Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold358
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: 447680
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 23201 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:406720 original size:49 final size:49
Alignment explanation
Indices: 406654--406751 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
406644 GTAATAAGTT
406654 TTACAGTATGATGGAATTATAGTATAAAAATTTCGTTAAGAAATTTTAC
1 TTACAGTATGATGGAATTATAGTATAAAAATTTCGTTAAGAAATTTTAC
406703 TTACAGTATGATGGAATTATAGTATAAAAATTTCGTTAAGAAATTTTAC
1 TTACAGTATGATGGAATTATAGTATAAAAATTTCGTTAAGAAATTTTAC
406752 CGTTTAAATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (49 bp):
TTACAGTATGATGGAATTATAGTATAAAAATTTCGTTAAGAAATTTTAC
Found at i:411150 original size:807 final size:807
Alignment explanation
Indices: 409597--411211 Score: 3151
Period size: 807 Copynumber: 2.0 Consensus size: 807
409587 ATGAAAGTAT
409597 GTTTGGTTGTTTAATTTAATATGTTCGGTAAGTTTAAGTTTCCTTTATACGAGCTTAATAAGCAC
1 GTTTGGTTGTTTAATTTAATATGTTCGGTAAGTTTAAGTTTCCTTTATACGAGCTTAATAAGCAC
*
409662 TAGTTGCTTATATATTTGTTTTCTTTGTTCGTAGATCATCGAAAAGCTTGATTGGTTGGAATCTT
66 TAGTTGCTTATATATTTGTTTTCTTTGTTCGTAGATCATCGAAAAGCTCGATTGGTTGGAATCTT
*
409727 GTCGAAGCATCGTCACACTCTCTATTCGTCATATTGGTAGTTTTGGTTAATGGTTATAAATGGCA
131 GTCGAAGCATCGTCACACTATCTATTCGTCATATTGGTAGTTTTGGTTAATGGTTATAAATGGCA
409792 TGTGATAGGGTTAAAAGGTTATTCAAGTGAATTGGCTTGTTTTGAGTTGTGTCAAGCTTATTGTG
196 TGTGATAGGGTTAAAAGGTTATTCAAGTGAATTGGCTTGTTTTGAGTTGTGTCAAGCTTATTGTG
* *
409857 GTTAATGATGTTAAATGATGACATGTAAATAATATGAGCAAATATGAGTGGATGAACCCTTATGC
261 GTTAATGATGTGAAATGATAACATGTAAATAATATGAGCAAATATGAGTGGATGAACCCTTATGC
409922 ATACTCTATAGATAGTAGATATTAAATGGTATGATGGCAAGTTTTGAAAATGGTTATTTTGGCAT
326 ATACTCTATAGATAGTAGATATTAAATGGTATGATGGCAAGTTTTGAAAATGGTTATTTTGGCAT
409987 GGTTGATATAGGTTCTAAATAGAACTTTAAGATGTTGAATGGGACTAAGTTGGTATGTAAATTGT
391 GGTTGATATAGGTTCTAAATAGAACTTTAAGATGTTGAATGGGACTAAGTTGGTATGTAAATTGT
410052 GGTGCCTTTGAATGGTATATTGGTTAGATATAGGATGGATGAATGTTTGGCATGTTGTTGGTGTT
456 GGTGCCTTTGAATGGTATATTGGTTAGATATAGGATGGATGAATGTTTGGCATGTTGTTGGTGTT
410117 TTGAATGTGCTTTTGATCATATGAAATAGGCTAGGTATGATTTGATAATGAAGTGATTATATGAT
521 TTGAATGTGCTTTTGATCATATGAAATAGGCTAGGTATGATTTGATAATGAAGTGATTATATGAT
410182 GTGTGTGTGATATGTGTTTTGGTCATGAACTTATGATGTTAAAATTGATGTGTTTTAGGGGATTT
586 GTGTGTGTGATATGTGTTTTGGTCATGAACTTATGATGTTAAAATTGATGTGTTTTAGGGGATTT
*
410247 GAATGTGATTTAAGCATGTGAAAGTAGCTATAAAGGGTATGGCTTGGTGGTTAAGAAAGGGTATT
651 GAATGTGATTTAAGCATGTGAAAGTAGCTATAAAGGGTATGGCTTGGTGGTTAAGAAAGGGGATT
410312 TGAAATGGTTTGTTTTATAGGTAATTTGTGTTGCACATGACCTGGGACATGAGCTGTCACACGGC
716 TGAAATGGTTTGTTTTATAGGTAATTTGTGTTGCACATGACCTGGGACATGAGCTGTCACACGGC
410377 TATGTGCCACACATGGCCTGACCACAC
781 TATGTGCCACACATGGCCTGACCACAC
410404 GTTTGGTTGTTTAATTTAATATGTTCGGTAAGTTTAAGTTTCCTTTATACGAGCTTAATAAGCAC
1 GTTTGGTTGTTTAATTTAATATGTTCGGTAAGTTTAAGTTTCCTTTATACGAGCTTAATAAGCAC
410469 TAGTTGCTTATATATTTGTTTTCTTTGTTCGTAGATCATCGAAAAGCTCGATTGGTTGGAATCTT
