size: 23
18645 TAATTTCACA
*
18655 GAGGTTAACAAAATTTCATG-GG
1 GAGGTTATCAAAATTTCATGTGG
*
18677 GAGGTTATCAAAATTTTA-GTGG
1 GAGGTTATCAAAATTTCATGTGG
*
18699 GAGATTATCAAAATTTCAT
1 GAGGTTATCAAAATTTCAT
18718 AGTGTGGTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (23 bp):
GAGGTTATCAAAATTTCATGTGG
Found at i:18858 original size:22 final size:21
Alignment explanation
Indices: 18790--18867 Score: 61
Period size: 22 Copynumber: 3.6 Consensus size: 21
18780 ATGAGTTCAT
18790 CAAAA-TTTATAGTA-AGTTAA
1 CAAAATTTTATAG-AGAGTTAA
* * **
18810 CAAAATTTTGATAGTGTGGTTCT
1 CAAAATTTT-ATAGAG-AGTTAA
18833 CAAAATTTTATAGAGAGATTAA
1 CAAAATTTTATAGAGAG-TTAA
*
18855 CAAAATTTCATAG
1 CAAAATTTTATAG
18868 GTAAGTTATC
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
20 5 0.11
21 4 0.09
22 23 0.52
23 12 0.27
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (21 bp):
CAAAATTTTATAGAGAGTTAA
Found at i:18907 original size:22 final size:21
Alignment explanation
Indices: 18882--19021 Score: 101
Period size: 22 Copynumber: 6.6 Consensus size: 21
18872 GTTATCGTAA
18882 CAAAATTTCATAAGATGGTTAT
1 CAAAATTTCAT-AGATGGTTAT
* *
18904 CAAAATTTCATGAGGTGGTTTT
1 CAAAATTTCAT-AGATGGTTAT
*
18926 CAAAATTTCAT-GA-GGTTAC
1 CAAAATTTCATAGATGGTTAT
* *
18945 CAAAATTTTATTGGGA-GGTTTAT
1 CAAAATTTCA-T-AGATGG-TTAT
* *
18968 AAAAATTTCATAG-TGAGGTAT
1 CAAAATTTCATAGATG-GTTAT
* *
18989 CACAATTT-ATGGTATGGTTAT
1 CAAAATTTCATAG-ATGGTTAT
19010 CAAAATTTCATA
1 CAAAATTTCATA
19022 AAGTGATTAC
Statistics
Matches: 91, Mismatches: 18, Indels: 18
0.72 0.14 0.14
Matches are distributed among these distances:
19 13 0.14
20 5 0.05
21 22 0.24
22 40 0.44
23 11 0.12
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (21 bp):
CAAAATTTCATAGATGGTTAT
Found at i:18950 original size:41 final size:44
Alignment explanation
Indices: 18882--19065 Score: 125
Period size: 44 Copynumber: 4.3 Consensus size: 44
18872 GTTATCGTAA
* *
18882 CAAAATTTCATAAGATGGTTATCAAAATTTCA-TGAGGTGGTTT-T
1 CAAAATTTCAT-AGATGGTTACCAAAATTTCATTG-GGAGGTTTAT
*
18926 CAAAATTTCAT-GA-GGTTACCAAAATTTTATTGGGAGGTTTAT
1 CAAAATTTCATAGATGGTTACCAAAATTTCATTGGGAGGTTTAT
* * * * *
18968 AAAAATTTCATAG-TGAGGTATCACAATTT-A-TGGTATGG-TTAT
1 CAAAATTTCATAGATG-GTTACCAAAATTTCATTGGGA-GGTTTAT
* * * * * *
19010 CAAAATTTCATAAAGTGATTACCAATATTTTATCGGAAGG-TTAT
1 CAAAATTTCATAGA-TGGTTACCAAAATTTCATTGGGAGGTTTAT
*
19054 CAAATTTTCATA
1 CAAAATTTCATA
19066 ATGTAATATG
Statistics
Matches: 112, Mismatches: 18, Indels: 20
0.75 0.12 0.13
Matches are distributed among these distances:
41 21 0.19
42 34 0.30
43 13 0.12
44 41 0.37
45 3 0.03
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (44 bp):
CAAAATTTCATAGATGGTTACCAAAATTTCATTGGGAGGTTTAT
Found at i:19115 original size:22 final size:22
Alignment explanation
Indices: 19079--19195 Score: 69
Period size: 22 Copynumber: 5.4 Consensus size: 22
19069 TAATATGCGC
*
19079 TTAACAACATTTCATTGGGAAG
1 TTAACAAAATTTCATTGGGAAG
* * **
19101 TTATCAAAATTTCATAGGGCGG
1 TTAACAAAATTTCATTGGGAAG
* **
19123 TTAACAAAATTT-ATTAGGTGG
1 TTAACAAAATTTCATTGGGAAG
** * *
19144 TTATTAAAATTTTATAGGG-AG
