Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1371
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: 47206
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:3084 original size:47 final size:47
Alignment explanation
Indices: 3033--3512 Score: 737
Period size: 47 Copynumber: 10.1 Consensus size: 47
3023 TTAGGATTTT
*
3033 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
3080 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
*
3127 ATGTGATG-ATGTGAACATGCGTATGTGTGATAATGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
***
3173 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA--C--ATGCGTATGTGTGATAAGGCCGAATGGCCA
3224 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
***
3271 ATGTGATGAATGTGAACCTGTATATATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA-C---ATGCGTATGTGTGATAAGGCCGAATGGCCA
3322 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
3369 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
* * *
3416 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
** * * *
3463 ATGTGATGAATGTGAACATGAATATATGTGGTAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
3510 ATG
1 ATG
3513 CGAAACGTGT
Statistics
Matches: 402, Mismatches: 22, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
46 45 0.11
47 268 0.67
48 1 0.00
49 2 0.00
50 1 0.00
51 85 0.21
ACGTcount: A:0.31, C:0.12, G:0.30, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
Found at i:3131 original size:94 final size:94
Alignment explanation
Indices: 3033--3512 Score: 746
Period size: 98 Copynumber: 5.0 Consensus size: 94
3023 TTAGGATTTT
*
3033 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
*
3098 TGCGTATGTGTGATAAGGCCGAATGGCCA
66 TGCATATGTGTGATAAGGCCGAATGGCCA
*
3127 ATGTGATG-ATGTGAACATGCGTATGTGTGATAATGCCGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA--
**
3191 CGTATATATATGTGTGATAAGGCCGAATGGCCA
64 C--ATGCATATGTGTGATAAGGCCGAATGGCCA
3224 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-C
**
3289 TGTATATATATGTGTGATAAGGCCGAATGGCCA
65 ---ATGCATATGTGTGATAAGGCCGAATGGCCA
3322 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
*
3387 TGCGTATGTGTGATAAGGCCGAATGGCCA
66 TGCATATGTGTGATAAGGCCGAATGGCCA
* * *
3416 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
* * * *
3481 TGAATATATGTGGTAAGGCCGAATGGCTA
66 TGCATATGTGTGATAAGGCCGAATGGCCA
3510 ATG
1 ATG
3513 CGAAACGTGT
Statistics
Matches: 364, Mismatches: 16, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
93 53 0.15
94 124 0.34
95 1 0.00
97 38 0.10
98 148 0.41
ACGTcount: A:0.31, C:0.12, G:0.30, T:0.26
Consensus pattern (94 bp):
ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
TGCATATGTGTGATAAGGCCGAATGGCCA
Found at i:3228 original size:24 final size:24
Alignment explanation
Indices: 3200--3275 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
3190 CCGTATATAT
3200 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
* * **
3224 ATGTGATGA-ATGTG--AACAT-GCGT
1 ATGTG-TGATAAG-GCCGA-ATGGCCA
3247 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
3271 ATGTG
1 ATGTG
3276 ATGAATGTGA
Statistics
Matches: 37, Mismatches: 8, Indels: 14
0.63 0.14 0.24
Matches are distributed among these distances:
22 4 0.11
23 12 0.32
24 17 0.46
25 4 0.11
ACGTcount: A:0.29, C:0.13, G:0.33, T:0.25
Consensus pattern (24 bp):
ATGTGTGATAAGGCCGAATGGCCA
Found at i:3552 original size:46 final size:46
Alignment explanation
Indices: 3486--3576 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
3476 GAACATGAAT
* * *
3486 ATATGTGGTAAGGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
* * *
3532 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATG
3577 TGTATATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.33, C:0.09, G:0.32, T:0.26
Consensus pattern (46 bp):
ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
Found at i:3583 original size:141 final size:140
Alignment explanation
Indices: 3033--3561 Score: 600
Period size: 145 Copynumber: 3.7 Consensus size: 140
3023 TTAGGATTTT
* ** * * *
3033 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGAATATATGTGATAAGGCCGAATGGCCAATGCGA-GAACGTGAACA
* * * * * *
3098 TGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATG-ATGTGAACATGCGTATGTGTGATAATG
65 TGCGTATGTGTGATAAAGCCAAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGG
3162 CCGAATGGCCA
130 CCGAATGGCCA
** * *
3173 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTG
1 ATGTGATGAATGTGAACATG-A-ATATA--TGTGATAAGGCCGAATGGCCAATGCGA-GAACGTG
