Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold306
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: 585619
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 41328 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:510759 original size:23 final size:23
Alignment explanation
Indices: 510731--510847 Score: 71
Period size: 23 Copynumber: 5.1 Consensus size: 23
510721 AATTACTAAT
510731 TTGCACAGAAGTGTCACTTTCAA
1 TTGCACAGAAGTGTCACTTTCAA
* *
510754 TTGCACCAG-AGTGTCACTGTCAG
1 TTGCA-CAGAAGTGTCACTTTCAA
* * * *
510777 TTCCACCGGAGTGTCTCTGTT-AA
1 TTGCACAGAAGTGTCACT-TTCAA
* *
510800 TTGCATC-GAAGTGCCA-TGATCAA
1 TTGCA-CAGAAGTGTCACT-TTCAA
* * *
510823 TTGCACAAAAGTTTCACTTTAAA
1 TTGCACAGAAGTGTCACTTTCAA
510846 TT
1 TT
510848 TGCGTGTTGA
Statistics
Matches: 70, Mismatches: 17, Indels: 14
0.69 0.17 0.14
Matches are distributed among these distances:
22 6 0.09
23 58 0.83
24 6 0.09
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (23 bp):
TTGCACAGAAGTGTCACTTTCAA
Found at i:514905 original size:132 final size:131
Alignment explanation
Indices: 514667--514975 Score: 334
Period size: 132 Copynumber: 2.3 Consensus size: 131
514657 TCTCTATTGA
* ** *
514667 GTATTTGTATTTTGGGA-TAGTGGCAGAAGTGATGTTTTGACCACAACGATTGACTTCTCCATCA
1 GTATTTGTATTTTGGGAGT-GTGACAGAAGTGATG-TTTGACCACAACGATAAAATTCTCCATCA
* ** * * *
514731 AAATAATTTATATTTTGAGAGAGCCATAAAAGTGATGTTTTGACCATAACAGTTGACTTATTTGC
64 AAAGAATTTATATTCCGAAAGAGCCATAAAAGTGA-GTTTTGACCAAAACAGTTGACTTATTCGC
*
514796 TATG
128 TAGG
* * * *
514800 GTATTTATATTTTGAGAGTGTGACAGAAGTGATGTTTGACCACAACGATAAAATTCTTCATTAAA
1 GTATTTGTATTTTGGGAGTGTGACAGAAGTGATGTTTGACCACAACGATAAAATTCTCCATCAAA
** * ** *
514865 AGAATTTATATTCCGAAAGAGTGATGAAAGTG-GCTCTTTGACCAAAATGGTTGACTTCTTCGCT
66 AGAATTTATATTCCGAAAGAGCCATAAAAGTGAG-T-TTTGACCAAAACAGTTGACTTATTCGCT
514929 AGG
129 AGG
** *
514932 GTATTTGTATTTTGGGAGAATGACAGAAATGATGTTGTGACCAC
1 GTATTTGTATTTTGGGAGTGTGACAGAAGTGATGTT-TGACCAC
514976 CACAATTGAT
Statistics
Matches: 146, Mismatches: 26, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
130 1 0.01
131 1 0.01
132 107 0.73
133 36 0.25
134 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (131 bp):
GTATTTGTATTTTGGGAGTGTGACAGAAGTGATGTTTGACCACAACGATAAAATTCTCCATCAAA
AGAATTTATATTCCGAAAGAGCCATAAAAGTGAGTTTTGACCAAAACAGTTGACTTATTCGCTAG
G
Found at i:515041 original size:133 final size:131
Alignment explanation
Indices: 514602--515115 Score: 423
Period size: 133 Copynumber: 3.9 Consensus size: 131
514592 TTTTATTAAT
* * * * * **
514602 AGAATTTGTATTTTGAAAGAGTGACGAAAGTGGCGTTTT-AGCCACAATGG-TCACTTC-TCTAT
1 AGAATTTATATTCTGAAAGAGTGATGAAAGTGGCGTTTTGA-CCACAACGGTTGACTTCTTCGCT
* * * * * *
514664 TGAGTATTTGTATTTTGGGATAGTGGCAGAAGTGATGTTTTGACCACAACGATTGACTTCTCCAT
65 AGGGTATTTGTATTTTGGGAGAGTGACAGAAGTGATG-TTTGACCACAACGATTGAATTCTCTAT
514729 CAAA
129 -AAA
* * * ** * ** * * * *
514733 ATAATTTATATTTTGAGAGAGCCATAAAAGTGATGTTTTGACCATAACAGTTGACTTATTTGCTA
1 AGAATTTATATTCTGAAAGAGTGATGAAAGTGGCGTTTTGACCACAACGGTTGACTTCTTCGCTA
* * * * **
514798 TGGTATTTATATTTTGAGAGTGTGACAGAAGTGATGTTTGACCACAACGATAAAATTCT-TCATT
66 GGGTATTTGTATTTTGGGAGAGTGACAGAAGTGATGTTTGACCACAACGATTGAATTCTCT-A-T
514862 AAA
129 AAA
* * *
514865 AGAATTTATATTCCGAAAGAGTGATGAAAGTGGC-TCTTTGACCAAAATGGTTGACTTCTTCGCT
1 AGAATTTATATTCTGAAAGAGTGATGAAAGTGGCGT-TTTGACCACAACGGTTGACTTCTTCGCT
* * * * *
514929 AGGGTATTTGTATTTTGGGAGAATGACAGAAATGATGTTGTGACCACCACAATTGATTTCTCTAC
65 AGGGTATTTGTATTTTGGGAGAGTGACAGAAGTGATGTT-TGACCACAACGATTGAATTCTCTA-
