Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022488.1 Corchorus olitorius cultivar O-4 contig22521, 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: 95461
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:22 original size:2 final size:2
Alignment explanation
Indices: 17--51 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
7 TATACGTAGA
17 AT AT AT AT 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 AT AT AT AT A
52 CGTACACATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16228 original size:42 final size:42
Alignment explanation
Indices: 16176--16259 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
16166 AATCAAAAGC
16176 CTTGGACAATGAAATGAAAATATAGGAAAATACAAACAGAAA
1 CTTGGACAATGAAATGAAAATATAGGAAAATACAAACAGAAA
*
16218 CTTGGGCAATGAAATGAAAATATAGGAAAATACAAACAGAAA
1 CTTGGACAATGAAATGAAAATATAGGAAAATACAAACAGAAA
16260 AATTCACAGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.56, C:0.10, G:0.18, T:0.17
Consensus pattern (42 bp):
CTTGGACAATGAAATGAAAATATAGGAAAATACAAACAGAAA
Found at i:26593 original size:16 final size:17
Alignment explanation
Indices: 26558--26596 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
26548 TAAAGTTGCA
26558 ATATTATTATATTATAT
1 ATATTATTATATTATAT
26575 ATATTATTA-ATTA-ACT
1 ATATTATTATATTATA-T
26591 ATATTA
1 ATATTA
26597 AGGGCTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.05
16 11 0.52
17 9 0.43
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATTATTATATTATAT
Found at i:28373 original size:28 final size:28
Alignment explanation
Indices: 28330--28388 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
28320 GTAGTAAGTA
*
28330 TTTCCCCCATTCCTTCAATCATTTTACT
1 TTTCCCCCATTCCTTCAATCATTTCACT
*
28358 TTTCCCCCATTTCTTCAATCATTTCACT
1 TTTCCCCCATTCCTTCAATCATTTCACT
28386 TTT
1 TTT
28389 AGGGTGGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.49
Consensus pattern (28 bp):
TTTCCCCCATTCCTTCAATCATTTCACT
Found at i:28966 original size:25 final size:25
Alignment explanation
Indices: 28932--28980 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
28922 TCTTCGCTCT
28932 CGTTTCTGTGAAATTTAATAAACAA
1 CGTTTCTGTGAAATTTAATAAACAA
28957 CGTTTCTGTGAAATTTAATAAACA
1 CGTTTCTGTGAAATTTAATAAACA
28981 GAAAACTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (25 bp):
CGTTTCTGTGAAATTTAATAAACAA
Found at i:29869 original size:78 final size:78
Alignment explanation
Indices: 29780--29938 Score: 282
Period size: 78 Copynumber: 2.0 Consensus size: 78
29770 AGATTTATAG
* *
29780 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTTATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAGTT
*
29845 TACCATTTTACTA
66 TACCATTTAACTA
*
29858 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATTTAATATCTTTATAACTATTTCAGTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAGTT
29923 TACCATTTAACTA
66 TACCATTTAACTA
29936 TTT
1 TTT
29939 CAACTAGAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.35, C:0.14, G:0.01, T:0.51
Consensus pattern (78 bp):
TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAGTT
TACCATTTAACTA
Found at i:30625 original size:18 final size:18
Alignment explanation
Indices: 30598--30632 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
30588 ATATACGGTG
30598 TTAATTAATTTT-AATTA
1 TTAATTAATTTTCAATTA
30615 TTAATTTAATTTTCAATT
1 TTAA-TTAATTTTCAATT
30633 TATTTAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 8 0.50
19 4 0.25
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAATTAATTTTCAATTA
Found at i:33272 original size:29 final size:29
Alignment explanation
Indices: 33232--33322 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 29
33222 GATAACGTTA
33232 GGCCCTTATTTGGCCAAATTAAAAGACCG
1 GGCCCTTATTTGGCCAAATTAAAAGACCG
** * * ***
33261 GGCCCTTATTTGAG-CATTTTGGTAAACATTA
1 GGCCCTTATTTG-GCCAAATT--AAAAGACCG
33292 GGCCCTTATTTGGCCAAATTAAAAGACCG
1 GGCCCTTATTTGGCCAAATTAAAAGACCG
33321 GG
1 GG
33323 ACCGGGCCCT
Statistics
Matches: 44, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
29 22 0.50
30 2 0.05
31 20 0.45
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (29 bp):
GGCCCTTATTTGGCCAAATTAAAAGACCG
Found at i:33362 original size:66 final size:60
Alignment explanation
Indices: 33200--33429 Score: 345
Period size: 60 Copynumber: 3.7 Consensus size: 60
33190 AACTGACGCT
*
33200 GGGCCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACC
1 GGGCCCTTATTTGAGCATTTTGGCA-AACGTTAGGCCCTTATTTGGCCAAATTAAAAGACC
* *
33260 GGGCCCTTATTTGAGCATTTTGGTAAACATTAGGCCCTTATTTGGCCAAATTAAAAGACCGGGAC
1 GGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATT-AAA-A----GAC
33325 C
60 C
*
33326 GGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC
1 GGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACC
*
33386 GGGCCCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTG
1 GGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
33430 AGCAATTAGC
Statistics
Matches: 157, Mismatches: 6, Indels: 14
0.89 0.03 0.08
Matches are distributed among these distances:
60 94 0.60
61 4 0.03
62 1 0.01
64 1 0.01
65 3 0.02
66 54 0.34
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.32
Consensus pattern (60 bp):
GGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACC
Found at i:33425 original size:126 final size:126
Alignment explanation
Indices: 33200--33429 Score: 399
Period size: 126 Copynumber: 1.8 Consensus size: 126
33190 AACTGACGCT
33200 GGGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACCGGGCC
1 GGGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACCGGGCC
*
33265 CTTATTTGAGCATTTTGGTAAACATTAGGCCCTTATTTGGCCAAATTAAAAGACCGGGACC
66 CTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGACCGGGACC
* *
33326 GGGCCCTTATTTGAGCATTTTGGCA-AACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGGC
1 GGGCCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACCGGGC
**
33390 CCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTG
65 CCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTG
33430 AGCAATTAGC
Statistics
Matches: 98, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
126 97 0.99