* * * *
3238 AACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACCTGTATATATATGTG
61 AACATGCGTATGTGTGATAAAGCCAAATGGCCAATGTGATGAATGTGAACATG--CATATA--TG
*
3303 TGATAAGGCCGAATGGCCA
122 AGATAAGGCCGAATGGCCA
** * * *
3322 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGAATATATGTGATAAGGCCGAATGGCCAATGCGA-GAACGTGAACA
* *
3387 TGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGG
65 TGCGTATGTGTGATAAAGCCAAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGG
3452 CCGAATGGCCA
130 CCGAATGGCCA
* *
3463 ATGTGATGAATGTGAACATGAATATATGTGGTAAGGCCGAATGGCTAATGCGA-AACGTGTATGA
1 ATGTGATGAATGTGAACATGAATATATGTGATAAGGCCGAATGGCCAATGCGAGAACGTG-A--A
* *
3527 GATG-GATATGTG-G-TAAAGCCAAATGGCTAATGTGA
63 CATGCG-TATGTGTGATAAAGCCAAATGGCCAATGTGA
3562 GATATGTATG
Statistics
Matches: 346, Mismatches: 30, Indels: 26
0.86 0.07 0.06
Matches are distributed among these distances:
139 5 0.01
140 37 0.11
141 69 0.20
142 13 0.04
143 5 0.01
144 76 0.22
145 97 0.28
147 6 0.02
149 38 0.11
ACGTcount: A:0.31, C:0.12, G:0.30, T:0.26
Consensus pattern (140 bp):
ATGTGATGAATGTGAACATGAATATATGTGATAAGGCCGAATGGCCAATGCGAGAACGTGAACAT
GCGTATGTGTGATAAAGCCAAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGC
CGAATGGCCA
Found at i:3804 original size:37 final size:36
Alignment explanation
Indices: 3720--3864 Score: 245
Period size: 37 Copynumber: 4.0 Consensus size: 36
3710 GGAAATATAT
3720 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTG
3756 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT-TG
3793 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGA-TTTG
* * *
3830 TCCGGGTAAGACCCGATAACTTCATGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
3865 CGTCTGAGCT
Statistics
Matches: 104, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
36 37 0.36
37 65 0.62
38 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.26
Consensus pattern (36 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTG
Found at i:5398 original size:40 final size:40
Alignment explanation
Indices: 5115--5386 Score: 454
Period size: 40 Copynumber: 6.8 Consensus size: 40
5105 GAGAATTGAG
* * *
5115 AGTGATATATCTGGGCTAAGTCCCGAAGAGCACTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
* *
5155 AGTGATATATCCGGGCTAAGTCCCAAGAAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
5195 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
5235 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
5275 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
*
5315 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTCCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
* * * *
5355 GGTGTTATATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCA
5387 ATCATGCTGG
Statistics
Matches: 220, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 220 1.00
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
Found at i:5603 original size:25 final size:25
Alignment explanation
Indices: 5562--5613 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
5552 TGTGTATTAA
5562 TGAATGAATAAGAGCACTATGTGTG
1 TGAATGAATAAGAGCACTATGTGTG
* *
5587 TGAATG-ATTAGAGGCACTGTGTGTG
1 TGAATGAATAAGA-GCACTATGTGTG
5612 TG
1 TG
5614 CGAATTCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.29, C:0.08, G:0.33, T:0.31
Consensus pattern (25 bp):
TGAATGAATAAGAGCACTATGTGTG
Found at i:9228 original size:47 final size:47
Alignment explanation
Indices: 9177--9706 Score: 772
Period size: 47 Copynumber: 11.1 Consensus size: 47
9167 TTAGGATTTT
*
9177 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
*
9224 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
* *
9271 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCAAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
***
9318 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA--C--ATGCGTATGTGTGATAAGGCCGAATGGCCA
9369 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
*** *
9416 ATGTGATGAATGTGAACCTGTATATATATATGCGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA-C-----ATGCGTATGTGTGATAAGGCCGAATGGCCA
9469 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
*
9516 ATGTGATGAATGTGAACATGCGTATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
*
9563 ATGTGATGAATGTAAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
* * *
9610 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
* ** * * *
9657 ATGTGATGAATGTAAACATGAATATATGTGGTAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
9704 ATG
1 ATG
9707 CGAAACGTGT
Statistics
