Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3612
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: 89565
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Found at i:3606 original size:38 final size:39
Alignment explanation
Indices: 3526--3667 Score: 193
Period size: 38 Copynumber: 3.7 Consensus size: 39
3516 GCTACTTGCT
3526 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GTTATAGTAACTCGCA
3566 CAAATGCCTTCGGGACTTAGCCCGTTA-AGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGTTATAGTAACTCGCA
** * *
3604 CAAATGCCTTC-GG--TTAGCCCGGAATAGATCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGTTATAG-TAACTCGCA
3641 CAAATGCGCTTCGGGACTTAGCCCGTT
1 CAAATGC-CTTCGGGACTTAGCCCGTT
3668 TCATCGAATA
Statistics
Matches: 90, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
35 9 0.10
36 2 0.02
37 16 0.18
38 26 0.29
39 6 0.07
40 23 0.26
41 8 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGTTATAGTAACTCGCA
Found at i:10587 original size:40 final size:39
Alignment explanation
Indices: 10543--10682 Score: 200
Period size: 37 Copynumber: 3.7 Consensus size: 39
10533 GCTACTTGCT
10543 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
10583 CAAATGCCTTCGGGACTTAGCCC-GT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
* * *
10620 CAAATGCCTTC-GG--TTAGCCCGGAATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCGCA
10657 CAAATGCCTTCGGGACTTAGCCCGGT
1 CAAATGCCTTCGGGACTTAGCCCGGT
10683 TATCATCCGA
Statistics
Matches: 90, Mismatches: 4, Indels: 12
0.85 0.04 0.11
Matches are distributed among these distances:
34 7 0.08
35 1 0.01
36 2 0.02
37 44 0.49
38 3 0.03
39 1 0.01
40 32 0.36
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
Found at i:18603 original size:40 final size:40
Alignment explanation
Indices: 18559--18786 Score: 325
Period size: 40 Copynumber: 5.7 Consensus size: 40
18549 GCTACTTGCT
*
18559 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
18599 CAAATGCCTTCAGGACTTAGCCCGGTTATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
18639 CAAATGCATTCGGGACTTAGCCCAGTTATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
18679 CAAATGCCTTCGGGACTTAGCCTGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * * * *
18719 CAAATGCCTTCTGG-CTTAGCCTGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
18758 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
18787 CATCCGAATA
Statistics
Matches: 168, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
38 1 0.01
39 33 0.20
40 133 0.79
41 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.27
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:26149 original size:13 final size:12
Alignment explanation
Indices: 26125--26172 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 12
26115 GATGGATCAT
26125 AATAATAACTAA
1 AATAATAACTAA
26137 AATAATAAACTAA
1 AATAAT-AACTAA
*
26150 AATAGTAACATAA
1 AATAATAAC-TAA
26163 AA-AAT-ACTAA
1 AATAATAACTAA
26173 TTTGATGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 3 0.09
11 2 0.06
12 11 0.34
13 16 0.50
ACGTcount: A:0.67, C:0.08, G:0.02, T:0.23
Consensus pattern (12 bp):
AATAATAACTAA
Found at i:26380 original size:13 final size:13
