Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007209.1 Corchorus capsularis cultivar CVL-1 contig07230, 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: 59221
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:3621 original size:21 final size:21
Alignment explanation
Indices: 3597--3639 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3587 TAACGTGAGT
3597 AATAAAGACTACCAAAAATTC
1 AATAAAGACTACCAAAAATTC
3618 AATAAAGACTACCAAAAATTC
1 AATAAAGACTACCAAAAATTC
3639 A
1 A
3640 CATTTCAGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.19, G:0.05, T:0.19
Consensus pattern (21 bp):
AATAAAGACTACCAAAAATTC
Found at i:4371 original size:24 final size:25
Alignment explanation
Indices: 4324--4372 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
4314 TGTAAAGGAC
*
4324 AATTTTAATAGATTTTAGTGTTAAA
1 AATTTTAATAGATTTTACTGTTAAA
* *
4349 AATTTTAAT-GATTTTTCTTTTAAA
1 AATTTTAATAGATTTTACTGTTAAA
4373 TTACTCCACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (25 bp):
AATTTTAATAGATTTTACTGTTAAA
Found at i:8855 original size:55 final size:53
Alignment explanation
Indices: 8763--8865 Score: 136
Period size: 55 Copynumber: 1.9 Consensus size: 53
8753 ACAAAACGTT
* * *
8763 TCATTGTATATGATGGTCAAACCCCAAATTTTAATAGTCAAATCTAAAAAAACA
1 TCATTGTACATGAGGGTCAAACCCCAAATTCTAATAGTCAAATC-AAAAAAACA
*
8817 TCATTGTACATGCAGGGTCAAACCCCAAAGTTCT-ATAGTCATATCAAAA
1 TCATTGTACATG-AGGGTCAAACCCCAAA-TTCTAATAGTCAAATCAAAA
8866 TGTGTATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
54 15 0.35
55 25 0.58
56 3 0.07
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (53 bp):
TCATTGTACATGAGGGTCAAACCCCAAATTCTAATAGTCAAATCAAAAAAACA
Found at i:11493 original size:20 final size:20
Alignment explanation
Indices: 11468--11508 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
11458 TACTCTCGGA
11468 GGTCAA-AGTCAAAAGTCAAC
1 GGTCAACAG-CAAAAGTCAAC
11488 GGTCAACAGCAAAAGTCAAC
1 GGTCAACAGCAAAAGTCAAC
11508 G
1 G
11509 CTGATGTGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (20 bp):
GGTCAACAGCAAAAGTCAAC
Found at i:12301 original size:2 final size:2
Alignment explanation
Indices: 12289--12321 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
12279 TTTCCAATGT
*
12289 TA TA T- TA TA TA TA CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12322 AGAAAGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:12347 original size:29 final size:28
Alignment explanation
Indices: 12314--12374 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
12304 TATATATATA
12314 TATATAT-AAGAAAGAAAAATTAAAGGCAT
1 TATATATCAA-AAAG-AAAATTAAAGGCAT
* *
12343 TATATTTCTAAAAGAAAATTAAAGGCAT
1 TATATATCAAAAAGAAAATTAAAGGCAT
12371 TATA
1 TATA
12375 AACATGAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 18 0.62
29 10 0.34
30 1 0.03
ACGTcount: A:0.54, C:0.05, G:0.11, T:0.30
Consensus pattern (28 bp):
TATATATCAAAAAGAAAATTAAAGGCAT
Found at i:15506 original size:54 final size:54
Alignment explanation
Indices: 15435--15800 Score: 403
Period size: 54 Copynumber: 6.8 Consensus size: 54
15425 GAATGACCGG
* * * ** *
15435 ACCGGATCAATTCGAGATCAACTCTAACCGCTAAAAACTTC-TAGAGACGACCAC
1 ACCGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTCTTGGA-ACGACCAC
* * *
15489 ACCGGATCAATTGGAGATCAACTATGACCACCGAAAACTTCTTGGAATGACCGC
1 ACCGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTCTTGGAACGACCAC
* * *
15543 ACTGGATCAATTGGAGATCAACTCTGACCACTGAAAATTTCTT-GACACGACCAC
1 ACCGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTCTTGGA-ACGACCAC
** * * *
15597 ACCTAATCAATTGGGGATCAACTCTGACCACCGAAAACTTCTTGGAATGACCGC
1 ACCGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTCTTGGAACGACCAC
* * * * * * * *
15651 ACTGAATCAATTCGAAATCAAATCTGAACTCCGAAAACTTCTTGGAATGACCAC