1 TTAACAAAATTTCATTGGGAAG
* *
19165 TGTAGCAAAATTTTATAT-GGAAG
1 T-TAACAAAATTTCAT-TGGGAAG
19188 TTAACAAA
1 TTAACAAA
19196 TTTTAATATT
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
21 18 0.25
22 52 0.71
23 3 0.04
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (22 bp):
TTAACAAAATTTCATTGGGAAG
Found at i:19161 original size:21 final size:21
Alignment explanation
Indices: 19100--19225 Score: 69
Period size: 22 Copynumber: 5.8 Consensus size: 21
19090 TCATTGGGAA
*
19100 GTTATCAAAATTTCATAGGGCG
1 GTTATCAAAATTTTATA-GGCG
* *
19122 GTTAACAAAA-TTTATTAGGTG
1 GTTATCAAAATTTTA-TAGGCG
*
19143 GTTATTAAAATTTTATAGG-G
1 GTTATCAAAATTTTATAGGCG
* **
19163 AGTGTAGCAAAATTTTATATGGAA
1 -GT-TATCAAAATTTTATA-GGCG
* * *
19187 GTTAAC-AAATTTTAATATTGAG
1 GTTATCAAAATTTT-ATA-GGCG
*
19209 GTTCTCAAAATTTTATA
1 GTTATCAAAATTTTATA
19226 ATCTCGTCAT
Statistics
Matches: 83, Mismatches: 13, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
20 1 0.01
21 27 0.33
22 44 0.53
23 11 0.13
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.39
Consensus pattern (21 bp):
GTTATCAAAATTTTATAGGCG
Found at i:19441 original size:22 final size:21
Alignment explanation
Indices: 19410--19553 Score: 92
Period size: 22 Copynumber: 6.6 Consensus size: 21
19400 TGAATATTTT
19410 TATGAAATTTTGATAACTACCC
1 TATGAAATTTTGATAACTA-CC
* *
19432 TATTAAATTTTGATAATTACC
1 TATGAAATTTTGATAACTACC
* ** * *
19453 TATGAAATTGTGATAGGTTGCA
1 TATGAAATTTTGATA-ACTACC
* * *
19475 TATAAAACTTTGATAACCTAAC
1 TATGAAATTTTGATAA-CTACC
* *
19497 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTGAT-AA-CTACC
*
19520 TATGAAATTTTG-TAACCTTCCC
1 TATGAAATTTTGATAA-C-TACC
*
19542 TATGAGATTTTG
1 TATGAAATTTTG
19554 TTAATCTCCC
Statistics
Matches: 95, Mismatches: 23, Indels: 8
0.75 0.18 0.06
Matches are distributed among these distances:
21 19 0.20
22 59 0.62
23 17 0.18
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (21 bp):
TATGAAATTTTGATAACTACC
Found at i:20990 original size:46 final size:45
Alignment explanation
Indices: 20928--21024 Score: 151
Period size: 46 Copynumber: 2.1 Consensus size: 45
20918 GAAATTGTAC
*
20928 AACCTCGCTATGAAATTTTGATAAACCT-TCCTATAAAATTTTGAT
1 AACCTCGCTATAAAATTTTGATAAACCTCT-CTATAAAATTTTGAT
*
20973 AAACCTCTCTATAAAATTTTGATAAACCTCTCTATAAAATTTTGAT
1 -AACCTCGCTATAAAATTTTGATAAACCTCTCTATAAAATTTTGAT
21019 AACCTC
1 AACCTC
21025 CTTATGAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
45 6 0.12
46 41 0.85
47 1 0.02
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (45 bp):
AACCTCGCTATAAAATTTTGATAAACCTCTCTATAAAATTTTGAT
Found at i:21034 original size:22 final size:21
Alignment explanation
Indices: 20613--21276 Score: 243
Period size: 22 Copynumber: 30.7 Consensus size: 21
20603 ATTACACTAT
* *
20613 TTTTGATAACTTTCTTATGAAA
1 TTTTGATAAC-CTCCTATGAAA
*
20635 TTTTAATAACCTTCCTATGAAA
1 TTTTGATAACC-TCCTATGAAA
* * * *
20657 TTTTAATAACGATACTATGGAA
1 TTTTGATAAC-CTCCTATGAAA
* * **
20679 TTTCGAGAACCTTTTTAT-AAA
1 TTTTGATAACC-TCCTATGAAA
** ** *
20700 TTTTTTTTAACCTTTTTATAAAA
1 -TTTTGATAACC-TCCTATGAAA
* * *
