Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3227
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: 43529
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.31
Found at i:7463 original size:40 final size:39
Alignment explanation
Indices: 7379--7559 Score: 204
Period size: 40 Copynumber: 4.6 Consensus size: 39
7369 TTGAATGATG
* * * *
7379 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
7419 TCCGGACTAAGATCCGAAGGTATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
7459 TCCGGGCTAAG-CCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
7497 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAA
*
7537 TCCGGGTTAAGTCCCGAAGGCAT
1 TCCGGGCTAAGT-CCGAAGGCAT
7560 AAATTGCTTA
Statistics
Matches: 122, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
38 33 0.27
40 81 0.66
41 8 0.07
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:8594 original size:27 final size:27
Alignment explanation
Indices: 8564--8618 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
8554 GGGTGTTACA
* *
8564 TGTAATACCC-TCGTAGGGTAAAATGAC
1 TGTAATACCCAT-GTAAGGTAAAAAGAC
8591 TGTAATACCCATGTAAGGTAAAAAGAC
1 TGTAATACCCATGTAAGGTAAAAAGAC
8618 T
1 T
8619 ATTTTACCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.25
Consensus pattern (27 bp):
TGTAATACCCATGTAAGGTAAAAAGAC
Found at i:8639 original size:27 final size:26
Alignment explanation
Indices: 8608--8715 Score: 101
Period size: 27 Copynumber: 4.0 Consensus size: 26
8598 CCCATGTAAG
*
8608 GTAAAAAGACTATTTTACCCTTATGT
1 GTAAAAAGACTATTTTGCCCTTATGT
*
8634 GTTAAAATGA-TAATTTTGCCCTTATGT
1 G-TAAAAAGACT-ATTTTGCCCTTATGT
* * *
8661 GATAAAATGACAAATTTGCCCTTATGT
1 G-TAAAAAGACTATTTTGCCCTTATGT
* * *
8688 GGAAAAATGACTGTTTTGCCCCTATGT
1 GTAAAAA-GACTATTTTGCCCTTATGT
8715 G
1 G
8716 ATGTATGTGA
Statistics
Matches: 67, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
26 6 0.09
27 61 0.91
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (26 bp):
GTAAAAAGACTATTTTGCCCTTATGT
Found at i:8667 original size:54 final size:54
Alignment explanation
Indices: 8609--8717 Score: 130
Period size: 54 Copynumber: 2.0 Consensus size: 54
8599 CCATGTAAGG
* * ** *
8609 TAAAAAGACTATTTTACCCTTATGTGTTAAAATGA-TAATTTTGCCCTTATGTGA
1 TAAAAAGACAAATTTACCCTTATGTGGAAAAATGACT-ATTTTGCCCCTATGTGA
* * *
8663 TAAAATGACAAATTTGCCCTTATGTGGAAAAATGACTGTTTTGCCCCTATGTGA
1 TAAAAAGACAAATTTACCCTTATGTGGAAAAATGACTATTTTGCCCCTATGTGA
8717 T
1 T
8718 GTATGTGATG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
54 45 0.98
55 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.38
Consensus pattern (54 bp):
TAAAAAGACAAATTTACCCTTATGTGGAAAAATGACTATTTTGCCCCTATGTGA
Found at i:9093 original size:18 final size:18
Alignment explanation
Indices: 9048--9086 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
9038 AGACTGGCAT
* *
9048 ACTGCTTACTGTTACTGC
1 ACTGATTACTGTTACTAC
*
9066 ATTGATTACTGTTACTAC
1 ACTGATTACTGTTACTAC
9084 ACT
1 ACT
9087 ATTTACTATT
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.41
Consensus pattern (18 bp):
ACTGATTACTGTTACTAC
Found at i:11203 original size:19 final size:19
Alignment explanation
Indices: 11179--11215 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
11169 GTCTCTCGGG
*
11179 CTTTTTTTTACTCATTTTC
1 CTTTTTATTACTCATTTTC
*
11198 CTTTTTATTACTTATTTT
1 CTTTTTATTACTCATTTT
11216 GATTTGCGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (19 bp):
CTTTTTATTACTCATTTTC
