Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold613
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: 121006
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Found at i:9655 original size:30 final size:30
Alignment explanation
Indices: 9619--9765 Score: 139
Period size: 28 Copynumber: 5.0 Consensus size: 30
9609 CAAGTCGATG
9619 ATACCCTTTCAAAGCTCACAAGTCAGTGGC
1 ATACCCTTTCAAAGCTCACAAGTCAGTGGC
* *
9649 ATACCCTTTCAAAGCCCACAAGTCAGTAGC
1 ATACCCTTTCAAAGCTCACAAGTCAGTGGC
* * *
9679 --ACCTTTTCAAAACCCACAAGAT-AGTGG-
1 ATACCCTTTCAAAGCTCACAAG-TCAGTGGC
* *
9706 -TATCTTTTCAAAGCTCACAAGTCAGTGGC
1 ATACCCTTTCAAAGCTCACAAGTCAGTGGC
9735 AT--CCTTTCAAAGCCTACACAAGT-AGGTGGC
1 ATACCCTTTCAAAG-CT-CACAAGTCA-GTGGC
9765 A
1 A
9766 ACTCTTTTTT
Statistics
Matches: 100, Mismatches: 9, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
27 1 0.01
28 53 0.53
29 4 0.04
30 42 0.42
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (30 bp):
ATACCCTTTCAAAGCTCACAAGTCAGTGGC
Found at i:9976 original size:45 final size:46
Alignment explanation
Indices: 9921--10047 Score: 148
Period size: 47 Copynumber: 2.8 Consensus size: 46
9911 ATCTTAAAGT
* * * *
9921 TCGATATCGCTGGCATTGAATCAGCATATTGGCACCTTT-ATTAGC
1 TCGATGTCGCTGGCCTTGAATTAGCACATTGGCACCTTTCATTAGC
* * *
9966 TCGATGTCGCTGGCCTTGAATTAGCACATTGTCCACTTTTCCTTAGC
1 TCGATGTCGCTGGCCTTGAATTAGCACATTG-GCACCTTTCATTAGC
* * *
10013 TCAATGTCGTTGGCCTTGAATTGGCACATTGGCAC
1 TCGATGTCGCTGGCCTTGAATTAGCACATTGGCAC
10048 TCCTCTCATC
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
45 27 0.39
46 9 0.13
47 33 0.48
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.34
Consensus pattern (46 bp):
TCGATGTCGCTGGCCTTGAATTAGCACATTGGCACCTTTCATTAGC
Found at i:15463 original size:2 final size:2
Alignment explanation
Indices: 15456--15480 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15446 ATAATGTATT
15456 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
15481 TTAATATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15825 original size:36 final size:36
Alignment explanation
Indices: 15778--15856 Score: 149
Period size: 36 Copynumber: 2.2 Consensus size: 36
15768 GGAAAAATTA
15778 ATTAAAATTCTAGCCTAAGTAAAACATTTTTACTTC
1 ATTAAAATTCTAGCCTAAGTAAAACATTTTTACTTC
15814 ATTAAAATTCTAGCCTAAGTAAAACATTTTTACTTC
1 ATTAAAATTCTAGCCTAAGTAAAACATTTTTACTTC
15850 ATGTAAA
1 AT-TAAA
15857 TATAAACAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 38 0.90
37 4 0.10
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (36 bp):
ATTAAAATTCTAGCCTAAGTAAAACATTTTTACTTC
Found at i:21376 original size:29 final size:29
Alignment explanation
Indices: 21334--21389 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
21324 ATTGTTAGCT
*
21334 GTAGTTTGGCTATTAGGCATAATTAAGCA
1 GTAGTTTGGCTATTAGGCAAAATTAAGCA
*
21363 GTAGTTTGGTTATTAGGCAAAATTAAG
1 GTAGTTTGGCTATTAGGCAAAATTAAG
21390 TTATCAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.36
Consensus pattern (29 bp):
GTAGTTTGGCTATTAGGCAAAATTAAGCA
Found at i:24938 original size:28 final size:27
Alignment explanation
Indices: 24883--24948 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
24873 GCCACCCATT
* *
24883 TGTTTGTTAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATAGTGGTTATTTTG
24910 TGTTTGTCAAAAATAGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATAGTGGTTAT--TTTG
*
24938 TATTTGTCAAA
1 TGTTTGTCAAA
24949 TATGGAGACT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 19 0.56
28 14 0.41
ACGTcount: A:0.24, C:0.06, G:0.21, T:0.48
Consensus pattern (27 bp):
TGTTTGTCAAAAATAGTGGTTATTTTG
Found at i:24971 original size:25 final size:24
Alignment explanation
Indices: 24938--25002 Score: 87
Period size: 25 Copynumber: 2.7 Consensus size: 24
24928 GTTTCCTTTG
24938 TATTTGTC-AAATATGGAGACTTGTT