20723 TTTTGTTAACCTCCTTAAGGAA
1 TTTTGATAACCTCC-TATGAAA
*
20745 TTTTGA-AGACCTCACTATGAATT
1 TTTTGATA-ACCTC-CTATGAA-A
* *
20768 TTTTTATAACTTCCTAATGAAA
1 TTTTGATAACCTCCT-ATGAAA
* * *
20790 TTTTGATTACCAACACTATGAGA
1 TTTTGATAACC-TC-CTATGAAA
* *
20813 TGTTGATAACCTCCATATGATA
1 TTTTGATAACCTCC-TATGAAA
* * *
20835 TATTGATAACCACGTTATGAAAA
1 TTTTGATAACCTC-CTATG-AAA
*
20858 TTTT-AAAACCTCCATATG-AA
1 TTTTGATAACCTCC-TATGAAA
* * *
20878 TTGTT-AGTAATCACACTCTGAAA
1 TT-TTGA-TAACCTC-CTATGAAA
* *
20901 -TTTGATAATCACACTATGAAA
1 TTTTGATAACCTC-CTATGAAA
* *
20922 TTGT-ACAACCTCGCTATGAAA
1 TTTTGATAACCTC-CTATGAAA
*
20943 TTTTGATAAACCTTCCTATAAAA
1 TTTTGAT-AACC-TCCTATGAAA
*
20966 TTTTGATAAACCTCTCTATAAAA
1 TTTTGAT-AACCTC-CTATGAAA
*
20989 TTTTGATAAACCTCTCTATAAAA
1 TTTTGAT-AACCTC-CTATGAAA
21012 TTTTGATAACCTCCTTATGAAA
1 TTTTGATAACCTCC-TATGAAA
* * *
21034 TCTTGAT----TACTA-CAAA
1 TTTTGATAACCTCCTATGAAA
* * **
21050 TTTTGATAACCTCCCCATCATT
1 TTTTGATAACCT-CCTATGAAA
* *
21072 TTTTGATAACCTCATTATGCAA
1 TTTTGATAACCTC-CTATGAAA
* *
21094 TTTTGTTAATCTCCCTATGAAA
1 TTTTGATAACCT-CCTATGAAA
* * *
21116 TTTTGATCTACATACTATGAAA
1 TTTTGAT-AACCTCCTATGAAA
*
21138 TTTTGATAACCCTCTTATGAAA
1 TTTTGATAA-CCTCCTATGAAA
* *
21160 TTTTGA-AAACTAAACTATGAAA
1 TTTTGATAACCT--CCTATGAAA
*
21182 TTTTGATATCCTCC-ATGAAA
1 TTTTGATAACCTCCTATGAAA
* *
21202 TTTTGATTA-CTCCATAATAAAA
1 TTTTGATAACCTCC-T-ATGAAA
* *
21224 GTTTAATAACCTGCC----AAA
1 TTTTGATAACCT-CCTATGAAA
* *
21242 -TTTGGTAACCATACTATGAAA
1 TTTTGATAACC-TCCTATGAAA
21263 TTTTGATAACCTCC
1 TTTTGATAACCTCC
21277 CCAGAAATAC
Statistics
Matches: 485, Mismatches: 105, Indels: 105
0.70 0.15 0.15
Matches are distributed among these distances:
16 9 0.02
17 11 0.02
18 6 0.01
19 4 0.01
20 20 0.04
21 54 0.11
22 264 0.54
23 110 0.23
24 7 0.01
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (21 bp):
TTTTGATAACCTCCTATGAAA
Found at i:21317 original size:22 final size:22
Alignment explanation
Indices: 21287--21457 Score: 91
Period size: 22 Copynumber: 7.9 Consensus size: 22
21277 CCAGAAATAC
* * *
21287 CATTATGAAATTTTGGTAATCA
1 CATTTTGAAATTTTGATAACCA
* *
21309 CATTTTGAAAATTTGATAACCT
1 CATTTTGAAATTTTGATAACCA
*
21331 C-TTTATGAAATTTTGATAACCT
1 CATTT-TGAAATTTTGATAACCA
* * * *
21353 C--TATAAAATTTTGTTGACC-
1 CATTTTGAAATTTTGATAACCA
* * *
21372 CCTCTATGAAATTTTGATAATCA
1 CAT-TTTGAAATTTTGATAACCA
* *
21395 CATTAT-ATAATTTTGATAACCT
1 CATTTTGA-AATTTTGATAACCA
*** *
21417 TGCTTTGAAATTTTGATAACAA
1 CATTTTGAAATTTTGATAACCA
* *
21439 CACTATGAAATTTTGATAA
1 CATTTTGAAATTTTGATAA
21458 TCTTCCTATA
Statistics
Matches: 116, Mismatches: 26, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
19 1 0.01
20 13 0.11
21 5 0.04
22 94 0.81
23 3 0.03
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.42
Consensus pattern (22 bp):
CATTTTGAAATTTTGATAACCA
Found at i:21409 original size:44 final size:42
Alignment explanation
Indices: 21290--21478 Score: 136
Period size: 44 Copynumber: 4.4 Consensus size: 42
21280 GAAATACCAT
* * * * *
21290 TATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAATCACATTAT-AAATTTTGAT-ACCCCTC
