Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3304
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: 95272
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4410 original size:12 final size:12
Alignment explanation
Indices: 4365--4422 Score: 59
Period size: 12 Copynumber: 4.9 Consensus size: 12
4355 AAACCTTACT
4365 TTTATATTA-TA
1 TTTATATTATTA
*
4376 TATATAATTATCTA
1 TTTAT-ATTAT-TA
4390 TTTA-A-TATTA
1 TTTATATTATTA
4400 TTTATATTATTA
1 TTTATATTATTA
*
4412 ATTATATTATT
1 TTTATATTATT
4423 TAATTTTCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
10 6 0.15
11 8 0.21
12 20 0.51
14 5 0.13
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTATATTATTA
Found at i:4441 original size:23 final size:21
Alignment explanation
Indices: 4394--4446 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 21
4384 TATCTATTTA
*
4394 ATATTATTTATATTATTAATT
1 ATATTATTTATATTATAAATT
*
4415 ATATTATTTAATTTTCATAAATT
1 ATATTATTT-ATATT-ATAAATT
4438 ATATTATTT
1 ATATTATTT
4447 TTCATCGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 9 0.32
22 4 0.14
23 15 0.54
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATTATTTATATTATAAATT
Found at i:4524 original size:15 final size:16
Alignment explanation
Indices: 4492--4537 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
4482 TATTATTTAA
*
4492 TTATTTATATATATAT
1 TTATTTACATATATAT
4508 TTATTTACATA-ATAT
1 TTATTTACATATATAT
*
4523 TTATTTATATATATA
1 TTATTTACATATATA
4538 CTAGTCACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATTTACATATATAT
Found at i:9284 original size:49 final size:51
Alignment explanation
Indices: 9158--9303 Score: 197
Period size: 49 Copynumber: 2.9 Consensus size: 51
9148 TATGTAGCTA
* *
9158 GGTCGCATGTGTAGTACTAAGTACAGGCTACTATGCGTACCCGATAACTTC
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCGATAACTTC
* * * * *
9209 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TT-
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCGATAACTTC
* *
9258 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCGATA
9304 GTTTGGCTAC
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
49 40 0.49
50 2 0.02
51 40 0.49
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (51 bp):
GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCGATAACTTC
Found at i:18593 original size:37 final size:37
Alignment explanation
Indices: 18536--18674 Score: 165
Period size: 37 Copynumber: 4.1 Consensus size: 37
18526 TTACGAAGTC
* * * *
18536 TACCCGGACATAATCTCCACACGAAGTTATCGGGTCT
1 TACCCGGACAAAATCCCCACACGTAGTCATCGGGTCT
18573 TACCCGGACAAAATCCCCACACGTAGTCATCGGGTCT
1 TACCCGGACAAAATCCCCACACGTAGTCATCGGGTCT
18610 TA--CGGACAAAAT--CCACACGTA-TCATC--GTCT
1 TACCCGGACAAAATCCCCACACGTAGTCATCGGGTCT
18640 TACCC-G-CAAAATCCCCACACGTA-TCATC-GGTCT
1 TACCCGGACAAAATCCCCACACGTAGTCATCGGGTCT
18673 TA
1 TA
18675 GAGCTCGGAT
Statistics
Matches: 93, Mismatches: 4, Indels: 14
0.84 0.04 0.13
Matches are distributed among these distances:
30 12 0.13
31 1 0.01
32 20 0.22
33 15 0.16
35 10 0.11
37 35 0.38
ACGTcount: A:0.29, C:0.33, G:0.16, T:0.22
Consensus pattern (37 bp):
TACCCGGACAAAATCCCCACACGTAGTCATCGGGTCT
Found at i:18929 original size:47 final size:47
Alignment explanation
Indices: 18788--19013 Score: 339
Period size: 47 Copynumber: 4.8 Consensus size: 47
18778 CCCTTCGGGA
* * * * *
18788 CTTATCACAT-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
18834 CCTGTCACATATATACACTTTCACATTTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACA-TTCATCACATCGGCCATTAGGC
18882 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