Found at i:12125 original size:27 final size:27
Alignment explanation
Indices: 12087--12251 Score: 213
Period size: 27 Copynumber: 6.1 Consensus size: 27
12077 TGGGAAAAAT
*
12087 AATGACCGAAATACCCCAATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* ** *
12114 AATGACCAAAATATTCCCATTGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* * * *
12141 AATAACTGAAATACCCCTATAGGGCAA
1 AATGACCGAAATACCCCCATAGGGTAA
*
12168 AATGACCGAAATACCCCCATAAGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
*
12195 AATGACCGAAATACCCCCATAAGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* *
12222 AATAACCTAAATACCCCCATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
12249 AAT
1 AAT
12252 AACTGTAATA
Statistics
Matches: 117, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 117 1.00
ACGTcount: A:0.44, C:0.23, G:0.15, T:0.18
Consensus pattern (27 bp):
AATGACCGAAATACCCCCATAGGGTAA
Found at i:12272 original size:54 final size:54
Alignment explanation
Indices: 12094--12281 Score: 214
Period size: 54 Copynumber: 3.5 Consensus size: 54
12084 AATAATGACC
* * ** *
12094 GAAATACCCCAATAGGGTAAAATGACCAAAATATTCCCATTGGGTAAAATAACT
1 GAAATACCCCTATAAGGTAAAATGACCAAAATACCCCCATAGGGTAAAATAACT
* * * * * *
12148 GAAATACCCCTATAGGGCAAAATGACCGAAATACCCCCATAAGGTAAAATGACC
1 GAAATACCCCTATAAGGTAAAATGACCAAAATACCCCCATAGGGTAAAATAACT
* * *
12202 GAAATACCCCCATAAGGTAAAATAACCTAAATACCCCCATAGGGTAAAATAACT
1 GAAATACCCCTATAAGGTAAAATGACCAAAATACCCCCATAGGGTAAAATAACT
* * * *
12256 GTAATACCCTTGTAAGGTAAAGTGAC
1 GAAATACCCCTATAAGGTAAAATGAC
12282 TGTAAGGTAA
Statistics
Matches: 111, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 111 1.00
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.20
Consensus pattern (54 bp):
GAAATACCCCTATAAGGTAAAATGACCAAAATACCCCCATAGGGTAAAATAACT
Found at i:12285 original size:16 final size:16
Alignment explanation
Indices: 12266--12300 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
12256 GTAATACCCT
*
12266 TGTAAGGTAAAGTGAC
1 TGTAAGGTAAAATGAC
12282 TGTAAGGTAAAATGAC
1 TGTAAGGTAAAATGAC
12298 TGT
1 TGT
12301 TTTGCCCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.06, G:0.29, T:0.29
Consensus pattern (16 bp):
TGTAAGGTAAAATGAC
Found at i:12464 original size:27 final size:27
Alignment explanation
Indices: 12287--12502 Score: 186
Period size: 27 Copynumber: 8.0 Consensus size: 27
12277 GTGACTGTAA
*
12287 GGTAAAATGACTGTTTTGCCCTTATGT
1 GGTAAAATGACTATTTTGCCCTTATGT
*
12314 AGT-AAATGA-TAATTTTGCCCTTATGT
1 GGTAAAATGACT-ATTTTGCCCTTATGT
** ***
12340 TATAAAATGACGGCTTTGCCCTTATGT
1 GGTAAAATGACTATTTTGCCCTTATGT
* * *
12367 GGAAAAATTACTACTTTGCCCTTATGT
1 GGTAAAATGACTATTTTGCCCTTATGT
** ** * *
12394 TTTAAAATGACGGTTTTTCCCTTAAGT
1 GGTAAAATGACTATTTTGCCCTTATGT
* *
12421 GGTAAAATAAC-AGTTTTGCCCTTATGA
1 GGTAAAATGACTA-TTTTGCCCTTATGT
* *
12448 GGTAAAATGACTATTTTACACTTATGT
1 GGTAAAATGACTATTTTGCCCTTATGT
* **
12475 TGTAGGATGACTATTTTGCCCTTATGT
1 GGTAAAATGACTATTTTGCCCTTATGT
12502 G
1 G
12503 ATGTATGTTT
Statistics
Matches: 145, Mismatches: 39, Indels: 10
0.75 0.20 0.05
Matches are distributed among these distances:
25 1 0.01
26 21 0.14
27 122 0.84
28 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (27 bp):
GGTAAAATGACTATTTTGCCCTTATGT
Found at i:12497 original size:81 final size:80
Alignment explanation
Indices: 12286--12504 Score: 224
Period size: 81 Copynumber: 2.7 Consensus size: 80
12276 AGTGACTGTA