*
21334 TATGAAATTTTGATAA-C-C-TCTATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAATCACAT-TAT-AAATTTTGAT-ACCCCTC
* *
21376 TATGAAATTTTGATAATCACATTATATAATTTTGATAACCTTGC
1 TATGAAATTTTGATAATCACATTATA-AATTTTGATACCCCT-C
* * ** *
21420 TTTGAAATTTTGATAA-CAACACTATGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAATC-ACATTAT-AAATTTTGATACCCCT-C
21464 TAT-AAATTTTGATAA
1 TATGAAATTTTGATAA
21479 ACCGATCTCT
Statistics
Matches: 121, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
41 1 0.01
42 32 0.26
43 20 0.17
44 66 0.55
45 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (42 bp):
TATGAAATTTTGATAATCACATTATAAATTTTGATACCCCTC
Found at i:21466 original size:22 final size:22
Alignment explanation
Indices: 21314--21704 Score: 113
Period size: 22 Copynumber: 17.6 Consensus size: 22
21304 AATCACATTT
* * **
21314 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACTTCACTA
*
21336 TGAAATTTTGATAAC--CTCTA
1 TGAAATTTTGATAACTTCACTA
* * * ** *
21356 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACTTCACTA
21378 TGAAATTTTGATAA--TCACATTA
1 TGAAATTTTGATAACTTCAC--TA
* *
21400 T-ATAATTTTGATAACCTT-GCTT
1 TGA-AATTTTGATAA-CTTCACTA
**
21422 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACTTCACTA
21444 TGAAATTTTGATAATCTTC-CTA
1 TGAAATTTTGATAA-CTTCACTA
* *
21466 T-AAATTTTGATAAACCGATCTCTA
1 TGAAATTTTGAT-AA-C-TTCACTA
*
21490 TGAAATTTCGATAA--TCACTCTA
1 TGAAATTTTGATAACTTCA--CTA
*
21512 TGAGA-TTTGATAACCTT--CTA
1 TGAAATTTTGATAA-CTTCACTA
* *
21532 TCAAATTTTGGT-AC-TC-CTTA
1 TGAAATTTTGATAACTTCAC-TA
*
21552 TGAAATTGAGACTTTTATAATCTTCA-TA
1 TGAAA-T-----TTTGATAA-CTTCACTA
**
21580 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACTTCACTA
* *
21602 TGAAATTTTGATAAAC-TCCCCA
1 TGAAATTTTGAT-AACTTCACTA
* *
21624 TGAAATATT-AGTAACCTC-CTTA
1 TGAAATTTTGA-TAACTTCAC-TA
* *
21646 TGAAATTTTGTTAACGTACACTA
1 TGAAATTTTGATAAC-TTCACTA
* * *
21669 TAAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACTTCACTA
*
21691 TGACATTTTGATAA
1 TGAAATTTTGATAA
21705 TCTCTTTGAT
Statistics
Matches: 277, Mismatches: 49, Indels: 86
0.67 0.12 0.21
Matches are distributed among these distances:
18 1 0.00
19 2 0.01
20 33 0.12
21 35 0.13
22 148 0.53
23 21 0.08
24 11 0.04
25 10 0.04
26 4 0.01
27 2 0.01
28 8 0.03
29 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACTTCACTA
Found at i:21653 original size:66 final size:65
Alignment explanation
Indices: 21578--21943 Score: 232
Period size: 66 Copynumber: 5.3 Consensus size: 65
21568 ATAATCTTCA
* *
21578 TATGAAATTTTGATAACCACACTATGAAATTTTGATAAACTCCCCATGAAATATTAGTAACCTCC
1 TATGAAATTTTGATAACCACACTATGAAATTTCGATAACCTCCCCATGAAAT-TTAGTAACCTCC
21643 T
65 T
* * * * * * * *
21644 TATGAAATTTTGTTAACGTACACTAT-AAAATTCTTATAACCTCGCTATGACATTTTGATAATCT
1 TATGAAATTTTGATAAC-CACACTATGAAATTTC-GATAACCTCCCCATGAAATTTAG-TAA-C-
*
21708 CTTTGATAACATTT
61 C-----T--C--CT
* * * * * * * * * *
21722 CTATAAAATTGTGATAAGCACACTATGAAGTTTCAATAACCTTCCTAAGAAATTTTAATAACCTG
1 -TATGAAATTTTGATAACCACACTATGAAATTTCGATAACCTCCCCATGAAA-TTTAGTAACCTC
*
21787 AT
64 CT
* * * *
