Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020805.1 Corchorus olitorius cultivar O-4 contig20838, 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: 67737
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:724 original size:30 final size:30
Alignment explanation
Indices: 642--725 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 30
632 TACATACCAC
* * *
642 TAATTATTATTATTATTATAATAATAAGTT
1 TAATAATTATTATAATAATAATAATAAGTT
* ** *
672 TAATAATTATAATACCACTAATAATAAGTT
1 TAATAATTATTATAATAATAATAATAAGTT
702 TAATAATTATTATAATAATAATAA
1 TAATAATTATTATAATAATAATAA
726 CTCTAAATTA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (30 bp):
TAATAATTATTATAATAATAATAATAAGTT
Found at i:1028 original size:12 final size:13
Alignment explanation
Indices: 1004--1032 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
994 GTTTAGACTT
1004 ATATAGTATATAG
1 ATATAGTATATAG
1017 ATATAG-ATATAG
1 ATATAGTATATAG
1029 ATAT
1 ATAT
1033 TAGCAAGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (13 bp):
ATATAGTATATAG
Found at i:1776 original size:59 final size:59
Alignment explanation
Indices: 1684--1806 Score: 171
Period size: 60 Copynumber: 2.1 Consensus size: 59
1674 ACGTATGTGA
* *
1684 CTTAATTTAGGGCCATGCTTTTAATTTGATTAAATA-GGCCC-TAAGATATGCAAAAATG
1 CTTAATTCAAGGCCATGCTTTTAATTTGATTAAATAGGGCCCTTAAG-TATGCAAAAATG
*
1742 CTTAATTCAAGGCTCATGCTTTTAATTT-AGTTAAATAGGGCCCTTATGTATGCAAAAATG
1 CTTAATTCAAGGC-CATGCTTTTAATTTGA-TTAAATAGGGCCCTTAAGTATGCAAAAATG
1802 CTTAA
1 CTTAA
1807 ATAAGGGAGG
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
58 12 0.21
59 21 0.36
60 22 0.38
61 3 0.05
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (59 bp):
CTTAATTCAAGGCCATGCTTTTAATTTGATTAAATAGGGCCCTTAAGTATGCAAAAATG
Found at i:1942 original size:60 final size:60
Alignment explanation
Indices: 1874--2013 Score: 174
Period size: 61 Copynumber: 2.3 Consensus size: 60
1864 AGGATCACAT
* * *
1874 TTTACTAAATTCAAAGCATGGATAGTAAA-TTGAGTATTTTTAAATACGTTAGGACCCTA
1 TTTACTAAATTCAAAGCATGGATACTAAATTTGAGCATTTTCAAATACGTTAGGACCCTA
* * * *
1933 TTTATCTAAATTCAAAGCATGGATCCTAAATTTGAGCATTTTCAAATATGTTAGGATCTTA
1 TTTA-CTAAATTCAAAGCATGGATACTAAATTTGAGCATTTTCAAATACGTTAGGACCCTA
* *
1994 TTTAACCAAATTAAAAGCAT
1 TTT-ACTAAATTCAAAGCAT
2014 ATGGGCCCTA
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 4 0.06
60 23 0.33
61 41 0.59
62 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (60 bp):
TTTACTAAATTCAAAGCATGGATACTAAATTTGAGCATTTTCAAATACGTTAGGACCCTA
Found at i:5522 original size:331 final size:332
Alignment explanation
Indices: 4816--5698 Score: 1128
Period size: 331 Copynumber: 2.7 Consensus size: 332
4806 AGGGATCCAA
* * * * *
4816 CTCAATTTTGCATGATTTTTGGCTCCGAGACTACTTGAAATATTTATATTCATCTAATCAAATCT
1 CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCT
*
4881 CAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAT
66 CAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAA
*** * *
4946 ATTAATTTAGAAAAA-AT-AGGTTAACGATATTAGAAA-CGTCAAAAGCCCTTCAATCTTTTTGG
131 ATTAATTTAGAAAAATATGA-AAAAACGATATTA-AAAGCGTGAAAAGCCCTTCAATCTTTTTTG
* * ** *
5008 CATTGAA-T-TATATATTTTTCAAAAGTATTTTATCCAAAAATTGAGGAAATATCTTTCAGGTCA
194 CGTTGAATTATATATATTTTTTATGAGTATTTTATCCAAAAATTGAGGAAAAATCTTTCAGGTCA
*
5071 ATTTTTACAAAATTTTAGCAGAAATCATGGAATAACCATCACAGTTTTTAGCTAAAAAAGCGTTC
259 ATTTTTACAAAATTTTAGCAAAAATCATGG-ATAACCATCACAGTTTTTAGCTAAAAAAGCGTTC
5136 TGGGCCCCAG
323 TGGGCCCCAG
* * * *