66 TAGTTGCTTATATATTTGTTTTCTTTGTTCGTAGATCATCGAAAAGCTCGATTGGTTGGAATCTT
*
410534 GTCGGAGCATCGTCACACTATCTATTCGTCATATTGGTAGTTTTGGTTAATGGTTATAAATGGCA
131 GTCGAAGCATCGTCACACTATCTATTCGTCATATTGGTAGTTTTGGTTAATGGTTATAAATGGCA
*
410599 TGTGATAGGGTTAAAAGGTTATTCAAGTGAATTGGCTTGTTTTGAGTTGTGTTAAGCTTATTGTG
196 TGTGATAGGGTTAAAAGGTTATTCAAGTGAATTGGCTTGTTTTGAGTTGTGTCAAGCTTATTGTG
410664 GTTAATGATGTGAAATGATAACATGTAAATAATATGAGCAAATATGAGTGGATGAACCCTTATGC
261 GTTAATGATGTGAAATGATAACATGTAAATAATATGAGCAAATATGAGTGGATGAACCCTTATGC
410729 ATACTCTATAGATAGTAGATATTAAATGGTATGATGGCAAGTTTTGAAAATGGTTATTTTGGCAT
326 ATACTCTATAGATAGTAGATATTAAATGGTATGATGGCAAGTTTTGAAAATGGTTATTTTGGCAT
410794 GGTTGATATAGGTTCTAAATAGAACTTTAAGATGTTGAATGGGACTAAGTTGGTATGTAAATTGT
391 GGTTGATATAGGTTCTAAATAGAACTTTAAGATGTTGAATGGGACTAAGTTGGTATGTAAATTGT
410859 GGTGCCTTTGAATGGTATATTGGTTAGATATAGGATGGATGAATGTTTGGCATGTTGTTGGTGTT
456 GGTGCCTTTGAATGGTATATTGGTTAGATATAGGATGGATGAATGTTTGGCATGTTGTTGGTGTT
410924 TTGAATGTGCTTTTGATCATATGAAATAGGCTAGGTATGATTTGATAATGAAGTGATTATATGAT
521 TTGAATGTGCTTTTGATCATATGAAATAGGCTAGGTATGATTTGATAATGAAGTGATTATATGAT
410989 GTGTGTGTGATATGTGTTTTTGGTCATGAA-TTATGATGTTAAAATTGATGTGTTTTAGGGGATT
586 GTGTGTGTGATATGTG-TTTTGGTCATGAACTTATGATGTTAAAATTGATGTGTTTTAGGGGATT
411053 TGAATGTGATTTAAGCATGTGAAAGTAGCTATAAAGGGTATGGCTTGGTGGTTAAGAAAGGGGAT
650 TGAATGTGATTTAAGCATGTGAAAGTAGCTATAAAGGGTATGGCTTGGTGGTTAAGAAAGGGGAT
411118 TTGAAATGGTTTGTTTTATAGGTAATTTGTGTTGCACATGACCTGGGACATGAGCTGTCACACGG
715 TTGAAATGGTTTGTTTTATAGGTAATTTGTGTTGCACATGACCTGGGACATGAGCTGTCACACGG
411183 CTATGTGCCACACATGGCCTGACCACAC
780 CTATGTGCCACACATGGCCTGACCACAC
411211 G
1 G
411212 ATCATGTGTC
Statistics
Matches: 800, Mismatches: 7, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
807 787 0.98
808 13 0.02
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.38
Consensus pattern (807 bp):
GTTTGGTTGTTTAATTTAATATGTTCGGTAAGTTTAAGTTTCCTTTATACGAGCTTAATAAGCAC
TAGTTGCTTATATATTTGTTTTCTTTGTTCGTAGATCATCGAAAAGCTCGATTGGTTGGAATCTT
GTCGAAGCATCGTCACACTATCTATTCGTCATATTGGTAGTTTTGGTTAATGGTTATAAATGGCA
TGTGATAGGGTTAAAAGGTTATTCAAGTGAATTGGCTTGTTTTGAGTTGTGTCAAGCTTATTGTG
GTTAATGATGTGAAATGATAACATGTAAATAATATGAGCAAATATGAGTGGATGAACCCTTATGC
ATACTCTATAGATAGTAGATATTAAATGGTATGATGGCAAGTTTTGAAAATGGTTATTTTGGCAT
GGTTGATATAGGTTCTAAATAGAACTTTAAGATGTTGAATGGGACTAAGTTGGTATGTAAATTGT
GGTGCCTTTGAATGGTATATTGGTTAGATATAGGATGGATGAATGTTTGGCATGTTGTTGGTGTT
TTGAATGTGCTTTTGATCATATGAAATAGGCTAGGTATGATTTGATAATGAAGTGATTATATGAT
GTGTGTGTGATATGTGTTTTGGTCATGAACTTATGATGTTAAAATTGATGTGTTTTAGGGGATTT
GAATGTGATTTAAGCATGTGAAAGTAGCTATAAAGGGTATGGCTTGGTGGTTAAGAAAGGGGATT
TGAAATGGTTTGTTTTATAGGTAATTTGTGTTGCACATGACCTGGGACATGAGCTGTCACACGGC
TATGTGCCACACATGGCCTGACCACAC
Found at i:411925 original size:26 final size:25
Alignment explanation
Indices: 411887--411937 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
411877 AATGTTTTTT
* *
411887 TTTTTGCAAAAATAATATTATATTA
1 TTTTTGAAAAAATAATATGATATTA
*
411912 TTTTTGAAAGAAATATTATGATATTA
1 TTTTTGAAA-AAATAATATGATATTA
