Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold233
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: 993233
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.30
Warning! 80272 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:884998 original size:22 final size:22
Alignment explanation
Indices: 884972--885018 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
884962 TAACCTTGGA
*
884972 AACAAAAAGCTGATGCTTACAC
1 AACAAAAAGCTGACGCTTACAC
884994 AACAAAAAGCTGACGCTTACAC
1 AACAAAAAGCTGACGCTTACAC
885016 AAC
1 AAC
885019 CACCACCTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.26, G:0.13, T:0.15
Consensus pattern (22 bp):
AACAAAAAGCTGACGCTTACAC
Found at i:885489 original size:9 final size:9
Alignment explanation
Indices: 885477--885507 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
885467 GTCAAGATGA
*
885477 ATATATTTT
1 ATATATGTT
885486 ATATATGTT
1 ATATATGTT
885495 ATATATGTT
1 ATATATGTT
885504 ATAT
1 ATAT
885508 TAACATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (9 bp):
ATATATGTT
Found at i:887422 original size:20 final size:20
Alignment explanation
Indices: 887397--887443 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
887387 AGCTCGTTTC
*
887397 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
887417 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
887437 CAGCTCA
1 CAGCTCA
887444 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:910248 original size:21 final size:21
Alignment explanation
Indices: 910222--910263 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
910212 CACGACTTAG
910222 ATTACTTTTAATTTACTATTT
1 ATTACTTTTAATTTACTATTT
910243 ATTACTTTTAATTTACTATTT
1 ATTACTTTTAATTTACTATTT
910264 CATTCAATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTACTTTTAATTTACTATTT
Found at i:912403 original size:50 final size:50
Alignment explanation
Indices: 912345--912566 Score: 205
Period size: 50 Copynumber: 4.3 Consensus size: 50
912335 TATCTCAGAT
** * * *
912345 ATGGTCTTATATGGGAGTTCTCATATCAGTGCCCATGCCATGTCCTAGAC
1 ATGGTCTTATATGGGACCTCTCATATCGGTGCCAACGCCATGTCCTAGAC
* * *
912395 ATGTTCTTATGA-GGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTAT-ATGGGACCTCTCATATCGGTGCCAACGCCATGTCCTAGAC
* *
912445 ATGGTCTTACATTGGACCTCTCATATCGGTGCCAACGCCATGTCCCT-GAC
1 ATGGTCTTATATGGGACCTCTCATATCGGTGCCAACGCCATGT-CCTAGAC
* * * * * *
912495 ATGGCCTTACATGGGACCTCTAATAATCTCAATGATGCCAATGCCATGTCCCAGAC
1 ATGGTCTTATATGGGACCTCTCAT-A--TC---GGTGCCAACGCCATGTCCTAGAC
*
912551 ATGGTCTTACATGGGA
1 ATGGTCTTATATGGGA
912567 TCTTATTTCC
Statistics
Matches: 142, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
49 1 0.01
50 101 0.71
51 4 0.03
53 2 0.01
55 2 0.01
56 32 0.23
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
ATGGTCTTATATGGGACCTCTCATATCGGTGCCAACGCCATGTCCTAGAC
Found at i:912468 original size:100 final size:102
Alignment explanation
Indices: 912331--912566 Score: 246
Period size: 100 Copynumber: 2.3 Consensus size: 102
912321 TACTGTCAAT
* * * * ** * *