Alignment explanation
Indices: 26362--26459 Score: 85
Period size: 13 Copynumber: 7.5 Consensus size: 13
26352 AAAATGGGAT
*
26362 AAATAATTAAATA
1 AAATAAATAAATA
26375 AAATAAACATAAATA
1 AAAT-AA-ATAAATA
*
26390 GAAT-AATAAAATA
1 AAATAAAT-AAATA
*
26403 ACATAAATAAATA
1 AAATAAATAAATA
26416 AAAT-AATAGAAT-
1 AAATAAATA-AATA
*
26428 AAATAAATAAAGA
1 AAATAAATAAATA
* *
26441 AGATAAAAAAATA
1 AAATAAATAAATA
26454 AAATAA
1 AAATAA
26460 TAATAAGAAG
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
12 12 0.18
13 42 0.62
14 5 0.07
15 9 0.13
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.21
Consensus pattern (13 bp):
AAATAAATAAATA
Found at i:26399 original size:18 final size:18
Alignment explanation
Indices: 26362--26455 Score: 85
Period size: 17 Copynumber: 5.4 Consensus size: 18
26352 AAAATGGGAT
*
26362 AAATAATTA-AATAAAATA
1 AAATAAATAGAAT-AAATA
26380 AACATAAATAGAAT-AATA
1 AA-ATAAATAGAATAAATA
26398 AAATAACATA-AATAAATA
1 AAATAA-ATAGAATAAATA
26416 AAAT-AATAGAATAAAT-
1 AAATAAATAGAATAAATA
*
26432 AAATAAAGA-AGATAAA-A
1 AAATAAATAGA-ATAAATA
26449 AAATAAA
1 AAATAAA
26456 ATAATAATAA
Statistics
Matches: 66, Mismatches: 2, Indels: 17
0.78 0.02 0.20
Matches are distributed among these distances:
16 8 0.12
17 30 0.45
18 19 0.29
19 6 0.09
20 3 0.05
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.21
Consensus pattern (18 bp):
AAATAAATAGAATAAATA
Found at i:26402 original size:8 final size:8
Alignment explanation
Indices: 26331--26462 Score: 56
Period size: 8 Copynumber: 15.6 Consensus size: 8
26321 AACATAATCA
26331 AATAAGAAT
1 AATAA-AAT
26340 AATAAAATT
1 AATAAAA-T
*
26349 ACTAAAAT
1 AATAAAAT
*
26357 GGGAT-AAAT
1 --AATAAAAT
*
26366 AATTAAATAA
1 AA-TAAA-AT
26376 AATAAACAT
1 AATAAA-AT
*
26385 AAATAGAAT
1 -AATAAAAT
26394 AATAAAAT
1 AATAAAAT
*
26402 AACATAAAT
1 AATA-AAAT
26411 AAATAAAAT
1 -AATAAAAT
*
26420 AATAGAAT
1 AATAAAAT
26428 AA-ATAAAT
1 AATA-AAAT
*
26436 AA-AGAA-
1 AATAAAAT
* *
26442 GATAAAAA
1 AATAAAAT
26450 AATAAAAT
1 AATAAAAT
26458 AATAA
1 AATAA
26463 TAAGAAGAAG
Statistics
Matches: 93, Mismatches: 18, Indels: 25
0.68 0.13 0.18
Matches are distributed among these distances:
6 1 0.01
7 7 0.08
8 40 0.43
9 33 0.35
10 12 0.13
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.23
Consensus pattern (8 bp):
AATAAAAT
Found at i:26452 original size:21 final size:21
Alignment explanation
Indices: 26407--26465 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 21
26397 AAAATAACAT
*
26407 AAATAAATAAAATAATAGAAT
1 AAATAAATAAAATAATAGAAA
26428 AAATAAATAAAGA-AGATA-AAA
1 AAATAAATAAA-ATA-ATAGAAA
26449 AAATAAAATAATAATAA
1 AAAT-AAATAA-AATAA
26466 GAAGAAGAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
21 18 0.56
22 12 0.38
23 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (21 bp):
AAATAAATAAAATAATAGAAA
Found at i:31847 original size:45 final size:45
Alignment explanation
Indices: 31744--31947 Score: 170
Period size: 45 Copynumber: 4.6 Consensus size: 45
31734 AATGAGAAAT
* * * ** *
31744 ACCATAGTTGAAAGATATTATGGCATTAAACC-GGAGTGA-ATAAG
1 ACCATGGTTGAAAGATACTATGGCACTAAACCAAAAAT-ATATAAG
* *
31788 ACTATAGTTGAAAGATACTATGGCACTAAACCAAAAATATATAAG
1 ACCATGGTTGAAAGATACTATGGCACTAAACCAAAAATATATAAG
