Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3425
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: 82484
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:13096 original size:30 final size:30
Alignment explanation
Indices: 13062--13158 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
13052 TAAACTAAAA
13062 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
13092 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
13122 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
13151 ATGAGCTA
1 -TGAGCTA
13159 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:15324 original size:12 final size:12
Alignment explanation
Indices: 15309--15339 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
15299 TTCTTTTTGC
15309 TTTTCAAAGGCT
1 TTTTCAAAGGCT
15321 TTTTCAAAGGCT
1 TTTTCAAAGGCT
15333 TTTTCAA
1 TTTTCAA
15340 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:15416 original size:6 final size:6
Alignment explanation
Indices: 15400--15449 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
15390 TTTCTTTTTA
*
15400 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
15449 T
1 T
15450 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:15432 original size:37 final size:37
Alignment explanation
Indices: 15389--15459 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
15379 CTTGCCTCTC
15389 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
15426 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
15460 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:15460 original size:16 final size:16
Alignment explanation
Indices: 15385--15445 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
15375 GCCTCTTGCC
*
15385 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
15401 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
15417 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
15433 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
15446 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:16392 original size:22 final size:23
Alignment explanation
Indices: 16367--16413 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
16357 TTTTATATAC
16367 TTCGA-TTTTTTTAAAATTTTTT
1 TTCGATTTTTTTTAAAATTTTTT
*
16389 TTCGATTTTTTTTCAAATTTTTT
1 TTCGATTTTTTTTAAAATTTTTT
16412 TT
1 TT
16414 TTCGAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.70
Consensus pattern (23 bp):
TTCGATTTTTTTTAAAATTTTTT
Found at i:16411 original size:14 final size:14
Alignment explanation
Indices: 16394--16425 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
16384 TTTTTTTCGA
16394 TTTTTTTTCAAATT
1 TTTTTTTTCAAATT
*
16408 TTTTTTTTCGAATT
1 TTTTTTTTCAAATT
16422 TTTT
1 TTTT
16426 CTCTCTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (14 bp):
TTTTTTTTCAAATT
Found at i:16438 original size:25 final size:25
Alignment explanation
Indices: 16367--16428 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 25
16357 TTTTATATAC
*
16367 TTCGATTTTTT-T-AAA-ATTTTTT
1 TTCGATTTTTTCTCAAATTTTTTTT
*
16389 TTCGATTTTTTTTCAAATTTTTTTT
1 TTCGATTTTTTCTCAAATTTTTTTT
16414 TTCGAATTTTTTCTC
1 TTCG-ATTTTTTCTC
16429 TCTTTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 11 0.32
23 1 0.03
24 3 0.09
25 10 0.29
26 9 0.26
ACGTcount: A:0.18, C:0.10, G:0.05, T:0.68
Consensus pattern (25 bp):
TTCGATTTTTTCTCAAATTTTTTTT
Found at i:16515 original size:13 final size:13
Alignment explanation
Indices: 16497--16521 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16487 ATTACAACTC
16497 AATTTTTTTTTTT
1 AATTTTTTTTTTT
16510 AATTTTTTTTTT
1 AATTTTTTTTTT
16522 CACGTTCGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
AATTTTTTTTTTT
Found at i:18144 original size:30 final size:30
Alignment explanation
Indices: 18110--18206 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
18100 TAAACTAAAA
18110 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
18140 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
18170 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
18199 ATGAGCTA
1 -TGAGCTA