1 ACCGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTCTTGGAACGACCAC
* * ** * * *
15705 ACCGGATCAATTCGAGATCCACTCTGACCATTGAAAATTTCTTGAAACGACCGC
1 ACCGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTCTTGGAACGACCAC
*
15759 ACCGGATCAATTGGGGATCAACTCTGACCACCGAAAACTTCT
1 ACCGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTCT
15801 ACGAAAGACC
Statistics
Matches: 258, Mismatches: 51, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
53 2 0.01
54 251 0.97
55 5 0.02
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (54 bp):
ACCGGATCAATTGGAGATCAACTCTGACCACCGAAAACTTCTTGGAACGACCAC
Found at i:15854 original size:162 final size:161
Alignment explanation
Indices: 15519--15812 Score: 471
Period size: 162 Copynumber: 1.8 Consensus size: 161
15509 ACTATGACCA
* * *
15519 CCGAAAACTTCTTGGAATGACCGCACTGGATCAATTGGAGATCAACTCTGACCACTGAAAATTTC
1 CCGAAAACTTCTTGGAATGACCACACCGGATCAATTCGAGATCAACTCTGACCACTGAAAATTTC
* * ** *
15584 TTGACACGACCACACCTAATCAATTGGGGATCAACTCTGACCACCGAAAACTTCTTGGAATGACC
66 TTGAAACGACCACACCGAATCAATTGGGGATCAACTCTGACCACCGAAAACTTCTACGAAAGACC
15649 GCACTGAATCAATTCGAAATCAAATCTGAACT
131 GCACTGAATCAATTCG-AATCAAATCTGAACT
* *
15681 CCGAAAACTTCTTGGAATGACCACACCGGATCAATTCGAGATCCACTCTGACCATTGAAAATTTC
1 CCGAAAACTTCTTGGAATGACCACACCGGATCAATTCGAGATCAACTCTGACCACTGAAAATTTC
* *
15746 TTGAAACGACCGCACCGGATCAATTGGGGATCAACTCTGACCACCGAAAACTTCTACGAAAGACC
66 TTGAAACGACCACACCGAATCAATTGGGGATCAACTCTGACCACCGAAAACTTCTACGAAAGACC
15811 GC
131 GC
15813 CTAGGGTCTT
Statistics
Matches: 120, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
162 120 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.22
Consensus pattern (161 bp):
CCGAAAACTTCTTGGAATGACCACACCGGATCAATTCGAGATCAACTCTGACCACTGAAAATTTC
TTGAAACGACCACACCGAATCAATTGGGGATCAACTCTGACCACCGAAAACTTCTACGAAAGACC
GCACTGAATCAATTCGAATCAAATCTGAACT
Found at i:15903 original size:54 final size:55
Alignment explanation
Indices: 15790--15903 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 55
15780 CTCTGACCAC
* * *
15790 CGAAAACTTCTACGAAAGACCGCCTAGGGTCTTCTTCTGATCTACTTAGATCTTT
1 CGAAAACTTCTACGAAAGACCGCCCAGGGTCATCTTCTGATCAACTTAGATCTTT
** *
15845 -GAAAACTTCTGTGAAAGACCGCCCAGGGTCATCTTCTGATCAACTTATAT-TTT
1 CGAAAACTTCTACGAAAGACCGCCCAGGGTCATCTTCTGATCAACTTAGATCTTT
15898 CGAAAA
1 CGAAAA
15904 TTTTGAAAGA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
53 3 0.06
54 49 0.94
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (55 bp):
CGAAAACTTCTACGAAAGACCGCCCAGGGTCATCTTCTGATCAACTTAGATCTTT
Found at i:16896 original size:7 final size:6
Alignment explanation
Indices: 16875--16904 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
16865 TTCGGAAACC
16875 TTTTGT TTTTGT TTTTGTT TTTTGT TTTTG
1 TTTTGT TTTTGT TTTTG-T TTTTGT TTTTG
16905 GACCTCAGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (6 bp):
TTTTGT
Found at i:16898 original size:13 final size:12
Alignment explanation
Indices: 16875--16904 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
16865 TTCGGAAACC
16875 TTTTGTTTTTGT
1 TTTTGTTTTTGT
16887 TTTTGTTTTTTGT
1 TTTTG-TTTTTGT
16900 TTTTG
1 TTTTG
16905 GACCTCAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (12 bp):
TTTTGTTTTTGT
Found at i:23902 original size:13 final size:13
Alignment explanation
Indices: 23856--23903 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
23846 ATCATTTTTT
23856 TCTCTTTTCTTAC
1 TCTCTTTTCTTAC
* *
23869 TCT-TTTTACTAAT
1 TCTCTTTT-CTTAC
23882 TACTCTTTTCTTAC
1 T-CTCTTTTCTTAC
23896 TCTCTTTT
1 TCTCTTTT
23904 ATTTATTACC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
12 4 0.14
13 14 0.50
14 6 0.21
15 4 0.14
ACGTcount: A:0.12, C:0.25, G:0.00, T:0.62
Consensus pattern (13 bp):
TCTCTTTTCTTAC
Found at i:23918 original size:29 final size:28