514994 TAAGA
128 TAA-A
* ** * ****
514999 A-AATTTTTATAGTGATAGAGTGATGAAAGTGGCGTTTTGACCACAACGACCAACTTCTTCGCTA
1 AGAATTTATATTCTGAAAGAGTGATGAAAGTGGCGTTTTGACCACAACGGTTGACTTCTTCGCTA
* * * *
515063 GGGTATTTGTATTTTGGAAGAGTGAC--AAGTAATTTTTTGACCACAATGATTGA
66 GGGTATTTGTATTTTGGGAGAGTGACAGAAGTGA-TGTTTGACCACAACGATTGA
515116 CTCCTCCTGT
Statistics
Matches: 298, Mismatches: 74, Indels: 22
0.76 0.19 0.06
Matches are distributed among these distances:
131 54 0.18
132 114 0.38
133 126 0.42
134 4 0.01
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (131 bp):
AGAATTTATATTCTGAAAGAGTGATGAAAGTGGCGTTTTGACCACAACGGTTGACTTCTTCGCTA
GGGTATTTGTATTTTGGGAGAGTGACAGAAGTGATGTTTGACCACAACGATTGAATTCTCTATAA
A
Found at i:520286 original size:10 final size:10
Alignment explanation
Indices: 520279--520323 Score: 65
Period size: 10 Copynumber: 4.5 Consensus size: 10
520269 TGTTAACATA
520279 TTTTAACACAT
1 TTTTAACAC-T
*
520290 GTTTAACACT
1 TTTTAACACT
520300 TTTT-ACACT
1 TTTTAACACT
520309 TTTTAACACT
1 TTTTAACACT
520319 TTTTA
1 TTTTA
520324 CCTTATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
9 9 0.29
10 14 0.45
11 8 0.26
ACGTcount: A:0.29, C:0.18, G:0.02, T:0.51
Consensus pattern (10 bp):
TTTTAACACT
Found at i:520296 original size:11 final size:10
Alignment explanation
Indices: 520271--520323 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
520261 TTACCTTATG
*
520271 TTAACATATT
1 TTAACACATT
520281 TTAACACATGT
1 TTAACACAT-T
520292 TTAACAC-TT
1 TTAACACATT
* *
520301 TTTACACTTT
1 TTAACACATT
*
520311 TTAACACTTT
1 TTAACACATT
520321 TTA
1 TTA
520324 CCTTATTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
9 7 0.18
10 23 0.61
11 8 0.21
ACGTcount: A:0.32, C:0.17, G:0.02, T:0.49
Consensus pattern (10 bp):
TTAACACATT
Found at i:520309 original size:9 final size:9
Alignment explanation
Indices: 520295--520324 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
520285 CACATGTTTA
520295 ACACTTTTT
1 ACACTTTTT
520304 ACACTTTTT
1 ACACTTTTT
520313 AACACTTTTT
1 -ACACTTTTT
520323 AC
1 AC
520325 CTTATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (9 bp):
ACACTTTTT
Found at i:520332 original size:20 final size:20
Alignment explanation
Indices: 520256--520334 Score: 74
Period size: 19 Copynumber: 4.0 Consensus size: 20
520246 TGAAGAAAAT
*
520256 ACTTTTTACCTTATGTTAAC
1 ACTTTTTACCTTATTTTAAC
* **
520276 A-TATTTTAACACATGTTTAAC
1 ACT-TTTTACCTTAT-TTTAAC
520297 ACTTTTTACAC-T-TTTTAAC
1 ACTTTTTAC-CTTATTTTAAC
520316 ACTTTTTACCTTATTTTAA
1 ACTTTTTACCTTATTTTAA
520335 TTAAATAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
18 1 0.02
19 17 0.36
20 16 0.34
21 11 0.23
22 2 0.04
ACGTcount: A:0.29, C:0.18, G:0.03, T:0.51
Consensus pattern (20 bp):
ACTTTTTACCTTATTTTAAC
Found at i:521401 original size:20 final size:20
Alignment explanation
Indices: 521363--521401 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
521353 GTAAATTGGT
*
521363 AAATAAAAGAAAAACTAAAC
1 AAATAAAACAAAAACTAAAC
521383 AAATAAAACACAAAA-TAAA
1 AAATAAAACA-AAAACTAAA
521402 GATGATATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.77, C:0.10, G:0.03, T:0.10
Consensus pattern (20 bp):
AAATAAAACAAAAACTAAAC
Found at i:523349 original size:30 final size:30
Alignment explanation
Indices: 523307--523369 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
523297 TTTGGGAGTC
523307 ACATGGTCGTGTGACACACACGGCCTAGCT
1 ACATGGTCGTGTGACACACACGGCCTAGCT
523337 ACATGG-CTGTGTGACACACACGGCCTAGCT