21789 ACTATGAAATTTTGGTAACCACACTATGAAATTTCGATAACCTTCCCATGAAATTTTGATAACTT
1 --TATGAAATTTTGATAACCACACTATGAAATTTCGATAACCTCCCCATGAAATTTAG-TAACCT
*
21854 CCA
63 CCT
* * * * *
21857 TATGAAATTTTGGTAACCACATTATGGAATTTCGATAACCTCCTCATGAAATTATATTAACCAT-
1 TATGAAATTTTGATAACCACACTATGAAATTTCGATAACCTCCCCATGAAATT-TAGTAACC-TC
21921 CT
64 CT
21923 TATGAAATTTTGATAACCACA
1 TATGAAATTTTGATAACCACA
21944 TAGAGACCAG
Statistics
Matches: 229, Mismatches: 50, Indels: 42
0.71 0.16 0.13
Matches are distributed among these distances:
66 98 0.43
67 30 0.13
68 50 0.22
69 1 0.00
71 1 0.00
74 1 0.00
76 2 0.01
77 1 0.00
78 24 0.10
79 21 0.09
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.36
Consensus pattern (65 bp):
TATGAAATTTTGATAACCACACTATGAAATTTCGATAACCTCCCCATGAAATTTAGTAACCTCCT
Found at i:21654 original size:114 final size:115
Alignment explanation
Indices: 21449--21655 Score: 253
Period size: 112 Copynumber: 1.8 Consensus size: 115
21439 CACTATGAAA
* * * * *
21449 TTTTGATAATCTTCCTATAAATTTTGATAAACCGATCTCTATGAAATTTCGATAATCACTCTATG
1 TTTTGATAATCTTCATATAAATTTTGATAAACCGATCACTATGAAATTTCGATAAACACCCCATG
* *
21514 AGATTTGATAACCTTCTATCAAATTTTGGTACTCCTTATGAAATTGAGAC
66 AAATTTGATAACCTCCTATCAAATTTTGGTACTCCTTATGAAATTGAGAC
* *
21564 TTTT-ATAATCTTCATATGAAATTTTGAT-AACC-A-CACTATGAAATTTTGATAAACTCCCCAT
1 TTTTGATAATCTTCATAT-AAATTTTGATAAACCGATCACTATGAAATTTCGATAAACACCCCAT
*
21625 GAAATATT-AGTAACCTCCTTATGAAATTTTG
65 GAAAT-TTGA-TAACCTCC-TATCAAATTTTG
21656 TTAACGTACA
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
112 27 0.35
113 10 0.13
114 27 0.35
115 14 0.18
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (115 bp):
TTTTGATAATCTTCATATAAATTTTGATAAACCGATCACTATGAAATTTCGATAAACACCCCATG
AAATTTGATAACCTCCTATCAAATTTTGGTACTCCTTATGAAATTGAGAC
Found at i:21781 original size:22 final size:22
Alignment explanation
Indices: 21757--21940 Score: 135
Period size: 22 Copynumber: 8.3 Consensus size: 22
21747 TGAAGTTTCA
* *
21757 ATAACCTTCCTAAGAAATTTTA
1 ATAACCTTCCTATGAAATTTTG
*
21779 ATAACCTGATACTATGAAATTTTG
1 ATAACCT--TCCTATGAAATTTTG
* * *
21803 GTAACC-ACACTATGAAATTTCG
1 ATAACCTTC-CTATGAAATTTTG
*
21825 ATAACCTTCCCATGAAATTTTG
1 ATAACCTTCCTATGAAATTTTG
21847 ATAA-CTTCCATATGAAATTTTG
1 ATAACCTTCC-TATGAAATTTTG
* * * * *
21869 GTAACC-ACATTATGGAATTTCG
1 ATAACCTTC-CTATGAAATTTTG
*
21891 ATAACC-TCCTCATGAAATTAT-
1 ATAACCTTCCT-ATGAAATTTTG
* *
21912 ATTAACCATCTTATGAAATTTTG
1 A-TAACCTTCCTATGAAATTTTG
21935 ATAACC
1 ATAACC
21941 ACATAGAGAC
Statistics
Matches: 126, Mismatches: 25, Indels: 22
0.73 0.14 0.13
Matches are distributed among these distances:
21 7 0.06
22 96 0.76
23 6 0.05
24 17 0.13
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.35
Consensus pattern (22 bp):
ATAACCTTCCTATGAAATTTTG
Found at i:22496 original size:166 final size:173
Alignment explanation
Indices: 22159--22500 Score: 468
Period size: 176 Copynumber: 2.0 Consensus size: 173
22149 AATAGTAAAG
* * *
22159 GAAATTTGTATGTTCATCAACGAAAATCAATTTGACAAACTTATAATTCGGTTTAAATTGAAAGT
1 GAAATTTGCATGTTAATCAACGAAAATCAATTTGACAAACTTATAATTCGGTCTAAATTGAAAGT