Alignment explanation
Indices: 23859--23931 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 28
23849 ATTTTTTTCT
*
23859 CTTTTCTTACTCT-TTTTACTAATTACT
1 CTTTTCTTACTCTCTTTTACTAATTACA
* *
23886 CTTTTCTTACTCTCTTTTATTTATTACCA
1 CTTTTCTTACTCTCTTTTACTAATTA-CA
23915 C-TTT-TTACTCTTCTTTT
1 CTTTTCTTACTC-TCTTTT
23932 TTCTTATACT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 19 0.47
28 19 0.47
29 2 0.05
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (28 bp):
CTTTTCTTACTCTCTTTTACTAATTACA
Found at i:24016 original size:21 final size:21
Alignment explanation
Indices: 23977--24116 Score: 165
Period size: 21 Copynumber: 6.5 Consensus size: 21
23967 CTGATCACCC
23977 TTTTACTCTTTACTGATTACTA
1 TTTTACTC-TTACTGATTACTA
* * *
23999 TTTTATTCTTACTAATTACCA
1 TTTTACTCTTACTGATTACTA
*
24020 TTTTGCTCTTACTGATTACTA
1 TTTTACTCTTACTGATTACTA
24041 TTTTACTCTTACTGATTACTA
1 TTTTACTCTTACTGATTACTA
24062 TTTTACTCTTTACTGATTACCT-
1 TTTTACTC-TTACTGATTA-CTA
* * *
24084 TCTTACTTTTTACTGATTTCTA
1 TTTTAC-TCTTACTGATTACTA
24106 TTTTTACTCTT
1 -TTTTACTCTT
24117 TTTTACTTAT
Statistics
Matches: 100, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
21 58 0.58
22 34 0.34
23 8 0.08
ACGTcount: A:0.21, C:0.19, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTACTCTTACTGATTACTA
Found at i:24148 original size:53 final size:51
Alignment explanation
Indices: 24089--24243 Score: 161
Period size: 53 Copynumber: 2.9 Consensus size: 51
24079 TACCTTCTTA
* *
24089 CTTTTTACTGATTTCTATTTTTACTCTTTTTTACTTATTACCATTTTCTTACT
1 CTTTTTACTGATTTCTATTTTTA-TCTTTTTTACTGAATACCATTTT-TTACT
24142 CTTTTTACTGATTATCCT-TTTCTTA-CTTTTTTACTGAATACCATTTTTTACT
1 CTTTTTACTGATT-T-CTATTT-TTATCTTTTTTACTGAATACCATTTTTTACT
* * * *
24194 CTTTTTTACTGAATACCATTTTTATTCTTTTTACCACTGAATACCATTTT
1 C-TTTTTACTGATTTCTATTTTTA-TCTTTTT--TACTGAATACCATTTT
24244 AACTCCTTTT
Statistics
Matches: 87, Mismatches: 6, Indels: 16
0.80 0.06 0.15
Matches are distributed among these distances:
51 4 0.05
52 9 0.10
53 50 0.57
54 4 0.05
55 20 0.23
ACGTcount: A:0.20, C:0.19, G:0.03, T:0.57
Consensus pattern (51 bp):
CTTTTTACTGATTTCTATTTTTATCTTTTTTACTGAATACCATTTTTTACT
Found at i:24200 original size:28 final size:27
Alignment explanation
Indices: 24106--24299 Score: 193
Period size: 28 Copynumber: 7.1 Consensus size: 27
24096 CTGATTTCTA
* *
24106 TTTTTACTCTTTTTTACTTATTACCAT
1 TTTTTACTCTTTTTTACTGAATACCAT
*
24133 TTTCTTACTC-TTTTTACTGATTATCC-T
1 TTT-TTACTCTTTTTTACTGAATA-CCAT
24160 TTTCTTA--CTTTTTTACTGAATACCAT
1 TTT-TTACTCTTTTTTACTGAATACCAT
24186 TTTTTACTCTTTTTTACTGAATACCA-
1 TTTTTACTCTTTTTTACTGAATACCAT
* *
24212 TTTTTATTCTTTTTACCACTGAATACCA-
1 TTTTTACTCTTTTT--TACTGAATACCAT
*
24240 TTTTAACTCCTTTTTTTACTGAATACCATT
1 TTTTTACT-C-TTTTTTACTGAATACCA-T
* * *
24270 TTTTTATTCTTTTCTACTGATTACCAT
1 TTTTTACTCTTTTTTACTGAATACCAT
24297 TTT
1 TTT
24300 CACTTTACTA
Statistics
Matches: 144, Mismatches: 11, Indels: 24
0.80 0.06 0.13
Matches are distributed among these distances:
25 6 0.04
26 29 0.20
27 45 0.31
28 51 0.35
29 2 0.01
30 11 0.08
ACGTcount: A:0.21, C:0.20, G:0.03, T:0.57
Consensus pattern (27 bp):
TTTTTACTCTTTTTTACTGAATACCAT
Found at i:24308 original size:21 final size:21
Alignment explanation
Indices: 24284--24328 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
24274 TATTCTTTTC
* *
24284 TACTGATTACCATTTTCACTT
1 TACTAATTACCATTTACACTT
* *
24305 TACTAATTACTATTTACTCTT
1 TACTAATTACCATTTACACTT
24326 TAC
1 TAC
24329 CATTTTACTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.22, G:0.02, T:0.49
Consensus pattern (21 bp):
TACTAATTACCATTTACACTT
Found at i:24327 original size:7 final size:7
Alignment explanation
Indices: 24311--24524 Score: 91
Period size: 7 Copynumber: 29.7 Consensus size: 7
24301 ACTTTACTAA
*
24311 TTACTAT