* *
31833 ATCATGGTTGAAAGATACTATGGCA-TCAAATCCAATACA-A-ATAAG
1 ACCATGGTTGAAAGATACTATGGCACT-AAA-CCAA-AAATATATAAG
* *** *
31878 ACCATAGTTGAAAGATACTATGGCACTACTTCAAGAATATATAAG
1 ACCATGGTTGAAAGATACTATGGCACTAAACCAAAAATATATAAG
31923 ACCATGGTT-AGAAGATA-TCATGGCA
1 ACCATGGTTGA-AAGATACT-ATGGCA
31948 TCATTTGGAG
Statistics
Matches: 132, Mismatches: 18, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
43 1 0.01
44 37 0.28
45 86 0.65
46 6 0.05
47 2 0.02
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (45 bp):
ACCATGGTTGAAAGATACTATGGCACTAAACCAAAAATATATAAG
Found at i:31902 original size:90 final size:90
Alignment explanation
Indices: 31782--31950 Score: 252
Period size: 90 Copynumber: 1.9 Consensus size: 90
31772 AACCGGAGTG
* *
31782 AATAAGACTATAGTTGAAAGATACTATGGCACTAAACCAAAAATATATAAGATCATGGTT-GAAA
1 AATAAGACCATAGTTGAAAGATACTATGGCACTAAACCAAAAATATATAAGACCATGGTTAG-AA
31846 GATA-CTATGGCATCAAATCCAATACA
65 GATATC-ATGGCATCAAATCCAATACA
*** *
31872 AATAAGACCATAGTTGAAAGATACTATGGCACTACTTCAAGAATATATAAGACCATGGTTAGAAG
1 AATAAGACCATAGTTGAAAGATACTATGGCACTAAACCAAAAATATATAAGACCATGGTTAGAAG
31937 ATATCATGGCATCA
66 ATATCATGGCATCA
31951 TTTGGAGCAA
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
90 69 0.97
91 2 0.03
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25
Consensus pattern (90 bp):
AATAAGACCATAGTTGAAAGATACTATGGCACTAAACCAAAAATATATAAGACCATGGTTAGAAG
ATATCATGGCATCAAATCCAATACA
Found at i:43048 original size:64 final size:66
Alignment explanation
Indices: 42966--43119 Score: 258
Period size: 64 Copynumber: 2.3 Consensus size: 66
42956 TTCACTTGGA
* *
42966 ATCACTCATGCGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACAT-GG-CATCCCG
1 ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGACATCCCG
43029 T
66 T
43030 ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
1 ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGG--ACATCC
43095 CGT
64 CGT
43098 ATCACACATGTGACCTAGCTAC
1 ATCACACATGTGACCTAGCTAC
43120 TATATAGTAT
Statistics
Matches: 84, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
64 52 0.62
65 2 0.02
68 30 0.36
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.31
Consensus pattern (66 bp):
ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGACATCCCG
T
Found at i:43136 original size:68 final size:65
Alignment explanation
Indices: 42924--43145 Score: 229
Period size: 64 Copynumber: 3.3 Consensus size: 65
42914 CTATCCGATT
* * * * *
42924 TATCT-CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACTCATGCGACCTAGCTAC
1 TATCTACGTAGCTCTCTTGTCTACATGG-GT-CATC-C--CGTATCACACATGTGACCTAGCTAC
42988 ATTTA
61 ATTTA
*
42993 TCTCTCACGTAGCTCTCTTGTCTACAT-GG-CATCCCGTATCACACATGTGACCTAGCTACATTT
1 TATCT-ACGTAGCTCTCTTGTCTACATGGGTCATCCCGTATCACACATGTGACCTAGCTACATTT
43056 A
65 A
*
43057 TCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCCCGTATCACACATGTGACCTAGCTACTA
1 TATCT-ACGTAGCTCTCTTGTCTACATGGG-T-CATCCCGTATCACACATGTGACCTAGCTAC-A
*
43122 TATA
62 TTTA
43126 GTATCT-CGTAGC-CTTCTTGT
1 -TATCTACGTAGCTC-TCTTGT
43146 ACACATGATG
Statistics
Matches: 136, Mismatches: 8, Indels: 19
0.83 0.05 0.12
Matches are distributed among these distances:
64 53 0.39
65 2 0.01
66 1 0.01
67 4 0.03
68 42 0.31
69 9 0.07
70 5 0.04
71 20 0.15
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.35
Consensus pattern (65 bp):
TATCTACGTAGCTCTCTTGTCTACATGGGTCATCCCGTATCACACATGTGACCTAGCTACATTTA
Found at i:44800 original size:60 final size:60
Alignment explanation
Indices: 44686--44800 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
44676 ATTTGGGGTG
* * * *
44686 AAGTAAAAATAGGGGAACGTATGTGCAATCAGGGGTGCCGTAGTACAAACAGGGGCACAA
1 AAGTAAAAACAGGGGAACGTATGTGCAATCAAGGGTACCGAAGTACAAACAGGGGCACAA
* * * * * *
44746 AAGTACAAACAGGGGCAGGTATGTTCAATCAAGGGTACCGAAGTAGAAATAGGGG
1 AAGTAAAAACAGGGGAACGTATGTGCAATCAAGGGTACCGAAGTACAAACAGGGG
44801 TACGTATGTG
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.38, C:0.14, G:0.32, T:0.16
Consensus pattern (60 bp):
AAGTAAAAACAGGGGAACGTATGTGCAATCAAGGGTACCGAAGTACAAACAGGGGCACAA
Found at i:46320 original size:27 final size:27
Alignment explanation
Indices: 46279--46332 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
46269 TGTCATGTGA
* *
46279 AATTGAATGGCAAATTATTGTTACATG
1 AATTGAATGGCAAATTACTATTACATG
**
46306 AATTGAATGTTAAATTACTATTACATG
1 AATTGAATGGCAAATTACTATTACATG
46333 GGTTGTATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (27 bp):
AATTGAATGGCAAATTACTATTACATG
Found at i:49707 original size:27 final size:25
Alignment explanation
Indices: 49653--49707 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 25
49643 AAAACTCTTC
* *
49653 TAAAAGAAAACTCAAGAGAAATTCT
1 TAAAAGAAAACTAAAGAGAAATTAT
*
49678 TAAAAGAAAAATCTAAAGAGAATTTAT
1 TAAAAG-AAAA-CTAAAGAGAAATTAT
49705 TAA
1 TAA
49708 CTCAAAAGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 6 0.24
26 4 0.16
27 15 0.60
ACGTcount: A:0.58, C:0.07, G:0.11, T:0.24
Consensus pattern (25 bp):
TAAAAGAAAACTAAAGAGAAATTAT
Found at i:53686 original size:15 final size:15
Alignment explanation
Indices: 53647--53687 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
53637 CAAGGAAACC
53647 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
*
53662 -ATATAGAGAAATCCA
1 GA-ATAAAGAAATCCA
53677 GAATAAAGAAA
1 GAATAAAGAAA
53688 CCCAAGATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (15 bp):
GAATAAAGAAATCCA
Found at i:56209 original size:46 final size:46
Alignment explanation
Indices: 56142--56267 Score: 225
Period size: 46 Copynumber: 2.7 Consensus size: 46
56132 AACCCGCCCC
* *
56142 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
56188 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
56234 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
56268 TGCTCAACCA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 77 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:58514 original size:15 final size:17
Alignment explanation
Indices: 58479--58516 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
58469 ATCAAGTAGA
58479 CTTTTATCACTCAAGGT
1 CTTTTATCACTCAAGGT
*
58496 CTTTTTTCACTC-A-GT
1 CTTTTATCACTCAAGGT
58511 CTTTTA
1 CTTTTA
58517 AATTTTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 7 0.37
16 1 0.05
17 11 0.58
ACGTcount: A:0.18, C:0.24, G:0.08, T:0.50
Consensus pattern (17 bp):
CTTTTATCACTCAAGGT