22224 TTTAATTAATTTTTAATAATAAAATTATACTAAATTTTAATAATGAAAATTTAGAAATATATTTG
66 TTTAATTAA-TTTT-AT-ATAAAATTATACTAAATTTTAATAATGAAAATTTAGAAATATATTTG
*
22289 AAAAAAAGGGTGCAATTGGAAAACATAAAGTTCCCCATTATTCGTA
128 AAAAAAAGGGTACAATTGGAAAACATAAAGTTCCCCATTATTCGTA
* * *
22335 GAAATTTGCATGTTAATCAATGAAAATCAATTTTACAAACTTATAA-TCGGGTCTAAATTGAAAT
1 GAAATTTGCATGTTAATCAACGAAAATCAATTTGACAAACTTATAATTC-GGTCTAAATTGAAAG
**
22399 TTTATAATTAA-TTT-T-T-AAA-TA-A-TAAATTTTAATAATGTCAATTTAGAAATATATTTG-
65 TTT-TAATTAATTTTATATAAAATTATACTAAATTTTAATAATGAAAATTTAGAAATATATTTGA
***
22456 AAAAAAGGGTACAATTGGAAAACATAAAGTTTTGCATTATTCGTA
129 AAAAAAGGGTACAATTGGAAAACATAAAGTTCCCCATTATTCGTA
22501 ATTTTGTATA
Statistics
Matches: 152, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
166 41 0.27
167 33 0.22
168 1 0.01
169 2 0.01
170 3 0.02
171 1 0.01
173 1 0.01
175 5 0.03
176 58 0.38
177 7 0.05
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (173 bp):
GAAATTTGCATGTTAATCAACGAAAATCAATTTGACAAACTTATAATTCGGTCTAAATTGAAAGT
TTTAATTAATTTTATATAAAATTATACTAAATTTTAATAATGAAAATTTAGAAATATATTTGAAA
AAAAGGGTACAATTGGAAAACATAAAGTTCCCCATTATTCGTA
Found at i:23955 original size:43 final size:44
Alignment explanation
Indices: 23887--23991 Score: 124
Period size: 43 Copynumber: 2.4 Consensus size: 44
23877 TTGAATATTT
* * * *
23887 TTATGAAAATTTGATAACTACCCTATTAAATTTTGATAACCACC
1 TTATGAAATTTTGATAACTACCCTATAAAATTGTGATAAACACC
* *
23931 TTATGAAATTTTGATAATTA-CCTATAAAATTGTGATAAACTCC
1 TTATGAAATTTTGATAACTACCCTATAAAATTGTGATAAACACC
*
23974 ATATGAAACTTTT-ATAAC
1 TTATGAAA-TTTTGATAAC
23992 CTAACTATGA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
43 30 0.58
44 22 0.42
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (44 bp):
TTATGAAATTTTGATAACTACCCTATAAAATTGTGATAAACACC
Found at i:24000 original size:22 final size:21
Alignment explanation
Indices: 23975--24072 Score: 63
Period size: 21 Copynumber: 4.5 Consensus size: 21
23965 ATAAACTCCA
23975 TATGAAACTTTTATAACCTAAC
1 TATGAAA-TTTTATAACCTAAC
* **
23997 TATGAAAATTTAATAAACCTTCC
1 TATG-AAATTTTAT-AACCTAAC
* **
24020 TATGAAATTTTGTAACCTTCC
1 TATGAAATTTTATAACCTAAC
* **
24041 TATG-ATTTTTGATAACCTCCC
1 TATGAAATTTT-ATAACCTAAC
*
24062 TGTGAAATTTT
1 TATGAAATTTT
24073 GTTAATATCC
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
20 5 0.08
21 23 0.37
22 21 0.34
23 13 0.21
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (21 bp):
TATGAAATTTTATAACCTAAC
Found at i:24038 original size:21 final size:22
Alignment explanation
Indices: 23888--24073 Score: 136
Period size: 22 Copynumber: 8.5 Consensus size: 22
23878 TGAATATTTT
* *
23888 TATGAAAATTTGATAA-CTACCC
1 TATGAAATTTTGATAACCT-TCC
* *
23910 TATTAAATTTTGATAACC-ACC
1 TATGAAATTTTGATAACCTTCC
23931 TTATGAAATTTTGATAA--TTACC
1 -TATGAAATTTTGATAACCTT-CC
* * *
23953 TATAAAATTGTGATAAAC-TCC
1 TATGAAATTTTGATAACCTTCC
**
23974 ATATGAAACTTTT-ATAACCTAAC
1 -TATGAAA-TTTTGATAACCTTCC
* *
23997 TATGAAAATTTAATAAACCTTCC
1 TATGAAATTTTGAT-AACCTTCC
24020 TATGAAATTTTG-TAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* *
24041 TATG-ATTTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