1 TATTTGTCAAAAT-TGGAGACTTG-T
*
24963 TATTTGTCAAAATTGGTGACTTGT
1 TATTTGTCAAAATTGGAGACTTGT
*
24987 TGTTTGTCAAAATTGG
1 TATTTGTCAAAATTGG
25003 TGGCTAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
24 16 0.43
25 17 0.46
26 4 0.11
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.45
Consensus pattern (24 bp):
TATTTGTCAAAATTGGAGACTTGT
Found at i:24997 original size:24 final size:25
Alignment explanation
Indices: 24938--25004 Score: 93
Period size: 24 Copynumber: 2.7 Consensus size: 25
24928 GTTTCCTTTG
*
24938 TATTTGTC-AAATATGGAGACTTGTT
1 TATTTGTCAAAAT-TGGTGACTTGTT
24963 TATTTGTCAAAATTGGTGACTTG-T
1 TATTTGTCAAAATTGGTGACTTGTT
*
24987 TGTTTGTCAAAATTGGTG
1 TATTTGTCAAAATTGGTG
25005 GCTAATTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
24 18 0.46
25 17 0.44
26 4 0.10
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.45
Consensus pattern (25 bp):
TATTTGTCAAAATTGGTGACTTGTT
Found at i:27581 original size:21 final size:22
Alignment explanation
Indices: 27552--27597 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
27542 GGTTCAGACA
**
27552 AGTAGTACTCCGCAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
27574 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
27595 AGT
1 AGT
27598 TTCAACAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:29503 original size:25 final size:24
Alignment explanation
Indices: 29475--29599 Score: 97
Period size: 27 Copynumber: 4.9 Consensus size: 24
29465 AAGCCACCCA
29475 TTTGTTTGTCAAAAATGGTGGTTATT
1 TTTGTTTGTCAAAAATGGTGG-T-TT
29501 TTGTGTTTGTCAAAAATGGTGGTTT
1 TT-TGTTTGTCAAAAATGGTGGTTT
* * *
29526 CCTTTGTATTTGTCAAATATGGAGGCTTG
1 --TTTG--TTTGTCAAAAATGGTGG-TTT
* * **
29555 TTTATTTGTCAAAATTGGTGACTT
1 TTTGTTTGTCAAAAATGGTGGTTT
* *
29579 GTTGTTTGTCAAAATTGGTGG
1 TTTGTTTGTCAAAAATGGTGG
29600 CTAATTTTTA
Statistics
Matches: 80, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
24 19 0.24
25 15 0.19
26 5 0.06
27 24 0.30
28 15 0.19
29 2 0.03
ACGTcount: A:0.22, C:0.07, G:0.25, T:0.46
Consensus pattern (24 bp):
TTTGTTTGTCAAAAATGGTGGTTT
Found at i:29532 original size:28 final size:27
Alignment explanation
Indices: 29477--29547 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
29467 GCCACCCATT
29477 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
29504 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
29532 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
29548 AGGCTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:30539 original size:3 final size:3
Alignment explanation
Indices: 30531--30569 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
30521 GGTTTAGATG
**
30531 ATA ATA ATA ACG ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
30570 GATGAGTGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:32440 original size:2 final size:2
Alignment explanation
Indices: 32433--32474 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
32423 TAACGCTTTA
32433 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32475 TACAAACCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36767 original size:2 final size:2
Alignment explanation
Indices: 36760--36789 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
36750 GTGATGATTC
*
36760 AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36790 CTGTTCTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37302 original size:22 final size:22
Alignment explanation
Indices: 37274--37315 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
37264 TATTAAAAAA
37274 TATTTTTAT-ATTAATATTTATT
1 TATTTTTATAATTAA-ATTTATT
37296 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
37316 AATAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATT
Found at i:43380 original size:3 final size:3
Alignment explanation