912331 GCCATATCTCAGATATGGTCTTATATGGGAGTTCTCATATCAGTGCCCATGCCATGT-CCTAGAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAGTGCCAACGCCATGTCCCT-GAC
** * * *
912395 ATGTTCTTATGA-GGGACCTC-TCATCTC-GGTGCCAAC
65 ATGGCCTTA-CATGGGACCTCATAATCTCAGATGCCAAC
* *
912431 GCCATGTCCCAGACATGGTCTTACATTGGACCTCTCATATCGGTGCCAACGCCATGTCCCTGACA
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAGTGCCAACGCCATGTCCCTGACA
*
912496 TGGCCTTACATGGGACCTCTAATAATCTCAATGATGCCAAT
66 TGGCCTTACATGGGACCTC--ATAATCTC-A-GATGCCAAC
912537 GCCATGTCCCAGACATGGTCTTACATGGGA
1 GCCATGTCCCAGACATGGTCTTACATGGGA
912567 TCTTATTTCC
Statistics
Matches: 111, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
99 1 0.01
100 65 0.59
101 3 0.03
103 6 0.05
106 36 0.32
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (102 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAGTGCCAACGCCATGTCCCTGACA
TGGCCTTACATGGGACCTCATAATCTCAGATGCCAAC
Found at i:923308 original size:20 final size:20
Alignment explanation
Indices: 923209--923359 Score: 78
Period size: 20 Copynumber: 7.5 Consensus size: 20
923199 AATTATTGAA
* *
923209 TGATTGCACTTACATGCACC
1 TGATTGCACTTACGTGCCCC
* * * *
923229 TGTTTGTACTT-CGATACCTC
1 TGATTGCACTTACG-TGCCCC
* *
923249 TAATTGCACTTATGTGCCCC
1 TGATTGCACTTACGTGCCCC
* * *
923269 T-ATTTGTAC-TGCGGTACCCC
1 TGA-TTGCACTTAC-GTGCCCC
923289 TGATTGCACTTACGTGCCCC
1 TGATTGCACTTACGTGCCCC
* * *
923309 T-ATTTGTACTT-CGGTACTCC
1 TGA-TTGCACTTAC-GTGCCCC
*
923329 TGATTGCACTTATGTGCCCC
1 TGATTGCACTTACGTGCCCC
*
923349 TGTTTGCACTT
1 TGATTGCACTT
923360 TGATAACCCT
Statistics
Matches: 94, Mismatches: 27, Indels: 20
0.67 0.19 0.14
Matches are distributed among these distances:
19 5 0.05
20 84 0.89
21 5 0.05
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.38
Consensus pattern (20 bp):
TGATTGCACTTACGTGCCCC
Found at i:923342 original size:80 final size:80
Alignment explanation
Indices: 923209--923411 Score: 239
Period size: 80 Copynumber: 2.5 Consensus size: 80
923199 AATTATTGAA
* * *
923209 TGATTGCACTTACATGCACCTGTTTGTACTTCGATACCTCTAATTGCACTTATGTGCCCCTATTT
1 TGATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCTCTAATTGCACTTATGTGCCCCTATTT
* * *
923274 GTACTGCGGTACCCC
66 GCACTGCGATAACCC
* * *
923289 TGATTGCACTTACGTGCCCCTATTTGTACTTCGGTA-CTCCTGATTGCACTTATGTGCCCCTGTT
1 TGATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCT-CTAATTGCACTTATGTGCCCCTATT
**
923353 TGCACTTTGATAACCC
65 TGCACTGCGATAACCC
* * * *
923369 TGGTTGCACTT-CTGTGCCCCTGGTTATACTTCGGTAACTCTAA
1 TGATTGCACTTAC-GTGCCCCTGTTTGTACTTCGGTACCTCTAA
923412 ATCAAATATT
Statistics
Matches: 104, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
79 3 0.03
80 99 0.95
81 2 0.02
ACGTcount: A:0.17, C:0.28, G:0.18, T:0.37
Consensus pattern (80 bp):
TGATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCTCTAATTGCACTTATGTGCCCCTATTT
GCACTGCGATAACCC
Found at i:923390 original size:40 final size:40
Alignment explanation
Indices: 923209--923406 Score: 202
Period size: 40 Copynumber: 5.0 Consensus size: 40
923199 AATTATTGAA
** * * *
923209 TGATTGCACTTACATGCACCTGTTTGTACTTCGAT-ACCTC