*
24062 TGTGAAATTTTG
1 TATGAAATTTTG
24074 TTAATATCCT
Statistics
Matches: 130, Mismatches: 21, Indels: 26
0.73 0.12 0.15
Matches are distributed among these distances:
20 6 0.05
21 44 0.34
22 59 0.45
23 21 0.16
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:26983 original size:6 final size:6
Alignment explanation
Indices: 26972--27031 Score: 75
Period size: 6 Copynumber: 10.0 Consensus size: 6
26962 TTATATATGG
* * * *
26972 TATAGA TATAGA TATAGA TATATA TATATA TATATA TATATA TATGTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
*
27020 TGTATA TATATA
1 TATATA TATATA
27032 CACACTAGTA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (6 bp):
TATATA
Found at i:26998 original size:4 final size:4
Alignment explanation
Indices: 26972--27031 Score: 75
Period size: 4 Copynumber: 15.0 Consensus size: 4
26962 TTATATATGG
* * * *
26972 TATA GATA TAGA TATA GATA TATA TATA TATA TATA TATA TATA TGTA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
*
27020 TGTA TATA TATA
1 TATA TATA TATA
27032 CACACTAGTA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (4 bp):
TATA
Found at i:28031 original size:42 final size:43
Alignment explanation
Indices: 27986--28070 Score: 134
Period size: 45 Copynumber: 1.9 Consensus size: 43
27976 CTAAATTCTA
*
27986 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTC
1 CTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTATA--C
*
28031 CTCCATCTCTATATAATTCATCAAAATAAAGCTAATATTA
1 CTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTA
28071 ATTGTTGCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (43 bp):
CTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTATAC
Found at i:31517 original size:21 final size:22
Alignment explanation
Indices: 31491--31533 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
31481 AAGAAGGTTA
31491 TACCA-TCTTCTTATTCAAGGT
1 TACCATTCTTCTTATTCAAGGT
*
31512 TACCATTCTTCTTATTTAAGGT
1 TACCATTCTTCTTATTCAAGGT
31534 CACTAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (22 bp):
TACCATTCTTCTTATTCAAGGT
Found at i:32285 original size:160 final size:159
Alignment explanation
Indices: 32089--32407 Score: 548
Period size: 160 Copynumber: 2.0 Consensus size: 159
32079 GATAGTTTAG
*
32089 GAGTGAAAGTTCCAAATTAAAAGTTCAATAGAAAAATTGTATCGATTTTGATAGTTTAAGGACTG
1 GAGTGAAAGTTCCAAATTAAAAATTCAATAGAAAAATTGTATCGATTTTGATAGTTTAAGGACTG
*
32154 AAAGTTGCAAATTAAAAGTTTAGGGGAAAAATGTCATTTTTATAAAAATTTAGGGGGAATGAACT
66 AAAGTTGCAAATTAAAAGTTTAGGGG-AAAATGTCATTTTTATAAAAAATTAGGGGGAATGAACT
*
32219 TAAATTGACATGAATGCCTTCGATAAACTT
130 TAAATTGACATGAATGACTTCGATAAACTT
* *
32249 GAGTGATAGTTCCAAATTAAAAATTCAATTGAAAAATTGTATCGATTTTGATAGTTTAAGGACTG
1 GAGTGAAAGTTCCAAATTAAAAATTCAATAGAAAAATTGTATCGATTTTGATAGTTTAAGGACTG
* *
32314 AAAGTTGCAAATTAAAAGTTTAGGGGGAAATGTCATTTTTATAAAAAATTAGGGGGATTGAACTT
66 AAAGTTGCAAATTAAAAGTTTAGGGGAAAATGTCATTTTTATAAAAAATTAGGGGGAATGAACTT
* *
32379 AAATTGTCATGAATGACTTTGATAAACTT
131 AAATTGACATGAATGACTTCGATAAACTT
32408 AAGTTGTTGC
Statistics
Matches: 150, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