127 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.32
Consensus pattern (126 bp):
GGGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACCGGGCC
CTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGACCGGGACC
Found at i:34518 original size:19 final size:19
Alignment explanation
Indices: 34494--34530 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
34484 AAGCCACAAA
34494 ATTATCAAAGATATTCATG
1 ATTATCAAAGATATTCATG
34513 ATTATCAAAGATATTCAT
1 ATTATCAAAGATATTCAT
34531 TTCTTATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (19 bp):
ATTATCAAAGATATTCATG
Found at i:37504 original size:29 final size:30
Alignment explanation
Indices: 37461--37536 Score: 136
Period size: 29 Copynumber: 2.5 Consensus size: 30
37451 CTAAATGGAT
37461 AAAATGACCCCGAACTATCACAAAAAGGAC
1 AAAATGACCCCGAACTATCACAAAAAGGAC
37491 AAAATG-CCCCGAACTATCACAAAAAGGAC
1 AAAATGACCCCGAACTATCACAAAAAGGAC
37520 AAAATGACCCCTGAACT
1 AAAATGACCCC-GAACT
37537 TTCAATTGGA
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
29 29 0.66
30 10 0.23
31 5 0.11
ACGTcount: A:0.47, C:0.28, G:0.13, T:0.12
Consensus pattern (30 bp):
AAAATGACCCCGAACTATCACAAAAAGGAC
Found at i:40921 original size:3 final size:3
Alignment explanation
Indices: 40913--40938 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40903 TGAAATTGAT
40913 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
40939 TGAATAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:44537 original size:13 final size:14
Alignment explanation
Indices: 44513--44541 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
44503 AAAAACAACT
44513 GAAAAGCACTTCTG
1 GAAAAGCACTTCTG
44527 GAAAA-CACTTCTG
1 GAAAAGCACTTCTG
44540 GA
1 GA
44542 TTTTCCGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (14 bp):
GAAAAGCACTTCTG
Found at i:47288 original size:23 final size:23
Alignment explanation
Indices: 47253--47315 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
47243 TGGGGAAGTT
* *
47253 AAGGTTTAGAATCGAGGGCTTTA
1 AAGGGTTAAAATCGAGGGCTTTA
* * *
47276 AATGGTTAAAATCGAAGGCTTTT
1 AAGGGTTAAAATCGAGGGCTTTA
*
47299 GAGGGTTAAAATCGAGG
1 AAGGGTTAAAATCGAGG
47316 ATTTTCGAGG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (23 bp):
AAGGGTTAAAATCGAGGGCTTTA
Found at i:47325 original size:23 final size:23
Alignment explanation
Indices: 47279--47327 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
47269 GGCTTTAAAT
*
47279 GGTTAAAATCGAAGGCTTTTGAG
1 GGTTAAAATCGAAGGATTTTGAG
47302 GGTTAAAATCG-AGGATTTTCGAG
1 GGTTAAAATCGAAGGATTTT-GAG
47325 GGT
1 GGT
47328 CTGAAGAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.29, C:0.08, G:0.33, T:0.31
Consensus pattern (23 bp):
GGTTAAAATCGAAGGATTTTGAG
Found at i:48197 original size:21 final size:20
Alignment explanation
Indices: 48172--48218 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 20
48162 AGTGCCAGAT
48172 GGGGTGGTGGGGCTTGCTCC-
1 GGGGTGGT-GGGCTTGCTCCA
* *
48192 GGGG-GTTGGGCTTGTTCCA
1 GGGGTGGTGGGCTTGCTCCA
48211 GGGGTGGT
1 GGGGTGGT
48219 CGATGGCGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 10 0.45
19 6 0.27