411938 AACTATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (25 bp):
TTTTTGAAAAAATAATATGATATTA
Found at i:412983 original size:17 final size:18
Alignment explanation
Indices: 412953--412995 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
412943 TTAATTGAGA
*
412953 AATTAATTTAATTTGATT
1 AATTAAATTAATTTGATT
412971 AATTAAATT-ATTTGATT
1 AATTAAATTAATTTGATT
*
412988 AAATAAAT
1 AATTAAAT
412996 AATATTTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
AATTAAATTAATTTGATT
Found at i:413868 original size:21 final size:21
Alignment explanation
Indices: 413842--413883 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
413832 AACTTGAATC
413842 CGATGAAATTTCTAATAACTT
1 CGATGAAATTTCTAATAACTT
* *
413863 CGATGAAGTTTCTAGTAACTT
1 CGATGAAATTTCTAATAACTT
413884 TGACATGTAT
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:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (21 bp):
CGATGAAATTTCTAATAACTT
Found at i:417844 original size:24 final size:24
Alignment explanation
Indices: 417798--417845 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
417788 CCTGCAAACC
* *
417798 AAAATAAACCCAATTTTATAAATG
1 AAAATAAACCAAATTTGATAAATG
417822 AAAATAAAACCAAATTTGA-AAATG
1 AAAAT-AAACCAAATTTGATAAATG
417846 TCCATAGTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.58, C:0.10, G:0.06, T:0.25
Consensus pattern (24 bp):
AAAATAAACCAAATTTGATAAATG
Found at i:419078 original size:3 final size:3
Alignment explanation
Indices: 419063--419107 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
419053 AAACCATTTA
*
419063 ATT ATT TTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
419108 TATGTATTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:419239 original size:24 final size:24
Alignment explanation
Indices: 419212--419272 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
419202 GAAATCATAG
419212 TGTATTATTATTCTAAAA-TTATTA-
1 TGTATTATTATT-TAAAAGTTA-TAC
*
419236 TGTATTATTACTTAAAAGTTATAC
1 TGTATTATTATTTAAAAGTTATAC
*
419260 TATATTATTATTT
1 TGTATTATTATTT
419273 TTTCAATTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 7 0.22
24 25 0.78
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (24 bp):
TGTATTATTATTTAAAAGTTATAC
Found at i:423410 original size:38 final size:35
Alignment explanation
Indices: 423331--423415 Score: 134
Period size: 35 Copynumber: 2.4 Consensus size: 35
423321 GATTTTCTTC
*
423331 CAAATTATTATTCATTCATTCATAATTATATGGTA
1 CAAATTATTATTCATTCATTCATAATCATATGGTA
*
423366 CAAATTATTATTCATTCGTTCATAATCATATGGTA
1 CAAATTATTATTCATTCATTCATAATCATATGGTA
* *
423401 CAACTAATTATTCAT
1 CAAATTATTATTCAT
423416 GAATTTATAC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (35 bp):
CAAATTATTATTCATTCATTCATAATCATATGGTA
Found at i:424124 original size:27 final size:26
Alignment explanation
Indices: 424077--424127 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
424067 AAAAGGGAGC
** *
424077 AAAAGAAAAAAATCAAGATCAAAACA
1 AAAAGAAAAAAAGAAAAATCAAAACA
424103 AAAAGAAGAAAAAGAAAAATCAAAA