* * * * *
12286 AGGTAAAATGACTGTTTTGCCCTTATGTAGTAAATGA-TAATTTTGCCCTTATGTTATAAAATGA
1 AGGTAAAATGACTATTTTGCCCTTATGTTGTAAATGACT-ATTTTGCCCTTAAGTGATAAAATAA
*
12350 CGGCTTTGCCCTTATG
65 CAGCTTTGCCCTTATG
* * * * * ** * *
12366 TGGAAAAATTACTACTTTGCCCTTATGTTTTAAAATGACGGTTTTTCCCTTAAGTGGTAAAATAA
1 AGGTAAAATGACTATTTTGCCCTTATGTTGT-AAATGACTATTTTGCCCTTAAGTGATAAAATAA
*
12431 CAGTTTTGCCCTTATG
65 CAGCTTTGCCCTTATG
* * * *
12447 AGGTAAAATGACTATTTTACACTTATGTTGTAGGATGACTATTTTGCCCTTATGTGAT
1 AGGTAAAATGACTATTTTGCCCTTATGTTGTA-AATGACTATTTTGCCCTTAAGTGAT
12505 GTATGTTTAT
Statistics
Matches: 107, Mismatches: 29, Indels: 5
0.76 0.21 0.04
Matches are distributed among these distances:
80 25 0.23
81 82 0.77
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.40
Consensus pattern (80 bp):
AGGTAAAATGACTATTTTGCCCTTATGTTGTAAATGACTATTTTGCCCTTAAGTGATAAAATAAC
AGCTTTGCCCTTATG
Found at i:13547 original size:154 final size:154
Alignment explanation
Indices: 13265--13573 Score: 501
Period size: 154 Copynumber: 2.0 Consensus size: 154
13255 ATAAACAAGA
* *
13265 TTTTGAAATTAATAACATTTTAAAGTAAATGCTTTTGATAGTGACGCATGGTTTTAAATTATTTT
1 TTTTGAAATTAATAACATTTTAAAGTAAATGCTTTTGATAGTGACGCAAGGTTTAAAATTATTTT
* * * *
13330 CTAGATCATACAAATAGGCTAAATAAACATTCGGCTTTTCAAACAATATCATGCTTTAGGAAAAG
66 CTAGATCACACAAAGAGGCTAAATAAACATTCGGCTTTTCAAACAATATCATGCTTTACGAAAAA
*
13395 CACTTCAATGTGAGATCGCTAGAT
131 CACTTCAATGTGAGATCGCCAGAT
*
13419 TTTTGAAATTAATAACGTTTTAAAGTAAATGCTTTTGATAGTGACGCAAGGTTTAAAATTATTTT
1 TTTTGAAATTAATAACATTTTAAAGTAAATGCTTTTGATAGTGACGCAAGGTTTAAAATTATTTT
* *
13484 CTAGATCACACAAAGAGGCTAAATAAACATTGGGCTTTTCAAACGATATCATGCTTTACGAAAAA
66 CTAGATCACACAAAGAGGCTAAATAAACATTCGGCTTTTCAAACAATATCATGCTTTACGAAAAA
* * *
13549 TACTTCAGTGTGATATCGCCAGAT
131 CACTTCAATGTGAGATCGCCAGAT
13573 T
1 T
13574 CGGCCATAGT
Statistics
Matches: 142, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
154 142 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (154 bp):
TTTTGAAATTAATAACATTTTAAAGTAAATGCTTTTGATAGTGACGCAAGGTTTAAAATTATTTT
CTAGATCACACAAAGAGGCTAAATAAACATTCGGCTTTTCAAACAATATCATGCTTTACGAAAAA
CACTTCAATGTGAGATCGCCAGAT
Found at i:14994 original size:20 final size:19
Alignment explanation
Indices: 14942--14995 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
14932 GCTAAAAGTA
14942 AGCTCGGTTGAGCTCAAACG
1 AGCT-GGTTGAGCTCAAACG
** *
14962 AGCTGGAACGAGCTCAAATG
1 AGCTGG-TTGAGCTCAAACG
14982 AGCTGAGTTGAGCT
1 AGCTG-GTTGAGCT
14996 GGACGGAGCT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.28, C:0.20, G:0.31, T:0.20
Consensus pattern (19 bp):
AGCTGGTTGAGCTCAAACG
Found at i:16567 original size:18 final size:19
Alignment explanation
Indices: 16544--16582 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
16534 TTTATCTCAA
*
16544 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
16562 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
16581 TT
1 TT
16583 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:16621 original size:18 final size:18
Alignment explanation
Indices: 16600--16649 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
16590 AAACTCTTTT
16600 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* * *
16618 TCATTTTCTTTTCCACTC
1 TCATTCTCTTTTTCAATC
*
16636 TCAATCTCTTTTTC
1 TCATTCTCTTTTTC
16650 TTTTTCTTTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.14, C:0.30, G:0.00, T:0.56
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:16716 original size:42 final size:42