18929 CTTATCACATATATACACTTTCACATTCATCATATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
18976 CTT-TCACATGTATATACACTTTCACATTCATCACATCG
1 CTTATCACA--TATATACACTTTCACATTCATCACATCG
19014 AATCCTAATC
Statistics
Matches: 165, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
46 13 0.08
47 85 0.52
48 67 0.41
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:18990 original size:95 final size:95
Alignment explanation
Indices: 18788--19013 Score: 341
Period size: 95 Copynumber: 2.4 Consensus size: 95
18778 CCCTTCGGGA
* * * * *
18788 CTTATCACAT-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCACATATATACAC
18852 TTTCACATTTCATCACATCGGCCATTAGGC
66 TTTCACATTTCATCACATCGGCCATTAGGC
* *
18882 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCACATATATACAC
*
18947 TTTCACA-TTCATCATATCGGCCATTAGGC
66 TTTCACATTTCATCACATCGGCCATTAGGC
18976 CTT-TCACATGTATATACACTTTCACATTCATCACATCG
1 CTTATCACA--TATATACACTTTCACATTCATCACATCG
19014 AATCCTAATC
Statistics
Matches: 121, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
93 5 0.04
94 34 0.28
95 82 0.68
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.33
Consensus pattern (95 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCACATATATACAC
TTTCACATTTCATCACATCGGCCATTAGGC
Found at i:24720 original size:45 final size:45
Alignment explanation
Indices: 24644--24852 Score: 271
Period size: 45 Copynumber: 4.7 Consensus size: 45
24634 AATATCGCAC
* * * **
24644 AATAATATTCAGGCCTTTGAGCCAAGCAGGCTATGATGCCGGTGA
1 AATACTATTCGGGCCTTTGAGCCTAGCAGGCTACAATGCCGGTGA
* *
24689 GATACTATTCGGGCCTTTGAGCCTAGTAGGCTACAATGCCGGTGA
1 AATACTATTCGGGCCTTTGAGCCTAGCAGGCTACAATGCCGGTGA
* *
24734 GATACTATTCGGGCCTTTGAGCCTAGCAGGCTACAATGCCAGTGA
1 AATACTATTCGGGCCTTTGAGCCTAGCAGGCTACAATGCCGGTGA
** *
24779 AATACTATTCGGGCCTTCAAGCCTAGCAGGCTATAATGCCGGTGA
1 AATACTATTCGGGCCTTTGAGCCTAGCAGGCTACAATGCCGGTGA
*
24824 AATGA-TA-TCGGG-CTTCGAGCCTAGCAGGC
1 AAT-ACTATTCGGGCCTTTGAGCCTAGCAGGC
24853 GAAATGTAGG
Statistics
Matches: 148, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
43 16 0.11
44 5 0.03
45 126 0.85
46 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.24
Consensus pattern (45 bp):
AATACTATTCGGGCCTTTGAGCCTAGCAGGCTACAATGCCGGTGA
Found at i:25980 original size:49 final size:49
Alignment explanation
Indices: 25759--25982 Score: 205
Period size: 49 Copynumber: 4.7 Consensus size: 49
25749 TTAAGTTGCC
* * * *
25759 GATGCCATGTCGCAGACATGGTCTTACACTGGCTATCTTCATCGAGGTT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCATTGAGGCT
* ** * * *
25808 GGTGCCATGTCCCAGACATGGTCTTACACTAACTCTCAT-GTATAAGTGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCAT-TGAG-GCT
* * * *
25858 GATG-CATGTCCCAGACAT-GTCTTACACTAGC-ATGAAGC-TT-A-GCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTAT-CATCATTGAGGCT
**
25902 GATG-CATGTCCCAGA-AACGTCTTACACTGGCTATCATCATTGAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCATTGAGGCT
*
25949 GATGCCATGTCCCAGACATGGTCTTTCACTGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCT
25983 CTCACATAAC
Statistics
Matches: 140, Mismatches: 24, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
43 1 0.01
44 31 0.22
45 4 0.03
46 2 0.01
47 8 0.06
48 26 0.19
49 63 0.45
50 5 0.04
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (49 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATCATTGAGGCT
Found at i:27410 original size:20 final size:20
Alignment explanation
Indices: 27385--27422 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27375 TTTTCATACA
*
27385 CATTAACCACATTAAAAAGG
1 CATTAACAACATTAAAAAGG
*
27405 CATTAATAACATTAAAAA
1 CATTAACAACATTAAAAA
27423 ACACTATTAA