Indices: 43372--43458 Score: 64
Period size: 3 Copynumber: 31.0 Consensus size: 3
43362 TTATTTAATA
*
43372 TAT TAT TA- TAT TAT T-T TA- TAT TATT TAT TAA TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
* * *
43414 TAT TA- TAT TAT TAT T-T AAT ATAT TAT T-T AAA TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
43456 TAT
1 TAT
43459 ATTTAAATAT
Statistics
Matches: 67, Mismatches: 7, Indels: 20
0.71 0.07 0.21
Matches are distributed among these distances:
2 14 0.21
3 48 0.72
4 5 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:43383 original size:8 final size:8
Alignment explanation
Indices: 43361--43461 Score: 81
Period size: 8 Copynumber: 13.0 Consensus size: 8
43351 CTAAGGTCCA
43361 ATTAT-TT
1 ATTATATT
*
43368 AATATATT
1 ATTATATT
43376 ATTATATT
1 ATTATATT
*
43384 ATTTTA-T
1 ATTATATT
43391 ATTAT-TT
1 ATTATATT
43398 ATTA-ATAT
1 ATTATAT-T
43406 ATTATTATT
1 ATTA-TATT
43415 ATTATATT
1 ATTATATT
43423 ATTAT-TT
1 ATTATATT
*
43430 AATATATT
1 ATTATATT
*
43438 ATT-TAAAT
1 ATTAT-ATT
43446 ATTATTATT
1 ATTA-TATT
43455 -TTATATT
1 ATTATATT
43462 TAAATATCGT
Statistics
Matches: 76, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
7 26 0.34
8 40 0.53
9 7 0.09
10 3 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATTATATT
Found at i:43431 original size:29 final size:29
Alignment explanation
Indices: 43361--43460 Score: 109
Period size: 29 Copynumber: 3.4 Consensus size: 29
43351 CTAAGGTCCA
43361 ATTATTTAATATATTATTATATTATTTTATATT
1 ATTATTTAATATATTA-T-TATTA--TTATATT
43394 ATT-TATTAATATATTATTATTATTATATT
1 ATTAT-TTAATATATTATTATTATTATATT
*
43423 ATTATTTAATATATTA-T-TTA-AATATT
1 ATTATTTAATATATTATTATTATTATATT
*
43449 ATTATTTTATAT
1 ATTATTTAATAT
43461 TTAAATATCG
Statistics
Matches: 63, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
26 16 0.25
27 3 0.05
28 1 0.02
29 21 0.33
30 1 0.02
31 5 0.08
32 2 0.03
33 14 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
ATTATTTAATATATTATTATTATTATATT
Found at i:44733 original size:20 final size:20
Alignment explanation
Indices: 44705--44779 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
44695 TCATACCCTG
44705 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
44725 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
44745 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
44765 ATGTATCGATACATT
1 ATGTATCGATACATT
44780 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:44772 original size:40 final size:39
Alignment explanation
Indices: 44705--44782 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
44695 TCATACCCTG
* *
44705 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
44745 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
44783 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:45718 original size:23 final size:23
Alignment explanation
Indices: 45691--45746 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
45681 AGCCTTTGAC
45691 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
45714 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
45736 CATGCATTTTT
1 CATGCATTTTT
45747 AACATGTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 22 0.69
23 10 0.31
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:45753 original size:20 final size:21
Alignment explanation
Indices: 45699--45753 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
45689 ACCATGCATT
**
45699 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
**
45720 TTTTTTTATTATGTTTCATGCA
1 -TTTTTTAACATGTTTCATGCA
45742 -TTTTTAACATGT
1 TTTTTTAACATGT
45754 CCAGCATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 10 0.32
22 21 0.68
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTTTTAACATGTTTCATGCA
Found at i:49628 original size:22 final size:22
Alignment explanation