Alignment explanation
Indices: 16653--16749 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
16643 CTTTTTCTTT
* * *
16653 TTCTTTCA-TTTCTTTGTTTCTTTTCTCGATTTCATTCAAGA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
16694 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
*
16736 TCCTCTCATTTTCT
1 TTCTCTCATTTTCT
16750 CTCATAATCT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 7 0.14
42 44 0.86
ACGTcount: A:0.14, C:0.24, G:0.05, T:0.57
Consensus pattern (42 bp):
TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
Found at i:16727 original size:21 final size:21
Alignment explanation
Indices: 16660--16727 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
16650 TTTTTCTTTC
*
16660 ATTTCTTTGTTTCTTTTCTCG
1 ATTTCTTTGTTTCTTCTCTCG
* *****
16681 ATTTCATTCAAGATTCTCTC-
1 ATTTCTTTGTTTCTTCTCTCG
16701 ATTTTCTTTGTTTCTTCTCTCG
1 A-TTTCTTTGTTTCTTCTCTCG
16723 ATTTC
1 ATTTC
16728 ATTCAAAATC
Statistics
Matches: 32, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.12, C:0.22, G:0.07, T:0.59
Consensus pattern (21 bp):
ATTTCTTTGTTTCTTCTCTCG
Found at i:19223 original size:20 final size:19
Alignment explanation
Indices: 19171--19224 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
19161 GCTGAAAGTA
19171 AGCTCGGTTGAGCTCAAACG
1 AGCT-GGTTGAGCTCAAACG
** *
19191 AGCTGGAACGAGCTCAAATG
1 AGCTGG-TTGAGCTCAAACG
19211 AGCTGAGTTGAGCT
1 AGCTG-GTTGAGCT
19225 GGACGGAGCT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.28, C:0.20, G:0.31, T:0.20
Consensus pattern (19 bp):
AGCTGGTTGAGCTCAAACG
Found at i:21738 original size:27 final size:27
Alignment explanation
Indices: 21703--21870 Score: 214
Period size: 27 Copynumber: 6.2 Consensus size: 27
21693 GAGATAAAAT
*
21703 AATGACCGAAATACCTCTCTAGGGTAA
1 AATGACCGAAATACCTCTATAGGGTAA
21730 AATGACCGAAATACCTCTATAGGGTAA
1 AATGACCGAAATACCTCTATAGGGTAA
*
21757 AATGACCGAAATATCC-CCATAGGGTAA
1 AATGACCGAAATA-CCTCTATAGGGTAA
* *
21784 AATGACTGAAATACCCCTATAGGGTAA
1 AATGACCGAAATACCTCTATAGGGTAA
* *
21811 AATGATCGAAATACCCCTATAGGGTAA
1 AATGACCGAAATACCTCTATAGGGTAA
* * * *
21838 AATGACTGTAATACCATC-GTACGGTAA
1 AATGACCGAAATACC-TCTATAGGGTAA
21865 AATGAC
1 AATGAC
21871 TGTGGGTAAG
Statistics
Matches: 126, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
26 2 0.02
27 121 0.96
28 3 0.02
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (27 bp):
AATGACCGAAATACCTCTATAGGGTAA
Found at i:21923 original size:27 final size:27
Alignment explanation
Indices: 21882--22058 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
21872 GTGGGTAAGG
*
21882 TAAAATGACTGTTTTGCCCTTATATGT
1 TAAAATGACTGTTTTGCCCTTATGTGT
** *
21909 TAAAATGACAATTTTTCCCTTATGT-T
1 TAAAATGACTGTTTTGCCCTTATGTGT
* * *
21935 ATAAAATGACGGCTTTGCCCTTATGTGGC
1 -TAAAATGACTGTTTTGCCCTTATGT-GT
* *
21964 AAAAAT-ACTGTTTTGCCCTTATGTTT
1 TAAAATGACTGTTTTGCCCTTATGTGT
* *
21990 TAAAATGACAGTTTTGCCCTTATGTGG
1 TAAAATGACTGTTTTGCCCTTATGTGT
* * *
22017 TAAAATGACGGTTTTGCCCTTATGAGG
1 TAAAATGACTGTTTTGCCCTTATGTGT
*
22044 TAAAATGACTATTTT
1 TAAAATGACTGTTTT
22059 ACAATTATGT
Statistics
Matches: 124, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
26 6 0.05
27 113 0.91
28 5 0.04
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (27 bp):
TAAAATGACTGTTTTGCCCTTATGTGT
Found at i:22066 original size:27 final size:27
Alignment explanation
Indices: 22009--22085 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 27