1 ACATGGTC-GTGTGACACACACGGCCTAGCT
523367 ACA
1 ACA
523370 CGACTCTGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 1 0.03
30 31 0.97
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.19
Consensus pattern (30 bp):
ACATGGTCGTGTGACACACACGGCCTAGCT
Found at i:528568 original size:50 final size:50
Alignment explanation
Indices: 528502--528612 Score: 168
Period size: 50 Copynumber: 2.2 Consensus size: 50
528492 GAAAGGAGCG
* *
528502 CAAACCATCCACTAAGGGAGGAAGGAGCCCAATCGTCCACTTGAGGTGCC
1 CAAACCATCCACTAAGGCAGGAAGGAGCCCAACCGTCCACTTGAGGTGCC
* * *
528552 TAAACCGTCCAGTAAGGCAGGAAGGAGCCCAACCGTCCACTTGAGGTGCC
1 CAAACCATCCACTAAGGCAGGAAGGAGCCCAACCGTCCACTTGAGGTGCC
*
528602 CAAACTATCCA
1 CAAACCATCCA
528613 TGGGACTTGG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.14
Consensus pattern (50 bp):
CAAACCATCCACTAAGGCAGGAAGGAGCCCAACCGTCCACTTGAGGTGCC
Found at i:530739 original size:16 final size:16
Alignment explanation
Indices: 530718--530748 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
530708 CCATTATATG
530718 CGAGCTATCTGTATTA
1 CGAGCTATCTGTATTA
*
530734 CGAGCTATGTGTATT
1 CGAGCTATCTGTATT
530749 GCAAACTATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (16 bp):
CGAGCTATCTGTATTA
Found at i:534293 original size:42 final size:43
Alignment explanation
Indices: 534210--534350 Score: 142
Period size: 44 Copynumber: 3.3 Consensus size: 43
534200 TCCCAGATGT
* * * *
534210 GGTCTTACATGTAATCAAATATCGATGTCACTGTCCCAGACAA
1 GGTCTTACACGAAATCAAATATCGATGCCAATGTCCCAGACAA
* * *
534253 GGTCTTACACGAAATCATATA-CGATGCCAATGTCCTAGACAT
1 GGTCTTACACGAAATCAAATATCGATGCCAATGTCCCAGACAA
* * **
534295 GGTCTTACACGTAAATCTCAA-ATCGATGCCAACGTCCCAGACGT
1 GGTCTTACACG-AAATC-AAATATCGATGCCAATGTCCCAGACAA
*
534339 GGTCTTGCACGA
1 GGTCTTACACGA
534351 TAAAACATAT
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
42 28 0.34
43 25 0.30
44 29 0.35
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (43 bp):
GGTCTTACACGAAATCAAATATCGATGCCAATGTCCCAGACAA
Found at i:534342 original size:44 final size:44
Alignment explanation
Indices: 534191--534354 Score: 142
Period size: 42 Copynumber: 3.8 Consensus size: 44
534181 AGCTCATACA
* ** * *
534191 ATGCCAACATCCCAGATGTGGTCTTACATGT-AATC-AAATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAATCTCAA-ATCG
* * *
534234 ATGTC-ACTGTCCCAGACAAGGTCTTACACG-AAA--TCATATACG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGTAAATCTCAAAT-CG
* *
534276 ATGCCAATGTCCTAGACATGGTCTTACACGTAAATCTCAAATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAATCTCAAATCG
* *
534320 ATGCCAACGTCCCAGACGTGGTCTTGCACGATAAA
1 ATGCCAACGTCCCAGACATGGTCTTACACG-TAAA
534355 ACATATCAAA
Statistics
Matches: 95, Mismatches: 17, Indels: 16
0.74 0.13 0.12
Matches are distributed among these distances:
41 2 0.02
42 29 0.31
43 27 0.28
44 28 0.29
45 9 0.09
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.25
Consensus pattern (44 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAATCTCAAATCG
Found at i:537750 original size:42 final size:42
Alignment explanation
Indices: 537691--537788 Score: 169
Period size: 42 Copynumber: 2.3 Consensus size: 42
537681 GGTGAATCGA
* *
537691 GTGTGGGCTACCTTGCACCTAACACATTCAGGGCACACGCCC
1 GTGTGGTCTACCCTGCACCTAACACATTCAGGGCACACGCCC
*
537733 GTGTGGTCTACCCTGCACCTAACGCATTCAGGGCACACGCCC
1 GTGTGGTCTACCCTGCACCTAACACATTCAGGGCACACGCCC
537775 GTGTGGTCTACCCT
1 GTGTGGTCTACCCT
537789 TAATTGACAC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.18, C:0.36, G:0.24, T:0.21