20 6 0.27
ACGTcount: A:0.02, C:0.15, G:0.55, T:0.28
Consensus pattern (20 bp):
GGGGTGGTGGGCTTGCTCCA
Found at i:51578 original size:14 final size:15
Alignment explanation
Indices: 51559--51589 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
51549 AAAAAGAAGA
51559 TTTTTATTTTT-ATT
1 TTTTTATTTTTCATT
51573 TTTTTATTTTTCATT
1 TTTTTATTTTTCATT
51588 TT
1 TT
51590 ATCTCTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTATTTTTCATT
Found at i:51780 original size:22 final size:22
Alignment explanation
Indices: 51755--52351 Score: 194
Period size: 22 Copynumber: 27.3 Consensus size: 22
51745 ATTACGCTAT
*
51755 TTTTGATGACC-TCCTTATGAAA
1 TTTTGATAACCTTCC-TATGAAA
51777 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* ** * *
51799 TTTTAATAACGATACTATGGAA
1 TTTTGATAACCTTCCTATGAAA
* * * **
51821 TTTCGA-GATCTTTTTAT-AAA
1 TTTTGATAACCTTCCTATGAAA
** *
51841 TTTTTTTTAACCTTCTTATGAAA
1 -TTTTGATAACCTTCCTATGAAA
* * * *
51864 TTTTGTTAACCTCCCTAAGGAA
1 TTTTGATAACCTTCCTATGAAA
* * *
51886 TTTTAAAAATC-TCACTATGAAA
1 TTTTGATAACCTTC-CTATGAAA
*
51908 TTTTGATAA-CTTCCCAATGAAA
1 TTTTGATAACCTT-CCTATGAAA
*
51930 TTTTGATAA-CTGAT-CTATGAGA
1 TTTTGATAACCT--TCCTATGAAA
* * *
51952 TGTTGATAA-CTTACATATG-AT
1 TTTTGATAACCTT-CCTATGAAA
* *
51973 TTATTGATAACC-ACATTATGAAA
1 TT-TTGATAACCTTC-CTATGAAA
* * *
51996 ATTT-AAAAACTTCCATATG-AA
1 TTTTGATAACCTTCC-TATGAAA
*
52017 TTGTTAGTAATCACCTT-C--TGAAA
1 TT-TT-G--ATAACCTTCCTATGAAA
*
52040 TTTTGAT-A-CTCACACTATGAAA
1 TTTTGATAACCT-TC-CTATGAAA
* * * *
52062 TTGTAATAACC-TCGTTATTAAA
1 TTTTGATAACCTTC-CTATGAAA
*
52084 TTTTGATAAACCTTCCTATAAAA
1 TTTTGAT-AACCTTCCTATGAAA
* *
52107 TTTTGATAAACCTCCCTATAAAA
1 TTTTGAT-AACCTTCCTATGAAA
52130 TTTTGATAACC-TCCTTATGAAA
1 TTTTGATAACCTTCC-TATGAAA
* *
52152 TCTTGATAA-----CTA-CAAA
1 TTTTGATAACCTTCCTATGAAA
*
52168 TTTTGATAACCTCTCCCTAT-AATTT
1 TTTTGATAACCT-T-CCTATGAA--A
* *
52193 TTTTGATAACC-TCATTATGGAA
1 TTTTGATAACCTTC-CTATGAAA
* * *
52215 TTTTGTTAATCTCCCTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* * *
52237 TTTTGATCTA-CATACTATGAAA
1 TTTTGAT-AACCTTCCTATGAAA
* *
52259 TTTTGATAACCCTCTTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* **
52281 TTTTGA-AAACTAAACTATGAAA
1 TTTTGATAACCT-TCCTATGAAA
* *
52303 TTTTGATAATCTTCATATGAAA
1 TTTTGATAACCTTCCTATGAAA
* *
52325 TTTTGATATCC-TCC-CTGAAA
1 TTTTGATAACCTTCCTATGAAA
52345 TTTTGAT
1 TTTTGAT
52352 TACTCCATAA
Statistics
Matches: 422, Mismatches: 103, Indels: 102
0.67 0.16 0.16
Matches are distributed among these distances:
16 11 0.03
17 4 0.01
18 2 0.00
19 2 0.00
20 16 0.04
21 28 0.07
22 268 0.64
23 69 0.16
24 5 0.01
25 12 0.03
26 5 0.01
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.41
Consensus pattern (22 bp):
TTTTGATAACCTTCCTATGAAA
Found at i:52107 original size:23 final size:23
Alignment explanation
Indices: 52081--52160 Score: 110
Period size: 23 Copynumber: 3.5 Consensus size: 23
52071 CCTCGTTATT
52081 AAATTTTGATAAACCTTCCTATA
1 AAATTTTGATAAACCTTCCTATA
*
52104 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTTCCTATA
*
52127 AAATTTTGAT-AACC-TCCTTATG
