Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold153
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: 3137677
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 24 of 24
Found at i:3086138 original size:58 final size:56
Alignment explanation
Indices: 3086059--3086177 Score: 138
Period size: 58 Copynumber: 2.1 Consensus size: 56
3086049 AGTTACCTTC
* *
3086059 AAAATTTATTTATATCATTCAAAT-TTGAAGATAACTAT-T-AAATATGAATATGTTCAA
1 AAAATTTATTTATATCATTCAAATATT-AA-A-AAATATATAAAATATGAATAT-TTAAA
3086116 AAAATTT-TTTATATCTCATTCAAATATTAAAAAATATATAAAATATGAATATTTAAA
1 AAAATTTATTTATA--TCATTCAAATATTAAAAAATATATAAAATATGAATATTTAAA
3086173 AAAAT
1 AAAAT
3086178 AAAAAAATTA
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
56 11 0.20
57 18 0.33
58 24 0.44
59 2 0.04
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.39
Consensus pattern (56 bp):
AAAATTTATTTATATCATTCAAATATTAAAAAATATATAAAATATGAATATTTAAA
Found at i:3091334 original size:9 final size:9
Alignment explanation
Indices: 3091320--3091356 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
3091310 AGAGAGCTGG
3091320 CTCCTTCTT
1 CTCCTTCTT
3091329 CTCCTTCTT
1 CTCCTTCTT
*
3091338 CTCCTACTT
1 CTCCTTCTT
3091347 CTTCCTTCTT
1 C-TCCTTCTT
3091357 TTTTTTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 18 0.72
10 7 0.28
ACGTcount: A:0.03, C:0.43, G:0.00, T:0.54
Consensus pattern (9 bp):
CTCCTTCTT
Found at i:3091367 original size:12 final size:12
Alignment explanation
Indices: 3091352--3091377 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3091342 TACTTCTTCC
3091352 TTCTTTTTTTTT
1 TTCTTTTTTTTT
3091364 TTCTTTTTTTTT
1 TTCTTTTTTTTT
3091376 TT
1 TT
3091378 TCAACTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTCTTTTTTTTT
Found at i:3091373 original size:13 final size:13
Alignment explanation
Indices: 3091355--3091379 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3091345 TTCTTCCTTC
3091355 TTTTTTTTTTTCT
1 TTTTTTTTTTTCT
3091368 TTTTTTTTTTTC
1 TTTTTTTTTTTC
3091380 AACTGTAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTTTTTTTTTCT
Found at i:3091871 original size:21 final size:20
Alignment explanation
Indices: 3091847--3091892 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3091837 TTTTAATCAG
*
3091847 ATTTATCACTTTATTAATTTT
1 ATTTATCAATTT-TTAATTTT
*
3091868 ATTTATTAATTTTTAATTTT
1 ATTTATCAATTTTTAATTTT
*
3091888 TTTTA
1 ATTTA
3091893 AAATTGGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTATCAATTTTTAATTTT
Found at i:3091874 original size:13 final size:13
Alignment explanation
Indices: 3091856--3091880 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3091846 GATTTATCAC
3091856 TTTATTAATTTTA
1 TTTATTAATTTTA
3091869 TTTATTAATTTT
1 TTTATTAATTTT
3091881 TAATTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTAATTTTA
Found at i:3092752 original size:33 final size:33
Alignment explanation
Indices: 3092710--3092789 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 33
3092700 AAAAAAATAT
*
3092710 TTTTATTTTAAATTTAATAATATTA-AGATAAA
1 TTTTATTTTAAATTTAATAATATTATAAATAAA
* *
3092742 TTTTATTTTTAATTAAATAATATTATAAATAAA
1 TTTTATTTTAAATTTAATAATATTATAAATAAA
* *
3092775 TATTATCTTAAATTT
1 TTTTATTTTAAATTT