Consensus pattern (42 bp):
GTGTGGTCTACCCTGCACCTAACACATTCAGGGCACACGCCC
Found at i:537942 original size:21 final size:21
Alignment explanation
Indices: 537895--537936 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
537885 CTAAACTAAT
*
537895 TCATAACACATGATCACTAGA
1 TCATAACACATGATCACAAGA
*
537916 TCATAACATATGATCACAAGA
1 TCATAACACATGATCACAAGA
537937 CTATAATCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.21, G:0.10, T:0.24
Consensus pattern (21 bp):
TCATAACACATGATCACAAGA
Found at i:548419 original size:44 final size:43
Alignment explanation
Indices: 548371--548478 Score: 153
Period size: 43 Copynumber: 2.5 Consensus size: 43
548361 TGTCCCAGAC
** *
548371 ATGGTCTTACATGGAAATCTCGTATCGCTGCCAATAGCCCAGCT
1 ATGGTCTTACAT-GAAATCTCAAATCGATGCCAATAGCCCAGCT
**
548415 ATGGTCTTACACAAAATCTCAAATCGATGCCAATAGCCCAGCT
1 ATGGTCTTACATGAAATCTCAAATCGATGCCAATAGCCCAGCT
*
548458 ATGATCTTACATGAAATCTCA
1 ATGGTCTTACATGAAATCTCA
548479 CCTCAGAAGT
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 45 0.80
44 11 0.20
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (43 bp):
ATGGTCTTACATGAAATCTCAAATCGATGCCAATAGCCCAGCT
Found at i:548634 original size:31 final size:31
Alignment explanation
Indices: 548593--548799 Score: 265
Period size: 31 Copynumber: 6.7 Consensus size: 31
548583 ATCCAATGCT
* *
548593 CAAATC-AATTCGGTAATATATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* * * *
548623 CGAATGAAATTCGGCAATGTATATCTACATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
**
548654 CAAATC-AATTCGATAATGTATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
548684 CAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* * *
548715 CAAATCAAATTCGGTAATGTATATCTATAAA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* *
548746 CAATTCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
548777 CAAATCAAATTTGGCAATGTATA
1 CAAATCAAATTCGGCAATGTATA
548800 AAACATATAC
Statistics
Matches: 151, Mismatches: 24, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
30 30 0.20
31 121 0.80
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATATCCATATA
Found at i:548819 original size:93 final size:92
Alignment explanation
Indices: 548593--548810 Score: 276
Period size: 92 Copynumber: 2.4 Consensus size: 92
548583 ATCCAATGCT
* * ** * * *
548593 CAAATC-AATTCGGTAATATATATCCATATACGAATGAAATTCGGCAATGTATATCTACATACAA
1 CAAATCAAATTCGGCAATGTATAAACATATACAAATCAAATTCGGCAATGTATATCTACAAACAA
*
548657 ATCAATTCGATAATGTATATCCATATA
66 ATCAATTCGACAATGTATATCCATATA
* * *
548684 CAAATCAAATTCGGCAATGTATAACCATATACAAATCAAATTCGGTAATGTATATCTATAAACAA
1 CAAATCAAATTCGGCAATGTATAAACATATACAAATCAAATTCGGCAATGTATATCTACAAACAA
* * *
548749 TTCAAATTCGGCAATGTATATCTATATA
66 ATC-AATTCGACAATGTATATCCATATA
*
548777 CAAATCAAATTTGGCAATGTATAAAACATATACA
1 CAAATCAAATTCGGCAATGTAT-AAACATATACA
548811 TTTAAATTCA
Statistics
Matches: 110, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
91 6 0.05
92 52 0.47
93 42 0.38
94 10 0.09
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.31
Consensus pattern (92 bp):
CAAATCAAATTCGGCAATGTATAAACATATACAAATCAAATTCGGCAATGTATATCTACAAACAA
ATCAATTCGACAATGTATATCCATATA
Found at i:552970 original size:95 final size:95
Alignment explanation
Indices: 552846--553036 Score: 330
Period size: 95 Copynumber: 2.0 Consensus size: 95
552836 CTGAGTTCAA
* *
552846 TAATAAAATTATTAAATGGACTGAATTTTT-TCATTTAGATAAAGATAGACCTCGTACGGATTTA
1 TAATAAAAATATTAAATGGACTGAATTTTTCT-ATTTAGATAAAGATAGACCTCGTACAGATTTA