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:0.55, C:0.16, G:0.05, T:0.24
Consensus pattern (20 bp):
CATTAACAACATTAAAAAGG
Found at i:30368 original size:2 final size:2
Alignment explanation
Indices: 30363--30387 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30353 AATATATATA
30363 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
30388 ACTTTGATAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:34666 original size:38 final size:38
Alignment explanation
Indices: 34624--34727 Score: 149
Period size: 38 Copynumber: 2.7 Consensus size: 38
34614 GGCTTAAAGA
* *
34624 CCCGCAGGCTATATGCTGGAATTATATCCGGGTTAAAT
1 CCCGCAGGCTATGTGCTGGTATTATATCCGGGTTAAAT
34662 CCCGCAGGCT-TCGTGCTGGTATTATATCCGGGTTAAAT
1 CCCGCAGGCTAT-GTGCTGGTATTATATCCGGGTTAAAT
*
34700 CCCGAAGGCCTA-GTGCTGGTATTATATC
1 CCCGCAGG-CTATGTGCTGGTATTATATC
34728 TGAGTTTAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
37 1 0.02
38 57 0.95
39 2 0.03
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (38 bp):
CCCGCAGGCTATGTGCTGGTATTATATCCGGGTTAAAT
Found at i:42271 original size:16 final size:16
Alignment explanation
Indices: 42250--42281 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
42240 TATGTGTGAA
42250 AGTCGTATATATATAT
1 AGTCGTATATATATAT
42266 AGTCGTATATATATAT
1 AGTCGTATATATATAT
42282 TATATTCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (16 bp):
AGTCGTATATATATAT
Found at i:42772 original size:39 final size:39
Alignment explanation
Indices: 42717--42828 Score: 161
Period size: 39 Copynumber: 2.9 Consensus size: 39
42707 TTCAGTGATG
*
42717 TATATCTGGACTTAGGGTCCGCAAGCTATGTGCTGGAAT
1 TATATCTGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
* * *
42756 TATATCTGAACATAGGGTCCGTAGGCTATGTGCTGGAAT
1 TATATCTGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
* * *
42795 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCT
1 TATATCTGGACTTAGGGTCCGCAGGCTATGTGCT
42829 AGAAATATGT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (39 bp):
TATATCTGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
Found at i:54542 original size:34 final size:34
Alignment explanation
Indices: 54499--54565 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
54489 ATATTCAGAG
54499 TAGACATCCACAAAACAAGGTTTAGAAATAATGT
1 TAGACATCCACAAAACAAGGTTTAGAAATAATGT
* *
54533 TAGATATCCATAAAACAAGGTTTAGAAATAATG
1 TAGACATCCACAAAACAAGGTTTAGAAATAATG
54566 GTTCTGCATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (34 bp):
TAGACATCCACAAAACAAGGTTTAGAAATAATGT
Found at i:57320 original size:51 final size:49
Alignment explanation
Indices: 57242--57382 Score: 192
Period size: 49 Copynumber: 2.8 Consensus size: 49
57232 AGCTAGGTCG
*
57242 CATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGATCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAA-TT-GATCA
* * * * * * *
57293 CGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGATAATTGGTCG
1 CATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTGATCA
57342 CATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
57383 GTTTGGCTAC
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
49 39 0.50
50 2 0.03
51 37 0.47
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (49 bp):
CATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTGATCA
Found at i:57367 original size:49 final size:51
Alignment explanation
Indices: 57237--57382 Score: 197
Period size: 51 Copynumber: 2.9 Consensus size: 51
57227 TATGTAGCTA
*
57237 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTC
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCGATAACTTC
* * * * * *
57288 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGATAA-TT-