3092790 TTTAAAAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
32 23 0.57
33 17 0.43
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (33 bp):
TTTTATTTTAAATTTAATAATATTATAAATAAA
Found at i:3092817 original size:14 final size:15
Alignment explanation
Indices: 3092791--3092826 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
3092781 CTTAAATTTT
*
3092791 TTAAAAAATATAATC
1 TTAAAAAATATAATA
3092806 TTAAAAAA-ATAATA
1 TTAAAAAATATAATA
3092820 TTAAAAA
1 TTAAAAA
3092827 TTATTTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (15 bp):
TTAAAAAATATAATA
Found at i:3093152 original size:3 final size:3
Alignment explanation
Indices: 3093140--3093195 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
3093130 ATTTCTGGCT
3093140 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3093187 TAA TAA TAA
1 TAA TAA TAA
3093196 GAAATTTGAG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3093818 original size:78 final size:78
Alignment explanation
Indices: 3093727--3093884 Score: 280
Period size: 78 Copynumber: 2.0 Consensus size: 78
3093717 ATCACCCTAC
*
3093727 ATAATAATTAACTAAGAAAGCTAATTTGAGCAAAGAACAACTGGCATTTGATTTGATGTTGATTC
1 ATAATAATCAACTAAGAAAGCTAATTTGAGCAAAGAACAACTGGCATTTGATTTGATGTTGATTC
*
3093792 AAATATATGAAGA
66 AAAAATATGAAGA
* *
3093805 ATAATAATCAACTAAGAAAGCTAATTTGAGCAAAGAACAATTGGCATTTGATTTGATGTTGGTTC
1 ATAATAATCAACTAAGAAAGCTAATTTGAGCAAAGAACAACTGGCATTTGATTTGATGTTGATTC
3093870 AAAAATATGAAGA
66 AAAAATATGAAGA
3093883 AT
1 AT
3093885 TTCTTCTATG
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.30
Consensus pattern (78 bp):
ATAATAATCAACTAAGAAAGCTAATTTGAGCAAAGAACAACTGGCATTTGATTTGATGTTGATTC
AAAAATATGAAGA
Found at i:3093926 original size:48 final size:48
Alignment explanation
Indices: 3093852--3093952 Score: 193
Period size: 48 Copynumber: 2.1 Consensus size: 48
3093842 CAATTGGCAT
3093852 TTGATTTGATGTTGGTTCAAAAATATGAAGAATTTCTTCTATGTTGAA
1 TTGATTTGATGTTGGTTCAAAAATATGAAGAATTTCTTCTATGTTGAA
*
3093900 TTGATTTGATGTTGGTTCAAATATATGAAGAATTTCTTCTATGTTGAA
1 TTGATTTGATGTTGGTTCAAAAATATGAAGAATTTCTTCTATGTTGAA
3093948 TTGAT
1 TTGAT
3093953 CTAAACATAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.46
Consensus pattern (48 bp):
TTGATTTGATGTTGGTTCAAAAATATGAAGAATTTCTTCTATGTTGAA
Found at i:3096192 original size:606 final size:607
Alignment explanation
Indices: 3094776--3096621 Score: 2872
Period size: 606 Copynumber: 3.0 Consensus size: 607
3094766 TTAGCACCAA
* * * * *
3094776 ATTTCTTAAGCATGGCATGGGCAACAACTAAGATTGCCGAAGGTGTTTTTAGGTGATTCGGAGGC
1 ATTTCTTAAGCATGGCATGAGCAGCAACTAAGATTGCTGAAGGTGTTTTTAGGTGGTTC-GTGGC
** * * * * * *
3094841 CCGGGCCTCACGGAGATGGAAACAATGCATCAAAGTTCTACTTCCGATGCGTCTTCTGATGCTTA
65 CCGACCCTCACGGAGATGGACACAGTGCATCAAAGTTCTGCTTCTGATGCGTCTTTTAATGCTTA
* * * * * * *
3094906 AATCACT-GTTTGAGGGAGCACCGAACCCTAGAAGCCACCTCAACAAAAAATCTAGTGCAGAAAG
130 AATCAGTAG-TCGAGGAACCACTGAACCCTAAAAGCCACCTCAACAAAAAATCTAGTGCAGCAAG
* *
3094970 GCCTTCAAAACTAAATTTAAAACGTGAAAGATATACAAAAGACGCTTAAAAGGCTTTAGAAACCT
194 GCCTTCAAAACAAAATTTAAAACGT----G--------AA-A---TT-------TTTACAAACCT
* * * * *
3095035 AAAGCATTAACAAAACAATA-TATCCAAAAGGTAATTAGGTTGATTTGGAATCGGAAGTAGAAAA