1 AAATTTTGATAAACCTTCC-TATA
*
52149 AAATCTTGATAA
1 AAATTTTGATAA
52161 CTACAAATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.04
22 16 0.31
23 33 0.65
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (23 bp):
AAATTTTGATAAACCTTCCTATA
Found at i:52234 original size:85 final size:84
Alignment explanation
Indices: 52081--52332 Score: 199
Period size: 85 Copynumber: 2.9 Consensus size: 84
52071 CCTCGTTATT
* *
52081 AAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCCTT
1 AAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTCACTATAAAATTTTGATAACCTCCCT
52146 ATGAAATCTTGATAACTAC
66 ATGAAATCTTGATAACTAC
** * ** * *
52165 AAATTTTGAT-AACCTCTCCCTATAATTTTTTTGAT-AACCTCATTATGGAATTTTGTTAATCTC
1 AAATTTTGATAAACCT-T-CCTATAA-AATTTTGATAAACCTCACTATAAAATTTTGATAACCTC
* *
52228 CCTATGAAATTTTGATCTACATACTATG
63 CCTATGAAATCTTGA--T--A-ACTA-C
* * * * * * * *
52256 AAATTTTGAT-AACCCTCTTATGAAATTTTGA-AAA-CTAAACTATGAAATTTTGATAATCTTCA
1 AAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCT-CACTATAAAATTTTGATAACCTCCC
*
52318 TATGAAATTTTGATA
65 TATGAAATCTTGATA
52333 TCCTCCCTGA
Statistics
Matches: 135, Mismatches: 22, Indels: 22
0.75 0.12 0.12
Matches are distributed among these distances:
83 5 0.04
84 12 0.09
85 42 0.31
86 8 0.06
87 3 0.02
88 40 0.30
89 6 0.04
90 5 0.04
91 14 0.10
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (84 bp):
AAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTCACTATAAAATTTTGATAACCTCCCT
ATGAAATCTTGATAACTAC
Found at i:52496 original size:22 final size:22
Alignment explanation
Indices: 52446--52497 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
52436 TCACATTTTG
*
52446 AAAA-TTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTCTAT
* *
52467 GAAATTTTGATTACCTCTCTAT
1 AAAATTTTGATAACCTCTCTAT
52489 AAAATTTTG
1 AAAATTTTG
52498 TTGACCATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTCTAT
Found at i:52971 original size:2 final size:2
Alignment explanation
Indices: 52964--53003 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
52954 AAGCATCTAC
52964 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
53004 TATTTGTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54041 original size:168 final size:167
Alignment explanation
Indices: 53763--54268 Score: 809
Period size: 168 Copynumber: 3.0 Consensus size: 167
53753 ATTAGTCTCC
* * * *
53763 ATGGCTTAGGGTCTGTTCGGAATGCCCTTTCAGTGTGATTGGGCTGCCTTTTAGATCCATTCGGG
1 ATGGCTTAGGGTCTGTTCGGCATGCCCTCTCAGTGTGATTGGGCTGCCTTTTGGATCCATTCGTG
*
53828 CCGCAAGCCTCTGTTCGGCAAGACCTAGCAGCCCGTTTGAGCTCAAGTACGAGACTAATCCCTTT
66 -CGCAAGCCTCTGTTCGGCAAGACCTAGCAACCCGTTTGAGCTCAAGTACGAGACTAATCCCTTT
53893 TAGGCTGGAAATATTAAAGAGTTAAATCCTCTCGTCAA
130 TAGGCTGGAAATATTAAAGAGTTAAATCCTCTCGTCAA
* * *
53931 ATGGCTTAGGGTCTGTTCAGCATGCCCTCTCATTGTGATCGGGCTGCCTTTTGGATCCATTCGTG
1 ATGGCTTAGGGTCTGTTCGGCATGCCCTCTCAGTGTGATTGGGCTGCCTTTTGGATCCATTCGTG
* *
53996 TCGCAAGCCTCTGTTCGGCAATACCT-GACAACCTGTTTGAGCTCAAGTACGAGACTAATCCCTT
66 -CGCAAGCCTCTGTTCGGCAAGACCTAG-CAACCCGTTTGAGCTCAAGTACGAGACTAATCCCTT
* *