1 TGATTGCACTTATGTGCCCCTATTTGTACTTCGGTAACC-C
* * *
923249 TAATTGCACTTATGTGCCCCTATTTGTACTGCGGTACCCC
1 TGATTGCACTTATGTGCCCCTATTTGTACTTCGGTAACCC
*
923289 TGATTGCACTTACGTGCCCCTATTTGTACTTCGGT-ACTCC
1 TGATTGCACTTATGTGCCCCTATTTGTACTTCGGTAAC-CC
* * * *
923329 TGATTGCACTTATGTGCCCCTGTTTGCACTTTGATAACCC
1 TGATTGCACTTATGTGCCCCTATTTGTACTTCGGTAACCC
* * ** *
923369 TGGTTGCACTTCTGTGCCCCTGGTTATACTTCGGTAAC
1 TGATTGCACTTATGTGCCCCTATTTGTACTTCGGTAAC
923407 TCTAAATCAA
Statistics
Matches: 131, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
39 1 0.01
40 126 0.96
41 4 0.03
ACGTcount: A:0.17, C:0.28, G:0.18, T:0.37
Consensus pattern (40 bp):
TGATTGCACTTATGTGCCCCTATTTGTACTTCGGTAACCC
Found at i:923393 original size:20 final size:20
Alignment explanation
Indices: 923252--923390 Score: 93
Period size: 20 Copynumber: 7.0 Consensus size: 20
923242 ATACCTCTAA
* *
923252 TTGCACTTATGTGCCCCTAT
1 TTGCACTTCTGTGCCCCTGT
* * * * *
923272 TTGTACTGCGGTACCCCTGA
1 TTGCACTTCTGTGCCCCTGT
*
923292 TTGCACTTAC-GTGCCCCTAT
1 TTGCACTT-CTGTGCCCCTGT
* * * * *
923312 TTGTACTTCGGTACTCCTGA
1 TTGCACTTCTGTGCCCCTGT
*
923332 TTGCACTTATGTGCCCCTGT
1 TTGCACTTCTGTGCCCCTGT
** *
923352 TTGCACTT-TGATAACCCTGG
1 TTGCACTTCTG-TGCCCCTGT
923372 TTGCACTTCTGTGCCCCTG
1 TTGCACTTCTGTGCCCCTG
923391 GTTATACTTC
Statistics
Matches: 87, Mismatches: 28, Indels: 8
0.71 0.23 0.07
Matches are distributed among these distances:
19 3 0.03
20 81 0.93
21 3 0.03
ACGTcount: A:0.14, C:0.30, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGCACTTCTGTGCCCCTGT
Found at i:924545 original size:22 final size:22
Alignment explanation
Indices: 924504--924577 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
924494 CAGCAGAGCT
* *
924504 GCCAGTAACCAGAATGGCTA-AGA
1 GCCA-TAAACAGAATAGCTATA-A
* *
924527 GCCGTAAACAGGATAGCTATAA
1 GCCATAAACAGAATAGCTATAA
* *
924549 GCTATAAACAGAATAGCTACAA
1 GCCATAAACAGAATAGCTATAA
924571 GCCATAA
1 GCCATAA
924578 GTACAGTAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
22 37 0.90
23 4 0.10
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.16
Consensus pattern (22 bp):
GCCATAAACAGAATAGCTATAA
Found at i:924642 original size:32 final size:32
Alignment explanation
Indices: 924569--924678 Score: 123
Period size: 32 Copynumber: 3.5 Consensus size: 32
924559 GAATAGCTAC
* ** *
924569 AAGCCATAAGTA-CAGTAATATGAGTGGCATA
1 AAGCCATCAGTAGCAGTAATATGACCGGCACA
*
924600 AAGCCATCAGTAGCAGTGATATGACCGGCACA
1 AAGCCATCAGTAGCAGTAATATGACCGGCACA
* * ** *
924632 CAGCCCTCAGTAATAGTAATATGATCGGCACA
1 AAGCCATCAGTAGCAGTAATATGACCGGCACA
924664 AAGCCATCAGTAGCA
1 AAGCCATCAGTAGCA
924679 TCGCAGCAAA
Statistics
Matches: 63, Mismatches: 15, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
31 11 0.17
32 52 0.83
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (32 bp):
AAGCCATCAGTAGCAGTAATATGACCGGCACA
Found at i:924729 original size:26 final size:26
Alignment explanation
Indices: 924678--924731 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
924668 CATCAGTAGC
*
924678 ATCGCAGCAAAGCTGCCAGCAATAGT