552910 GATCGAGGAAAAGCTAAAGCTTCAGATTAAT
65 GATCGAGGAAAAGCTAAAGCTTCAGATTAAT
*
552941 TAATAAAAATATTAAATGGACTGAATTTTTCTATTTAGATAAAGATAGACCTTGTACAGATTTAG
1 TAATAAAAATATTAAATGGACTGAATTTTTCTATTTAGATAAAGATAGACCTCGTACAGATTTAG
*
553006 ATCGGGGAAAAGCTAAAGCTTCAGATTAAT
66 ATCGAGGAAAAGCTAAAGCTTCAGATTAAT
553036 T
1 T
553037 GACTTCGTTG
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
95 90 0.99
96 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (95 bp):
TAATAAAAATATTAAATGGACTGAATTTTTCTATTTAGATAAAGATAGACCTCGTACAGATTTAG
ATCGAGGAAAAGCTAAAGCTTCAGATTAAT
Found at i:553218 original size:41 final size:41
Alignment explanation
Indices: 553156--553304 Score: 183
Period size: 41 Copynumber: 3.6 Consensus size: 41
553146 AAAAAATTGA
* * *
553156 TGAATTGCACATGA-ATGCCCCTATTTGTACCTCGGTACCCC
1 TGAATTGCACA-GACGTGCCCCTGTTTGTACTTCGGTACCCC
* *
553197 TGAATTGCACAGACGTACCCCTGTTTGTACTTCGGTACCCT
1 TGAATTGCACAGACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * * *
553238 TGAATTGTACATATGTCCCCCTGTTTGTACTTCGATACCCC
1 TGAATTGCACAGACGTGCCCCTGTTTGTACTTCGGTACCCC
*
553279 TGAATTGCACACACGTGCCCCTGTTT
1 TGAATTGCACAGACGTGCCCCTGTTT
553305 AGACTTCAAA
Statistics
Matches: 92, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 2 0.02
41 90 0.98
ACGTcount: A:0.20, C:0.30, G:0.17, T:0.32
Consensus pattern (41 bp):
TGAATTGCACAGACGTGCCCCTGTTTGTACTTCGGTACCCC
Found at i:553236 original size:20 final size:20
Alignment explanation
Indices: 553211--553280 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
553201 TTGCACAGAC
553211 GTACCCCTGTTTGTACTTCG
1 GTACCCCTGTTTGTACTTCG
* * * **
553231 GTACCCTTGAATTGTACATAT
1 GTACCCCTG-TTTGTACTTCG
*
553252 GTCCCCCTGTTTGTACTTCG
1 GTACCCCTGTTTGTACTTCG
*
553272 ATACCCCTG
1 GTACCCCTG
553281 AATTGCACAC
Statistics
Matches: 36, Mismatches: 13, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
20 22 0.61
21 14 0.39
ACGTcount: A:0.16, C:0.30, G:0.17, T:0.37
Consensus pattern (20 bp):
GTACCCCTGTTTGTACTTCG
Found at i:556900 original size:42 final size:42
Alignment explanation
Indices: 556836--556922 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
556826 GTAAAGCATA
* *
556836 AAGAGTTAGTTTTGAGTGCATGTAAAGTATAAGAATTTTAAT
1 AAGAATTAGTTTTGAGTGCATGTAAAGTATAAGAATTTGAAT
*
556878 AAGAATTAGTTTTGAGTGCATGTAAAGTATAATAATTTGAAT
1 AAGAATTAGTTTTGAGTGCATGTAAAGTATAAGAATTTGAAT
556920 AAG
1 AAG
556923 TATAAGAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.37
Consensus pattern (42 bp):
AAGAATTAGTTTTGAGTGCATGTAAAGTATAAGAATTTGAAT
Found at i:558313 original size:27 final size:27
Alignment explanation
Indices: 558252--558316 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
558242 CAAAAAAGTT
*
558252 AAAGCCTTTGTGGAAATCTATGAAATG
1 AAAGCCTTTGTGGAAATCTATAAAATG
* * *
558279 AAAACCTTTGTGGCAATTTATAAAATTG
1 AAAGCCTTTGTGGAAATCTATAAAA-TG
558307 -AAGCCTTTGT
1 AAAGCCTTTGT
558317 AGCGATCTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 30 0.94
28 2 0.06
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.34
Consensus pattern (27 bp):
AAAGCCTTTGTGGAAATCTATAAAATG
Found at i:558509 original size:27 final size:27
Alignment explanation
Indices: 558486--558714 Score: 253
Period size: 27 Copynumber: 8.5 Consensus size: 27
558476 AGGTATGGTA
* * *
558486 AACTCTGAAAGAATGGTACATATGACG
1 AACTCTAAAAGAATAGTACATATGGCG
* * *
558513 AACTATAAAATAATAGTACATATGGAG
1 AACTCTAAAAGAATAGTACATATGGCG
*
558540 AACTCTGGAAA-AATAGTACATATGGCG
1 AACTCT-AAAAGAATAGTACATATGGCG