Found at i:60593 original size:22 final size:22
Alignment explanation
Indices: 60568--60668 Score: 139
Period size: 22 Copynumber: 4.6 Consensus size: 22
60558 TGCAGGGCTC
* *
60568 ACACGCCTGTGTAGTCCAAGGG
1 ACACGCCCGTGTGGTCCAAGGG
* * *
60590 ACACGCCTGTGTGGTCCATGAG
1 ACACGCCCGTGTGGTCCAAGGG
*
60612 ACACGCCCGTGTGGTCCATGGG
1 ACACGCCCGTGTGGTCCAAGGG
*
60634 ACATGCCCGTGTGGTCCAAGGG
1 ACACGCCCGTGTGGTCCAAGGG
60656 ACACGCCCGTGTG
1 ACACGCCCGTGTG
60669 ACCCTAGAAC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 71 1.00
ACGTcount: A:0.18, C:0.30, G:0.34, T:0.19
Consensus pattern (22 bp):
ACACGCCCGTGTGGTCCAAGGG
Found at i:63674 original size:22 final size:22
Alignment explanation
Indices: 63622--63720 Score: 103
Period size: 22 Copynumber: 4.4 Consensus size: 22
63612 AAGCTGATGT
*
63622 AGTAAGCTCTATTGAGCTGAA-
1 AGTAAGCTCTATCGAGCTGAAC
63643 ATGGTAAGCTCTATCGAGCTGAAC
1 A--GTAAGCTCTATCGAGCTGAAC
* *
63667 AGTAAGCTCTATTGAGTTGAAC
1 AGTAAGCTCTATCGAGCTGAAC
*
63689 AGTAAGCTC-ATACGAACTGAAAC
1 AGTAAGCTCTAT-CGAGCTG-AAC
*
63712 GGTAAGCTC
1 AGTAAGCTC
63721 CAATAAGCTA
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
21 3 0.05
22 32 0.48
23 30 0.45
24 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.25
Consensus pattern (22 bp):
AGTAAGCTCTATCGAGCTGAAC
Found at i:63675 original size:45 final size:45
Alignment explanation
Indices: 63622--63720 Score: 123
Period size: 45 Copynumber: 2.2 Consensus size: 45
63612 AAGCTGATGT
*
63622 AGTAAGCTCTATTGAGCTGAA-ATGGTAAGCTC-TATCGAGCTG-AAC
1 AGTAAGCTCTATTGAGCTGAACA--GTAAGCTCATA-CGAACTGAAAC
*
63667 AGTAAGCTCTATTGAGTTGAACAGTAAGCTCATACGAACTGAAAC
1 AGTAAGCTCTATTGAGCTGAACAGTAAGCTCATACGAACTGAAAC
*
63712 GGTAAGCTC
1 AGTAAGCTC
63721 CAATAAGCTA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
44 14 0.29
45 33 0.69
46 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.25
Consensus pattern (45 bp):
AGTAAGCTCTATTGAGCTGAACAGTAAGCTCATACGAACTGAAAC
Found at i:74985 original size:16 final size:16
Alignment explanation
Indices: 74964--74996 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
74954 GGCTAAAAGA
74964 AAAAGAAAAGATGAGC
1 AAAAGAAAAGATGAGC
*
74980 AAAAGAAGAGATGAGC
1 AAAAGAAAAGATGAGC
74996 A
1 A
74997 GAGAATTCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.27, T:0.06
Consensus pattern (16 bp):
AAAAGAAAAGATGAGC
Found at i:78280 original size:39 final size:40
Alignment explanation
Indices: 78203--78349 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
78193 TAGCTCCTCG
* * *
78203 TTCAAGTGCCTTCGGGACATAGCCC-GATTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
78243 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
78282 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
78322 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
78350 ATTAGTATCT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 25 0.27
40 67 0.73
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:78389 original size:40 final size:40
Alignment explanation
Indices: 78246--78376 Score: 192
Period size: 40 Copynumber: 3.3 Consensus size: 40
78236 TAACTCATTC
* * * *
78246 AATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAGTATCTCGCACA
78286 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
*
78326 AAGGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
*
78366 AATACCTTCGG
1 AATGCCTTCGG
78377 ATCTTAGTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
39 3 0.04
40 80 0.96
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
Found at i:78389 original size:80 final size:80
Alignment explanation
Indices: 78249--78429 Score: 192
Period size: 80 Copynumber: 2.3 Consensus size: 80
78239 CTCATTCAAT
* * *
78249 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGACTTAACCCGGA-ATT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGGACTTAACCCGGATA-T
*
78313 AGT-A-TCTCGCACAAA
65 AGTCACT-TAGCACAAA
* * **
78328 GGCCTTCGGGACTTAACCCGGA-ATTAGTATCTCGCACAAATACCTTC-GGATCTTAGTCCGGAT
1 -GCCTTCGGGACTTAACCCGGATATTA-AAACTCGCACAAATACCTTCGGGA-CTTAACCCGGAT
78391 ATAGTCACTTAGCACAAA
63 ATAGTCACTTAGCACAAA
* *
78409 GCCTTTGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
78430 CAGCATTCAA
Statistics
Matches: 86, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
79 6 0.07
80 69 0.80
81 10 0.12
82 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGGACTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:82100 original size:50 final size:51
Alignment explanation
Indices: 82025--82196 Score: 258
Period size: 50 Copynumber: 3.4 Consensus size: 51
82015 TGCAATTCAC
82025 AAAAAAAAAAAAAAAAAAAAAAAAAAA-AAAAAAAAAAAAAAAAAAAATAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAATAA
82075 AAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAA-AA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAATAA
* *
82125 AAAAAAAAAAAAAAAAAAAAAAAAAAACGATTAAAAAAACAAAAAAAGAAATAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAC-A--AAAAAAAAAAAAAAAAAAATAA
* * *
82179 ACACAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAA
82197 GTCTTTAACA
Statistics
Matches: 112, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
50 57 0.51
51 21 0.19
53 17 0.15
54 17 0.15
ACGTcount: A:0.93, C:0.03, G:0.02, T:0.02
Consensus pattern (51 bp):
AAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAATAA
Found at i:82171 original size:1 final size:1
Alignment explanation
Indices: 82025--82151 Score: 236
Period size: 1 Copynumber: 127.0 Consensus size: 1
82015 TGCAATTCAC
*
82025 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
82090 AAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
82152 CGATTAAAAA
Statistics
Matches: 122, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
1 122 1.00
ACGTcount: A:0.98, C:0.01, G:0.00, T:0.01
Consensus pattern (1 bp):
A
Found at i:87482 original size:38 final size:40
Alignment explanation
Indices: 87438--87515 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 40
87428 AACTCCCGAT
*
87438 GCCTTCGGAC-TAACCC-GGAA-TAGTATTCTCGCACAAAG
1 GCCTTCGGACTTAACCCGGGAATTAGGA-TCTCGCACAAAG
87476 GCCTTCGGACTTTAACCCGGGAATTAGGATCTCGCACAAA
1 GCCTTCGGAC-TTAACCCGGGAATTAGGATCTCGCACAAA
87516 TACCCGGACT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
38 10 0.29
40 6 0.17
41 15 0.43
42 4 0.11
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (40 bp):
GCCTTCGGACTTAACCCGGGAATTAGGATCTCGCACAAAG
Done.