54060 TTAGG-TCGGAAACATTAAAAAGTTAAATCCTCTCGTCAA
129 TTAGGCT-GGAAATATTAAAGAGTTAAATCCTCTCGTCAA
*
54099 ATGGCTTAGGGTCTGTTCGGCATGCCCTCTCAGTGTGATTGGGCTGCCTTTTGGATCCATTCATG
1 ATGGCTTAGGGTCTGTTCGGCATGCCCTCTCAGTGTGATTGGGCTGCCTTTTGGATCCATTCGTG
*
54164 CTGCAAGCCTCTGTTCGGTAAGACCTAGCAACCCGTTTGAGCTCAAGTACGAGACTAATCCCTTT
66 C-GCAAGCCTCTGTTCGGCAAGACCTAGCAACCCGTTTGAGCTCAAGTACGAGACTAATCCCTTT
* *
54229 TAGGCCGGAAATATTAAAGAGTTAAATCCTCTCATCAA
130 TAGGCTGGAAATATTAAAGAGTTAAATCCTCTCGTCAA
54267 AT
1 AT
54269 ACACTTATGA
Statistics
Matches: 309, Mismatches: 24, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
167 3 0.01
168 305 0.99
169 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (167 bp):
ATGGCTTAGGGTCTGTTCGGCATGCCCTCTCAGTGTGATTGGGCTGCCTTTTGGATCCATTCGTG
CGCAAGCCTCTGTTCGGCAAGACCTAGCAACCCGTTTGAGCTCAAGTACGAGACTAATCCCTTTT
AGGCTGGAAATATTAAAGAGTTAAATCCTCTCGTCAA
Found at i:59084 original size:16 final size:15
Alignment explanation
Indices: 59063--59092 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
59053 TTAAACAGAT
59063 TTTTTTTTCCTTTTTC
1 TTTTTTTT-CTTTTTC
59079 TTTTTTTTCTTTTT
1 TTTTTTTTCTTTTT
59093 AATTAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTTTTTCTTTTTC
Found at i:76826 original size:20 final size:20
Alignment explanation
Indices: 76798--76836 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
76788 TAAAAAAATA
76798 GTTGAGGAAGGGGTTTGTTT
1 GTTGAGGAAGGGGTTTGTTT
*
76818 GTTGGGGAAGGGGTTTGTT
1 GTTGAGGAAGGGGTTTGTT
76837 AGCTCATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.00, G:0.49, T:0.38
Consensus pattern (20 bp):
GTTGAGGAAGGGGTTTGTTT
Found at i:77882 original size:26 final size:23
Alignment explanation
Indices: 77836--77882 Score: 58
Period size: 26 Copynumber: 1.9 Consensus size: 23
77826 TTGGGTCAGC
*
77836 CTTAAATTTTTAAATGTTTAATT
1 CTTAAATTTTTAAATGGTTAATT
77859 CTTAAATTTATTTGAAATGGTTAA
1 CTTAAA-TT-TTT-AAATGGTTAA
77883 AATTATAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 2 0.10
25 3 0.15
26 9 0.45
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (23 bp):
CTTAAATTTTTAAATGGTTAATT
Found at i:79068 original size:11 final size:10
Alignment explanation
Indices: 79048--79072 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
79038 AAAATTTTGG
79048 TTTTTATTTT
1 TTTTTATTTT
79058 TTTTTATTTT
1 TTTTTATTTT
79068 TTTTT
1 TTTTT
79073 CTCTCTCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:81091 original size:111 final size:111
Alignment explanation
Indices: 80948--81158 Score: 327
Period size: 111 Copynumber: 1.9 Consensus size: 111
80938 ACAACAAATC
* * ** *
80948 AATTAAGTATAAGGCCATTATTCAAAATAATGTGATGGTTATCAACAGAA-TCAAATGCAAGTTA
1 AATTAAGTATAAGGCCATTAATCAAAATAATGTGAAGGCCATCAACA-AAGTCAAATGCAAGTAA
81012 TGGTACATACACCCATATAGCCATATGTAAAACAGAGAGGGAATATT
65 TGGTACATACACCCATATAGCCATATGTAAAACAGAGAGGGAATATT
*
81059 AATTAAGTA-AATGGCCATTAATCAAAATAATGTGAAGGCCATCAACAAAGTTAAATGCAAGTAA
1 AATTAAGTATAA-GGCCATTAATCAAAATAATGTGAAGGCCATCAACAAAGTCAAATGCAAGTAA
*
81123 TGGTACTTACACCCATATAGCCATATGTAAAACAGA
65 TGGTACATACACCCATATAGCCATATGTAAAACAGA