1 AAAAGAA-AAAAAGAAAAATCAAAA
424128 ATCAAGGTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.76, C:0.08, G:0.10, T:0.06
Consensus pattern (26 bp):
AAAAGAAAAAAAGAAAAATCAAAACA
Found at i:425049 original size:7 final size:7
Alignment explanation
Indices: 425037--425295 Score: 493
Period size: 7 Copynumber: 37.0 Consensus size: 7
425027 TTGGAGTCAA
425037 AAAAATG
1 AAAAATG
425044 AAAAATG
1 AAAAATG
425051 AAAAATG
1 AAAAATG
425058 AAAAATG
1 AAAAATG
425065 AAAAATG
1 AAAAATG
425072 AAAAATG
1 AAAAATG
425079 AAAAATG
1 AAAAATG
425086 AAAAATG
1 AAAAATG
425093 AAAAATG
1 AAAAATG
425100 AAAAATG
1 AAAAATG
425107 AAAAATG
1 AAAAATG
425114 AAAAATG
1 AAAAATG
425121 AAAAATG
1 AAAAATG
425128 AAAAATG
1 AAAAATG
425135 AAAAATG
1 AAAAATG
425142 AAAAATG
1 AAAAATG
425149 AAAAATG
1 AAAAATG
425156 AAAAATG
1 AAAAATG
425163 AAAAATG
1 AAAAATG
425170 AAAAATG
1 AAAAATG
425177 AAAAATG
1 AAAAATG
425184 AAAAATG
1 AAAAATG
425191 AAAAATG
1 AAAAATG
425198 AAAAATG
1 AAAAATG
425205 AAAAATG
1 AAAAATG
425212 AAAAATG
1 AAAAATG
425219 AAAAATG
1 AAAAATG
425226 AAAAATG
1 AAAAATG
425233 AAAAATG
1 AAAAATG
425240 AAAAATG
1 AAAAATG
425247 AAAAATG
1 AAAAATG
425254 AAAAATG
1 AAAAATG
425261 AAAAATG
1 AAAAATG
425268 -AAAATG
1 AAAAATG
425274 AAAAATG
1 AAAAATG
*
425281 AAAAAATA
1 -AAAAATG
425289 AAAAATG
1 AAAAATG
425296 GAGACGCTAA
Statistics
Matches: 248, Mismatches: 2, Indels: 4
0.98 0.01 0.02
Matches are distributed among these distances:
6 6 0.02
7 236 0.95
8 6 0.02
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:428228 original size:79 final size:79
Alignment explanation
Indices: 428092--428245 Score: 263
Period size: 79 Copynumber: 1.9 Consensus size: 79
428082 TTGCAGTAGA
* * *
428092 GCTGGTTAAAGATAGTAGATCTTGCCTTCCTGCGTTAAGAGCGAAGCAGATCCAAAACAAAGCCT
1 GCTGGTTAAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCCAAAACAAAGCCT
428157 TGCCTCCATCCACT
66 TGCCTCCATCCACT
* *
428171 GCTGGTTAAAGATGGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAACAAAGCCT
1 GCTGGTTAAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCCAAAACAAAGCCT
428236 TGCCTCCATC
66 TGCCTCCATC
428246 GGTTGCAGTG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 70 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (79 bp):
GCTGGTTAAAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCCAAAACAAAGCCT
TGCCTCCATCCACT
Found at i:428603 original size:139 final size:139
Alignment explanation
Indices: 428429--428984 Score: 925
Period size: 139 Copynumber: 4.0 Consensus size: 139
428419 AGTGTAAAGA
*
428429 AGCAGATTGAAGCCGGTAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAAAGGATCTTA
1 AGCAGATGGAAGCCGGTAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAAAGGATCTTA
428494 TCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGA
66 TCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGA
*
428559 TTACAGCAG
131 TTACAGCGG
** * *
428568 AGCAGATGGAAGCTAGTAATCCTATCTCCCTGAGATTATAGTGGAGCGGATTAAAATAAAGGATC
1 AGCAGATGGAAGCCGGTAATCCTATCTCCCTGAGATTACAGTGGAGTGGATT--AA-AAAGGATC