1 TTACTCT
24318 TTACTCT
1 TTACTCT
24325 TTAC-CATT
1 TTACTC--T
*
24333 TTACTTT
1 TTACTCT
**
24340 TTACTGA
1 TTACTCT
24347 TTACTCT
1 TTACTCT
*
24354 TTACTTT
1 TTACTCT
24361 TTAC-CATT
1 TTACTC--T
24369 TTAC-CTT
1 TTACTC-T
**
24376 TTACTGA
1 TTACTCT
24383 TTACTCT
1 TTACTCT
*
24390 TTACTTT
1 TTACTCT
24397 TTAC-CATT
1 TTACTC--T
*
24405 TTACCCT
1 TTACTCT
* **
24412 TAACTGA
1 TTACTCT
24419 TTACTCT
1 TTACTCT
*
24426 TTACTTT
1 TTACTCT
24433 TTAC-CATT
1 TTACTC--T
24441 TTACTCT
1 TTACTCT
**
24448 TTACTGA
1 TTACTCT
*
24455 TTACTAT
1 TTACTCT
*
24462 TTACTTT
1 TTACTCT
24469 TTAC-CAT
1 TTACTC-T
24476 TATACTCT
1 T-TACTCT
**
24484 TTACTGA
1 TTACTCT
24491 TTACTCT
1 TTACTCT
24498 TTACTCT
1 TTACTCT
24505 TTAC-CATT
1 TTACTC--T
24513 TTACTCT
1 TTACTCT
24520 TTACT
1 TTACT
24525 GATTACCCTT
Statistics
Matches: 156, Mismatches: 33, Indels: 36
0.69 0.15 0.16
Matches are distributed among these distances:
6 2 0.01
7 119 0.76
8 31 0.20
9 4 0.03
ACGTcount: A:0.21, C:0.22, G:0.02, T:0.54
Consensus pattern (7 bp):
TTACTCT
Found at i:24350 original size:36 final size:36
Alignment explanation
Indices: 24290--24557 Score: 380
Period size: 36 Copynumber: 7.5 Consensus size: 36
24280 TTTCTACTGA
* * * *
24290 TTACCATTTT-CACTTTACTAATTACTATTTACTCT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
*
24325 TTACCATTTTACTTTTTACTGATTACTCTTTACTTT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
24361 TTACCATTTTAC-CTTTTACTGATTACTCTTTACTTT
1 TTACCATTTTACTC-TTTACTGATTACTCTTTACTTT
* *
24397 TTACCATTTTACCCTTAACTGATTACTCTTTACTTT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
*
24433 TTACCATTTTACTCTTTACTGATTACTATTTACTTT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
* *
24469 TTACCATTATACTCTTTACTGATTACTCTTTACTCT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
* *
24505 TTACCATTTTACTCTTTACTGATTACCCTTT-GTTCT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTT-T
*
24541 TTACCATTTTAGTCTTT
1 TTACCATTTTACTCTTT
24558 TTAACTTGAT
Statistics
Matches: 211, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
35 11 0.05
36 199 0.94
37 1 0.00
ACGTcount: A:0.21, C:0.22, G:0.03, T:0.54
Consensus pattern (36 bp):
TTACCATTTTACTCTTTACTGATTACTCTTTACTTT
Found at i:24632 original size:38 final size:38
Alignment explanation
Indices: 24589--24662 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
24579 ATCTTTTGAC
**
24589 CTTAATTACTGATATACTGACT-ACTTCTTTTACTTTCT
1 CTTAATTACCAATATACTG-CTCACTTCTTTTACTTTCT
* *
24627 CTTAATTACCAATTTACTGCTCCCTTCTTTTACTTT
1 CTTAATTACCAATATACTGCTCACTTCTTTTACTTT
24663 TACTACATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 2 0.06
38 29 0.94
ACGTcount: A:0.22, C:0.24, G:0.04, T:0.50
Consensus pattern (38 bp):
CTTAATTACCAATATACTGCTCACTTCTTTTACTTTCT
Found at i:24690 original size:32 final size:32
Alignment explanation
Indices: 24650--24918 Score: 206
Period size: 32 Copynumber: 8.1 Consensus size: 32
24640 TTACTGCTCC
*
24650 CTTCTTTTACTTTTACTACATTCTACTAA-TA
1 CTTCTTTTACTTTTACTCCATTCTACTAATTA
* *
24681 TCTTCTTTTACCTTGATTCTTAATTACCCATT-TACTGATTA
1 -CTTCTTTTA-C----TT-TT-ACT--CCATTCTACTAATTA
* * *
24722 CTTCTTTTACTCTTACTCCATTCTGCTGATTA
1 CTTCTTTTACTTTTACTCCATTCTACTAATTA
* * *
24754 CCTT-TTTTACTTTTACTCAATTCTATTGATTA
1 -CTTCTTTTACTTTTACTCCATTCTACTAATTA
* *
24786 CTTATTTTACTTTTACTCCATTCTACTGATTA
1 CTTCTTTTACTTTTACTCCATTCTACTAATTA
* * *
24818 TTTCTTTTACTTTTACTCCATTTTACTGATTA
1 CTTCTTTTACTTTTACTCCATTCTACTAATTA
* * *
24850 CTTCCTCTTACTTTTACTCCATT-TGCTGATTA
1 CTT-CTTTTACTTTTACTCCATTCTACTAATTA
* *
24882 CTTCCTCTTACTTTCACTCCATTCTAC-AGATTA
1 CTT-CTTTTACTTTTACTCCATTCTACTA-ATTA
24915 CTTC
1 CTTC
24919 CTCTTTTACT
Statistics
Matches: 200, Mismatches: 21, Indels: 32
0.79 0.08 0.13
Matches are distributed among these distances:
31 8 0.04
32 129 0.64
33 33 0.17
34 2 0.01
35 1 0.00
37 2 0.01
38 2 0.01
39 3 0.01
40 14 0.07
41 6 0.03
ACGTcount: A:0.20, C:0.25, G:0.04, T:0.52
Consensus pattern (32 bp):
CTTCTTTTACTTTTACTCCATTCTACTAATTA
Found at i:24762 original size:72 final size:72
Alignment explanation
Indices: 24626--24763 Score: 179
Period size: 72 Copynumber: 1.9 Consensus size: 72
24616 TTTTACTTTC
* * * *
24626 TCTTAATTACCAATTTACTGCTCCCTTCTTTTACTTTTACTACATTCTACTAATATCTTCTTTTA
1 TCTTAATTACCAATTTACTGATCACTTCTTTTACTCTTACTACATTCTACTAATACCTTCTTTTA
24691 CCTTGAT
66 CCTTGAT
* * * * *
24698 TCTTAATTACCCATTTACTGATTACTTCTTTTACTCTTACTCCATTCTGCTGATTACCTT-TTTT
1 TCTTAATTACCAATTTACTGATCACTTCTTTTACTCTTACTACATTCTACT-AATACCTTCTTTT
24762 AC
65 AC
24764 TTTTACTCAA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
72 50 0.89
73 6 0.11
ACGTcount: A:0.21, C:0.25, G:0.04, T:0.50
Consensus pattern (72 bp):
TCTTAATTACCAATTTACTGATCACTTCTTTTACTCTTACTACATTCTACTAATACCTTCTTTTA
CCTTGAT
Found at i:24787 original size:64 final size:64
Alignment explanation
Indices: 24704--24918 Score: 276
Period size: 64 Copynumber: 3.4 Consensus size: 64
24694 TGATTCTTAA
*
24704 TTAC-CCATT-TACTGATTACTTCTTTTACTCTTACTCCATTCTGCTGATTACCTT-TTTTACTT
1 TTACTCCATTCTACTGATTACTTCTTTTACTTTTACTCCATTCTGCTGATTA-CTTCTTTTACTT
* * * * *
24766 TTACTCAATTCTATTGATTACTTATTTTACTTTTACTCCATTCTACTGATTATTTCTTTTACTT
1 TTACTCCATTCTACTGATTACTTCTTTTACTTTTACTCCATTCTGCTGATTACTTCTTTTACTT
* * *
24830 TTACTCCATTTTACTGATTACTTCCTCTTACTTTTACTCCATT-TGCTGATTACTTCCTCTTACT
1 TTACTCCATTCTACTGATTACTT-CTTTTACTTTTACTCCATTCTGCTGATTACTT-CTTTTACT
24894 T
64 T
* *
24895 TCACTCCATTCTACAGATTACTTC
1 TTACTCCATTCTACTGATTACTTC
24919 CTCTTTTACT
Statistics
Matches: 131, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
62 4 0.03
63 6 0.05
64 76 0.58
65 45 0.34
ACGTcount: A:0.20, C:0.25, G:0.04, T:0.51
Consensus pattern (64 bp):
TTACTCCATTCTACTGATTACTTCTTTTACTTTTACTCCATTCTGCTGATTACTTCTTTTACTT
Found at i:24814 original size:96 final size:96
Alignment explanation
Indices: 24704--24918 Score: 267
Period size: 96 Copynumber: 2.2 Consensus size: 96
24694 TGATTCTTAA
* *
24704 TTAC-CCATT-TACTGATTACTTCTTTTACTCTTACTCCATTCTGCTGATTACCTT-TTTTACTT
1 TTACTCCATTCTACTGATTACTTCTTTTACTCTTACTCCATTCTACTGATTA-CTTCTCTTACTT
* *
24766 TTACTCAATTCTATTGATTACTT-ATTTTACTT
65 TTACTCAATT-TACTGATTACTTCATCTTACTT
* * *
24798 TTACTCCATTCTACTGATTATTTCTTTTACTTTTACTCCATTTTACTGATTACTTCCTCTTACTT
1 TTACTCCATTCTACTGATTACTTCTTTTACTCTTACTCCATTCTACTGATTACTT-CTCTTACTT
* * *
24863 TTACTCCATTTGCTGATTACTTCCTCTTACTT
65 TTACTCAATTTACTGATTACTTCATCTTACTT
* *
24895 TCACTCCATTCTACAGATTACTTC
1 TTACTCCATTCTACTGATTACTTC
24919 CTCTTTTACT
Statistics
Matches: 103, Mismatches: 13, Indels: 7
0.84 0.11 0.06
Matches are distributed among these distances:
94 4 0.04
95 8 0.08
96 47 0.46
97 44 0.43
ACGTcount: A:0.20, C:0.25, G:0.04, T:0.51
Consensus pattern (96 bp):
TTACTCCATTCTACTGATTACTTCTTTTACTCTTACTCCATTCTACTGATTACTTCTCTTACTTT
TACTCAATTTACTGATTACTTCATCTTACTT
Found at i:24860 original size:17 final size:17
Alignment explanation
Indices: 24840--24893 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
24830 TTACTCCATT
24840 TTACTGATTACTTCCTC
1 TTACTGATTACTTCCTC
*
24857 TTACT-TTTAC-TCCAT-
1 TTACTGATTACTTCC-TC
*
24872 TTGCTGATTACTTCCTC
1 TTACTGATTACTTCCTC
24889 TTACT
1 TTACT
24894 TTCACTCCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
15 7 0.24
16 10 0.34
17 12 0.41
ACGTcount: A:0.17, C:0.28, G:0.06, T:0.50
Consensus pattern (17 bp):
TTACTGATTACTTCCTC
Found at i:25005 original size:38 final size:38
Alignment explanation
Indices: 24957--25029 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
24947 TGAATTAAAC
*
24957 TAATCTACTGATTACTATTACTTTGACTCTTAATTACT