81159 AAAGGCATAT
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
110 4 0.04
111 87 0.96
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.26
Consensus pattern (111 bp):
AATTAAGTATAAGGCCATTAATCAAAATAATGTGAAGGCCATCAACAAAGTCAAATGCAAGTAAT
GGTACATACACCCATATAGCCATATGTAAAACAGAGAGGGAATATT
Found at i:82793 original size:12 final size:12
Alignment explanation
Indices: 82776--82800 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
82766 CAGTCAATCA
82776 TCGAACCAAAAT
1 TCGAACCAAAAT
82788 TCGAACCAAAAT
1 TCGAACCAAAAT
82800 T
1 T
82801 TGATTTAGAA
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:0.48, C:0.24, G:0.08, T:0.20
Consensus pattern (12 bp):
TCGAACCAAAAT
Found at i:83023 original size:17 final size:17
Alignment explanation
Indices: 83001--83038 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
82991 CAGAGGAGAA
83001 AGATGAAGAAAAAATGG
1 AGATGAAGAAAAAATGG
*
83018 AGATGAAGAGAAAATGG
1 AGATGAAGAAAAAATGG
83035 AGAT
1 AGAT
83039 CACCGCTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.32, T:0.13
Consensus pattern (17 bp):
AGATGAAGAAAAAATGG
Found at i:84103 original size:12 final size:11
Alignment explanation
Indices: 84071--84097 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
84061 AGTAAATGAG
84071 AAAAGACAAAA
1 AAAAGACAAAA
84082 AAAAGACAAAA
1 AAAAGACAAAA
84093 AAAAG
1 AAAAG
84098 TTCAAATGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.81, C:0.07, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAGACAAAA
Found at i:88070 original size:138 final size:137
Alignment explanation
Indices: 87843--88109 Score: 453
Period size: 138 Copynumber: 1.9 Consensus size: 137
87833 TTGCAATTGT
* * * *
87843 TTTTTTAAAATGAAAAAAGTTGACCAAGTTCAAAACTGGTTTAAAGACTGGTGGTACGTTGACTT
1 TTTTTTAAAATGAAAAAAGTTGACCAAGTCCAAAACCGGTTTAAAAACCGGTGGTACGTTGACTT
* *
87908 ACCAATTTTCTACACATACCGGTACCGGACTGGGCACCGATTTCCGATTCAACCGGTTGGATCGA
66 ACCAATTTTCTACACATACCGGTACCGGACTGGGCACCAATTCCCGATTCAACCGGTTGGATCGA
87973 CCGGTAA
131 CCGGTAA
87980 TTTTTTAAAATGAAAAAAAGTTGACCAAGTCCAAAACCGGTTTAAAAACCGGTGGTACGTTGACT
1 TTTTTTAAAATG-AAAAAAGTTGACCAAGTCCAAAACCGGTTTAAAAACCGGTGGTACGTTGACT
* *
88045 TGCCAATTTTCTACACATACTGGTACCGGACTGGGCACCAATTCCCGATTCAACCGGTTGGATCG
65 TACCAATTTTCTACACATACCGGTACCGGACTGGGCACCAATTCCCGATTCAACCGGTTGGATCG
88110 GCCGATCCAA
Statistics
Matches: 121, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
137 12 0.10
138 109 0.90
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (137 bp):
TTTTTTAAAATGAAAAAAGTTGACCAAGTCCAAAACCGGTTTAAAAACCGGTGGTACGTTGACTT
ACCAATTTTCTACACATACCGGTACCGGACTGGGCACCAATTCCCGATTCAACCGGTTGGATCGA
CCGGTAA
Found at i:92275 original size:13 final size:13
Alignment explanation
Indices: 92254--92283 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
92244 CTTTATGTGC
92254 CATAACTTATCCG
1 CATAACTTATCCG
*
92267 CATATCTTATCCG
1 CATAACTTATCCG
92280 CATA
1 CATA
92284 CGGTTTCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (13 bp):
CATAACTTATCCG
Found at i:94733 original size:60 final size:60
Alignment explanation