428633 TTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTG
63 TTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTG
428698 AGATTACAGCGG
128 AGATTACAGCGG
* * *
428710 AACAAATGGAAGCCGGTAATCCTATCTCCCTGATATTACAGTGGAGTGGATTAAAAAGGATCTTA
1 AGCAGATGGAAGCCGGTAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAAAGGATCTTA
* *
428775 TCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGATTGAAGCCAGAAATCTTATCTCCTTGAGA
66 TCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGA
428840 TTACAGCGG
131 TTACAGCGG
*
428849 AG-ATGATTGAAGCCGGTAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAAAGGATCTT
1 AGCA-GATGGAAGCCGGTAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAAAGGATCTT
* * * *
428913 ATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATGGAAGCTAGTAATCCTATCTCCCTGAG
65 ATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAG
428978 ATTACAG
130 ATTACAG
428985 TGAAGCGAAT
Statistics
Matches: 388, Mismatches: 25, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
138 1 0.00
139 254 0.65
140 2 0.01
141 2 0.01
142 129 0.33
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (139 bp):
AGCAGATGGAAGCCGGTAATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAAAGGATCTTA
TCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGA
TTACAGCGG
Found at i:428875 original size:44 final size:44
Alignment explanation
Indices: 428809--428894 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 44
428799 GATCGCACCA
* *
428809 GATTGAAGCCAGAAATCTTATCTCCTTGAGATTACAGCGGAGAT
1 GATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGAT
* * *
428853 GATTGAAGCCGGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 GATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAG
428895 TGGATTAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (44 bp):
GATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGAT
Found at i:428971 original size:95 final size:97
Alignment explanation
Indices: 428864--429046 Score: 298
Period size: 98 Copynumber: 1.9 Consensus size: 97
428854 ATTGAAGCCG
* * *
428864 GTAATCCTATCTCCCTGAGATTACAGTGGAGTGGATT-AA-AAAGGATCTTATCTCTCTGAAGTT
1 GTAATCCTATCTCCCTGAGATTACAGTGAAGCGAATTAAATAAAGGATCTTATCTCTCTGAAGTT
* *
428927 ACAGTAGAGTAGATCGCATCAGATGGAAGCTA
66 ACAATAGAATAGATCGCATCAGATGGAAGCTA
428959 GTAATCCTATCTCCCTGAGATTACAGTGAAGCGAATTAAAATAAAGGATCTTATCTCTCTGAAGT
1 GTAATCCTATCTCCCTGAGATTACAGTGAAGCGAATT-AAATAAAGGATCTTATCTCTCTGAAGT
429024 TACAATAGAATAGATCGCATCAG
65 TACAATAGAATAGATCGCATCAG
429047 GTCTTATCTC
Statistics
Matches: 80, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
95 34 0.43
97 2 0.03
98 44 0.55
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28
Consensus pattern (97 bp):
GTAATCCTATCTCCCTGAGATTACAGTGAAGCGAATTAAATAAAGGATCTTATCTCTCTGAAGTT
ACAATAGAATAGATCGCATCAGATGGAAGCTA
Found at i:429453 original size:24 final size:24
Alignment explanation
Indices: 429417--429464 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