Indices: 49594--49635 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
49584 ACCTAACATA
49594 TCACCCAACACACCTAATATGC
1 TCACCCAACACACCTAATATGC
* *
49616 TCACCTAATACACCTAATAT
1 TCACCCAACACACCTAATAT
49636 ATTTACCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.36, G:0.02, T:0.24
Consensus pattern (22 bp):
TCACCCAACACACCTAATATGC
Found at i:49643 original size:22 final size:22
Alignment explanation
Indices: 49584--49645 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
49574 TATCTTGCTT
* * *
49584 ACCTAACATA-TCACCCAACAC
1 ACCTAATATACTCACCTAATAC
*
49605 ACCTAATATGCTCACCTAATAC
1 ACCTAATATACTCACCTAATAC
* *
49627 ACCTAATATATTTACCTAA
1 ACCTAATATACTCACCTAA
49646 CATACCACCT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
21 8 0.24
22 25 0.76
ACGTcount: A:0.40, C:0.32, G:0.02, T:0.26
Consensus pattern (22 bp):
ACCTAATATACTCACCTAATAC
Found at i:52457 original size:38 final size:38
Alignment explanation
Indices: 52406--52484 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
52396 AGAAACACAA
52406 TTCTCTATATTTAAATAACTTTGCAACTTTGATTTTTT
1 TTCTCTATATTTAAATAACTTTGCAACTTTGATTTTTT
52444 TTCTCTATATTTAAATAACTTTGCAACTTTGATTTTTT
1 TTCTCTATATTTAAATAACTTTGCAACTTTGATTTTTT
52482 TTC
1 TTC
52485 AATATGCAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.25, C:0.14, G:0.05, T:0.56
Consensus pattern (38 bp):
TTCTCTATATTTAAATAACTTTGCAACTTTGATTTTTT
Found at i:57953 original size:23 final size:23
Alignment explanation
Indices: 57924--57974 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
57914 CAAGTTATAC
57924 TTTTTCAACCAAGATCATAAACT
1 TTTTTCAACCAAGATCATAAACT
* *
57947 TTTTTCAGCGAAGATCATAAACT
1 TTTTTCAACCAAGATCATAAACT
57970 TTTTT
1 TTTTT
57975 GGTTCAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (23 bp):
TTTTTCAACCAAGATCATAAACT
Found at i:60308 original size:16 final size:16
Alignment explanation
Indices: 60258--60310 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
60248 AGTGATTCTA
*
60258 AATAAGAGTTGTTTTG
1 AATAAGAGTTATTTTG
* *
60274 AACAATAGTTATTTTG
1 AATAAGAGTTATTTTG
60290 AATAAGAGTTATTTTG
1 AATAAGAGTTATTTTG
60306 AATAA
1 AATAA
60311 CAAACTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.40, C:0.02, G:0.17, T:0.42
Consensus pattern (16 bp):
AATAAGAGTTATTTTG
Found at i:60356 original size:16 final size:16
Alignment explanation
Indices: 60337--60383 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
60327 AAAGCTGTTT
60337 TAAATAATAGCTATTC
1 TAAATAATAGCTATTC
* *
60353 TAAACAAGAGCTATTC
1 TAAATAATAGCTATTC
*
60369 TGAATAATAGCTATT
1 TAAATAATAGCTATT
60384 TTTAACAACA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.34
Consensus pattern (16 bp):
TAAATAATAGCTATTC
Found at i:60462 original size:16 final size:16
Alignment explanation
Indices: 60443--60484 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
60433 TGAACGACTC
60443 TTATTCTGAATAAAAG
1 TTATTCTGAATAAAAG
* * *
60459 TTATTTTGAATTATAG
1 TTATTCTGAATAAAAG
60475 TTATTCTGAA
1 TTATTCTGAA
60485 CAAGAACTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.48
Consensus pattern (16 bp):
TTATTCTGAATAAAAG
Found at i:60496 original size:32 final size:31
Alignment explanation
Indices: 60443--60502 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
60433 TGAACGACTC
* *
60443 TTATTCTGAATAAAAGTTATTTTGAATTATAG
1 TTATTCTGAACAAAAGCTATTTT-AATTATAG
60475 TTATTCTGAACAAGAA-CTATTTTAATTA
1 TTATTCTGAACAA-AAGCTATTTTAATTA
60503 ATGACTGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 5 0.20
32 18 0.72
33 2 0.08
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (31 bp):
TTATTCTGAACAAAAGCTATTTTAATTATAG
Found at i:62008 original size:29 final size:27
Alignment explanation
Indices: 61975--62045 Score: 67
Period size: 29 Copynumber: 2.6 Consensus size: 27