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCGATAACTTC
* *
57337 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCGATA
57383 GTTTGGCTAC
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
49 39 0.48
50 2 0.02
51 40 0.49
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (51 bp):
GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCCGATAACTTC
Found at i:63256 original size:26 final size:26
Alignment explanation
Indices: 63227--63312 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
63217 AAGTAAATAA
63227 TAAGAATGAAAATAAAATCTAAAACC
1 TAAGAATGAAAATAAAATCTAAAACC
* * ** *
63253 TAAGAGAAGGGAAAA-ACTAAGGTAAATA-A
1 T-A-AGAA-TGAAAATA-AAATCTAAA-ACC
63282 TAAGAATGAAAATAAAATCTAAAACC
1 TAAGAATGAAAATAAAATCTAAAACC
63308 TAAGA
1 TAAGA
63313 GAAGGGAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
25 1 0.02
26 17 0.40
27 6 0.14
28 6 0.14
29 12 0.28
30 1 0.02
ACGTcount: A:0.60, C:0.08, G:0.14, T:0.17
Consensus pattern (26 bp):
TAAGAATGAAAATAAAATCTAAAACC
Found at i:63334 original size:31 final size:31
Alignment explanation
Indices: 63244--63336 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 31
63234 GAAAATAAAA
63244 TCTAAAACCTAAGAGAAGGGAAAAACTAAGG
1 TCTAAAACCTAAGAGAAGGGAAAAACTAAGG
* * **
63275 --T-AAA--TAATAAGAA-TG-AAAA-TAAAA
1 TCTAAAACCTAA-GAGAAGGGAAAAACTAAGG
63299 TCTAAAACCTAAGAGAAGGGAAAAACTAAGG
1 TCTAAAACCTAAGAGAAGGGAAAAACTAAGG
63330 TCTAAAA
1 TCTAAAA
63337 ATAAAGAGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 18
0.63 0.11 0.25
Matches are distributed among these distances:
24 3 0.07
25 4 0.09
26 5 0.11
27 7 0.16
28 7 0.16
29 5 0.11
30 4 0.09
31 10 0.22
ACGTcount: A:0.57, C:0.10, G:0.17, T:0.16
Consensus pattern (31 bp):
TCTAAAACCTAAGAGAAGGGAAAAACTAAGG
Found at i:63349 original size:55 final size:55
Alignment explanation
Indices: 63219--63330 Score: 224
Period size: 55 Copynumber: 2.0 Consensus size: 55
63209 CTCCCTAAAA
63219 GTAAATAATAAGAATGAAAATAAAATCTAAAACCTAAGAGAAGGGAAAAACTAAG
1 GTAAATAATAAGAATGAAAATAAAATCTAAAACCTAAGAGAAGGGAAAAACTAAG
63274 GTAAATAATAAGAATGAAAATAAAATCTAAAACCTAAGAGAAGGGAAAAACTAAG
1 GTAAATAATAAGAATGAAAATAAAATCTAAAACCTAAGAGAAGGGAAAAACTAAG
63329 GT
1 GT
63331 CTAAAAATAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.59, C:0.07, G:0.17, T:0.17
Consensus pattern (55 bp):
GTAAATAATAAGAATGAAAATAAAATCTAAAACCTAAGAGAAGGGAAAAACTAAG
Found at i:68751 original size:16 final size:17
Alignment explanation
Indices: 68722--68755 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
68712 AGAAATGCAT
68722 AAAAAGGGACTAAATTG
1 AAAAAGGGACTAAATTG
*
68739 AAAAA-GGAGTAAATTG
1 AAAAAGGGACTAAATTG
68755 A
1 A
68756 GTGATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.56, C:0.03, G:0.24, T:0.18
Consensus pattern (17 bp):
AAAAAGGGACTAAATTG
Found at i:71386 original size:34 final size:35
Alignment explanation
Indices: 71340--71423 Score: 134
Period size: 34 Copynumber: 2.4 Consensus size: 35
71330 GAATACATTA
71340 TGGGCCTAAGCCCATATTAGTAACAGT-AACAGTC
1 TGGGCCTAAGCCCATATTAGTAACAGTAAACAGTC
* * *
71374 TGGGCCTTAGCCCATTTTAGTATCAGTAAACAGTC
1 TGGGCCTAAGCCCATATTAGTAACAGTAAACAGTC
71409 TGGGCCTAAGCCCAT
1 TGGGCCTAAGCCCAT
71424 CGCAATATAG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
34 24 0.53
35 21 0.47
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.26
Consensus pattern (35 bp):
TGGGCCTAAGCCCATATTAGTAACAGTAAACAGTC
Found at i:71884 original size:27 final size:26
Alignment explanation
Indices: 71854--71925 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
71844 CTTAACATAT
*
71854 AAGGGCAAAATAGTCATTTTACCTTAC
1 AAGGG-AAAATAGTCATTTTACCCTAC