1 ATCGCAACAAAGCTGCCAGCAATAGT
* *
924704 ATCGCAACAAAGTTGCCAGTAATAGT
1 ATCGCAACAAAGCTGCCAGCAATAGT
924730 AT
1 AT
924732 ATGTGGCCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.20
Consensus pattern (26 bp):
ATCGCAACAAAGCTGCCAGCAATAGT
Found at i:924874 original size:24 final size:24
Alignment explanation
Indices: 924847--924952 Score: 124
Period size: 24 Copynumber: 4.4 Consensus size: 24
924837 CCATTCTCAG
924847 AATCAGTCATACAAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
* * *
924871 AATCAGTCATACCAGTAACAGACA
1 AATCAGTCATACAAATCACAGACA
**
924895 AATCAGTCATTTAAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
* *
924919 AATCAGTCAT-CTACATCACGGACA
1 AATCAGTCATAC-AAATCACAGACA
*
924943 AATCAATCAT
1 AATCAGTCAT
924953 TTACACTCGA
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.45, C:0.25, G:0.09, T:0.21
Consensus pattern (24 bp):
AATCAGTCATACAAATCACAGACA
Found at i:925031 original size:27 final size:27
Alignment explanation
Indices: 924994--925279 Score: 234
Period size: 27 Copynumber: 10.6 Consensus size: 27
924984 CACCAGAGGC
* * *
924994 ATTACGATCATTTTACCTTACACGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
** * **
925021 ATTTTGGTCATTTAACCCTATGGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
925048 ATTATGGTCATTTTACCTTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
**
925075 ATTACGGTCATTTTACCCTATGGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* ** * *
925102 TTTTTGGTCATTTTATCCTATAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* **
925129 ATTACGGTCATTTT-CCCTTATAGGGCC
1 ATTACGGTCATTTTACCC-TACAGGGGT
* *
925156 ATTACGATCATTTTACCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
925183 ATTACGATCATTTTACCCTA-TGGAGGT
1 ATTACGGTCATTTTACCCTACAGG-GGT
* ** * *
925210 TTTTTGATCATTTTACCCTACAAGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
925237 ATTACGATCATTTTACCTTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
*
925264 ATTATGGTCATTTTAC
1 ATTACGGTCATTTTAC
925280 AAATATTGGG
Statistics
Matches: 207, Mismatches: 48, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
26 4 0.02
27 199 0.96
28 4 0.02
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (27 bp):
ATTACGGTCATTTTACCCTACAGGGGT
Found at i:925062 original size:54 final size:54
Alignment explanation
Indices: 925001--925279 Score: 290
Period size: 54 Copynumber: 5.2 Consensus size: 54
924991 GGCATTACGA
* * ** *
925001 TCATTTTACCTTACACGGGTATTTTGGTCATTTAACCCTATGGGGGTATTATGG
1 TCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTATGGGGGTATTATGG
* * * *
925055 TCATTTTACCTTACAGGGGCATTACGGTCATTTTACCCTATGGGGGTTTTTTGG
1 TCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTATGGGGGTATTATGG
* * * ** * *
925109 TCATTTTATCCTATAGGGGTATTACGGTCATTTT-CCCTTATAGGGCCATTACGA
1 TCATTTTACCCTACAGGGGTATTACGGTCATTTTACCC-TATGGGGGTATTATGG
* * * * * *
925163 TCATTTTACCCTACAGGGGCATTACGATCATTTTACCCTATGGAGGTTTTTTGA
1 TCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTATGGGGGTATTATGG
* * * ** *
925217 TCATTTTACCCTACAAGGGTATTACGATCATTTTACCTTACAGGGGCATTATGG