429407 CCCGCAAACC
*
429417 AAAAT-AAACCCAATTTTATAAATG
1 AAAATAAAACCAAATTTTA-AAATG
429441 AAAATAAAACCAAATTTTAAAATG
1 AAAATAAAACCAAATTTTAAAATG
429465 TCCACAGTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.58, C:0.10, G:0.04, T:0.27
Consensus pattern (24 bp):
AAAATAAAACCAAATTTTAAAATG
Found at i:430684 original size:3 final size:3
Alignment explanation
Indices: 430678--430707 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
430668 AAACCATTTA
*
430678 ATT ATT ATT ATT AGT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
430708 TATGTACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:430842 original size:24 final size:24
Alignment explanation
Indices: 430812--430872 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
430802 GAAGTCATTG
430812 TGTATTATTATTCTAAAA-TTATTA-
1 TGTATTATTATT-TAAAAGTTA-TAC
*
430836 TGTATTATTACTTAAAAGTTATAC
1 TGTATTATTATTTAAAAGTTATAC
*
430860 TATATTATTATTT
1 TGTATTATTATTT
430873 TTTCATTTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 7 0.22
24 25 0.78
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (24 bp):
TGTATTATTATTTAAAAGTTATAC
Found at i:434285 original size:26 final size:24
Alignment explanation
Indices: 434217--434285 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 24
434207 GGACTCACCA
*
434217 CAGCTCGTATGAGCTTACCGTTTT
1 CAGCTCGAATGAGCTTACCGTTTT
*
434241 -AGCT-TAATAGAGCTTACCGTTTAT
1 CAGCTCGAAT-GAGCTTACCGTTT-T
434265 CAGCTCGAAATGAGCTTACCG
1 CAGCTCG-AATGAGCTTACCG
434286 ATCATGGCTC
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
22 2 0.05
23 17 0.46
24 1 0.03
25 4 0.11
26 10 0.27
27 3 0.08
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (24 bp):
CAGCTCGAATGAGCTTACCGTTTT
Found at i:437378 original size:26 final size:25
Alignment explanation
Indices: 437340--437390 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
437330 TAAAAATGTT
* *
437340 TTTTTGCAAAAATAATATTATATTA
1 TTTTTGAAAAAATAATATGATATTA
*
437365 TTTTTGAAAGAAATATTATGATATTA
1 TTTTTGAAA-AAATAATATGATATTA
437391 AACTATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (25 bp):
TTTTTGAAAAAATAATATGATATTA
Found at i:438429 original size:17 final size:18
Alignment explanation
Indices: 438399--438441 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
438389 TTAATTGAGA
*
438399 AATTAATTTAATTTGATT
1 AATTAAATTAATTTGATT
438417 AATTAAATT-ATTTGATT
1 AATTAAATTAATTTGATT
*
438434 AAATAAAT
1 AATTAAAT
438442 AATATTTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
AATTAAATTAATTTGATT
Found at i:443056 original size:2 final size:2
Alignment explanation
Indices: 443044--443077 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
443034 TTCACCTTCT
* *
443044 TA TA CA TA TA TA TA CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
443078 AGTGACGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:443059 original size:10 final size:10
Alignment explanation
Indices: 443044--443077 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
443034 TTCACCTTCT
443044 TATACATATA
