Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016118.1 Corchorus olitorius cultivar O-4 contig16151, 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: 52957
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:775 original size:33 final size:33
Alignment explanation
Indices: 711--800 Score: 101
Period size: 33 Copynumber: 2.7 Consensus size: 33
701 CATCTAATGT
* * *
711 TAATGTTAACATTTAC-AGAATTCTTCCATCACC
1 TAATATTAACATTT-CTAGAAATCTACCATCACC
*
744 TAATATTAACATTTCTAGAAATCTACTATCACC
1 TAATATTAACATTTCTAGAAATCTACCATCACC
* * *
777 TAATTTTTACATTTGTAGAAATCT
1 TAATATTAACATTTCTAGAAATCT
801 GCATTTCCAA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
32 1 0.02
33 48 0.98
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.40
Consensus pattern (33 bp):
TAATATTAACATTTCTAGAAATCTACCATCACC
Found at i:6002 original size:12 final size:12
Alignment explanation
Indices: 5985--6016 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
5975 ACATGGTAAT
5985 GAAAATAATGAA
1 GAAAATAATGAA
5997 GAAAATAATGAA
1 GAAAATAATGAA
6009 GAAAATAA
1 GAAAATAA
6017 GTTAATGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (12 bp):
GAAAATAATGAA
Found at i:8021 original size:20 final size:20
Alignment explanation
Indices: 7984--8022 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
7974 TACTATTATT
7984 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
8004 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
8023 AATGTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:8213 original size:22 final size:22
Alignment explanation
Indices: 8188--8336 Score: 101
Period size: 22 Copynumber: 6.7 Consensus size: 22
8178 TGTCTCTGTG
*
8188 TGGTTATCAAAATTTCGTAAGA
1 TGGTTATCAAAATTTCATAAGA
* *
8210 TGGTTATTATAATTTCATGAA-A
1 TGGTTATCAAAATTTCAT-AAGA
* * *
8232 AGGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
8254 TGGTTACCAAAATTTCATATAGA
1 TGGTTATCAAAATTTCATA-AGA
* *
8277 -AGTTATCAAAATTTCAT-AGCG
1 TGGTTATCAAAATTTCATAAG-A
* *
8298 TGGTT-CCAAAATTTCATAAAA
1 TGGTTATCAAAATTTCATAAGA
*
8319 TCAGGTTATAAAAATTTC
1 T--GGTTATCAAAATTTC
8337 TTAGGAATGT
Statistics
Matches: 95, Mismatches: 21, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
20 3 0.03
21 12 0.13
22 64 0.67
23 6 0.06
24 10 0.11
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:8456 original size:22 final size:22
Alignment explanation
Indices: 8399--8839 Score: 150
Period size: 22 Copynumber: 19.9 Consensus size: 22
8389 ATCAAAGAGA
* * * *
8399 TTATTAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGTGG
*
8421 TTAT-AAGAAATTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGTGG
* *
8443 TTAACAAAATTTCATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGTGG
* ** *
8465 TTA-CTAATATTTCATAAAGAGG
1 TTATC-AAAATTTCATAGTGTGG
* *
8487 TTATCAGAATTTCATATTGTGG
1 TTATCAAAATTTCATAGTGTGG
**
8509 TTATCAAAATTTTTTAGTGTGAG
1 TTATCAAAATTTCATAGTGTG-G
*
8532 -TATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-TGG
* *
8553 TTATAAAAGTCTCAATTTCATA-AG-GAG
1 TTAT-CAA-----AATTTCATAGTGTG-G
* * ** *
8580 -TACCAAAATTTGATAG-AAGA
1 TTATCAAAATTTCATAGTGTGG
* ** *
8600 TTATC-AAATCTCATAGAATGA
1 TTATCAAAATTTCATAGTGTGG
** *
8621 TTATTGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAGTG-T-GG
* * *
8645 TTTATCAAAATTT-ACAG-GAAGA
1 -TTATCAAAATTTCATAGTG-TGG
* *
8667 TTATCAAAATTTCGTAGTGTTG