**
558567 AACTCTAAAAGAATAGTATGTATGGCG
1 AACTCTAAAAGAATAGTACATATGGCG
* **
558594 AACTTTAAAAGAATAGTATGTATGGCG
1 AACTCTAAAAGAATAGTACATATGGCG
* *
558621 AACTCTAAAAGAATAGTACGTATGGTG
1 AACTCTAAAAGAATAGTACATATGGCG
558648 AACTCTAAAAGAATAGTACATATGGCG
1 AACTCTAAAAGAATAGTACATATGGCG
* * * ** *
558675 AACTCTGAAGGAATAATATGTATCGCG
1 AACTCTAAAAGAATAGTACATATGGCG
*
558702 AACTCTAAGAGAA
1 AACTCTAAAAGAA
558715 ATGGTTCCAT
Statistics
Matches: 173, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
26 3 0.02
27 167 0.97
28 3 0.02
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (27 bp):
AACTCTAAAAGAATAGTACATATGGCG
Found at i:559785 original size:25 final size:25
Alignment explanation
Indices: 559740--559795 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
559730 TTACGTATTT
* *
559740 AAAATTATTCTTGAGTTTTTTAAAA
1 AAAATTATTCATGAGTATTTTAAAA
*
559765 AAAATTATTCATG-GTAATTTTCAAA
1 AAAATTATTCATGAGT-ATTTTAAAA
*
559790 CAAATT
1 AAAATT
559796 TGTGGATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (25 bp):
AAAATTATTCATGAGTATTTTAAAA
Found at i:563230 original size:133 final size:133
Alignment explanation
Indices: 562724--563219 Score: 791
Period size: 133 Copynumber: 3.7 Consensus size: 133
562714 NNNNNNNNNN
**
562724 GGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGC-TC-CAC
1 GGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTG
* * ** *** * *
562787 T-ACTGCTTAGGGAGATAAGATCTAAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAA
66 TCAATGC--AGGAAGGCAAGATCTGCTATCTTTAATCTATTCCACTGCTGCCCAGGGAAGTAGAA
562851 TTACT
129 TTACT
*
562856 GGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCACCATCTTCGATCTGCTTCGCTG
1 GGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTG
* *
562921 TCAATGCAGGAAGGCAAGATCTGCTATATTTAATCTATTCCACTGCTGCCCAGGGAAATAGAATT
66 TCAATGCAGGAAGGCAAGATCTGCTATCTTTAATCTATTCCACTGCTGCCCAGGGAAGTAGAATT
*
562986 ATT
131 ACT
*
562989 GGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTG
1 GGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTG
*
563054 TCAATGCAGGAAGGCAAGATCTGCTATCTTTAATCTATTCCACTGCTGCACAGGGAAGTAGAATT
66 TCAATGCAGGAAGGCAAGATCTGCTATCTTTAATCTATTCCACTGCTGCCCAGGGAAGTAGAATT
563119 ACT
131 ACT
563122 GGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTG
1 GGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTG
*
563187 TCAATGCAGGAAGGCAAGATCTGTTATCTTTAA
66 TCAATGCAGGAAGGCAAGATCTGCTATCTTTAA
563220 CCTGCTCCAC
Statistics
Matches: 338, Mismatches: 23, Indels: 5
0.92 0.06 0.01
Matches are distributed among these distances:
132 57 0.17
133 275 0.81
134 2 0.01
135 4 0.01
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (133 bp):
GGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTTCGCTG
TCAATGCAGGAAGGCAAGATCTGCTATCTTTAATCTATTCCACTGCTGCCCAGGGAAGTAGAATT
ACT
Found at i:571230 original size:23 final size:22
Alignment explanation
Indices: 571186--571244 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
571176 TAAAGGGTAT
* *
571186 TTACAAATTAAATC-TCTAAGA
1 TTACAAATCATATCTTCTAAGA
571207 TTACAAAATCATATCTTCTAAGA
1 TTAC-AAATCATATCTTCTAAGA
*
571230 TTACATATCATATCT
1 TTACAAATCATATCT
571245 AAGATTGCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.12
22 18 0.55
23 11 0.33
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.37
Consensus pattern (22 bp):
TTACAAATCATATCTTCTAAGA
Found at i:571247 original size:19 final size:19
Alignment explanation
Indices: 571200--571316 Score: 126
Period size: 19 Copynumber: 5.8 Consensus size: 19