236 GAAGTATTAACAAAACAA-AGTCTCCAACAGGTATTTAGGTTGATTTGGAATCGGAAGTAGAAAA
* * * ** * *
3095099 AAAAA-GGACAAAGGAACAGACCTTTAGTACACGGTTGCGGGAACGGTGGTGCTGGCGGTGGTGG
300 AAAAAGGGAAAAAGGAACAGACCTTCAGTACAAGGTTGCGCCAACGGTGGCGCTGGAGGTGGTGG
* * * * * *
3095163 AGGCCGTTGCAGCTCAAGCCTCAATCTGATTCAATGTACAAATTTGGGTCTGGGCAACGCCATAA
365 AGGCAGTAGCAGCTCAAGCCTCAATCTGATTCAGTTTCCAAATTTGGTTCTGGGCAACGCCATAA
* *
3095228 TTCAGGCTAATCTTCTTCTTTCCTTCAATTTTCTCTTCAACCAAACACGAAACTCCCATAACATC
430 TTCAGGCTAATCTTCTTCTTTCCTCCAATTTTCTCCTCAACCAAACACGAAACTCCCATAACATC
*
3095293 AACCAAAACAAAGAGATCTAGGAAATTTTGAATCAAATATAGGAAAAAAATAAAGATTTTTTGCA
495 AACCACAACAAAGAGATCTAGGAAATTTTGAATCAAATATAGGAAAAAAATAAAGATTTTTTGCA
* *
3095358 CTATCTCTCTTTGCTGACAACATTTTGTTTAAGTATACACTATATACT
560 CTATCTCTCTTTGCTGACAACATTATGTTTAAGTATATACTATATACT
* *
3095406 ATTTCTTAAGCATGGCATGAGCAGAAACTAAGATTGTTGAAGGTGTTTTTAGGTGGTTCGTGGCC
1 ATTTCTTAAGCATGGCATGAGCAGCAACTAAGATTGCTGAAGGTGTTTTTAGGTGGTTCGTGGCC
* *
3095471 CGACCCTCACGGAGATGGACACAGTGCATCAAAGTTCTGCTTCTGATGAGTCTTTTAACGCTTAA
66 CGACCCTCACGGAGATGGACACAGTGCATCAAAGTTCTGCTTCTGATGCGTCTTTTAATGCTTAA
3095536 ATCAGTAGTCGAGGAACCACTGAACCCTAAAAGCCACCTCAACAAAAAATCTAGTGCAGCAAGGC
131 ATCAGTAGTCGAGGAACCACTGAACCCTAAAAGCCACCTCAACAAAAAATCTAGTGCAGCAAGGC
*
3095601 CTTCAAAACAAAATTTAAAACGTGAAATTTTTACAAACCTGAAGTATTAACAAAACAAAGTCCCC
196 CTTCAAAACAAAATTTAAAACGTGAAATTTTTACAAACCTGAAGTATTAACAAAACAAAGTCTCC
*
3095666 AACAGGTATTTAGGTTGATTTGGAATCGGAAGTAGAAAAAAAAAGGGAAAAAGGAACAGACATTC
261 AACAGGTATTTAGGTTGATTTGGAATCGGAAGTAGAAAAAAAAAGGGAAAAAGGAACAGACCTTC
*
3095731 AGTACAAGGTTGCGCCAACGGTGGCGCTGGAGGTGGTGGAGGCAGTAGCAGCTCAAGCTTCAATC
326 AGTACAAGGTTGCGCCAACGGTGGCGCTGGAGGTGGTGGAGGCAGTAGCAGCTCAAGCCTCAATC
*
3095796 TGATTCAGTTTCCAAATTTGGTTCTGGGCAACGCCATAATTCAGGCTAATCTTCTTCTTCCCTCC
391 TGATTCAGTTTCCAAATTTGGTTCTGGGCAACGCCATAATTCAGGCTAATCTTCTTCTTTCCTCC
3095861 AATTTTCTCCTCAACCAAACACGAAACTCCCATAACATCAACCACAACAAAGAGATCTAGGAAAT
456 AATTTTCTCCTCAACCAAACACGAAACTCCCATAACATCAACCACAACAAAGAGATCTAGGAAAT
**
3095926 TTTGAATCAAATATAGG-AAAAAATAAAGATTTTTTGCACTCGCTCTCTTTGCTGACAACATTAT
521 TTTGAATCAAATATAGGAAAAAAATAAAGATTTTTTGCACTATCTCTCTTTGCTGACAACATTAT
*
3095990 GTCTAAGTATATACTATATACT
586 GTTTAAGTATATACTATATACT
3096012 ATTTCTTAAGCATGGCATGAGCAGCAACTAAGATTGCTGAAGGTGTTTTTAGGTGGTTCGTGGCC
1 ATTTCTTAAGCATGGCATGAGCAGCAACTAAGATTGCTGAAGGTGTTTTTAGGTGGTTCGTGGCC
3096077 CGACCCTCACGGAGATGGACACAGTGCATCAAAGTTCTGCTTCTGATGCGTCTTTTAATGCTTAA
66 CGACCCTCACGGAGATGGACACAGTGCATCAAAGTTCTGCTTCTGATGCGTCTTTTAATGCTTAA
3096142 ATCAGTAGTCGAGGAACCACTGAACCCTAAAAGCCACCTCAACAAAAAATCTAGTGCAGCAAGGC
131 ATCAGTAGTCGAGGAACCACTGAACCCTAAAAGCCACCTCAACAAAAAATCTAGTGCAGCAAGGC
* *
3096207 CTTCAAAACAAAATTTAAAACGTGAAAGTTATACAAACCTGAAGTATTAACAAAACAAAGTCTCC
196 CTTCAAAACAAAATTTAAAACGTGAAATTTTTACAAACCTGAAGTATTAACAAAACAAAGTCTCC
3096272 AACAGGTATTTAGGTTGATTTGGAATCGGAAGTAGAAAAAAAAAGGGAAAAAGGAACAGACCTTC
261 AACAGGTATTTAGGTTGATTTGGAATCGGAAGTAGAAAAAAAAAGGGAAAAAGGAACAGACCTTC
3096337 AGTACAAGGTTGCGCCAACGGTGGCGCTGGAGGTGGTGGAGGCAGTAGCAGCTCAAGCCTCAATC
326 AGTACAAGGTTGCGCCAACGGTGGCGCTGGAGGTGGTGGAGGCAGTAGCAGCTCAAGCCTCAATC
*
3096402 TGATTCAGTTTCCAAATTTGGTTCTGGGCAACGCCATAATTCAGGATAATCTTCTTCTTTCCTCC
391 TGATTCAGTTTCCAAATTTGGTTCTGGGCAACGCCATAATTCAGGCTAATCTTCTTCTTTCCTCC