1 TTATCAAAATTTCATAGTGTGG
* * *
8689 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGTGTGG
* * *
8711 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGTGTGG
* *
8733 TTATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGTGTGG
* * * * *
8755 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAGTGTGG
** *
8777 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGTGG
* * * *
8799 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGTGG
*
8821 TTACCAAAATTTCATAGTG
1 TTATCAAAATTTCATAGTG
8840 GTATTTCTGG
Statistics
Matches: 314, Mismatches: 79, Indels: 52
0.71 0.18 0.12
Matches are distributed among these distances:
20 17 0.05
21 30 0.10
22 225 0.72
23 12 0.04
24 4 0.01
25 12 0.04
26 3 0.01
27 1 0.00
28 10 0.03
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGG
Found at i:8741 original size:66 final size:66
Alignment explanation
Indices: 8664--8812 Score: 172
Period size: 66 Copynumber: 2.3 Consensus size: 66
8654 ATTTACAGGA
* * ** * * * *
8664 AGATTATCAAAATTTCGTAGTGTTGTTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAAT
1 AGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTATCAAAATTACATAAA
8729 G
66 G
* * * *
8730 TGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAGAGAGGTTATCAAAATTTCATAAA
1 AGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTATCAAAATTACATAAA
8795 G
66 G
* *
8796 AGGTTATCAAATTTTCA
1 AGATTATCAAAATTTCA
8813 AAATGTGATT
Statistics
Matches: 68, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.34
Consensus pattern (66 bp):
AGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTATCAAAATTACATAAA
G
Found at i:8965 original size:22 final size:22
Alignment explanation
Indices: 8918--9420 Score: 307
Period size: 22 Copynumber: 23.0 Consensus size: 22
8908 TTATGGAGTA
*
8918 ATCAAAATTTCA-A-GGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
* *
8938 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
8960 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
* *
8982 TTCAAAATTTCATA-AGAGGGTT
1 ATCAAAATTTCATAGGGA-GGTT
* *
9004 ATCAAAATTTCATA-GTATGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
9025 GATCAAAATTTCATGGGGAGATT
1 -ATCAAAATTTCATAGGGAGGTT
* **
9048 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
9070 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
9092 ATTAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
9108 ATCAAGATTTTATAAGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
9130 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* *
9153 ATCGAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* *
9176 ATCAAAATTTTATAGGAAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
9199 ATCAAAATTTCATAGCGG-GGTT
1 ATCAAAATTTCATAG-GGAGGTT
* * * *
9221 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
9243 ATCAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* *
9265 A-CTAACAA-TTGATATGGAGGTT
1 ATC-AA-AATTTCATAGGGAGGTT
* * * ** **
9287 TTTAAATTTTCATAACGTTGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
9309 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
** * **
9331 ATCAGCATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
* *
9354 ATCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCATAGGGAGGTT
*
9376 ATCAAAATTTCATAGTGAGGTCT
1 ATCAAAATTTCATAGGGAGGT-T
*