1 TATACATATA
443054 TATACATATA
1 TATACATATA
*
443064 TATATATATA
1 TATACATATA
443074 TATA
1 TATA
443078 AGTGACGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (10 bp):
TATACATATA
Found at i:443971 original size:21 final size:22
Alignment explanation
Indices: 443934--443976 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
443924 TGGTTTGCTA
443934 CATTCGTGCAAAAAAACGCAAT
1 CATTCGTGCAAAAAAACGCAAT
*
443956 CATTCGTGC-CAAAAACGCAAT
1 CATTCGTGCAAAAAAACGCAAT
443977 AAATTTTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.42, C:0.26, G:0.14, T:0.19
Consensus pattern (22 bp):
CATTCGTGCAAAAAAACGCAAT
Found at i:444293 original size:19 final size:17
Alignment explanation
Indices: 444255--444294 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
444245 TTTTTTTCTA
*
444255 TATAAGTTTTCTAAATT
1 TATAAGTTTTCGAAATT
444272 TATAAGTTTTCGGAAATAT
1 TATAAGTTTTC-GAAAT-T
444291 TATA
1 TATA
444295 TCATAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 11 0.55
18 4 0.20
19 5 0.25
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (17 bp):
TATAAGTTTTCGAAATT
Found at i:444485 original size:17 final size:17
Alignment explanation
Indices: 444465--444557 Score: 67
Period size: 17 Copynumber: 5.9 Consensus size: 17
444455 TTATTTTCTA
444465 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
444482 TATAAGTTTTCT-AA--
1 TATAAGTTTTCTAAATT
*
444496 -ATAATTTTTCTAAATT
1 TATAAGTTTTCTAAATT
* * **
444512 TATTAG-TATAAAAATT
1 TATAAGTTTTCTAAATT
*
444528 TAGT-AG-TAT-TAAATT
1 TA-TAAGTTTTCTAAATT
444543 TATAAGTTTTCTAAA
1 TATAAGTTTTCTAAA
444558 AAAGTGTTCT
Statistics
Matches: 60, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
13 10 0.17
14 3 0.05
15 9 0.15
16 18 0.30
17 20 0.33
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.49
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:444492 original size:30 final size:30
Alignment explanation
Indices: 444458--444575 Score: 96
Period size: 30 Copynumber: 3.9 Consensus size: 30
444448 TATTGTTTTA
*
444458 TTTTCTATATAAGTTTTCTAAATTTATAAG
1 TTTTCTAAATAAGTTTTCTAAATTTATAAG
* *
444488 TTTTCTAAATAATTTTTCTAAATTTATTAG
1 TTTTCTAAATAAGTTTTCTAAATTTATAAG
* ** * *
444518 -TATAAAAATTTAGTAGTAT-TAAATTTATAAG
1 TTTTCTAAA-TAAGT--TTTCTAAATTTATAAG
* * *
444549 TTTTCTAAAAAAGTGTTCTAGATTTAT
1 TTTTCTAAATAAGTTTTCTAAATTTAT
444576 TATTAATAAA
Statistics
Matches: 65, Mismatches: 18, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
29 6 0.09
30 38 0.58
31 14 0.22
32 7 0.11
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (30 bp):
TTTTCTAAATAAGTTTTCTAAATTTATAAG
Found at i:444508 original size:13 final size:13
Alignment explanation
Indices: 444458--444510 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
444448 TATTGTTTTA
*
444458 TTTTCTATATAAG
1 TTTTCTAAATAAG
444471 TTTTCTAAATTTATAAG
1 TTTTCT-AA---ATAAG
*
444488 TTTTCTAAATAAT
1 TTTTCTAAATAAG
444501 TTTTCTAAAT
1 TTTTCTAAAT
444511 TTATTAGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
13 20 0.59
14 1 0.03