1 TCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTATGGGGGTATTATGG
925271 TCATTTTAC
1 TCATTTTAC
925280 AAATATTGGG
Statistics
Matches: 184, Mismatches: 39, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
53 3 0.02
54 178 0.97
55 3 0.02
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (54 bp):
TCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTATGGGGGTATTATGG
Found at i:925077 original size:81 final size:81
Alignment explanation
Indices: 924991--925279 Score: 335
Period size: 81 Copynumber: 3.6 Consensus size: 81
924981 ACCCACCAGA
* * * * *
924991 GGCATTACGATCATTTTACCTTACACGGGTATTTTGGTCATTTAACCCTATGGGGGTATTATGGT
1 GGCATTACGATCATTTTACCCTACAGGGGCATTATGGTCATTTTACCCTATGGGGGTATTATGGT
925056 CATTTTACCTTACAGG
66 CATTTTACCTTACAGG
* ** ** * * * *
925072 GGCATTACGGTCATTTTACCCTATGGGGGTTTTTTGGTCATTTTATCCTATAGGGGTATTACGGT
1 GGCATTACGATCATTTTACCCTACAGGGGCATTATGGTCATTTTACCCTATGGGGGTATTATGGT
* *
925137 CATTTTCCCTTATAGG
66 CATTTTACCTTACAGG
* * * * * * *
925153 GCCATTACGATCATTTTACCCTACAGGGGCATTACGATCATTTTACCCTATGGAGGTTTTTTGAT
1 GGCATTACGATCATTTTACCCTACAGGGGCATTATGGTCATTTTACCCTATGGGGGTATTATGGT
* *
925218 CATTTTACCCTACAAG
66 CATTTTACCTTACAGG
* *
925234 GGTATTACGATCATTTTACCTTACAGGGGCATTATGGTCATTTTAC
1 GGCATTACGATCATTTTACCCTACAGGGGCATTATGGTCATTTTAC
925280 AAATATTGGG
Statistics
Matches: 171, Mismatches: 37, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
81 171 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (81 bp):
GGCATTACGATCATTTTACCCTACAGGGGCATTATGGTCATTTTACCCTATGGGGGTATTATGGT
CATTTTACCTTACAGG
Found at i:925801 original size:121 final size:121
Alignment explanation
Indices: 925496--925767 Score: 517
Period size: 121 Copynumber: 2.2 Consensus size: 121
925486 CTTACTGAGG
* *
925496 ATTTTACCCATGTGGGCCCACAAGCCCATTGGGCCTACGCGGCTAATTTCAACCCATCGAGGCCC
1 ATTTTATCCGTGT-GGCCCACAAGCCCATTGGGCCTACGCGGCTAATTTCAACCCATCGAGGCCC
925561 ATAACGGCCCCAACTATGAAAACGTCACAGTCCAACAACACTTACCACATCACATAC
65 ATAACGGCCCCAACTATGAAAACGTCACAGTCCAACAACACTTACCACATCACATAC
925618 ATTTTATCCGTGTGGCCCACAAGCCCATTGGGCCTACGCGGCTAATTTCAACCCATCGAGGCCCA
1 ATTTTATCCGTGTGGCCCACAAGCCCATTGGGCCTACGCGGCTAATTTCAACCCATCGAGGCCCA
925683 TAACGGCCCCAACTATGAAAACGTCACAGTCCAACAACACTTACCACATCACATAC
66 TAACGGCCCCAACTATGAAAACGTCACAGTCCAACAACACTTACCACATCACATAC
925739 ATTTTATCCGTGTGGCCCACAAGCCCATT
1 ATTTTATCCGTGTGGCCCACAAGCCCATT
925768 AGGACCACAC
Statistics
Matches: 148, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
121 137 0.93
122 11 0.07
ACGTcount: A:0.29, C:0.35, G:0.16, T:0.21
Consensus pattern (121 bp):
ATTTTATCCGTGTGGCCCACAAGCCCATTGGGCCTACGCGGCTAATTTCAACCCATCGAGGCCCA
TAACGGCCCCAACTATGAAAACGTCACAGTCCAACAACACTTACCACATCACATAC
Found at i:927506 original size:17 final size:17
Alignment explanation
Indices: 927480--927512 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
927470 TATCTTATGG
927480 ATGATCTTATATGTAAC
1 ATGATCTTATATGTAAC
*
927497 ATGATGTTATATGTAA
1 ATGATCTTATATGTAA
927513 AAATAAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.42