18207 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:18654 original size:30 final size:30
Alignment explanation
Indices: 18620--18716 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
18610 AAAACTAAAA
18620 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
18650 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
18680 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
18709 ATGAGCTA
1 -TGAGCTA
18717 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:18854 original size:510 final size:509
Alignment explanation
Indices: 17862--18881 Score: 2013
Period size: 510 Copynumber: 2.0 Consensus size: 509
17852 TCATACATTG
17862 TACCGTCCAAAGGAATGTACCTACATGAAATAAACAAGTCATTAAGACATCTCATGAACACTCAT
1 TACCGTCCAAAGGAATGTACCTACATGAAATAAACAAGTCATTAAGACATCTCATGAACACTCAT
17927 AAATTCGGCATGATGTGAACACATTAATGTCATGCATTAATTCGGCTATGTGAACATAATCAATT
66 AAATTCGGCATGATGTGAACACATTAATGTCATGCATTAATTCGGCTATGTGAACATAATCAATT
17992 TATATAATGACAATGATATATTAATAACAAATATTAATATAAGACAAGTTTAATGCTTAAATGAA
131 TATATAATGACAATGATATATTAATAACAAATATTAATATAAGACAAGTTTAATGCTTAAATGAA
18057 TATGTGCAAATTTTTATTTAATGTATTAAAGACAAAACCGAGTTAAACTAAAATGAGCTAAGCTT
196 TATGTGCAAATTTTTATTTAATGTATTAAAGACAAAACCGAGTTAAACTAAAATGAGCTAAGCTT
18122 TAGCTCGTGAGCTAAAGTTGAGCTGAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTAGCT
261 TAGCTCGTGAGCTAAAGTTGAGCTGAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTAGCT
18187 CGTGAGCTAAATATGAGCTAGGAGTGAGCTCGGTTTAGCTCAGGCAAGTTGGATCGAGCTTGAAT
326 CGTGAGCTAAATATGAGCTAGGAGTGAGCTCGGTTTAGCTCAGGCAAGTTGGATCGAGCTTGAAT
* *
18252 AAGCTGGATTTGAGCTAGACGGAGCTCGTGGAGCTGGAAATGAGCTGGGATTAGCTTGCCAACAT
391 AAGCTGGATTTGAGCTAGACGGAGCTCGTGGAGCTGGAAACGAGCTGGGATCAGCTTGCCAACAT
18317 GTCAATGCTCGGCTTGACAGACTTGCTCGATGAAGTTCGCGGGGCGTGCTCGTA
456 GTCAATGCTCGGCTTGACAGACTTGCTCGATGAAGTTCGCGGGGCGTGCTCGTA
18371 TACCGTCCAAAGGAATGTACCTACATGAAATAAACAAGTCATTAAGACATCTCATGAACACTCAT
1 TACCGTCCAAAGGAATGTACCTACATGAAATAAACAAGTCATTAAGACATCTCATGAACACTCAT
18436 AAATTCGGCATGATGTGAACACATTAATGTCATGCATTAATTCGGCTATGTGAACATAATCAATT
66 AAATTCGGCATGATGTGAACACATTAATGTCATGCATTAATTCGGCTATGTGAACATAATCAATT
18501 TATATAATGACAATGATATATTAATAACAAATATTAATATAAGACAAGTTTAATGCTTAAATGAA
131 TATATAATGACAATGATATATTAATAACAAATATTAATATAAGACAAGTTTAATGCTTAAATGAA
18566 TATGTGCAAATTTTTATTTAATGTATTAAAGACAAAACCGAGTTAAAACTAAAATGAGCTAAGCT
196 TATGTGCAAATTTTTATTTAATGTATTAAAGACAAAACCGAGTT-AAACTAAAATGAGCTAAGCT
18631 TTAGCTCGTGAGCTAAAGTTGAGCTGAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTAGC
260 TTAGCTCGTGAGCTAAAGTTGAGCTGAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTAGC
18696 TCGTGAGCTAAATATGAGCTAGGAGTGAGCTCGGTTTAGCTCAGGCAAGTTGGATCGAGCTTGAA
325 TCGTGAGCTAAATATGAGCTAGGAGTGAGCTCGGTTTAGCTCAGGCAAGTTGGATCGAGCTTGAA
18761 TAAGCTGGATTTGAGCTAGACGGAGCTCGTGGAGCTGGAAACGAGCTGGGATCAGCTTGCCAACA
390 TAAGCTGGATTTGAGCTAGACGGAGCTCGTGGAGCTGGAAACGAGCTGGGATCAGCTTGCCAACA
18826 TGTCAATGCTCGGCTTGACAGACTTGCTCGATGAAGTTCGCGGGGCGTGCTCGTA
455 TGTCAATGCTCGGCTTGACAGACTTGCTCGATGAAGTTCGCGGGGCGTGCTCGTA
18881 T
1 T
18882 CATGGACGGT
Statistics
Matches: 508, Mismatches: 2, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
509 239 0.47
510 269 0.53
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (509 bp):
TACCGTCCAAAGGAATGTACCTACATGAAATAAACAAGTCATTAAGACATCTCATGAACACTCAT
AAATTCGGCATGATGTGAACACATTAATGTCATGCATTAATTCGGCTATGTGAACATAATCAATT
TATATAATGACAATGATATATTAATAACAAATATTAATATAAGACAAGTTTAATGCTTAAATGAA
TATGTGCAAATTTTTATTTAATGTATTAAAGACAAAACCGAGTTAAACTAAAATGAGCTAAGCTT
TAGCTCGTGAGCTAAAGTTGAGCTGAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTAGCT
CGTGAGCTAAATATGAGCTAGGAGTGAGCTCGGTTTAGCTCAGGCAAGTTGGATCGAGCTTGAAT
AAGCTGGATTTGAGCTAGACGGAGCTCGTGGAGCTGGAAACGAGCTGGGATCAGCTTGCCAACAT
GTCAATGCTCGGCTTGACAGACTTGCTCGATGAAGTTCGCGGGGCGTGCTCGTA
Found at i:22454 original size:17 final size:18
Alignment explanation
Indices: 22432--22472 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
22422 CATTTCTTTT
22432 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
**
22449 TCTTTTTTATCACTCATC
1 TCTTTTGAATCACTCATC
22467 T-TTTTG