5146 CTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCCTGAGATATCTATATTAATCTAATCAAATCT
1 CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCT
* ** * ** * * *
5211 CAACCACATTGGATTTAAAAATTTATTTTTAAAAGCATCTAAATTTTGTTTCAATTTAATTGGAA
66 CAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAA
*
5276 ATTAATTTAGAAAAATATGAAAAAACGATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTTGCG
131 ATTAATTTAGAAAAATATGAAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTTGCG
* * *
5341 TTAAATTATATATATATATTTTATGAGTATTTTATCCAAAAATTGAGGAAAAATTTTTCGGGTCA
196 TTGAATTATATATAT-T-TTTTATGAGTATTTTATCCAAAAATTGAGGAAAAATCTTTCAGGTCA
* * * * *
5406 TTTTTTACAAAATTTTAGCAAAAATCGT-G-T-ACCATCACGGTTTTTGGTTAAAAACAG-GTT-
259 ATTTTTACAAAATTTTAGCAAAAATCATGGATAACCATCACAGTTTTTAGCTAAAAA-AGCGTTC
**
5466 TCGGGCCCTGG
323 T-GGGCCCCAG
* * * *
5477 CTTAGTTTTGCATGATTTTTAGCGCC-AGCGCTCCTTGAAATATCTATATTCATCTAATAAAATC
1 CTCAGTTTTGCATGATTTTTGGCGCCAAG-ACTCCTTGAAATATCTATATTCATCTAATCAAATC
* * *
5541 TTAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTATA
65 TCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGA
* *
5606 AATTAATTCAGACTAAATATG-AAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATC-TTTTTG
130 AATTAATTTAGA-AAAATATGAAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTTG
*
5669 CGATGAATTATATAT-TTTTTTATGAGTATT
194 CGTTGAATTATATATATTTTTTATGAGTATT
5699 ATCGCTAAAA
Statistics
Matches: 476, Mismatches: 66, Indels: 25
0.84 0.12 0.04
Matches are distributed among these distances:
327 13 0.03
328 1 0.00
329 1 0.00
330 151 0.32
331 223 0.47
332 12 0.03
333 7 0.01
334 2 0.00
335 66 0.14
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (332 bp):
CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCT
CAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAA
ATTAATTTAGAAAAATATGAAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTTGCG
TTGAATTATATATATTTTTTATGAGTATTTTATCCAAAAATTGAGGAAAAATCTTTCAGGTCAAT
TTTTACAAAATTTTAGCAAAAATCATGGATAACCATCACAGTTTTTAGCTAAAAAAGCGTTCTGG
GCCCCAG
Found at i:5836 original size:20 final size:21
Alignment explanation
Indices: 5811--5856 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
5801 TATCATGTTT
5811 AAATTC-AAAATATATAATTA
1 AAATTCAAAAATATATAATTA
*
5831 AAATTCAAAAAATATATAATTC
1 AAATTC-AAAAATATATAATTA
5853 AAAT
1 AAAT
5857 CCATATTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.26
22 17 0.74
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATTCAAAAATATATAATTA
Found at i:5878 original size:21 final size:21
Alignment explanation
Indices: 5853--5914 Score: 88
Period size: 24 Copynumber: 2.8 Consensus size: 21
5843 TATATAATTC
5853 AAATCCATATTCATCTATAAA
1 AAATCCATATTCATCTATAAA
*
5874 AAATCCATATTCAAATCCCATAAA
1 AAATCCATATTC--AT-CTATAAA
5898 AAATCCATATTCATCTA
1 AAATCCATATTCATCTA
5915 ACCTAATGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
21 14 0.39
22 2 0.06
23 2 0.06
24 18 0.50
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATCCATATTCATCTATAAA
Found at i:9518 original size:21 final size:19
Alignment explanation
Indices: 9469--9526 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 19
9459 CTGTTTAGCA
*
9469 ACTGTACAAATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
9488 ACTATACAGATGAGATTAGGT
1 ACTGTACAGATGAGATTA--C
9509 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
9527 TTAGAGCAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.48
21 17 0.52