Consensus pattern (17 bp):
ATGATCTTATATGTAAC
Found at i:929105 original size:29 final size:29
Alignment explanation
Indices: 929062--929336 Score: 264
Period size: 29 Copynumber: 9.5 Consensus size: 29
929052 TTTCGACTAT
* *
929062 CGACTATCGACTATGAAAAGGGATGGTGA
1 CGACTATCAAATATGAAAAGGGATGGTGA
* **
929091 CGACTATCAAATATGAAAAGGGATAGTTT
1 CGACTATCAAATATGAAAAGGGATGGTGA
* * *
929120 CGACTATCGACTATGAAAAGGGATGGTAA
1 CGACTATCAAATATGAAAAGGGATGGTGA
* *
929149 CGACCATCAAATATGAATAGGGATGGTGA
1 CGACTATCAAATATGAAAAGGGATGGTGA
*
929178 CGACCATCAAATATGAAAAGGGATGGTGA
1 CGACTATCAAATATGAAAAGGGATGGTGA
* * *
929207 CAACCATCAACTATGAAAAGGGATGGTGA
1 CGACTATCAAATATGAAAAGGGATGGTGA
* * **
929236 CGA-TCATTAAATATGAAAAGGGATAGTTT
1 CGACT-ATCAAATATGAAAAGGGATGGTGA
* * * **
929265 TGACTATCAATTATGAAAAGGGATAGTTT
1 CGACTATCAAATATGAAAAGGGATGGTGA
* **** *
929294 TGACTATTGGTTATGAAAGGGGATGGTGA
1 CGACTATCAAATATGAAAAGGGATGGTGA
*
929323 CGACCATCAAATAT
1 CGACTATCAAATAT
929337 AAATGCACTA
Statistics
Matches: 203, Mismatches: 41, Indels: 4
0.82 0.17 0.02
Matches are distributed among these distances:
29 202 1.00
30 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.24
Consensus pattern (29 bp):
CGACTATCAAATATGAAAAGGGATGGTGA
Found at i:929309 original size:87 final size:87
Alignment explanation
Indices: 929073--929336 Score: 339
Period size: 87 Copynumber: 3.0 Consensus size: 87
929063 GACTATCGAC
929073 TATGAAAAGGGATGGTGACGACTATCAAATATGAAAAGGGATAGTTTCGACTATCGACTATGAAA
1 TATGAAAAGGGATGGTGACGACTATCAAATATGAAAAGGGATAGTTTCGACTATCGACTATGAAA
*
929138 AGGGATGGTAACGACCATCAAA
66 AGGGATGGTGACGACCATCAAA
* * * ** * * *
929160 TATGAATAGGGATGGTGACGACCATCAAATATGAAAAGGGATGGTGACAACCATCAACTATGAAA
1 TATGAAAAGGGATGGTGACGACTATCAAATATGAAAAGGGATAGTTTCGACTATCGACTATGAAA
* *
929225 AGGGATGGTGACGATCATTAAA
66 AGGGATGGTGACGACCATCAAA
* *** * * * **
929247 TATGAAAAGGGATAGTTTTGACTATCAATTATGAAAAGGGATAGTTTTGACTATTGGTTATGAAA
1 TATGAAAAGGGATGGTGACGACTATCAAATATGAAAAGGGATAGTTTCGACTATCGACTATGAAA
*
929312 GGGGATGGTGACGACCATCAAA
66 AGGGATGGTGACGACCATCAAA
929334 TAT
1 TAT
929337 AAATGCACTA
Statistics
Matches: 146, Mismatches: 31, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
87 146 1.00
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.25
Consensus pattern (87 bp):
TATGAAAAGGGATGGTGACGACTATCAAATATGAAAAGGGATAGTTTCGACTATCGACTATGAAA
AGGGATGGTGACGACCATCAAA
Found at i:931111 original size:20 final size:20
Alignment explanation
Indices: 931088--931126 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
931078 TTCTTTCTTC
931088 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
931108 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
931127 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:931545 original size:56 final size:50
Alignment explanation
Indices: 931377--931569 Score: 179
Period size: 50 Copynumber: 3.7 Consensus size: 50
931367 TTTCTTGTAC
* * * * ** * * *
931377 TGCCAATGTCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTAA
* * * * **