1 TCTTTTG
22473 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Found at i:28492 original size:13 final size:13
Alignment explanation
Indices: 28471--28505 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
28461 ATAAGTTGCT
* *
28471 GTTAGTTAAATTA
1 GTTAATTAAATAA
28484 GTTAATTAAATAA
1 GTTAATTAAATAA
28497 GTTAATTAA
1 GTTAATTAA
28506 TTTGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (13 bp):
GTTAATTAAATAA
Found at i:35253 original size:20 final size:20
Alignment explanation
Indices: 35230--35276 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
35220 GGGTTAAGAT
*
35230 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
35250 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
35270 TGAGCTG
1 TGAGCTG
35277 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:36998 original size:48 final size:48
Alignment explanation
Indices: 36946--37051 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
36936 TTGTCTTTTC
*
36946 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
36994 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
37042 TTTCTTTTTC
1 TTTCTTTTTC
37052 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:39666 original size:20 final size:20
Alignment explanation
Indices: 39643--39688 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
39633 GGGTTAAGAT
*
39643 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
39663 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
39683 TGAGCT
1 TGAGCT
39689 TGAAACGAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.22, C:0.13, G:0.35, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:44925 original size:38 final size:39
Alignment explanation
Indices: 44779--45001 Score: 263
Period size: 40 Copynumber: 5.6 Consensus size: 39
44769 TTGAATGATG
* * * *
44779 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
44819 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* *
44859 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
44898 T-CGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
44936 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
44977 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
45002 AACGAGGAGC
Statistics
Matches: 161, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
38 35 0.22
39 35 0.22
40 81 0.50
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:52824 original size:40 final size:39
Alignment explanation
Indices: 52740--52963 Score: 265
Period size: 40 Copynumber: 5.6 Consensus size: 39
52730 TTGAATGATG
* * * *
52740 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
52780 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
52820 TCCGGGCTAAG-CCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
52858 TCCGGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCC-GAAGGCATTTGTGCGAGTTACTAAA
*
52898 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
52939 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
52964 AACGAGGAGC
Statistics
Matches: 163, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
38 34 0.21
39 2 0.01
40 115 0.71
41 12 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:52943 original size:80 final size:79
Alignment explanation
Indices: 52740--52963 Score: 276
Period size: 78 Copynumber: 2.8 Consensus size: 79
52730 TTGAATGATG
* * * * *
52740 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCGAAGGCATT
*
52804 TGTGCGAGATACTAAT
64 TGTGCGAGATACTAAA
* *
52820 TCCGGGCTAAG--CCGAAGGCATTGGTGCGAGTTACTA-AATCCGGGTTAAGTCCTGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTAAGTCC-GAAGGCATT
*
52882 TGTGCGAGTTACTAAA
64 TGTGCGAGATACTAAA
* *
52898 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGT-CCGAAGGCATTT
52963 G
65 G
52964 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
77 4 0.03
78 55 0.44
79 6 0.05
80 55 0.44
81 4 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCGAAGGCATTTG
TGCGAGATACTAAA
Found at i:54970 original size:12 final size:12
Alignment explanation
Indices: 54953--54977 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54943 AAAAGAGAAG