21999 AGTTTTGCCC
** * **
22009 TTATGTGGTAAAATGACGGTTTTGCCC
1 TTATGTGGTAAAATGACTATTTTACAA
*
22036 TTATGAGGTAAAATGACTATTTTACAA
1 TTATGTGGTAAAATGACTATTTTACAA
* **
22063 TTATGTTGTAGGATGACTATTTT
1 TTATGTGGTAAAATGACTATTTT
22086 TCCCTTATGT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.42
Consensus pattern (27 bp):
TTATGTGGTAAAATGACTATTTTACAA
Found at i:22067 original size:81 final size:80
Alignment explanation
Indices: 21879--22098 Score: 262
Period size: 81 Copynumber: 2.7 Consensus size: 80
21869 ACTGTGGGTA
* * *
21879 AGGTAAAATGACTGTTTTGCCCTTATATGTTAAAATGACAATTTTTCCCTTATGTTATAAAATGA
1 AGGTAAAATGACTGTTTTGCCCTTATGTTTTAAAATGAC-ATTTTTCCCTTATGTGATAAAATGA
21944 CGGCTTTGCCCTTATG
65 CGGCTTTGCCCTTATG
* * * *
21960 TGGCAAAAAT-ACTGTTTTGCCCTTATGTTTTAAAATGACAGTTTTGCCCTTATGTGGTAAAATG
1 AGG-TAAAATGACTGTTTTGCCCTTATGTTTTAAAATGACA-TTTTTCCCTTATGTGATAAAATG
*
22024 ACGGTTTTGCCCTTATG
64 ACGGCTTTGCCCTTATG
* * ** * **
22041 AGGTAAAATGACTATTTTACAATTATGTTGTAGGATGACTATTTTTCCCTTATGTGAT
1 AGGTAAAATGACTGTTTTGCCCTTATGTTTTAAAATGAC-ATTTTTCCCTTATGTGAT
22099 GTATGTTTAT
Statistics
Matches: 116, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
80 6 0.05
81 104 0.90
82 6 0.05
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (80 bp):
AGGTAAAATGACTGTTTTGCCCTTATGTTTTAAAATGACATTTTTCCCTTATGTGATAAAATGAC
GGCTTTGCCCTTATG
Found at i:22446 original size:18 final size:18
Alignment explanation
Indices: 22420--22456 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
22410 GGACTTGCAT
22420 ACTGCTTACTGTTACTGC
1 ACTGCTTACTGTTACTGC
*
22438 ACTGTTTACTGTTACTGC
1 ACTGCTTACTGTTACTGC
22456 A
1 A
22457 ATGGGCCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.24, G:0.16, T:0.41
Consensus pattern (18 bp):
ACTGCTTACTGTTACTGC
Found at i:25231 original size:26 final size:24
Alignment explanation
Indices: 25193--25307 Score: 112
Period size: 23 Copynumber: 4.8 Consensus size: 24
25183 GACTCACCGT
* *
25193 AGCTCGTATGAGCTTACTGATATATT
1 AGCTCGTAAGAGCTTACTGAT-T-TC
25219 AGCTCGTAAGAGCTTACTG-TTCTC
1 AGCTCGTAAGAGCTTACTGATT-TC
* *
25243 AGCTCGTATGAGTTTACT-ATTTC
1 AGCTCGTAAGAGCTTACTGATTTC
* *
25266 AGCTCGTCAGAGCTTACCG-TTTC
1 AGCTCGTAAGAGCTTACTGATTTC
25289 AGCTC-TATAGAGCTTACTG
1 AGCTCGTA-AGAGCTTACTG
25308 TCCATCAAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
22 1 0.01
23 35 0.47
24 20 0.27
25 1 0.01
26 18 0.24
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.36
Consensus pattern (24 bp):
AGCTCGTAAGAGCTTACTGATTTC
Found at i:25696 original size:43 final size:43
Alignment explanation
Indices: 25635--25723 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
25625 TATGTTTAGG
25635 TATTTGGTAATTGAATTAAATACATCTTGATTATTGCATTGAT
1 TATTTGGTAATTGAATTAAATACATCTTGATTATTGCATTGAT
25678 TATTTGGTAATTGAATTAAATACATCTTGATTATTGCATTGAT
1 TATTTGGTAATTGAATTAAATACATCTTGATTATTGCATTGAT
25721 TAT
1 TAT
25724 GTATAAATGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (43 bp):
TATTTGGTAATTGAATTAAATACATCTTGATTATTGCATTGAT
Found at i:29924 original size:28 final size:27
Alignment explanation
Indices: 29857--29926 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 27
29847 AGAATATGAT
* *
29857 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTAACCATGCA
* *
29884 GCACTAAGTGTGCGAATCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TAACCATGCA
*
29912 GCACTAAGGGTGCGA
1 GCACTAAGTGTGCGA