931427 TGCCCATGCCATGTCCTAGACATGATCTTACAGGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTAA
**
931477 TGCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT---CT---TAA
931533 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
931570 TCTCATTCCC
Statistics
Matches: 114, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
50 76 0.67
53 2 0.02
56 36 0.32
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTAA
Found at i:940962 original size:62 final size:62
Alignment explanation
Indices: 940865--940990 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
940855 TATCCATTTC
940865 AGCTATTACTTGGGTGTTTTTGTTTGAGCTGTACGAGATGAAGTTCTCATATACGGTTCTCA
1 AGCTATTACTTGGGTGTTTTTGTTTGAGCTGTACGAGATGAAGTTCTCATATACGGTTCTCA
940927 AGCTATTACTTGGGTGTTTTTGTTTGAGCTGTACGAGATGAAGTTCTCATATACGGTTCTCA
1 AGCTATTACTTGGGTGTTTTTGTTTGAGCTGTACGAGATGAAGTTCTCATATACGGTTCTCA
940989 AG
1 AG
940991 GGGGGGTCCT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.21, C:0.14, G:0.25, T:0.40
Consensus pattern (62 bp):
AGCTATTACTTGGGTGTTTTTGTTTGAGCTGTACGAGATGAAGTTCTCATATACGGTTCTCA
Found at i:944448 original size:14 final size:14
Alignment explanation
Indices: 944429--944455 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
944419 TTGAGTTGAA
944429 TCGAGTTAAATTAT
1 TCGAGTTAAATTAT
944443 TCGAGTTAAATTA
1 TCGAGTTAAATTA
944456 AAAAATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (14 bp):
TCGAGTTAAATTAT
Found at i:944697 original size:20 final size:18
Alignment explanation
Indices: 944672--944710 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
944662 CTTTATATAT
944672 ATTTTAGAACTTTTTTAAAA
1 ATTTTAGAA--TTTTTAAAA
*
944692 ATTTTATAATTTTTAAAA
1 ATTTTAGAATTTTTAAAA
944710 A
1 A
944711 AATATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
20 8 0.44
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTTTAGAATTTTTAAAA
Found at i:944749 original size:18 final size:19
Alignment explanation
Indices: 944728--944767 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
944718 ATTTTGAGAT
*
944728 TTTTATAAA-TATTTTAAA
1 TTTTAAAAATTATTTTAAA
*
944746 TTTTAAAAATTATTTTGAA
1 TTTTAAAAATTATTTTAAA
944765 TTT
1 TTT
944768 GTTTGTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TTTTAAAAATTATTTTAAA
Found at i:975580 original size:13 final size:14
Alignment explanation
Indices: 975562--975590 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
975552 AAAATTGATT
975562 AAAAATCAAG-CAA
1 AAAAATCAAGTCAA
975575 AAAAATCAAGTCAA
1 AAAAATCAAGTCAA
975589 AA
1 AA
975591 GCCACTAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.69, C:0.14, G:0.07, T:0.10
Consensus pattern (14 bp):
AAAAATCAAGTCAA
Found at i:978996 original size:19 final size:20
Alignment explanation
Indices: 978958--978997 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
978948 AAACAAGCTT
*
978958 ATTGAGCTAGAAATGAGCTGA
1 ATTGAGCTA-AAACGAGCTGA
978979 ATTGAGCT-AAACGAGCTGA
1 ATTGAGCTAAAACGAGCTGA
978998 GATTAAGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.23
Consensus pattern (20 bp):
ATTGAGCTAAAACGAGCTGA
Done.