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.28
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:14608 original size:17 final size:17
Alignment explanation
Indices: 14554--14601 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
14544 ATCACCCCCC
* **
14554 AGATCACTAGTGATTTA
1 AGATCACCAGTGATGCA
14571 AGATCACCAGTGATGCA
1 AGATCACCAGTGATGCA
*
14588 AGATCACCGGTGAT
1 AGATCACCAGTGAT
14602 CAAAGATTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (17 bp):
AGATCACCAGTGATGCA
Found at i:23343 original size:22 final size:21
Alignment explanation
Indices: 23225--23455 Score: 81
Period size: 22 Copynumber: 10.4 Consensus size: 21
23215 AATGATATAT
* *
23225 AATTTCATAGAGAGATTATCGA
1 AATTTCATAG-GAGGTTATCAA
**
23247 AATTTCATACTATGG-TATCAAA
1 AATTTCATAGGA-GGTTATC-AA
*
23269 AATTT-ATAGGGAGATTAAT-AA
1 AATTTCATA-GGAGGTT-ATCAA
23290 AATTTCATAGAGAGGGTTATCAAA
1 AATTTCATAG-GA-GGTTATC-AA
**
23314 AAAATCATATGGAGGTTATCAA
1 AATTTCATA-GGAGGTTATCAA
* * *
23336 AATTTCATAGAAAAGTTTATTAA
1 AATTTCATAG--GAGGTTATCAA
* * *
23359 AATTTCATAGTTAAGTTATCAG
1 AATTTCATAG-GAGGTTATCAA
* * * *
23381 TATTTCATTGGGAGTTTATCAC
1 AATTTCA-TAGGAGGTTATCAA
* ** ** *
23403 AATTTCTTAAAATAATCATCAA
1 AATTTCATAGGA-GGTTATCAA
* *
23425 AATTTCATAGTGTGTTTATCAA
1 AATTTCATAG-GAGGTTATCAA
23447 AATTTCATA
1 AATTTCATA
23456 AAAATATTTA
Statistics
Matches: 150, Mismatches: 43, Indels: 32
0.67 0.19 0.14
Matches are distributed among these distances:
21 20 0.13
22 86 0.57
23 32 0.21
24 11 0.07
25 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (21 bp):
AATTTCATAGGAGGTTATCAA
Found at i:25378 original size:16 final size:16
Alignment explanation
Indices: 25357--25389 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
25347 CTATGCGCTG
25357 ACCCTACAAGCATGAA
1 ACCCTACAAGCATGAA
25373 ACCCTACAAGCATGAA
1 ACCCTACAAGCATGAA
25389 A
1 A
25390 ATGCATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.30, G:0.12, T:0.12
Consensus pattern (16 bp):
ACCCTACAAGCATGAA
Found at i:30805 original size:29 final size:30
Alignment explanation
Indices: 30768--30837 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
30758 ACTTGTAATT
*
30768 GTAGAGGGACTAAATTGATCGTTT-TTGT-A
1 GTAGAGGGACCAAATTGA-CGTTTATTGTAA
*
30797 GTAGAGGGACCAAATTGACTTTTATTGTAA
1 GTAGAGGGACCAAATTGACGTTTATTGTAA
*
30827 GTATAGGGACC
1 GTAGAGGGACC
30838 TGGCAGCTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.11
29 21 0.58
30 11 0.31
ACGTcount: A:0.30, C:0.10, G:0.27, T:0.33
Consensus pattern (30 bp):
GTAGAGGGACCAAATTGACGTTTATTGTAA
Found at i:36094 original size:29 final size:28
Alignment explanation
Indices: 36044--36099 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
36034 TTTTAATAAG
* *
36044 TATTCTTTTTAGGTATTTAACTTCTTTTT
1 TATTCTTTTTAGATATTCAACTT-TTTTT
36073 TATT-TTTTTAGATGATTCAACTTTTTT
1 TATTCTTTTTAGAT-ATTCAACTTTTTT
36100 ATAAATTACG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.20, C:0.09, G:0.07, T:0.64
Consensus pattern (28 bp):
TATTCTTTTTAGATATTCAACTTTTTTT
Found at i:36224 original size:15 final size:15
Alignment explanation
Indices: 36204--36234 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
36194 CTTCTAATAC
36204 TATTATAATATATAA
1 TATTATAATATATAA
*
36219 TATTATAATTTATAA
1 TATTATAATATATAA
36234 T
1 T
36235 CATGAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTATAATATATAA
Found at i:38709 original size:660 final size:649
Alignment explanation
Indices: 37425--39202 Score: 2062