1 TAATCCACTGATTACTATTACTTTGACTCTTAATTACT
*
24995 TAATCCACTGATTACTATTATTTTGACTCTTAATT
1 TAATCCACTGATTACTATTACTTTGACTCTTAATT
25030 TATTGGGGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.48
Consensus pattern (38 bp):
TAATCCACTGATTACTATTACTTTGACTCTTAATTACT
Found at i:27810 original size:23 final size:23
Alignment explanation
Indices: 27783--27830 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
27773 AGTACTAATG
*
27783 CTAAATTACTAATTAAAATTATT
1 CTAAATTACTAATTAAAAATATT
27806 CTAAATTACTAATTAAAAATATT
1 CTAAATTACTAATTAAAAATATT
27829 CT
1 CT
27831 TGTGTTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (23 bp):
CTAAATTACTAATTAAAAATATT
Found at i:27952 original size:28 final size:28
Alignment explanation
Indices: 27890--27987 Score: 92
Period size: 28 Copynumber: 3.5 Consensus size: 28
27880 ATTAAGTAGG
* * * *
27890 AAAATGACTAAAATGTCCCCCTGAGTGTC
1 AAAATGACCAAAAT-ACCCCCTGAATGCC
*
27919 AAAATGGCCAAAATACCCCCTGAATGCC
1 AAAATGACCAAAATACCCCCTGAATGCC
* *
27947 AGAATGACCAAAATA-CCCCT-AACTGCA
1 AAAATGACCAAAATACCCCCTGAA-TGCC
*
27974 AAAAAGACCAAAAT
1 AAAATGACCAAAAT
27988 GATAAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
26 2 0.03
27 20 0.34
28 24 0.41
29 12 0.21
ACGTcount: A:0.44, C:0.27, G:0.13, T:0.16
Consensus pattern (28 bp):
AAAATGACCAAAATACCCCCTGAATGCC
Found at i:27982 original size:27 final size:28
Alignment explanation
Indices: 27926--27987 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
27916 GTCAAAATGG
* * *
27926 CCAAAATACCCCCTGAATGCCAGAATGA
1 CCAAAATACCCCCTGAATGCAAAAAAGA
27954 CCAAAATA-CCCCT-AACTGCAAAAAAGA
1 CCAAAATACCCCCTGAA-TGCAAAAAAGA
27981 CCAAAAT
1 CCAAAAT
27988 GATAAAGCAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 2 0.07
27 20 0.67
28 8 0.27
ACGTcount: A:0.47, C:0.31, G:0.10, T:0.13
Consensus pattern (28 bp):
CCAAAATACCCCCTGAATGCAAAAAAGA
Found at i:28120 original size:26 final size:25
Alignment explanation
Indices: 28091--28140 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
28081 TATTATTAAA
28091 ATGCAAC-AATACTAAGCTAAATGAAG
1 ATGCAACTAATA-TAA-CTAAATGAAG
*
28117 ATGCAACTAATATTACTAAATGAA
1 ATGCAACTAATATAACTAAATGAA
28141 AATATGCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
26 9 0.41
27 4 0.18
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.24
Consensus pattern (25 bp):
ATGCAACTAATATAACTAAATGAAG
Found at i:28602 original size:21 final size:21
Alignment explanation
Indices: 28572--28618 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
28562 GCCCTGTTCT
* * *
28572 TGCCTAATTTCTTCTTGTGTC
1 TGCCTAATTTCTCCTTGCGAC
*
28593 TGCCTCATTTCTCCTTGCGAC
1 TGCCTAATTTCTCCTTGCGAC
28614 TGCCT
1 TGCCT
28619 TAACTGTTGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.32, G:0.15, T:0.45
Consensus pattern (21 bp):
TGCCTAATTTCTCCTTGCGAC
Found at i:29891 original size:6 final size:6
Alignment explanation
Indices: 29875--29910 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
29865 CATAAATATC
* *
29875 CAAAAA AAAAAA CAAAAA CAAAAA CAAAAA TAAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA
29911 ATGCAACCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.86, C:0.11, G:0.00, T:0.03
Consensus pattern (6 bp):
CAAAAA
Found at i:30633 original size:25 final size:24
Alignment explanation
Indices: 30582--30670 Score: 72
Period size: 24 Copynumber: 3.6 Consensus size: 24
30572 GTAAATGAAA
*
30582 AAAAAAGTAAAAATAGTAGATAAAT
1 AAAAAAG-ATAAATAGTAGATAAAT
* *
30607 AAAAAAGATAAATACGTATATAGAT
1 AAAAAAGATAAATA-GTAGATAAAT
* * *
30632 -AAATAGATAAATAAGTAGGTAAACA
1 AAAAAAGATAAAT-AGTAGATAAA-T
*
30657 AAAAAATATAAATA
1 AAAAAAGATAAATA
30671 AATATATAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
24 23 0.46
25 17 0.34
26 10 0.20
ACGTcount: A:0.65, C:0.02, G:0.11, T:0.21