61965 GATTCAATCC
61975 TATTTAAATTATAATTTAATTAATAAAAA
1 TATTT-AATTATAATTTAATT-ATAAAAA
* *
62004 TATTTTTATT-TATATTTAATTATATAAA
1 TA-TTTAATTATA-ATTTAATTATAAAAA
62032 T-TTTAA-TATAATTT
1 TATTTAATTATAATTT
62046 TTTAATATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
25 5 0.14
26 6 0.17
28 9 0.25
29 13 0.36
30 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TATTTAATTATAATTTAATTATAAAAA
Found at i:66563 original size:2 final size:2
Alignment explanation
Indices: 66556--66584 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
66546 AGAATATGAA
66556 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 A
66585 GAAAAAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:75111 original size:24 final size:25
Alignment explanation
Indices: 75077--75125 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
75067 AATCTTGAAC
75077 TTTATAATTTTATT-TAAGTAAATA
1 TTTATAATTTTATTGTAAGTAAATA
* *
75101 TTTATATTTTTATTGTAATTAAATA
1 TTTATAATTTTATTGTAAGTAAATA
75126 AATTTTTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
TTTATAATTTTATTGTAAGTAAATA
Found at i:75271 original size:30 final size:28
Alignment explanation
Indices: 75232--75299 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 28
75222 AATTTAAATA
*
75232 AAAATTAAAAGTTAA-GAATTTATTTGAGTGT
1 AAAA-TAAAAATTAATG-ATTTATTTGA--GT
75263 AAAATAAAAATTAATGATTTATTTGAGT
1 AAAATAAAAATTAATGATTTATTTGAGT
75291 AAAATAAAA
1 AAAATAAAA
75300 TATAAAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
28 11 0.31
30 19 0.54
31 5 0.14
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (28 bp):
AAAATAAAAATTAATGATTTATTTGAGT
Found at i:75739 original size:27 final size:27
Alignment explanation
Indices: 75704--75755 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
75694 TTAAAATAAA
*
75704 TTATTATTATAATAATTTTATTTTACT
1 TTATCATTATAATAATTTTATTTTACT
*
75731 TTATCATTATTATAATTTTATTTTA
1 TTATCATTATAATAATTTTATTTTA
75756 TTTCAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (27 bp):
TTATCATTATAATAATTTTATTTTACT
Found at i:76128 original size:20 final size:21
Alignment explanation
Indices: 76074--76130 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
76064 ATATATTAAT
*
76074 AATTACTATTTATA-TATACAA
1 AATTA-TATTTAAATTATACAA
76095 AATT-TATTCATAAATTATA-AA
1 AATTATATT--TAAATTATACAA
76116 AATTATATTTAAATT
1 AATTATATTTAAATT
76131 TTTAGTAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
19 4 0.13
20 6 0.19
21 13 0.42
22 8 0.26
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTATATTTAAATTATACAA
Found at i:76151 original size:14 final size:14
Alignment explanation
Indices: 76132--76159 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
76122 ATTTAAATTT
76132 TTAGTAAACAATAA
1 TTAGTAAACAATAA
76146 TTAGTAAACAATAA
1 TTAGTAAACAATAA
76160 CGAAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (14 bp):
TTAGTAAACAATAA
Found at i:77602 original size:13 final size:14
Alignment explanation
Indices: 77578--77627 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 14
77568 ATATATTTTA
77578 AAAATAAAATAATT
1 AAAATAAAATAATT
77592 AAAAT-AAATAA-T
1 AAAATAAAATAATT
*
77604 -AAATAAAAT-TTT
1 AAAATAAAATAATT
*
77616 AAAAAAAAATAA
1 AAAATAAAATAA
77628 AAATTCAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
11 4 0.14
12 6 0.21
13 14 0.48
14 5 0.17
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAATAAAATAATT
Found at i:77612 original size:25 final size:22
Alignment explanation
Indices: 77579--77628 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 22
77569 TATATTTTAA
77579 AAATAAAATAATTAAAATAAATAAT
1 AAATAAAAT-ATTAAAA-AAA-AAT
*
77604 AAATAAAATTTTAAAAAAAAAT
1 AAATAAAATATTAAAAAAAAAT
77626 AAA
1 AAA
77629 AATTCAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 6 0.25
23 3 0.12
24 6 0.25
25 9 0.38