9399 -TCAAAATTCCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
9420 A
1 A
9421 ATCTCCCTAC
Statistics
Matches: 375, Mismatches: 85, Indels: 44
0.74 0.17 0.09
Matches are distributed among these distances:
16 8 0.02
17 4 0.01
19 2 0.01
20 13 0.03
21 11 0.03
22 251 0.67
23 85 0.23
24 1 0.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:9160 original size:23 final size:23
Alignment explanation
Indices: 9106--9252 Score: 167
Period size: 23 Copynumber: 6.5 Consensus size: 23
9096 AAATTTGTAG
* *
9106 TTATCAAGATTTTATAAGGAGG-
1 TTATCAAAATTTTATAGGGAGGT
9128 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
*
9151 TTATCGAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
*
9174 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGGAGGT
*
9197 TTATCAAAATTTCATAGCGG-GG-
1 TTATCAAAATTTTATAG-GGAGGT
* * * * *
9219 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTTATAGGGAGGT
9241 TTATCAAAATTT
1 TTATCAAAATTT
9253 CAGAGTGTGA
Statistics
Matches: 111, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
21 2 0.02
22 47 0.42
23 61 0.55
24 1 0.01
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:9479 original size:22 final size:21
Alignment explanation
Indices: 9431--9530 Score: 76
Period size: 22 Copynumber: 4.6 Consensus size: 21
9421 ATCTCCCTAC
*
9431 GAAATTTTGATCTA-CATACTAT
1 GAAATTTTGAT-AACCAT-CTAT
* *
9453 AAAATTTTGATAACCCTCTTAT
1 GAAATTTTGATAACCATC-TAT
* * *
9475 GAAATTTTGAAAACTAAACTAT
1 GAAATTTTGATAAC-CATCTAT
* *
9497 GAAAATTTGATAACCTTCATAT
1 GAAATTTTGATAACCATC-TAT
9519 GAAATTTTGATA
1 GAAATTTTGATA
9531 TCCTCCCTAA
Statistics
Matches: 60, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
21 3 0.05
22 56 0.93
23 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (21 bp):
GAAATTTTGATAACCATCTAT
Found at i:9685 original size:22 final size:22
Alignment explanation
Indices: 9658--10291 Score: 245
Period size: 22 Copynumber: 28.5 Consensus size: 22
9648 ATTTTAAAAA
*
9658 TTTGATAACCTCTTTATGAAAT
1 TTTGATAACCTCTCTATGAAAT
*
9680 TTTGATAACCTCTCTATAAAAT
1 TTTGATAACCTCTCTATGAAAT
* * *
9702 TTTGTTGACCCCTCTATGAAAT
1 TTTGATAACCTCTCTATGAAAT
* *
9724 TTTGATAATCACAT-TAT-ATAAT
1 TTTGATAACCTC-TCTATGA-AAT
*
9746 TTTGATAACCT-TGCTTTGAAAT
1 TTTGATAACCTCT-CTATGAAAT
*** *
9768 TTTGATAATAACACTATGAAAT
1 TTTGATAACCTCTCTATGAAAT
*
9790 TTTGATAATCT-TCCTAT-AAAT
1 TTTGATAACCTCT-CTATGAAAT
9811 TTTGATAATCCGATCTCTATGAAAT
1 TTTGATAA-CC--TCTCTATGAAAT
** * * *
9836 TGGGATAATCACTCTATGAGA-
1 TTTGATAACCTCTCTATGAAAT
*
9857 TTTGATAACCT-TCTATCAAAT
1 TTTGATAACCTCTCTATGAAAT
*
9878 TTTGGT-A-CTC-CTTATGAAATT
1 TTTGATAACCTCTC-TATGAAA-T
* * *
9899 GAGACTTTTATAATCT-TCATATGAAAA
1 -----TTTGATAACCTCTC-TATGAAAT
* * *
9926 TTTGATAA-C-CAC-A-AAAAA
1 TTTGATAACCTCTCTATGAAAT
** * *
9944 AATGATAACCACACTATTG-AAT
1 TTTGATAACCTCTCTA-TGAAAT
* *
9966 TTTGATAACCTCCCCATGAAAT
1 TTTGATAACCTCTCTATGAAAT
*
9988 ATT-AGTAACCTC-CTTATGAAAT
1 TTTGA-TAACCTCTC-TATGAAAT
* * * *
10010 TTTGTTAACCACACTATAAAAT
1 TTTGATAACCTCTCTATGAAAT
* *
10032 TCTT-ATAACCTCGCTATGACATTT
1 T-TTGATAACCTCTCTATGA-A-AT
* *
10056 TGATAATGATAACCTTTCTATAAAAT
1 T--T--TGATAACCTCTCTATGAAAT
* * * *
10082 TGTAATAACCGCACTATGAAAT
1 TTTGATAACCTCTCTATGAAAT
** * *
10104 TTCAATAACCTTTCTAAGAAAT
1 TTTGATAACCTCTCTATGAAAT
* * *
10126 TTTAATAACTTGATCCTATGAAAT
1 TTTGATAACCT-CT-CTATGAAAT
* *
10150 TTTGGTAACCACGT-TATGAAAT