3096467 AATTTTCTCCTCAACCAAACACGAAACTCCCATAACATCAACCACAACAAAGAGATCTAGGAAAT
456 AATTTTCTCCTCAACCAAACACGAAACTCCCATAACATCAACCACAACAAAGAGATCTAGGAAAT
* *
3096532 TTTGAATCAAATATAGGAAAAAAATAAAGATTTTTTGCACTATCTCTCTTTGTTGACAACATTCT
521 TTTGAATCAAATATAGGAAAAAAATAAAGATTTTTTGCACTATCTCTCTTTGCTGACAACATTAT
*
3096597 GTTTAAGTATATACTATAAACT
586 GTTTAAGTATATACTATATACT
3096619 ATT
1 ATT
3096622 ACTAGAATTA
Statistics
Matches: 1139, Mismatches: 73, Indels: 31
0.92 0.06 0.02
Matches are distributed among these distances:
605 1 0.00
606 661 0.58
607 279 0.24
613 2 0.00
616 1 0.00
617 2 0.00
625 1 0.00
629 138 0.12
630 54 0.05
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (607 bp):
ATTTCTTAAGCATGGCATGAGCAGCAACTAAGATTGCTGAAGGTGTTTTTAGGTGGTTCGTGGCC
CGACCCTCACGGAGATGGACACAGTGCATCAAAGTTCTGCTTCTGATGCGTCTTTTAATGCTTAA
ATCAGTAGTCGAGGAACCACTGAACCCTAAAAGCCACCTCAACAAAAAATCTAGTGCAGCAAGGC
CTTCAAAACAAAATTTAAAACGTGAAATTTTTACAAACCTGAAGTATTAACAAAACAAAGTCTCC
AACAGGTATTTAGGTTGATTTGGAATCGGAAGTAGAAAAAAAAAGGGAAAAAGGAACAGACCTTC
AGTACAAGGTTGCGCCAACGGTGGCGCTGGAGGTGGTGGAGGCAGTAGCAGCTCAAGCCTCAATC
TGATTCAGTTTCCAAATTTGGTTCTGGGCAACGCCATAATTCAGGCTAATCTTCTTCTTTCCTCC
AATTTTCTCCTCAACCAAACACGAAACTCCCATAACATCAACCACAACAAAGAGATCTAGGAAAT
TTTGAATCAAATATAGGAAAAAAATAAAGATTTTTTGCACTATCTCTCTTTGCTGACAACATTAT
GTTTAAGTATATACTATATACT
Found at i:3098755 original size:2 final size:2
Alignment explanation
Indices: 3098711--3098737 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3098701 TTATTTCGTG
3098711 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3098738 GTTTAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3098773 original size:28 final size:27
Alignment explanation
Indices: 3098718--3098772 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
3098708 GTGTATATAT
*
3098718 ATATATATATATATATATATGTTTAAA
1 ATATATATATATATATAAATGTTTAAA
*
3098745 ATATGATATATTTATATAAAT-TTTAAA
1 ATAT-ATATATATATATAAATGTTTAAA
3098772 A
1 A
3098773 AATTAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (27 bp):
ATATATATATATATATAAATGTTTAAA
Found at i:3098875 original size:57 final size:57
Alignment explanation
Indices: 3098723--3098876 Score: 177
Period size: 57 Copynumber: 2.6 Consensus size: 57
3098713 TATATATATA
*
3098723 TATATATATATATATGTTTAAAATATGATATATTTATATAAATTTTAAAAAATTAATAATT
1 TATAT-TATATAAAT-TTT-AAA-ATGATATATTTATATAAATTTTAAAAAATTAATAATT
* * * * *
3098784 TATATTAAATAAATTTT--GATGATAGATATTTATATAAATTTTGACATATTAATAATT
1 TATATTATATAAATTTTAAAATGAT--ATATTTATATAAATTTTAAAAAATTAATAATT
*
3098841 TATATTATATAAATTTTAAAATGATATATGTATATA
1 TATATTATATAAATTTTAAAATGATATATTTATATA
3098877 TTTATATTAT
Statistics
Matches: 80, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
55 5 0.06
57 55 0.69
59 8 0.10
60 7 0.09
61 5 0.06
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (57 bp):
TATATTATATAAATTTTAAAATGATATATTTATATAAATTTTAAAAAATTAATAATT
Found at i:3098903 original size:11 final size:11
Alignment explanation
Indices: 3098873--3098897 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3098863 GATATATGTA
3098873 TATATTTATAT
1 TATATTTATAT
3098884 TATATTTATAT
1 TATATTTATAT
3098895 TAT
1 TAT