159 62 0.41
160 88 0.59
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (159 bp):
GAGTGAAAGTTCCAAATTAAAAATTCAATAGAAAAATTGTATCGATTTTGATAGTTTAAGGACTG
AAAGTTGCAAATTAAAAGTTTAGGGGAAAATGTCATTTTTATAAAAAATTAGGGGGAATGAACTT
AAATTGACATGAATGACTTCGATAAACTT
Found at i:32696 original size:2 final size:2
Alignment explanation
Indices: 32689--32752 Score: 56
Period size: 2 Copynumber: 31.5 Consensus size: 2
32679 GATATTTTAG
* * * * *
32689 AT AT AT AT AT AT AT AT AA AG AT AA AG AT AA AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
32731 AT AT GT AT CT AT ACT AT AT AT A
1 AT AT AT AT AT AT A-T AT AT AT A
32753 AAAGTACGAA
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
2 47 0.96
3 2 0.04
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.41
Consensus pattern (2 bp):
AT
Found at i:33989 original size:23 final size:24
Alignment explanation
Indices: 33957--34014 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
33947 GGAGATTAAC
*
33957 AAAATCTCATAGGGAAGG-TTACA
1 AAAATTTCATAGGGAAGGTTTACA
**
33980 AAAATTTCATA-GGAAGGTTTATT
1 AAAATTTCATAGGGAAGGTTTACA
34003 AAAATTTCATAG
1 AAAATTTCATAG
34015 TTAGGTTATC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.20
23 24 0.80
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31
Consensus pattern (24 bp):
AAAATTTCATAGGGAAGGTTTACA
Found at i:34199 original size:12 final size:12
Alignment explanation
Indices: 34182--34206 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34172 AGTTAAAACT
34182 TGTATATATATA
1 TGTATATATATA
34194 TGTATATATATA
1 TGTATATATATA
34206 T
1 T
34207 ATAACATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TGTATATATATA
Found at i:34819 original size:2 final size:2
Alignment explanation
Indices: 34814--34840 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
34804 GTTGAAAAAA
34814 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
34841 AAATATGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40155 original size:7 final size:7
Alignment explanation
Indices: 40143--40177 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
40133 ACACTCCATA
40143 AGCAACT
1 AGCAACT
40150 AGCAACT
1 AGCAACT
**
40157 ATTAACT
1 AGCAACT
40164 AGCAACT
1 AGCAACT
40171 AGCAACT
1 AGCAACT
40178 GCCTGATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.20
Consensus pattern (7 bp):
AGCAACT
Found at i:41530 original size:42 final size:43
Alignment explanation
Indices: 41479--41568 Score: 137
Period size: 45 Copynumber: 2.1 Consensus size: 43
41469 GCATTATCTA
* *
41479 ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAAT
1 ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTAAT
41521 ATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAACTAAT
1 ATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAACTAAT
41566 ATT
1 ATT
41569 AATTGTTGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
42 6 0.14
45 37 0.86
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.34
Consensus pattern (43 bp):
ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTAAT
Done.