Indices: 94640--94802 Score: 245
Period size: 60 Copynumber: 2.7 Consensus size: 60
94630 GCTAATTGTT
* * * * *
94640 CAAATAAGGGCCTAGCGTTTGCCCAAATGCTCAAATAAGGGTCCGATCTTTTGATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATATGGC
* * *
94700 CAAATAAGGGCCAAACGTTTGTCAAAATGCTCAAATAAGGACCCGATCTTTTAATATGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATATGGC
*
94760 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
94803 TGGCATCGAA
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 91 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATATGGC
Found at i:94738 original size:31 final size:31
Alignment explanation
Indices: 94700--94802 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 31
94690 TTGATTTGGC
94700 CAAATAAGGGCCAAACGTTTGTCAAAATGCT
1 CAAATAAGGGCCAAACGTTTGTCAAAATGCT
* * * *
94731 CAAATAAGGACCCGATC-TTT-T-AATATGGC-
1 CAAATAAGG-GCCAAACGTTTGTCAAAAT-GCT
* * *
94760 CAAATAAGGGCCTAATGTTTGCCAAAATGCT
1 CAAATAAGGGCCAAACGTTTGTCAAAATGCT
94791 CAAATAAGGGCC
1 CAAATAAGGGCC
94803 TGGCATCGAA
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 3 0.05
29 16 0.29
30 5 0.09
31 28 0.50
32 4 0.07
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.23
Consensus pattern (31 bp):
CAAATAAGGGCCAAACGTTTGTCAAAATGCT
Found at i:94911 original size:60 final size:59
Alignment explanation
Indices: 94843--95005 Score: 238
Period size: 60 Copynumber: 2.7 Consensus size: 59
94833 ATTGATGCCA
*
94843 GACTCTTATTGGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
1 GACTCTTATTTGAGCATTTT-GCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
* * *
94903 GGCTCTTATTTGAACATTTT-CAATAACGTTAGGCCCTTATTTGGCCCAATTAAAAGATCG
1 GACTCTTATTTGAGCATTTTGC-A-AACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
*
94963 GACCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTG
1 GACTCTTATTTGAGCATTTTG-CAAACGTTAGGCCCTTATTTG
95006 AGCAATTAGC
Statistics
Matches: 92, Mismatches: 7, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
58 1 0.01
59 1 0.01
60 88 0.96
61 1 0.01
62 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (59 bp):
GACTCTTATTTGAGCATTTTGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
Found at i:95003 original size:31 final size:29
Alignment explanation
Indices: 94847--95009 Score: 93
Period size: 31 Copynumber: 5.4 Consensus size: 29
94837 ATGCCAGACT
* *
94847 CTTATTGGAGCATTTTGGCAAACGTTAGGCC
1 CTTATTTGAGCATTTT--AAAACGTTAGGCC
** ** *
94878 CTTATTTG-GCCAAATTAAAA-GATCGGGCT
1 CTTATTTGAG-CATTTTAAAACG-TTAGGCC
*
94907 CTTATTTGAACATTTTCAATAACGTTAGGCC
1 CTTATTTGAGCATTTT-AA-AACGTTAGGCC
* * *
94938 CTTATTTG-GCCCA-ATTAAAA-GATCGGACC
1 CTTATTTGAG--CATTTTAAAACGTTAGG-CC
94967 CTTATTTGAGCATTTTGACAAACGTTAGGCC
1 CTTATTTGAGCATTTT-A-AAACGTTAGGCC
94998 CTTATTTGAGCA
1 CTTATTTGAGCA
95010 ATTAGCCTAA
Statistics
Matches: 98, Mismatches: 20, Indels: 28
0.67 0.14 0.19
Matches are distributed among these distances:
28 7 0.07
29 33 0.34
30 7 0.07
31 44 0.45
32 7 0.07
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (29 bp):
CTTATTTGAGCATTTTAAAACGTTAGGCC
Done.