* * *
71881 AAGGGTAAAACAATCATTTTACCCTAT
1 AAGGG-AAAATAGTCATTTTACCCTAC
*
71908 AAGGGAATTATAGTCATT
1 AAGGGAA-AATAGTCATT
71926 ATACATTATA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
26 2 0.06
27 34 0.94
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (26 bp):
AAGGGAAAATAGTCATTTTACCCTAC
Found at i:71970 original size:27 final size:27
Alignment explanation
Indices: 71894--72065 Score: 148
Period size: 27 Copynumber: 6.4 Consensus size: 27
71884 GGTAAAACAA
** * *
71894 TCATTTTACCCTATAAGGGAATTATAG
1 TCATTTTACCCTATGGGGGTATTTTAG
* ** * * *
71921 TCATTATACATTATAGAGATATTTTAG
1 TCATTTTACCCTATGGGGGTATTTTAG
* * *
71948 TCATTTTGCCATATGGGGGTA-TTTCG
1 TCATTTTACCCTATGGGGGTATTTTAG
*
71974 ATCATTTTACCCTATGAGGGTATTTTAG
1 -TCATTTTACCCTATGGGGGTATTTTAG
* *
72002 TCATTTTACCCTATCGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTTAG
** * *
72029 TCATTTTATTCTATGGGAGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTTAG
72056 TCATTTTACC
1 TCATTTTACC
72066 TGATTAAGGG
Statistics
Matches: 114, Mismatches: 29, Indels: 4
0.78 0.20 0.03
Matches are distributed among these distances:
26 4 0.04
27 106 0.93
28 4 0.04
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.44
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTTAG
Found at i:72044 original size:81 final size:81
Alignment explanation
Indices: 71893--72065 Score: 195
Period size: 81 Copynumber: 2.1 Consensus size: 81
71883 GGGTAAAACA
*
71893 ATCATTTTACCCTATAAGGGAATTATAGTCATTATACATTATAGAGATATTTTAGTCATTTTGCC
1 ATCATTTTACCCTATAAGGGAATTATAGTCATTATACACTATAGAGATATTTTAGTCATTTTGCC
*
71958 ATATGGGGGTATTTCG
66 ATATGGGAGTATTTCG
* * * * * * * * * **
71974 ATCATTTTACCCTATGAGGGTATTTTAGTCATTTTACCCTATCGGGGTATTTTGGTCATTTTATT
1 ATCATTTTACCCTATAAGGGAATTATAGTCATTATACACTATAGAGATATTTTAGTCATTTT-GC
*
72039 C-TATGGGAGTATTTTG
65 CATATGGGAGTATTTCG
*
72055 GTCATTTTACC
1 ATCATTTTACC
72066 TGATTAAGGG
Statistics
Matches: 76, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
81 75 0.99
82 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.44
Consensus pattern (81 bp):
ATCATTTTACCCTATAAGGGAATTATAGTCATTATACACTATAGAGATATTTTAGTCATTTTGCC
ATATGGGAGTATTTCG
Found at i:80227 original size:37 final size:37
Alignment explanation
Indices: 80168--80276 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
80158 AGTTCAGATG
* * *
80168 AAATCTCCACACGAAGTTATCGGGTCTTACTCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
80205 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
80242 TAATCTCCACATGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
80277 ATATATTTCC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:80624 original size:52 final size:50
Alignment explanation
Indices: 80423--80816 Score: 559
Period size: 48 Copynumber: 7.9 Consensus size: 50
80413 ACACATCGCC
* * *
80423 TACATAATTCACACTAGCTATTCGGCTTTACCACATATACATATCTC--A
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATA
* *
80471 TACATATTTCACACTAGCCATTCGGCTTTACAACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATA
* *
80521 TATATATTTCACATT-GACCATTCGGCTTTACCACATATGCATATCTCATA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCATA
* * *
80571 TATATATTTCACATTAACCATTCAGCTTTACCACATATACATATCTCATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--ATA
* **
80623 TACATATTTCGCATTAGCCATTTAGCTTTACCACATATACATATCTCATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--ATA
* *
80675 TATATATTTCGCATTAGCCATTCGGCTTTACCACATATACATATCTC--A
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATA
80723 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATA
80771 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCT
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCT
80817 TATGCATCAA
Statistics
Matches: 321, Mismatches: 19, Indels: 12
0.91 0.05 0.03
Matches are distributed among these distances:
48 137 0.43
49 1 0.00
50 88 0.27
52 95 0.30
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (50 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATA
Found at i:83627 original size:47 final size:45
Alignment explanation
Indices: 83576--83790 Score: 186
Period size: 46 Copynumber: 4.6 Consensus size: 45
83566 AAGTCGATTC
* *
83576 CATGTCCCAAACATGGTCTTACACTAACTATCGTCTCGTACTAGATG
1 CATGTCCCAGACAT-GTCTTACACTAGCTATCGTCTCGTACT-GATG
*
83623 CATGTCCCAGACATGTCTTACACTGGCT-TACGTCTCG-AGGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCTAT-CGTCTCGTA--CTGATG
*
83669 CATGTCCCAGACATGTCTTACACTAGC-ACTCGTCTCGATACCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTA-TCGTCTCG-TACTGATG
* * * * * * * *
83715 CCATGTCCTAGACATGGTCTAACACTGGCTCTCATAAT-GTGGCCGATG
1 -CATGTCCCAGACAT-GTCTTACACTAGCTATCGT-CTCGT-ACTGATG
*
83763 CATGTCCCAGATATGTCTTACACTAGCT
1 CATGTCCCAGACATGTCTTACACTAGCT
83791 CACAATAACC
Statistics
Matches: 140, Mismatches: 16, Indels: 25
0.77 0.09 0.14
Matches are distributed among these distances:
45 2 0.01
46 73 0.52
47 42 0.30
48 22 0.16
49 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (45 bp):
CATGTCCCAGACATGTCTTACACTAGCTATCGTCTCGTACTGATG
Found at i:85450 original size:39 final size:40
Alignment explanation
Indices: 85405--85515 Score: 98
Period size: 40 Copynumber: 2.8 Consensus size: 40
85395 CGGGGTTTAG
* * *
85405 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
85444 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * *
85484 CCGGATATAGTCGCTAGCACAAATGCCTTCGG
1 CCGGATATAACCACTAGCATAAAGGCCTTCGG
85516 ATCTTAGTCC
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
39 15 0.25
40 45 0.75
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:85475 original size:40 final size:40
Alignment explanation
Indices: 85428--85571 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
85418 CTCGCACAAG
* * * * *
85428 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
85468 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
85508 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
85549 GCCTTC-GGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
85572 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
39 3 0.03
40 71 0.77
41 18 0.20
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:93463 original size:39 final size:40
Alignment explanation
Indices: 93418--93585 Score: 106
Period size: 40 Copynumber: 4.2 Consensus size: 40
93408 CGGGGTTTAG
* * *
93418 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
93457 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
93497 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
93537 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
93578 CCGGATAT
1 CCGGATAT
93586 CATTCGAGTA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 18 0.17
40 61 0.56
41 27 0.25
42 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:93568 original size:41 final size:40
Alignment explanation
Indices: 93441--93585 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
93431 CTCGCACAAG
* * * * *
93441 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
93481 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
93521 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
93562 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
93586 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Done.