Matches: 440, Mismatches: 33, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
47 352 0.80
48 1 0.00
49 2 0.00
51 42 0.10
52 1 0.00
53 42 0.10
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
Found at i:9230 original size:22 final size:22
Alignment explanation
Indices: 9203--9277 Score: 57
Period size: 22 Copynumber: 3.3 Consensus size: 22
9193 CATGCGTATG
9203 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* *
9225 TGTGATGAATG-TGAACAT-G-CATA
1 TGTGAT-AAGGCCG-A-ATGGCCA-A
9248 TGTGTGATAAGGCCGAATGGCCAA
1 --TGTGATAAGGCCGAATGGCCAA
9272 TGTGAT
1 TGTGAT
9278 GGATGTGAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 15 0.38
23 8 0.20
24 8 0.20
25 9 0.22
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:9373 original size:24 final size:24
Alignment explanation
Indices: 9345--9420 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
9335 CCGTATATAT
9345 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
* * **
9369 ATGTGATGA-ATGTG--AACAT-GCGT
1 ATGTG-TGATAAG-GCCGA-ATGGCCA
9392 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
9416 ATGTG
1 ATGTG
9421 ATGAATGTGA
Statistics
Matches: 37, Mismatches: 8, Indels: 14
0.63 0.14 0.24
Matches are distributed among these distances:
22 4 0.11
23 12 0.32
24 17 0.46
25 4 0.11
ACGTcount: A:0.29, C:0.13, G:0.33, T:0.25
Consensus pattern (24 bp):
ATGTGTGATAAGGCCGAATGGCCA
Found at i:9522 original size:22 final size:22
Alignment explanation
Indices: 9495--9569 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
9485 CATGCGTATG
9495 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
9517 TGTGATGAATG-TGAACAT-GCGTATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
9542 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
9564 TGTGAT
1 TGTGAT
9570 GAATGTAAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 14 0.35
23 9 0.22
24 9 0.22
25 8 0.20
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:9746 original size:46 final size:46
Alignment explanation
Indices: 9680--9770 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
9670 AAACATGAAT
* * *
9680 ATATGTGGTAAGGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
* * *
9726 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATG
9771 TGTATATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.33, C:0.09, G:0.32, T:0.26
Consensus pattern (46 bp):
ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
Found at i:9962 original size:37 final size:37
Alignment explanation
Indices: 9913--10095 Score: 276
Period size: 37 Copynumber: 4.9 Consensus size: 37
9903 GGAAATATAT
*
9913 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
9950 TCCGGGTAAGACCTGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
9987 TCCGAGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
*
10024 TCTGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* * * *
10061 TCCGAGTAAGACCCGATAACTTCATGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
10096 CATCTGAGCT
Statistics
Matches: 133, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 133 1.00
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.28
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:12646 original size:8 final size:8
Alignment explanation
Indices: 12613--12654 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
12603 ATATTTTGTT
*
12613 TTCTTTTT
1 TTCTTTTA
*
12621 TTATTATTA
1 TTCTT-TTA
12630 TTC-TTTA
1 TTCTTTTA
12637 TTCTTTTA
1 TTCTTTTA
12645 TTCTTTTA
1 TTCTTTTA
12653 TT
1 TT
12655 TTTAATTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
7 6 0.21
8 19 0.66
9 4 0.14
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTA
Found at i:12649 original size:32 final size:31
Alignment explanation
Indices: 12604--12677 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
12594 TCATCGTAAA
*
12604 TATTTTGTT-TTCTTTT-TTTATT-ATTATTCTT
1 TATTTT-TTATTCTTTTATTT-TTAATTAATC-T
12635 TATTCTTTTATTCTTTTATTTTTAATTAATCT
1 TATT-TTTTATTCTTTTATTTTTAATTAATCT
12667 TATTTTTTATT
1 TATTTTTTATT
12678 TTAAATTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
31 13 0.34
32 16 0.42
33 9 0.24
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.74
Consensus pattern (31 bp):
TATTTTTTATTCTTTTATTTTTAATTAATCT
Found at i:14072 original size:24 final size:23
Alignment explanation
Indices: 14045--14096 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
14035 ACAAAGTTAT
* *
14045 TAAAATTTTGATATGTTTATAAAA
1 TAAAATTTTGACATG-TGATAAAA
14069 TAAAATTTTGACATGTGATAAAA