Consensus pattern (24 bp):
AAAAAAGATAAATAGTAGATAAAT
Found at i:30743 original size:17 final size:17
Alignment explanation
Indices: 30721--30777 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 17
30711 AGATAGATAA
*
30721 ATAATAGTATTACATAG
1 ATAATAGCATTACATAG
*
30738 ATAATAGCATTGCATAG
1 ATAATAGCATTACATAG
* *
30755 ATAATAGCAATAAATAG
1 ATAATAGCATTACATAG
30772 ATAATA
1 ATAATA
30778 ATAAATAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (17 bp):
ATAATAGCATTACATAG
Found at i:30785 original size:27 final size:27
Alignment explanation
Indices: 30755--30844 Score: 78
Period size: 27 Copynumber: 3.3 Consensus size: 27
30745 CATTGCATAG
*
30755 ATAATAGCAATAAATAGATAATAATAA
1 ATAATAGAAATAAATAGATAATAATAA
* * *
30782 ATAATA-ATTACAAATAGATAA-GA-AA
1 ATAATAGA-AATAAATAGATAATAATAA
*
30807 ATGAATAGTAAATAGATAGATAATAATAA
1 AT-AATAG-AAATAAATAGATAATAATAA
30836 ATAGATAGA
1 ATA-ATAGA
30845 TAAAGAAAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
25 4 0.08
26 5 0.10
27 27 0.56
28 4 0.08
29 8 0.17
ACGTcount: A:0.61, C:0.02, G:0.11, T:0.26
Consensus pattern (27 bp):
ATAATAGAAATAAATAGATAATAATAA
Found at i:30836 original size:18 final size:18
Alignment explanation
Indices: 30763--30847 Score: 70
Period size: 18 Copynumber: 4.7 Consensus size: 18
30753 AGATAATAGC
*
30763 AATAAATAGATAATAATA
1 AATAGATAGATAATAATA
30781 AATA-ATA-ATTACA-AATA
1 AATAGATAGA-TA-ATAATA
* * *
30798 GATAAGA-AAATGAATAGTA
1 AAT-AGATAGAT-AATAATA
30817 AATAGATAGATAATAATA
1 AATAGATAGATAATAATA
30835 AATAGATAGATAA
1 AATAGATAGATAA
30848 AGAAAATAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
16 1 0.02
17 11 0.20
18 31 0.57
19 11 0.20
ACGTcount: A:0.62, C:0.01, G:0.11, T:0.26
Consensus pattern (18 bp):
AATAGATAGATAATAATA
Found at i:31444 original size:2 final size:2
Alignment explanation
Indices: 31437--31469 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
31427 CTTATATTAA
31437 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 A
31470 ACGCCAGGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32930 original size:25 final size:25
Alignment explanation
Indices: 32902--32952 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
32892 ATGTTTACTC
32902 CAAGACTTGCAGAAGTTTTAATTGG
1 CAAGACTTGCAGAAGTTTTAATTGG
* ** *
32927 CAAGTCTTGTGGAAGTTTTAGTTGG
1 CAAGACTTGCAGAAGTTTTAATTGG
32952 C
1 C
32953 TCTAGGCTCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (25 bp):
CAAGACTTGCAGAAGTTTTAATTGG
Found at i:33358 original size:27 final size:27
Alignment explanation
Indices: 33328--33411 Score: 89
Period size: 27 Copynumber: 3.1 Consensus size: 27
33318 AGGCACGCCA
33328 AAGCCTCCGCAGTTGGGACTCATGCTG
1 AAGCCTCCGCAGTTGGGACTCATGCTG
* * **
33355 AAG-CTCCCGCAGTTGGGACTCTTCCCA
1 AAGCCT-CCGCAGTTGGGACTCATGCTG
* * *
33382 AAGCCTCCGTAGTTGGGACTTATGTTG
1 AAGCCTCCGCAGTTGGGACTCATGCTG
33409 AAG
1 AAG
33412 GACTCATGCC
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
26 2 0.05
27 40 0.91
28 2 0.05
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.25
Consensus pattern (27 bp):
AAGCCTCCGCAGTTGGGACTCATGCTG
Found at i:33371 original size:54 final size:54
Alignment explanation
Indices: 33284--33411 Score: 150
Period size: 54 Copynumber: 2.4 Consensus size: 54
33274 ATGCTCCCGT
* ** *
33284 AGTTGGCACTCATGCTGAAATTCCCGCAATTGGGAGGC-ACGCCAAAGCCTCCGC
1 AGTTGGGACTCATGCTGAAGCTCCCGCAATTGGGACGCTAC-CCAAAGCCTCCGC
* * * *
33338 AGTTGGGACTCATGCTGAAGCTCCCGCAGTTGGGACTCTTCCCAAAGCCTCCGT
1 AGTTGGGACTCATGCTGAAGCTCCCGCAATTGGGACGCTACCCAAAGCCTCCGC
* *
33392 AGTTGGGACTTATGTTGAAG
1 AGTTGGGACTCATGCTGAAG
33412 GACTCATGCC
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 62 0.98
55 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.23
Consensus pattern (54 bp):