3098898 TATTATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:3098915 original size:12 final size:12
Alignment explanation
Indices: 3098894--3098954 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
3098884 TATATTTATA
3098894 TTATTATTATTTT
1 TTATT-TTATTTT
* *
3098907 TTATTTTATGTA
1 TTATTTTATTTT
**
3098919 AAATTTTATTTT
1 TTATTTTATTTT
* * *
3098931 ATATTTTAATTA
1 TTATTTTATTTT
3098943 TTATTTTATTTT
1 TTATTTTATTTT
3098955 GTACCAATAT
Statistics
Matches: 36, Mismatches: 12, Indels: 1
0.73 0.24 0.02
Matches are distributed among these distances:
12 31 0.86
13 5 0.14
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (12 bp):
TTATTTTATTTT
Found at i:3098948 original size:24 final size:23
Alignment explanation
Indices: 3098877--3098954 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 23
3098867 TATGTATATA
*
3098877 TTTATATTATA-TTTA-TATTAT
1 TTTATTTTATATTTTATTATTAT
* **
3098898 TATTATTTTTTATTTTATGTAAAAT
1 T-TTATTTTATATTTTAT-TATTAT
3098923 TTTATTTTATATTTTAATTATTAT
1 TTTATTTTATATTTT-ATTATTAT
3098947 TTTATTTT
1 TTTATTTT
3098955 GTACCAATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.02
22 8 0.18
23 4 0.09
24 25 0.56
25 7 0.16
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.69
Consensus pattern (23 bp):
TTTATTTTATATTTTATTATTAT
Found at i:3100186 original size:21 final size:20
Alignment explanation
Indices: 3100162--3100200 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3100152 AACTCATAAT
3100162 TTAAAAAATTGTTTTTGAATC
1 TTAAAAAATT-TTTTTGAATC
**
3100183 TTAAATGATTTTTTTGAA
1 TTAAAAAATTTTTTTGAA
3100201 ATTTTTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (20 bp):
TTAAAAAATTTTTTTGAATC
Found at i:3103836 original size:2 final size:2
Alignment explanation
Indices: 3103829--3103862 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3103819 CCTCTTAACT
3103829 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3103863 CTTCTTAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3104749 original size:24 final size:24
Alignment explanation
Indices: 3104706--3104768 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 24
3104696 TAAAAACTCA
*
3104706 AATTATTATTT-TATAATTTTT-T
1 AATTAATATTTATATAATTTTTAT
3104728 ATATTAATATTTATATAATTTTTAT
1 A-ATTAATATTTATATAATTTTTAT
*
3104753 AATT-ATATTTAAATAA
1 AATTAATATTTATATAA
3104769 AAAATATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
22 1 0.03
23 20 0.56
24 13 0.36
25 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
AATTAATATTTATATAATTTTTAT
Found at i:3105149 original size:38 final size:38
Alignment explanation
Indices: 3105098--3105171 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 38
3105088 AAAAAATTAC
*
3105098 GGTTAAAATGCTTTCCT-TTTAAGGGGCCAGAAACTAAA
1 GGTTAAAATGCTTT-CTATTTAAAGGGCCAGAAACTAAA
*
3105136 GGTTAACATGCTTTCTATTTAAAGGGCCAGAAACTA
1 GGTTAAAATGCTTTCTATTTAAAGGGCCAGAAACTA
3105172 CAGTCCTCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 2 0.06
38 31 0.94
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (38 bp):
GGTTAAAATGCTTTCTATTTAAAGGGCCAGAAACTAAA
Found at i:3106471 original size:12 final size:12
Alignment explanation
Indices: 3106456--3106484 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3106446 AGGCAGGATA