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (22 bp):
AAATAAAATATTAAAAAAAAAT
Found at i:77647 original size:34 final size:35
Alignment explanation
Indices: 77567--77647 Score: 85
Period size: 39 Copynumber: 2.2 Consensus size: 35
77557 TTTATATTTT
*
77567 TATATATTTTAAAAATAAAATAATTAAAATAAATAA
1 TATAAATTTTAAAAATAAAATAA-TAAAATAAATAA
*
77603 TAAATAAAATTTTAAAAA-AAAATAA-AAATTCAAATAA
1 T--AT-AAATTTTAAAAATAAAATAATAAAAT-AAATAA
77640 TATAAATT
1 TATAAATT
77648 ATAACGGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
34 5 0.13
35 2 0.05
36 5 0.13
37 7 0.18
38 9 0.23
39 11 0.28
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (35 bp):
TATAAATTTTAAAAATAAAATAATAAAATAAATAA
Found at i:83247 original size:18 final size:18
Alignment explanation
Indices: 83220--83255 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
83210 TTCATTACTA
83220 GGGTTAAAAATCTATAAT
1 GGGTTAAAAATCTATAAT
* *
83238 GGGTTGAAAATCTGTAAT
1 GGGTTAAAAATCTATAAT
83256 TAAAAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (18 bp):
GGGTTAAAAATCTATAAT
Found at i:83290 original size:17 final size:17
Alignment explanation
Indices: 83259--83305 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
83249 CTGTAATTAA
* * *
83259 AAAAATTTATAATTTTT
1 AAAAATTTGTGATTTCT
83276 AAAAATTTGTGATTTCT
1 AAAAATTTGTGATTTCT
83293 -AAAATTTGTGATT
1 AAAAATTTGTGATT
83306 GATACTGATC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (17 bp):
AAAAATTTGTGATTTCT
Found at i:86018 original size:155 final size:156
Alignment explanation
Indices: 85727--86035 Score: 611
Period size: 155 Copynumber: 2.0 Consensus size: 156
85717 TTCCTAAATT
85727 GTATAGTATTTTTTTCTTGAAATCATGTCAAAATATTTTTCTAATGGTGTCTTATATGCCCTTGG
1 GTATAGTATTTTTTTCTTGAAATCATGTCAAAATATTTTTCTAATGGTGTCTTATATGCCCTTGG
85792 ATCATTCCGGATAAGGGAGTTACGATTTTTCGAACCTAAGCTATACAGAACCCCTGGAATCAATG
66 ATCATTCCGGATAAGGGAGTTACGATTTTTCGAACCTAAGCTATACAGAACCCCTGGAATCAATG
85857 AAATGCATTCTAGTTGGACCATTCTA
131 AAATGCATTCTAGTTGGACCATTCTA
85883 GTATAGTA-TTTTTTCTTGAAATCATGTCAAAATATTTTTCTAATGGTGTCTTATATGCCCTTGG
1 GTATAGTATTTTTTTCTTGAAATCATGTCAAAATATTTTTCTAATGGTGTCTTATATGCCCTTGG
85947 ATCATTCCGGATAAGGGAGTTACGATTTTTCGAACCTAAGCTATACAGAACCCCTGGAATCAATG
66 ATCATTCCGGATAAGGGAGTTACGATTTTTCGAACCTAAGCTATACAGAACCCCTGGAATCAATG
86012 AAATGCATTCTAGTTGGACCATTC
131 AAATGCATTCTAGTTGGACCATTC
86036 AGGCCCACTA
Statistics
Matches: 153, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
155 145 0.95
156 8 0.05
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (156 bp):
GTATAGTATTTTTTTCTTGAAATCATGTCAAAATATTTTTCTAATGGTGTCTTATATGCCCTTGG
ATCATTCCGGATAAGGGAGTTACGATTTTTCGAACCTAAGCTATACAGAACCCCTGGAATCAATG
AAATGCATTCTAGTTGGACCATTCTA
Found at i:88591 original size:53 final size:53
Alignment explanation
Indices: 88492--88592 Score: 150
Period size: 53 Copynumber: 1.9 Consensus size: 53
88482 ATAAAGGCTT
* *
88492 CTTAGATTCAGCAAAAAAACACTAAAAATTTTAATTTTAATTCTTATTCTCCC
1 CTTAGATTCAGCAAAAAAACACTAAAAATTTTAATTTCAATACTTATTCTCCC
* *
88545 CTTAGATTCAGCAAAAAAACAGTAAAAATTTTTATATTCAA-ACTTATT
1 CTTAGATTCAGCAAAAAAACACTAAAAATTTTAAT-TTCAATACTTATT
88593 TGGATTTCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
53 39 0.91
54 4 0.09
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.37
Consensus pattern (53 bp):
CTTAGATTCAGCAAAAAAACACTAAAAATTTTAATTTCAATACTTATTCTCCC
Found at i:93319 original size:20 final size:20
Alignment explanation
Indices: 93294--93331 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
93284 ATGGCCCAGC
* *
93294 ATCGATATATTCACTTATGT
1 ATCGATACATTAACTTATGT
93314 ATCGATACATTAACTTAT
1 ATCGATACATTAACTTAT
93332 TATATCAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (20 bp):
ATCGATACATTAACTTATGT
Found at i:94057 original size:33 final size:33
Alignment explanation