1 TTTGATAACCTC-TCTATGAAAT
*
10172 TTTGATAACCT-TTTCATGAAAT
1 TTTGATAACCTCTCT-ATGAAAT
*
10194 TTTGATAACTTC-CATATGAAAT
1 TTTGATAACCTCTC-TATGAAAT
* * * *
10216 TTTGGTAACCACACTATGGAAT
1 TTTGATAACCTCTCTATGAAAT
10238 TTTGATAACCTC-CTCATGAAAT
1 TTTGATAACCTCTCT-ATGAAAT
* * *
10260 TATAATAACCATCT-TATGATAT
1 TTTGATAACC-TCTCTATGAAAT
10282 TTTGATAACC
1 TTTGATAACC
10292 ACACAGAGAC
Statistics
Matches: 455, Mismatches: 104, Indels: 106
0.68 0.16 0.16
Matches are distributed among these distances:
18 10 0.02
19 5 0.01
20 19 0.04
21 36 0.08
22 306 0.67
23 12 0.03
24 24 0.05
25 12 0.03
26 6 0.01
27 3 0.01
28 22 0.05
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
TTTGATAACCTCTCTATGAAAT
Found at i:9700 original size:44 final size:44
Alignment explanation
Indices: 9628--9818 Score: 151
Period size: 44 Copynumber: 4.4 Consensus size: 44
9618 CCAGAACTAC
* * * * *
9628 TATGAAATTTTGGTGATCACATTTTAAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAACCACATTATAAAATTTTGATAACCTCTT
* * * * *
9672 TATGAAATTTTGATAACCTC-TCTATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACCACAT-TATAAAATTTTGATAACCTCTT
* *
9716 TATGAAATTTTGATAATCACATTATATAATTTTGATAACCT-TGCT
1 TATGAAATTTTGATAACCACATTATAAAATTTTGATAACCTCT--T
** * *
9761 T-TGAAATTTTGATAATAACACTATGAAATTTTGATAA--TCTT
1 TATGAAATTTTGATAACCACATTATAAAATTTTGATAACCTCTT
9802 CCTAT-AAATTTTGATAA
1 --TATGAAATTTTGATAA
9819 TCCGATCTCT
Statistics
Matches: 118, Mismatches: 21, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 16 0.14
44 98 0.83
45 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (44 bp):
TATGAAATTTTGATAACCACATTATAAAATTTTGATAACCTCTT
Found at i:10465 original size:20 final size:20
Alignment explanation
Indices: 10427--10465 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
10417 CATTGACATT
10427 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
10447 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
10466 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:10737 original size:13 final size:14
Alignment explanation
Indices: 10714--10758 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
10704 ATTCGGTCTA
10714 AATTGAAATTTT-AT
1 AATT-AAATTTTAAT
*
10728 AATTAAATTTTAAA
1 AATTAAATTTTAAT
*
10742 AAATAAATTTTAAT
1 AATTAAATTTTAAT
10756 AAT
1 AAT
10759 GTCAATTTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 7 0.27
14 19 0.73
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (14 bp):
AATTAAATTTTAAT
Found at i:13408 original size:61 final size:60
Alignment explanation
Indices: 13326--13441 Score: 144
Period size: 61 Copynumber: 1.9 Consensus size: 60
13316 TTTTTATCAT
* * * * * *
13326 CGTTTGTGAAAATGCTTAAATAAGG-GCTCAAAGGAAAAAAAATGCTTAAATCAAGGCCTAA
1 CGTTTGCGAAAATACTCAAATAAGGATC-CAAAGAAAAAAAAATGCTCAAAT-AAGGCCTAA
*
13387 CGTTTGCGAAAATACTCAAATAAGTATCCAAAGAAAAAAAAATGCTCAAATAAGG
1 CGTTTGCGAAAATACTCAAATAAGGATCCAAAGAAAAAAAAATGCTCAAATAAGG
13442 GTCCAACTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
60 4 0.09
61 42 0.89
62 1 0.02
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.22
Consensus pattern (60 bp):
CGTTTGCGAAAATACTCAAATAAGGATCCAAAGAAAAAAAAATGCTCAAATAAGGCCTAA
Found at i:13466 original size:61 final size:61
Alignment explanation
Indices: 13354--13472 Score: 145
Period size: 61 Copynumber: 2.0 Consensus size: 61
13344 AATAAGGGCT
* * *