Period size: 660 Copynumber: 2.7 Consensus size: 649
37415 TCGGTTCAGT
* * * * * * *
37425 TTTGCATGATTTTTGGTAGAAAGAATCCTTGCAATATCTATATTCATCTAACAAAATCTCAGCTA
1 TTTGCATGATTTTTGGCACAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATGTCAGCTA
* * **
37490 CATTGGAT-TCACGGA-TT-TTTTTACGAGCATCTAAATCTTATTTCGATTTAATTAGAAATAAA
66 CATTGGATATC-GGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTTA
** * ** * * * **
37552 TTCGGAAATTAATGGGAAAATGATATTAGAAGCGTGAAAAATTCTTTAATTTTTTTTGGTTTTGA
130 TTCGGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAACCCGTCAA-TCTTTTTGGCATTGA
* * * * * * *
37617 GTTATATATTTTTTCT-AGTTATTGTGGTAAAAAATTGAGGAAAAATTTTTCGGGTTAGTATTTC
194 ATTATATATTTTTTCTGA-ATATTATGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGT-TTTC
* * * * * *
37681 GAAAATTTAACCAAAATCGTGCACTAATCATCACGGTTTTTTTTTTTTGCTAAAAACGCGTTTCG
257 --------AGCCGAAATCGTGTACTAACCATCACGG------TTTTTGGCTAAAAACGC-TTTCC
* * * *
37746 GGGCCCCGGTTAAGTTTTGCATGATTTTAGGCAGAAAGTCTCCATGAAATATCTATATTCATCTA
307 GGGCCCCGGCTCAGTTTTGCATGATTTT-GGCAGAAAGACTCCTTGAAATATCTATATTCATCTA
* * *
37811 ATTAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATT
371 ATCAAATCTCAGCCAAATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATT
* * *
37876 TAATTAGAAATAAATTC----T-GGAAAAAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATT
436 TAATTAGAAATAAATTCAAAATAGGAAAAAAAAACGAGATTAGAAGCATGAAAAACCCTTCAATC
* *
37936 TTTTTGGCATTGAATTATATAATTTTCTGAGTATTGTGGGAAAAAATTGAGGAAAACTTTCGGGT
501 TTTTTGGCATTAAATTATATAATTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAACTTTCGGGT
* * * *
38001 CAATTTTCACAAAATTTTAGCCGAAAGCGTGTACTAACTATCACGGTTTTTGGCTAAATACGCGT
566 CAATTTTCACAAAATTTTAGCCGAAACCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCAT
** *
38066 TCCGGAGTGCCGGCTCAAG
631 TCCGGAGCCCCGACTCAAG
*
38085 TTTGCATGATTTTTGGCACAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATGTTAGCTA
1 TTTGCATGATTTTTGGCACAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATGTCAGCTA
* *
38150 CATTGGATATCGGGATTTGTTTTTACGAGCATCTCAATCTTGTTTTGATTTAATTAGAAATTTAT
66 CATTGGATATCGGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTTAT
38215 TCGGAAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAACCCGTCAATCTTTTTGGCATTGAA
131 TCGG-AAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAACCCGTCAATCTTTTTGGCATTGAA
**
38280 TTATATATTTTTTCTGAATATT-TCACAAAGAAATTGAGAAAAAACTTTTCGGGTCAGTTTTCAG
195 TTATATATTTTTTCTGAATATTATGGCAAA-AAATTGAGAAAAAACTTTTCGGGTCAGTTTTCAG
* ** ** *
38344 CCGAAATCGTGTACTAACCATCACGGTTTTCGGCTAAAAATACATTT-TAGGTCCCGGCTCAGTT
259 CCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGC-TTTCCGGGCCCCGGCTCAGTT
* * *
38408 TTGCATGATGTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATATCAGTCAA
323 TTGCATGAT-TTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCAA
* * * *
38473 ATTAGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTTGATTTAATTAGGAATAAATT
387 ATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATT
* *
38538 CATAAATAAGAAGAAGAAAGAAACACGAGATTAGAAGTATGAAAAA-CCTTCAATCTTTTTGGCG
452 CA-AAAT-AG--GAA-AAA-AAA-ACGAGATTAGAAGCATGAAAAACCCTTCAATCTTTTTGGCA
* *
38602 TTAAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAATACTTTTCGGGTCATTTT
510 TTAAATTATATA-ATTTTCTGAGTATTGTGGCAAAAAATTGAGGAAA-AC-TTTCGGGTCAATTT
** * * *
38667 TTGCAAAATTTTAGCCGAAACCGTGTACTAACCATCACGGTTTTTTGTTAAAAACGCATTTCGGA
572 TCACAAAATTTTAGCCGAAACCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCATTCCGGA
*
38732 GCCCCGACTCAAT
637 GCCCCGACTCAAG
* *
38745 TTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATAT-TCATATTCATCGAACCAAATGTCAGCC
1 TTTGCATGATTTTTGGCACAAAGACTCCTTGAAATATCT-ATATTCATCGAACCAAATGTCAGCT
**
38809 ACATTGGATAT-GAGGATTTGTTTTTACGAGCATCGGAATCTTGTTTCGATTTAATTAGAAATTT
65 ACATTGGATATCG-GGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTT
* * * *
38873 ATTTGG-AAAAAATAGAAAAATGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGA
129 ATTCGGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAACCCGTCAATCTTTTTGGCATTGA
* * * ** *
38937 ATTATATATTTTTTCTGAGTATTATGGCAAAAAATTGAGAATAAACGTTTCAAGTCAGTTTTTAG
194 ATTATATATTTTTTCTGAATATTATGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTCAG
* * * * *
39002 CCGAAATTGTGTACTAACCATCATGGTTTTTGACTAAAAACGCTTTCCGGAGCCCCGACTCAATT
259 CCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCTTTCCGG-GCCCCGGCTCAGTT
** * *
39067 TTGCATGATTTTTGGC-GCCGAGAGTCCTTGAAATATCTATATT-ATCTAATCAAATCTCAGGCA
323 TTGCATGA-TTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCA
* * * * * * * *
39130 TACTGGATTTGAA-GATTTGTTTTTATGAGTATTTGAATCTTATTTCGATTTAATTAAAAATTAA
386 AATTGGATTT-AAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAA
39194 TTCAAAATA
450 TTCAAAATA
39203 TATGAAACAA
Statistics
Matches: 961, Mismatches: 127, Indels: 64
0.83 0.11 0.06
Matches are distributed among these distances:
646 127 0.13
647 19 0.02
651 1 0.00
653 25 0.03
655 3 0.00
656 4 0.00
657 37 0.04
658 266 0.28
659 58 0.06
660 270 0.28
661 12 0.01
662 101 0.11
663 38 0.04
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (649 bp):
TTTGCATGATTTTTGGCACAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATGTCAGCTA
CATTGGATATCGGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTTAT
TCGGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAACCCGTCAATCTTTTTGGCATTGAAT
TATATATTTTTTCTGAATATTATGGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTCAGCC
GAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCTTTCCGGGCCCCGGCTCAGTTTTG
CATGATTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCAAATTG
GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAAA
ATAGGAAAAAAAAACGAGATTAGAAGCATGAAAAACCCTTCAATCTTTTTGGCATTAAATTATAT
AATTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAACTTTCGGGTCAATTTTCACAAAATTTTAG
CCGAAACCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCATTCCGGAGCCCCGACTCAAG
Found at i:47791 original size:3 final size:3
Alignment explanation
Indices: 47783--47840 Score: 107
Period size: 3 Copynumber: 19.0 Consensus size: 3
47773 TGATTAAACC
47783 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
47829 AAT AAT AAT AAT
1 AAT AAT AAT AAT
47841 TTTTTGGTGA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:51989 original size:31 final size:31
Alignment explanation
Indices: 51947--52051 Score: 115
Period size: 31 Copynumber: 3.4 Consensus size: 31
51937 GTTCAGGGGG
* *
51947 CAAAACGTACAAGTTCATTGGGCAAAATGTC
1 CAAAACGTACAAATTCATTGGGCAAAACGTC
* * *
51978 CAAAACATACAAATTTATTGGGTAAAACGTC
1 CAAAACGTACAAATTCATTGGGCAAAACGTC
* *
52009 CAAAACGTACAAATTCA-AGAGGCAAATCGTC
1 CAAAACGTACAAATTCATTG-GGCAAAACGTC
52040 C-AAACGCTACAA
1 CAAAACG-TACAA
52052 GTTTAAGAGG
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
30 6 0.10
31 56 0.90
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.20
Consensus pattern (31 bp):
CAAAACGTACAAATTCATTGGGCAAAACGTC
Done.