1 TAAAATTTTGACATGTGATAAAA
14092 -AAAAT
1 TAAAAT
14097 ATTTACGAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 5 0.19
23 7 0.27
24 14 0.54
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (23 bp):
TAAAATTTTGACATGTGATAAAA
Found at i:15599 original size:22 final size:20
Alignment explanation
Indices: 15567--15606 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
15557 TGAAAATAAT
*
15567 TATATAATAAATTTGTAAAA
1 TATATAATAAATATGTAAAA
15587 TATATAAGTTAAATATGTAA
1 TATATAA--TAAATATGTAA
15607 GTTGGGAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
22 10 0.59
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (20 bp):
TATATAATAAATATGTAAAA
Found at i:17919 original size:12 final size:12
Alignment explanation
Indices: 17902--17926 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17892 GTTAGAATTT
17902 AATTAAATTGAA
1 AATTAAATTGAA
17914 AATTAAATTGAA
1 AATTAAATTGAA
17926 A
1 A
17927 GACCAATTGT
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:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
AATTAAATTGAA
Found at i:18059 original size:5 final size:5
Alignment explanation
Indices: 18051--18077 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
18041 GTAATTTAAT
18051 AATTA AATTA AATTA AATTA AATTA AA
1 AATTA AATTA AATTA AATTA AATTA AA
18078 CCCAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATTA
Found at i:27358 original size:20 final size:21
Alignment explanation
Indices: 27320--27359 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
27310 GTTATAATGA
27320 CCACATGGGCGTGTTGCCCTT
1 CCACATGGGCGTGTTGCCCTT
27341 CCACATGGGCGT-TTGCCCT
1 CCACATGGGCGTGTTGCCCT
27360 GTTTCATGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.10, C:0.35, G:0.28, T:0.28
Consensus pattern (21 bp):
CCACATGGGCGTGTTGCCCTT
Found at i:29726 original size:46 final size:44
Alignment explanation
Indices: 29631--29839 Score: 199
Period size: 46 Copynumber: 4.5 Consensus size: 44
29621 GTGCCGACGC
*
29631 CATGTCCCAGACATAGTCTTACATTGACACATCTCATA-GCCGATG
1 CATGTCCCAGACAT-GTCTTACACTGACACATCTCA-AGGCCGATG
* *
29676 CATGTCTCAGACATGTCTTACACTGACTTACATTTCAAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTGAC--ACATCTCAAGGCCGATG
* * * *
29722 CATGTCGCATACATGTCTTACACTAACACTTATCTCAATGCCGATG
1 CATGTCCCAGACATGTCTTACACTGACAC--ATCTCAAGGCCGATG
* * *
29768 TCATGTCCCAAACATGGTCTTACACTGGCTC-TCAT-AATGTGGCCGATG
1 -CATGTCCCAGACAT-GTCTTACACTGACACATC-TCAA---GGCCGATG
29816 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
29840 ATCTCACACA
Statistics
Matches: 138, Mismatches: 15, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
44 14 0.10
45 18 0.13
46 62 0.45
47 25 0.18
48 19 0.14
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.29
Consensus pattern (44 bp):
CATGTCCCAGACATGTCTTACACTGACACATCTCAAGGCCGATG
Found at i:38558 original size:40 final size:40
Alignment explanation
Indices: 38481--38701 Score: 279
Period size: 40 Copynumber: 5.5 Consensus size: 40
38471 ACCCAAGTAT
* *
38481 CTTCGGGAT-TTAG-CCGGATATA-ACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* *
38520 CTTCGGGTCTTAGCTCGGATATAGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
38560 CTTCGGGACTTAACCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
38600 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * *
38640 CTTCGGATCTTAGTCCGGATATAGTCACTAGCACAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
38680 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
38702 CATTCGAATA
Statistics
Matches: 157, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.01
39 12 0.08
40 142 0.90
41 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:46777 original size:40 final size:40
Alignment explanation
Indices: 46700--46920 Score: 297
Period size: 40 Copynumber: 5.5 Consensus size: 40
46690 ACCCAAGTAT
* *
46700 CTTCGGGAT-TTAG-CCGGATATA-ACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGTC-ACTAGCACAAATGC
*
46739 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
46779 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
46819 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * *
46859 CTTCGGATCTTAGTCCGGATATAGTCACTAGCACAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
46899 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
46921 CATTCGAATA
Statistics
Matches: 161, Mismatches: 16, Indels: 9
0.87 0.09 0.05
Matches are distributed among these distances:
38 1 0.01
39 12 0.07
40 146 0.91
41 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Done.