571190 AAATTAAATC
*
571200 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
571220 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
*
571242 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
571263 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
* *
571282 TCTAGGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
571301 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
571317 CTCAAAAATT
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
19 50 0.58
21 18 0.21
22 7 0.08
23 11 0.13
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:571260 original size:21 final size:19
Alignment explanation
Indices: 571223--571316 Score: 152
Period size: 19 Copynumber: 4.8 Consensus size: 19
571213 AATCATATCT
*
571223 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
571242 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
571263 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
571282 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
571301 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
571317 CTCAAAAATT
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
19 51 0.73
21 19 0.27
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:579995 original size:43 final size:43
Alignment explanation
Indices: 579883--580126 Score: 305
Period size: 43 Copynumber: 5.7 Consensus size: 43
579873 TTTTAGAAAT
* * *
579883 AAACGCCGCTAAA-AGTCATAACCTTTAGCGGCGCTTTTGTCAC
1 AAACGCCGCTAAAGA-CCATGACCTTTAGCGGCGCTTTTCTCAC
* * *
579926 -AATGCCGCTAAAGACCATAACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCTCAC
* * *
579968 AAACGCCGCTATAGACCATGACATTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCTCAC
* *
580011 AAACGCCGCTAAAGACCATGACCTTTAACGGCGCATTTCTCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCTCAC
* *
580054 AAATGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTATCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGC-TTTTCTCAC
* * *
580098 AAACGCCGCTATAGAACA-AACCTTTAGCG
1 AAACGCCGCTAAAGACCATGACCTTTAGCG
580127 ACACTTCTCA
Statistics
Matches: 177, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
42 36 0.20
43 119 0.67
44 22 0.12
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCTCAC
Found at i:580124 original size:129 final size:128
Alignment explanation
Indices: 579883--580126 Score: 348
Period size: 129 Copynumber: 1.9 Consensus size: 128
579873 TTTTAGAAAT
* * * *
579883 AAACGCCGCTAAAAGTCATAACCTTTAGCGGCGCTTTTGTCACAATGCCGCTAAAGACCATAACC
1 AAACGCCGCTAAAAGCCATAACCTTTAACGGCGCATTTCTCACAATGCCGCTAAAGACCATAACC
* * *
579948 TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGACCATGACATTTAGCGGCGCTTTTCCCAC
66 TTTAGCGGCGCTTTTACCACAAACGCCGCTATAGAACATAACATTTAGCGGCGCTTTTCCCAC
* *
580011 AAACGCCGCT-AAAGACCATGACCTTTAACGGCGCATTTCTCACAAATGCCGCTAAAGACCATGA
1 AAACGCCGCTAAAAG-CCATAACCTTTAACGGCGCATTTCTCAC-AATGCCGCTAAAGACCATAA
* *
580075 CCTTTAGCGGCGCTTTTTATCACAAACGCCGCTATAGAACA-AACCTTTAGCG
64 CCTTTAGCGGCGC-TTTTACCACAAACGCCGCTATAGAACATAACATTTAGCG
580127 ACACTTCTCA
Statistics
Matches: 102, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
127 4 0.04
128 33 0.32
129 41 0.40
130 24 0.24
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (128 bp):
AAACGCCGCTAAAAGCCATAACCTTTAACGGCGCATTTCTCACAATGCCGCTAAAGACCATAACC
TTTAGCGGCGCTTTTACCACAAACGCCGCTATAGAACATAACATTTAGCGGCGCTTTTCCCAC
Found at i:580149 original size:86 final size:84
Alignment explanation
Indices: 579903--580152 Score: 265