29927 TTTGATTACG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 17 0.46
28 20 0.54
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTAACCATGCA
Found at i:29942 original size:55 final size:53
Alignment explanation
Indices: 29802--29953 Score: 178
Period size: 55 Copynumber: 2.8 Consensus size: 53
29792 TAAATTGTAC
* *
29802 AGCACTAAGTGTGCGATTCGATTATGTTGCACTAAGTGTGCGAAAAGAATATG
1 AGCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGAAAAGAATATG
* ** * ***
29855 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAATCTAACTATG
1 A-GCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGAAAAGAA-TATG
* *
29910 TAGCACTAAGGGTGCGATTTGATTACGTGGCACTAAGTGTGCGA
1 -AGCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGA
29954 GTTGAGTGAA
Statistics
Matches: 81, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
53 1 0.01
54 39 0.48
55 40 0.49
56 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (53 bp):
AGCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGAAAAGAATATG
Found at i:29958 original size:27 final size:27
Alignment explanation
Indices: 29803--29958 Score: 145
Period size: 27 Copynumber: 5.7 Consensus size: 27
29793 AAATTGTACA
* *
29803 GCACTAAGTGTGCG-ATTCGATTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
** *
29830 GCACTAAGTGTGCGAAAAGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
29857 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* *
29884 GCACTAAGTGTGCGAATCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * * *
29912 GCACTAAGGGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
29939 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
29959 GTGAATAGCA
Statistics
Matches: 105, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
27 82 0.78
28 23 0.22
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:37916 original size:54 final size:54
Alignment explanation
Indices: 37855--38005 Score: 173
Period size: 54 Copynumber: 2.8 Consensus size: 54
37845 TAAATTGTAC
*
37855 AGCACTAAGTGTGCGATTCGATTATGTTGCACTAAGTGTGCGAAAAGAA-TATG-
1 AGCACTAAGTGTGCGATT-GATTATGTGGCACTAAGTGTGCGAAAAGAACTATGT
** * ***
37908 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAATCTAACTATGT
1 A-GCACTAAGTGTGCG-ATTGATTATGTGGCACTAAGTGTGCGAAAAGAACTATGT
*
37964 AGCACTAAG-GTGCGATTTGATTACGTGGCACTAAGTGTGCGA
1 AGCACTAAGTGTGCGA-TTGATTATGTGGCACTAAGTGTGCGA
38006 GTTGAGTGAA
Statistics
Matches: 82, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
53 2 0.02
54 64 0.78
55 15 0.18
56 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTGATTATGTGGCACTAAGTGTGCGAAAAGAACTATGT
Found at i:38010 original size:27 final size:27
Alignment explanation
Indices: 37856--38010 Score: 145
Period size: 27 Copynumber: 5.7 Consensus size: 27
37846 AAATTGTACA
* *
37856 GCACTAAGTGTGCG-ATTCGATTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
** *
37883 GCACTAAGTGTGCGAAAAGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
37910 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* *
37937 GCACTAAGTGTGCGAATCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * *
37965 GCACTAAG-GTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
37991 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
38011 GTGAATAGCA
Statistics
Matches: 105, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
26 14 0.13
27 75 0.71
28 16 0.15
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Done.