13354 CAAAGGAAAAAAAATGCTTAAATCAAGGCCTAACGTTTGCGAAAATACTCAAATAAGTATC
1 CAAAGAAAAAAAAATGCTCAAATCAAGGCCTAACGTTTGAGAAAATACTCAAATAAGTATC
* *
13415 CAAAGAAAAAAAAATGCTCAAAT-AAGGGTCC-AAC-TTTTAGAAAATTGCTCAAATAAGT
1 CAAAGAAAAAAAAATGCTCAAATCAA-GG-CCTAACGTTTGAGAAAA-TACTCAAATAAGT
13473 CTCTGCCGTC
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
60 10 0.20
61 38 0.76
62 2 0.04
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.22
Consensus pattern (61 bp):
CAAAGAAAAAAAAATGCTCAAATCAAGGCCTAACGTTTGAGAAAATACTCAAATAAGTATC
Found at i:13538 original size:22 final size:22
Alignment explanation
Indices: 13492--13550 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
13482 CACTGTGTGG
*
13492 TTATCAAAATTCCATAATAAGA
1 TTATCAAAATTTCATAATAAGA
13514 TTATCAAAATTTCAT-ATGGAA-A
1 TTATCAAAATTTCATAAT--AAGA
*
13536 TTATCAAATTTTCAT
1 TTATCAAAATTTCAT
13551 TGTATGGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 2 0.06
22 29 0.88
23 2 0.06
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAATAAGA
Found at i:15046 original size:2 final size:2
Alignment explanation
Indices: 15039--15064 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15029 GCAACTTGAA
15039 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
15065 CACTTCTCTT
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):
AT
Found at i:15421 original size:17 final size:17
Alignment explanation
Indices: 15399--15431 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
15389 TTATATACTA
15399 TATGTTTAA-TATGCATG
1 TATG-TTAAGTATGCATG
15416 TATGTTAAGTATGCAT
1 TATGTTAAGTATGCAT
15432 TTGAGAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.45
Consensus pattern (17 bp):
TATGTTAAGTATGCATG
Found at i:20859 original size:6 final size:6
Alignment explanation
Indices: 20843--20880 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
20833 GGGAAATGGG
20843 AATTG- AATTGA AATTGA AATTGA AATTGA AATTGA AAT
1 AATTGA AATTGA AATTGA AATTGA AATTGA AATTGA AAT
20881 GAGAGCTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (6 bp):
AATTGA
Found at i:35497 original size:2 final size:2
Alignment explanation
Indices: 35490--35518 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35480 CACTTGTCAT
35490 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35519 TACATATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36158 original size:22 final size:23
Alignment explanation
Indices: 36119--36164 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
36109 AATTTACTAT
36119 TTTTATATTCATGATTAAGTGTG
1 TTTTATATTCATGATTAAGTGTG
*
36142 TTTTA-ATTACAT-ATTAATTGTG
1 TTTTATATT-CATGATTAAGTGTG
36164 T
1 T
36165 GTGGATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.28, C:0.04, G:0.13, T:0.54
Consensus pattern (23 bp):
TTTTATATTCATGATTAAGTGTG
Found at i:52335 original size:31 final size:30
Alignment explanation
Indices: 52266--52336 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
52256 TTGCCATAAA
*
52266 TCTCAAATAAGGGCCCGAACTTTATAAAAG
1 TCTCAAATAAGGGCCCCAACTTTATAAAAG
* *
52296 -GTCAAATAAGGGCCCCAACTTGTCA-GAAAG
1 TCTCAAATAAGGGCCCCAACTT-T-ATAAAAG
52326 TCTCAAATAAG
1 TCTCAAATAAG
52337 TCCATTTCGT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
29 19 0.56
30 5 0.15
31 10 0.29
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (30 bp):
TCTCAAATAAGGGCCCCAACTTTATAAAAG
Done.