Period size: 86 Copynumber: 2.9 Consensus size: 84
579893 AAAAGTCATA
* * * * *
579903 ACCTTTAGCGGCGCTTTTGTCAC-AATGCCGCTAAAGACCATAACCTTTAGCGGCGCTTTTCCCA
1 ACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGACCATAACCTTTAGC-GCACTTCTCACA
*
579967 CAAA-CGCCGCTATAGACCATG
65 -AAAGC-CCGCTAAAGACCATG
* ** * *
579988 ACATTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATGACCTTTAACGGCGCATTTCTCA
1 ACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGACCATAACCTTT-A--GCGCACTTCTCA
*
580053 CAAATG-CCGCTAAAGACCATG
63 CAAAAGCCCGCTAAAGACCATG
* *
580074 ACCTTTAGCGGCGCTTTTTATCACAAACGCCGCTATAGAACA-AACCTTTAGCGACACTTCTCAC
1 ACCTTTAGCGGCGC-TTTTATCACAAACGCCGCTAAAGACCATAACCTTTAGCG-CACTTCTCAC
580138 AAAAGCACCGCTAAA
64 AAAAGC-CCGCTAAA
580153 AACATATCAT
Statistics
Matches: 137, Mismatches: 19, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
83 3 0.02
84 13 0.09
85 21 0.15
86 64 0.47
87 26 0.19
88 8 0.06
89 2 0.01
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (84 bp):
ACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGACCATAACCTTTAGCGCACTTCTCACAA
AAGCCCGCTAAAGACCATG
Found at i:580149 original size:129 final size:128
Alignment explanation
Indices: 579903--580152 Score: 333
Period size: 129 Copynumber: 1.9 Consensus size: 128
579893 AAAAGTCATA
* * * *
579903 ACCTTTAGCGGCGCTTTTGTCACAATGCCGCTAAAGACCATAACCTTTAGCGGCGCTTTTCCCAC
1 ACCTTTAACGGCGCATTTCTCACAATGCCGCTAAAGACCATAACCTTTAGCGGCGCTTTTACCAC
* * * * * * *
579968 AAACGCCGCTATAGACCATGACATTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATG
66 AAACGCCGCTATAGAACATAACATTTAGCGACACTTCTCACACAAACACCGCTAAAGACCATG
* *
580031 ACCTTTAACGGCGCATTTCTCACAAATGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTTATC
1 ACCTTTAACGGCGCATTTCTCAC-AATGCCGCTAAAGACCATAACCTTTAGCGGCGC-TTTTACC
*
580096 ACAAACGCCGCTATAGAACA-AACCTTTAGCGACACTTCTCACA-AAAGCACCGCTAAA
64 ACAAACGCCGCTATAGAACATAACATTTAGCGACACTTCTCACACAAA-CACCGCTAAA
580153 AACATATCAT
Statistics
Matches: 105, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
128 23 0.22
129 58 0.55
130 24 0.23
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (128 bp):
ACCTTTAACGGCGCATTTCTCACAATGCCGCTAAAGACCATAACCTTTAGCGGCGCTTTTACCAC
AAACGCCGCTATAGAACATAACATTTAGCGACACTTCTCACACAAACACCGCTAAAGACCATG
Found at i:580639 original size:17 final size:18
Alignment explanation
Indices: 580609--580642 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
580599 ATTTAAATTA
580609 CGGTCGCGGTCGCGTTTT
1 CGGTCGCGGTCGCGTTTT
580627 CGGTCGC-GTCGCGTTT
1 CGGTCGCGGTCGCGTTT
580643 GTCACGGTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.00, C:0.29, G:0.38, T:0.32
Consensus pattern (18 bp):
CGGTCGCGGTCGCGTTTT
Found at i:585296 original size:23 final size:23
Alignment explanation
Indices: 585254--585297 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
585244 AGCTCTCCAT
*
585254 ATATAAACAAGAAGGAAAGAAAG
1 ATATAAACAAGAAGAAAAGAAAG
585277 ATATAAA-AAGAAGAAGAAGAA
1 ATATAAACAAGAAGAA-AAGAA
585298 GAAGGAGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.68, C:0.02, G:0.20, T:0.09
Consensus pattern (23 bp):
ATATAAACAAGAAGAAAAGAAAG
Found at i:585618 original size:20 final size:19
Alignment explanation
Indices: 585580--585619 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
585570 CATAAAAATA
* *
585580 TTAAAAAAAATTATTTTAT
1 TTAAAAAAAATGATGTTAT
585599 TTAAAATAAAATGATGTTAT
1 TTAAAA-AAAATGATGTTAT
585619 T
1 T
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
TTAAAAAAAATGATGTTAT
Done.