54953 AAATTCAAAAAA
1 AAATTCAAAAAA
54965 AAATTCAAAAAA
1 AAATTCAAAAAA
54977 A
1 A
54978 TTGAAAAAAA
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:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:56088 original size:6 final size:6
Alignment explanation
Indices: 56056--56162 Score: 65
Period size: 6 Copynumber: 17.5 Consensus size: 6
56046 AAAGAAATTG
* * ** *
56056 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
56103 AAAGAA ATCA-AA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
56154 AAAGAA AAA
1 AAAGAA AAA
56163 CCGAAAAAAG
Statistics
Matches: 74, Mismatches: 22, Indels: 11
0.69 0.21 0.10
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 8 0.11
8 4 0.05
ACGTcount: A:0.73, C:0.04, G:0.17, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:56143 original size:14 final size:13
Alignment explanation
Indices: 56124--56161 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
56114 AAAAGTGAGA
56124 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
56136 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
56151 GAAAAAGAAAA
1 GAAAAAGAAAA
56162 ACCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:56198 original size:12 final size:12
Alignment explanation
Indices: 56167--56198 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
56157 GAAAAACCGA
*
56167 AAAAAGAATTTG
1 AAAAAGAGTTTG
56179 AAAAAGAGTTTG
1 AAAAAGAGTTTG
56191 AAAAAGAG
1 AAAAAGAG
56199 AAGAGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (12 bp):
AAAAAGAGTTTG
Found at i:62322 original size:30 final size:30
Alignment explanation
Indices: 62288--62359 Score: 144
Period size: 30 Copynumber: 2.4 Consensus size: 30
62278 AGATTCAGTT
62288 TCTTGATTTTCTTGAAAACAAGAAAGTGAA
1 TCTTGATTTTCTTGAAAACAAGAAAGTGAA
62318 TCTTGATTTTCTTGAAAACAAGAAAGTGAA
1 TCTTGATTTTCTTGAAAACAAGAAAGTGAA
62348 TCTTGATTTTCT
1 TCTTGATTTTCT
62360 CTTTCTTTCG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (30 bp):
TCTTGATTTTCTTGAAAACAAGAAAGTGAA
Found at i:64141 original size:41 final size:41
Alignment explanation
Indices: 64079--64164 Score: 145
Period size: 41 Copynumber: 2.1 Consensus size: 41
64069 TTTAATTAGG
* *
64079 TGTTTTAAATATGGCTGGATGAATTTAATGCTGCCACTACA
1 TGTTATAAATATGCCTGGATGAATTTAATGCTGCCACTACA
*
64120 TGTTATAAATATGCCTGGATGAATTTAATGCTGCTACTACA
1 TGTTATAAATATGCCTGGATGAATTTAATGCTGCCACTACA
64161 TGTT
1 TGTT
64165 TGGCCGAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (41 bp):
TGTTATAAATATGCCTGGATGAATTTAATGCTGCCACTACA
Found at i:81028 original size:19 final size:18
Alignment explanation
Indices: 80992--81031 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
80982 TTTCCACTCG
*
80992 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
81010 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
81029 TTT
1 TTT
81032 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:82124 original size:13 final size:14
Alignment explanation
Indices: 82087--82122 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
82077 CTAGCTTCTC
82087 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
82101 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
82115 TTTTTTTT
1 TTTTTTTT
82123 CAATTGATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTTTTTCACAA
Found at i:82189 original size:23 final size:23
Alignment explanation
Indices: 82159--82203 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
82149 AATGGAAACC
82159 AATTTTTTTTAAAAATTTTTTTG
1 AATTTTTTTTAAAAATTTTTTTG
**
82182 AATTTTTTTTTCAAATTTTTTT
1 AATTTTTTTTAAAAATTTTTTT
82204 TGAAGAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (23 bp):
AATTTTTTTTAAAAATTTTTTTG
Found at i:82201 original size:24 final size:24
Alignment explanation
Indices: 82161--82207 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
82151 TGGAAACCAA
82161 TTTTTTTTAAAAATTTTTTTGAAT
1 TTTTTTTTAAAAATTTTTTTGAAT
* *
82185 TTTTTTTTCAAATTTTTTTTGAA
1 TTTTTTTTAAAAATTTTTTTGAA
82208 GAAACTATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (24 bp):
TTTTTTTTAAAAATTTTTTTGAAT
Done.