AGTTGGGACTCATGCTGAAGCTCCCGCAATTGGGACGCTACCCAAAGCCTCCGC
Found at i:36260 original size:33 final size:33
Alignment explanation
Indices: 36212--36275 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
36202 CCTAATATGA
** *
36212 GTGTTGTTTCCGATGACGCTAAATCTGTTTTAG
1 GTGTTGTTTCCGATGAAACAAAATCTGTTTTAG
**
36245 GTGTTGTTTGTGATGAAACAAAATCTGTTTT
1 GTGTTGTTTCCGATGAAACAAAATCTGTTTT
36276 GGATGCTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.22, C:0.11, G:0.23, T:0.44
Consensus pattern (33 bp):
GTGTTGTTTCCGATGAAACAAAATCTGTTTTAG
Found at i:36727 original size:30 final size:30
Alignment explanation
Indices: 36686--36748 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
36676 TCTTCAAGTG
*
36686 GGAGGGAATGATGCGCCCAAGG-CTTATCAT
1 GGAGAGAATGATGCG-CCAAGGACTTATCAT
*
36716 GGAGAGAATGATGTGCCAAGGACTTATCAT
1 GGAGAGAATGATGCGCCAAGGACTTATCAT
36746 GGA
1 GGA
36749 CTTGAAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 6 0.20
30 24 0.80
ACGTcount: A:0.30, C:0.16, G:0.33, T:0.21
Consensus pattern (30 bp):
GGAGAGAATGATGCGCCAAGGACTTATCAT
Found at i:37418 original size:43 final size:43
Alignment explanation
Indices: 37357--37443 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
37347 TTAAGTTAAG
37357 TTGATTAAATAAAGTTGAGGTTTATTCACCCAATTGATTATCT
1 TTGATTAAATAAAGTTGAGGTTTATTCACCCAATTGATTATCT
37400 TTGATTAAATAAAGTTGAGGTTTATTCACCCAATTGATTATCT
1 TTGATTAAATAAAGTTGAGGTTTATTCACCCAATTGATTATCT
37443 T
1 T
37444 AGCTTCATTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (43 bp):
TTGATTAAATAAAGTTGAGGTTTATTCACCCAATTGATTATCT
Found at i:37939 original size:27 final size:27
Alignment explanation
Indices: 37901--37956 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
37891 CACCGCGGGA
*
37901 CAGCCATGATTCCCGCTGCTGGCATAC
1 CAGCCACGATTCCCGCTGCTGGCATAC
*
37928 CAGCCACGATTCCCGCTGCTGGCTTAC
1 CAGCCACGATTCCCGCTGCTGGCATAC
37955 CA
1 CA
37957 ACTCTACCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.18, C:0.39, G:0.21, T:0.21
Consensus pattern (27 bp):
CAGCCACGATTCCCGCTGCTGGCATAC
Found at i:43820 original size:2 final size:2
Alignment explanation
Indices: 43813--43840 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43803 CCACAGCATC
43813 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43841 ACGAATATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52839 original size:21 final size:23
Alignment explanation
Indices: 52798--52861 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 23
52788 ATTTTGACAA
*
52798 AAAATTTCAATA-AG-CTCATGAC
1 AAAATTTCAA-AGAGCCTAATGAC
*
52820 -AAATTT-AAAGAGTCTAATGAC
1 AAAATTTCAAAGAGCCTAATGAC
52841 AAAAATTTCAAAGAGCCTAAT
1 -AAAATTTCAAAGAGCCTAAT
52862 ATTTTGAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
19 1 0.03
20 4 0.11
21 13 0.37
23 6 0.17
24 11 0.31
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (23 bp):
AAAATTTCAAAGAGCCTAATGAC
Found at i:52860 original size:24 final size:23
Alignment explanation
Indices: 52792--52861 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 23
52782 GCTAGTATTT
*
52792 TGACAAAAAATTTCAATA-AGCTCA
1 TGAC-AAAAATTTCAA-AGAGCTAA
52816 TGAC--AAATTT-AAAGAGTCTAA
1 TGACAAAAATTTCAAAGAG-CTAA
52837 TGACAAAAATTTCAAAGAGCCTAA
1 TGACAAAAATTTCAAAGAG-CTAA
52861 T
1 T
52862 ATTTTGAAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
19 1 0.03
20 4 0.10
21 13 0.33
23 6 0.15
24 15 0.38
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (23 bp):
TGACAAAAATTTCAAAGAGCTAA
Found at i:53105 original size:6 final size:6
Alignment explanation
Indices: 53094--53123 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
53084 TCCAAATAGA
53094 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT
53124 GCATGCAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
ACAAAT
Done.