3106456 ATAGGAGATGCC
1 ATAGGAGATGCC
3106468 ATAGGAGATGCC
1 ATAGGAGATGCC
3106480 ATAGG
1 ATAGG
3106485 CCTGTGAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.14, G:0.34, T:0.17
Consensus pattern (12 bp):
ATAGGAGATGCC
Found at i:3109684 original size:17 final size:17
Alignment explanation
Indices: 3109664--3109716 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
3109654 AATATTTTTT
3109664 TATTTTAAATTTAATAA
1 TATTTTAAATTTAATAA
* * *
3109681 TA--TTAAAATAAATAT
1 TATTTTAAATTTAATAA
*
3109696 TATTTTTAATTTAATAA
1 TATTTTAAATTTAATAA
3109713 TATT
1 TATT
3109717 ATGAATAAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
15 12 0.44
17 15 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTTTAAATTTAATAA
Found at i:3109703 original size:33 final size:34
Alignment explanation
Indices: 3109666--3109741 Score: 120
Period size: 33 Copynumber: 2.3 Consensus size: 34
3109656 TATTTTTTTA
3109666 TTTTAAATTTAATAATATTA-AAATAAATATTAT
1 TTTTAAATTTAATAATATTATAAATAAATATTAT
*
3109699 TTTT-AATTTAATAATATTATGAATAAATATTAT
1 TTTTAAATTTAATAATATTATAAATAAATATTAT
*
3109732 TTTAAAATTT
1 TTTTAAATTT
3109742 TTTAAAAGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
32 15 0.38
33 19 0.49
34 5 0.13
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (34 bp):
TTTTAAATTTAATAATATTATAAATAAATATTAT
Found at i:3109707 original size:32 final size:33
Alignment explanation
Indices: 3109663--3109737 Score: 125
Period size: 32 Copynumber: 2.3 Consensus size: 33
3109653 AAATATTTTT
3109663 TTATTTTAAATTTAATAATATTA-AAATAAATA
1 TTATTTTAAATTTAATAATATTATAAATAAATA
* *
3109695 TTATTTTTAATTTAATAATATTATGAATAAATA
1 TTATTTTAAATTTAATAATATTATAAATAAATA
3109728 TTATTTTAAA
1 TTATTTTAAA
3109738 ATTTTTTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 22 0.56
33 17 0.44
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (33 bp):
TTATTTTAAATTTAATAATATTATAAATAAATA
Found at i:3109840 original size:24 final size:22
Alignment explanation
Indices: 3109787--3109843 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 22
3109777 TTTTTTAAAA
* *
3109787 TTTTAAAAAATAATTTTTTTAT
1 TTTTTAAAATTAATTTTTTTAT
*
3109809 TTTCTAAAATTAATTATTATTTAT
1 TTTTTAAAATTAATT-TT-TTTAT
3109833 TTTTTAAAATT
1 TTTTTAAAATT
3109844 TTGTAATGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 12 0.41
23 2 0.07
24 15 0.52
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTTAAAATTAATTTTTTTAT
Found at i:3110635 original size:19 final size:18
Alignment explanation
Indices: 3110577--3110636 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
3110567 TTAAAAAGCT
*
3110577 AATAATTTATAATTTATATA
1 AATAATTTA-AATTAAT-TA
3110597 AAT-A-TTAATATTAAATTA
1 AATAATTTAA-ATT-AATTA
3110615 AATAATTTAAATTAATGTA
1 AATAATTTAAATTAAT-TA
3110634 AAT
1 AAT
3110637 TAGTCTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
17 1 0.03
18 14 0.41
19 12 0.35
20 7 0.21
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
AATAATTTAAATTAATTA
Found at i:3111956 original size:13 final size:13
Alignment explanation
Indices: 3111938--3111962 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3111928 AAAAACAATA
3111938 AATCATTTTTAAT
1 AATCATTTTTAAT
3111951 AATCATTTTTAA