Indices: 94011--94083 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
94001 AGGTGGAAAG
*
94011 AGATATTATGTTACATTTATTAAAGATAGTACT
1 AGATATTATGTTACATTTACTAAAGATAGTACT
* *
94044 AGATATT-TGGTTACATTTACTGAAGATATTACT
1 AGATATTAT-GTTACATTTACTAAAGATAGTACT
94077 AGATATT
1 AGATATT
94084 GCTATGCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 1 0.03
33 35 0.97
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (33 bp):
AGATATTATGTTACATTTACTAAAGATAGTACT
Found at i:99532 original size:2 final size:2
Alignment explanation
Indices: 99525--99560 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
99515 GAATCTCTTG
*
99525 AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
99561 GTACATTCCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:103621 original size:2 final size:2
Alignment explanation
Indices: 103614--103660 Score: 58
Period size: 2 Copynumber: 22.5 Consensus size: 2
103604 TTTGTGTAAT
* *
103614 TA TA TA TA TA TA AA CTCA TT TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA -T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
103658 TA T
1 TA T
103661 TAGAAGTGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 37 0.95
3 1 0.03
4 1 0.03
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:104363 original size:27 final size:27
Alignment explanation
Indices: 104310--104366 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 27
104300 AATTTTTATC
*
104310 ATTATATGAATATATTAAAAATAAATA
1 ATTATATGAATATAATAAAAATAAATA
*
104337 ATTATAT-AA-ATAAT-AAAATATATA
1 ATTATATGAATATAATAAAAATAAATA
104361 A-TATAT
1 ATTATAT
104367 TTTTTTACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 5 0.18
24 10 0.36
25 4 0.14
26 2 0.07
27 7 0.25
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (27 bp):
ATTATATGAATATAATAAAAATAAATA
Found at i:104432 original size:8 final size:8
Alignment explanation
Indices: 104419--104459 Score: 50
Period size: 7 Copynumber: 5.2 Consensus size: 8
104409 AAAAAGAAGA
104419 TATAATTT
1 TATAATTT
104427 TATAATTT
1 TATAATTT
*
104435 T-TAATTA
1 TATAATTT
104442 T-TAATTT
1 TATAATTT
104449 TATAAATTT
1 TAT-AATTT
104458 TA
1 TA
104460 AATAATCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 12 0.41
8 10 0.34
9 7 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TATAATTT
Found at i:105744 original size:75 final size:77
Alignment explanation
Indices: 105621--105774 Score: 242
Period size: 75 Copynumber: 2.0 Consensus size: 77
105611 GGTATATCAA
* * *
105621 AGCAATATATTGAGTTTGAATTGGAGATAATGTTGTGCTCGTTTTG-AAAATGAAAACACAAAAA
1 AGCAATATATTGAGTTTGAATTGGAGATAATGTTGTACTCGTTATGAAAAAAGAAAACACAAAAA
105685 -AAAAAAAAAAT
66 GAAAAAAAAAAT
*
105696 AGCAATATATTGAGTTTGGATTGGAGATAATGTTGTACTTC-TTATGAAAAAAGAAAACACAAAA
1 AGCAATATATTGAGTTTGAATTGGAGATAATGTTGTAC-TCGTTATGAAAAAAGAAAACACAAAA
105760 AGAAAAAAAAAAT
65 AGAAAAAAAAAAT
105773 AG
1 AG
105775 TTTCGAGACT
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
75 40 0.56
76 19 0.26
77 13 0.18
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (77 bp):
AGCAATATATTGAGTTTGAATTGGAGATAATGTTGTACTCGTTATGAAAAAAGAAAACACAAAAA
GAAAAAAAAAAT
Found at i:108143 original size:17 final size:17
Alignment explanation
Indices: 108123--108155 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
108113 ACGTAAAACT
108123 GTTTTTCAA-TTTTTTTA
1 GTTTTT-AACTTTTTTTA
108140 GTTTTTAACTTTTTTT
1 GTTTTTAACTTTTTTT
108156 TTAATTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.73
Consensus pattern (17 bp):
GTTTTTAACTTTTTTTA
Found at i:109365 original size:28 final size:28
Alignment explanation
Indices: 109304--109365 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
109294 ATATTAAGAT
* *
109304 TTAAATT-TTAAATTTATTAAATATTAA
1 TTAAATTATTAAATTAATTAAATATAAA
*
109331 -TAGATTATATAAATTAATTAAAT-TAAA