1 AATCATTTTTAA
3111963 AAGTTATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (13 bp):
AATCATTTTTAAT
Found at i:3113283 original size:2 final size:2
Alignment explanation
Indices: 3113276--3113320 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3113266 ATTGGTTCTA
3113276 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3113318 TC T
1 TC T
3113321 GCATCTGCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3118752 original size:13 final size:13
Alignment explanation
Indices: 3118725--3118757 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3118715 TTATATTATT
3118725 TAAAT-TTAAAAA
1 TAAATATTAAAAA
*
3118737 TAAATATTAAATA
1 TAAATATTAAAAA
3118750 TAAATATT
1 TAAATATT
3118758 TTTAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TAAATATTAAAAA
Found at i:3123713 original size:24 final size:25
Alignment explanation
Indices: 3123686--3123735 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
3123676 TTTTAATATA
3123686 TTAATAATTTATATTAA-ATAAATT
1 TTAATAATTTATATTAATATAAATT
*
3123710 TTAATATTTTATATTAATATAAATT
1 TTAATAATTTATATTAATATAAATT
3123735 T
1 T
3123736 CGATATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTAATAATTTATATTAATATAAATT
Found at i:3123741 original size:25 final size:24
Alignment explanation
Indices: 3123688--3123741 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
3123678 TTAATATATT
* *
3123688 AATAATTTATATTAAATAAATTTT
1 AATATTTTATATTAAATAAATTTC
3123712 AATATTTTATATTAATATAAATTTC
1 AATATTTTATATTAA-ATAAATTTC
*
3123737 GATAT
1 AATAT
3123742 ATTAATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
AATATTTTATATTAAATAAATTTC
Found at i:3123793 original size:21 final size:19
Alignment explanation
Indices: 3123760--3123831 Score: 51
Period size: 21 Copynumber: 3.6 Consensus size: 19
3123750 TACGTATTTA
3123760 TAAATTTTAATATAATATATT
1 TAAATTTT-ATAT-ATATATT
3123781 TAAATATTTATAT-TATTATT
1 TAAAT-TTTATATATA-TATT
* *
3123801 TATTTATTTTATATA-GTATT
1 TA--AATTTTATATATATATT
3123821 T-AATTTTATAT
1 TAAATTTTATAT
3123832 TTTAATTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
17 9 0.21
19 2 0.05
20 11 0.26
21 16 0.37
22 5 0.12
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (19 bp):
TAAATTTTATATATATATT
Found at i:3123802 original size:20 final size:20
Alignment explanation
Indices: 3123777--3123832 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
3123767 TAATATAATA
*
3123777 TATTTAAATATTTATATTAT
1 TATTTAAATATTTATATTAG
**
3123797 TATTTATTTATTT-TATATAG
1 TATTTAAATATTTATAT-TAG
3123817 TATTT-AAT-TTTATATT
1 TATTTAAATATTTATATT
3123833 TTAATTATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
18 4 0.14
19 7 0.24
20 18 0.62
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TATTTAAATATTTATATTAG
Found at i:3123804 original size:16 final size:15
Alignment explanation
Indices: 3123785--3123850 Score: 50
Period size: 16 Copynumber: 4.3 Consensus size: 15
3123775 TATATTTAAA
3123785 TATTTATATTATTATT
1 TATTTA-ATTATTATT
3123801 TATTT-ATT-TTATAT
1 TATTTAATTATTAT-T
*
3123815 AGTATTTAATT-TTATA
1 --TATTTAATTATTATT
3123831 T-TTTAATTATTATTT
1 TATTTAATTATTA-TT
3123846 TATTT
1 TATTT
3123851 TATACCCAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