1 TTAAATTAT-TAAATTAATTAAATATAAA
109358 TTAAATTA
1 TTAAATTA
109366 AAAATTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
26 5 0.18
27 4 0.14
28 19 0.68
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
TTAAATTATTAAATTAATTAAATATAAA
Found at i:109768 original size:29 final size:29
Alignment explanation
Indices: 109714--109769 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
109704 AATTTAAATT
*
109714 AATTTAAATTATTATTTAAATAATAAAAA
1 AATTTAAAATATTATTTAAATAATAAAAA
109743 AATTTAAAAT-TTACTTATAAAT-ATAAA
1 AATTTAAAATATTA-TT-TAAATAATAAA
109770 TATAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 3 0.12
29 16 0.67
30 5 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (29 bp):
AATTTAAAATATTATTTAAATAATAAAAA
Found at i:113966 original size:50 final size:50
Alignment explanation
Indices: 113891--114126 Score: 305
Period size: 50 Copynumber: 4.7 Consensus size: 50
113881 AGTTGCTTAG
*
113891 AGTCAACAATTAC-AGTCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGA-CCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
* *
113941 AGTCAACAATCACGACCACCTCTCTCTATTGTCAAAGGTTAGTGAAGAAT
1 AGTCAACAATTACGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
* * *
113991 AGTTAACAATTACGACCACCTCTCTCTCTTGTTAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
* ** * * *
114041 AGTCAATAATTACGGTCACCTCTCTCGATTGTCAAAAGTTGGTAAAGAAT
1 AGTCAACAATTACGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
* * *
114091 AGTTAACAATTAC-AGCCACTTCTCTCGATTGTCAAA
1 AGTCAACAATTACGA-CCACCTCTCTCTATTGTCAAA
114127 AACTTGTAAA
Statistics
Matches: 162, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
50 161 0.99
51 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.30
Consensus pattern (50 bp):
AGTCAACAATTACGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
Found at i:120208 original size:20 final size:20
Alignment explanation
Indices: 120161--120235 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
120151 AAAAAGACAT
*
120161 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
120180 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
120201 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
120221 AATGTATCGATACAT
1 AATGTATCGATACAT
120236 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:120229 original size:40 final size:39
Alignment explanation
Indices: 120158--120235 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
120148 GGTAAAAAGA
* *
120158 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
120197 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
120236 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:120935 original size:34 final size:32
Alignment explanation
Indices: 120771--121006 Score: 302
Period size: 31 Copynumber: 7.4 Consensus size: 32
120761 GATTTGAAAA
* ** **
120771 GGGTTGCCACTGACTTGCATGGGCTTTTAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
120803 GGGTTGCCACCGACTTGTGTGGG-TTTTGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
120834 GGGTTGCCGCCGACTTGTGT-GGC-TT-GAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
* *
120863 GGATTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
120895 GGGTTGCCACCGGCTTGTGTGGGCTTTGGGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTT--GGAAT
120929 GGGTTGCCACCGACTTGTGTGGGCTTT-GAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
120960 GGGTTGCCACCGACTTGTGTGGGTCTTTAGGAAT
1 GGGTTGCCACCGACTTGTGTGGG-CTTT-GGAAT
*
120994 GGGTTTCCACCGA
1 GGGTTGCCACCGA
Statistics
Matches: 182, Mismatches: 13, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
29 22 0.12
30 7 0.04
31 55 0.30
32 52 0.29
34 46 0.25
ACGTcount: A:0.14, C:0.19, G:0.35, T:0.32
Consensus pattern (32 bp):
GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
Done.