13 11 0.27
14 8 0.20
15 2 0.05
16 13 0.32
17 7 0.17
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (15 bp):
TATTTAATTATTATT
Found at i:3123806 original size:24 final size:22
Alignment explanation
Indices: 3123784--3123850 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
3123774 ATATATTTAA
3123784 ATATTTATATTATTATTTATTT
1 ATATTTATATTATTATTTATTT
*
3123806 AT-TTTATA-TAGTATTTAATTTT
1 ATATTTATATTATTATTT-A-TTT
3123828 ATATTT-TAATTATTATTTTATTT
1 ATATTTAT-ATTATTA-TTTATTT
3123851 TATACCCAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
20 7 0.19
21 7 0.19
22 8 0.22
23 7 0.19
24 5 0.14
25 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (22 bp):
ATATTTATATTATTATTTATTT
Found at i:3123851 original size:24 final size:24
Alignment explanation
Indices: 3123791--3123854 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
3123781 TAAATATTTA
*
3123791 TATTATTATTTATTTATTTTATATAG
1 TATT-TTATTT-TATATTTTATATAG
* *
3123817 TATTTAATTTTATATTTTA-ATTAT
1 TATTTTATTTTATATTTTATA-TAG
3123841 TATTTTATTTTATA
1 TATTTTATTTTATA
3123855 CCCAATATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 1 0.03
24 23 0.70
25 5 0.15
26 4 0.12
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TATTTTATTTTATATTTTATATAG
Found at i:3125197 original size:10 final size:10
Alignment explanation
Indices: 3125175--3125205 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
3125165 CCACACATAT
3125175 ATTAATATTAA
1 ATTAAT-TTAA
3125186 ATTAATTTAA
1 ATTAATTTAA
3125196 ATTAATTTAA
1 ATTAATTTAA
3125206 TTTTATCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.70
11 6 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
ATTAATTTAA
Found at i:3125205 original size:15 final size:16
Alignment explanation
Indices: 3125176--3125208 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3125166 CACACATATA
3125176 TTAATATTAAATTAAT
1 TTAATATTAAATTAAT
*
3125192 TTAA-ATTAATTTAAT
1 TTAATATTAAATTAAT
3125207 TT
1 TT
3125209 TATCTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAATATTAAATTAAT
Found at i:3129170 original size:20 final size:20
Alignment explanation
Indices: 3129145--3129182 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3129135 TAATATGAGA
*
3129145 TTAATATAAGATTGCAACTT
1 TTAATATAAGATTACAACTT
3129165 TTAATATAAGATTACAAC
1 TTAATATAAGATTACAAC
3129183 CGTTATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.37
Consensus pattern (20 bp):
TTAATATAAGATTACAACTT
Found at i:3135391 original size:22 final size:21
Alignment explanation
Indices: 3135358--3135398 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
3135348 TAATAAAATT
3135358 TATCAATATATTTATATTAAAA
1 TATCAATATATTTA-ATTAAAA
3135380 TATC-ATATTATTTAATTAA
1 TATCAATA-TATTTAATTAA
3135399 GTGTATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (21 bp):
TATCAATATATTTAATTAAAA
Found at i:3135423 original size:16 final size:16
Alignment explanation
Indices: 3135404--3135434 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3135394 ATTAAGTGTA
*
3135404 TATTTTTTAATTAAAT
1 TATTTTTAAATTAAAT
3135420 TATTTTTAAATTAAA
1 TATTTTTAAATTAAA
3135435 AAATATAATT
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTTTTAAATTAAAT
Done.