16 2 0.06
17 11 0.32
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.55
Consensus pattern (13 bp):
TTTTCTAAATAAG
Found at i:444543 original size:15 final size:16
Alignment explanation
Indices: 444506--444544 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
444496 ATAATTTTTC
*
444506 TAAATTTATTAGTATA
1 TAAATTTAGTAGTATA
*
444522 AAAATTTAGTAGTAT-
1 TAAATTTAGTAGTATA
444537 TAAATTTA
1 TAAATTTA
444545 TAAGTTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (16 bp):
TAAATTTAGTAGTATA
Found at i:444543 original size:61 final size:61
Alignment explanation
Indices: 444476--444623 Score: 174
Period size: 61 Copynumber: 2.4 Consensus size: 61
444466 ATAAGTTTTC
*
444476 TAAATTTATAAGTTTTCTAAATAATTTTTCTAAATTTATTAGT-ATAAAAATTTAGT-AGTAT
1 TAAATTTATAAGTTTTCTAAATAATTGTTCTAAATTTATTAGTAAT-AAAATTTA-TAAGTAT
* * * *
444537 TAAATTTATAAGTTTTCTAAAAAAGTGTTCTAGATTTATTATTAATAAAATTTATAAGTAT
1 TAAATTTATAAGTTTTCTAAATAATTGTTCTAAATTTATTAGTAATAAAATTTATAAGTAT
* * * * *
444598 CAATTTTACACGTTTTGTAAATAATT
1 TAAATTTATAAGTTTTCTAAATAATT
444624 ATATATATTT
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
60 1 0.01
61 70 0.96
62 2 0.03
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (61 bp):
TAAATTTATAAGTTTTCTAAATAATTGTTCTAAATTTATTAGTAATAAAATTTATAAGTAT
Found at i:445129 original size:8 final size:7
Alignment explanation
Indices: 445108--445144 Score: 56
Period size: 8 Copynumber: 5.0 Consensus size: 7
445098 CATAATAAAT
445108 TACATAA
1 TACATAA
445115 TACATAA
1 TACATAA
445122 TAACATAA
1 T-ACATAA
445130 TAACATAA
1 T-ACATAA
445138 TACATAA
1 TACATAA
445145 CTTATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 14 0.48
8 15 0.52
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (7 bp):
TACATAA
Found at i:445129 original size:15 final size:15
Alignment explanation
Indices: 445097--445144 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
445087 ATATATAACA
445097 ACATAATAA-AT--T
1 ACATAATAACATAAT
445109 ACATAAT-ACATAAT
1 ACATAATAACATAAT
445123 AACATAATAACATAAT
1 -ACATAATAACATAAT
445139 ACATAA
1 ACATAA
445145 CTTATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.03
12 9 0.29
14 1 0.03
15 13 0.42
16 7 0.23
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.27
Consensus pattern (15 bp):
ACATAATAACATAAT
Found at i:445166 original size:21 final size:21
Alignment explanation
Indices: 445140--445190 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
445130 TAACATAATA
* *
445140 CATAACTTATAT-ATAAGCTTG
1 CATAACTTACATAATAA-CTTC
445161 CATAACTTACATAATAACTTC
1 CATAACTTACATAATAACTTC
445182 CATAACTTA
1 CATAACTTA
445191 ATACACCACT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35
Consensus pattern (21 bp):
CATAACTTACATAATAACTTC
Found at i:445281 original size:9 final size:9
Alignment explanation
Indices: 445236--445462 Score: 134
Period size: 9 Copynumber: 25.2 Consensus size: 9
445226 CTCGTTATAA
445236 ACATAACTT
1 ACATAACTT
*
445245 GCATAACTT
1 ACATAACTT
*
445254 ACGTAATAACATA
1 AC---ATAAC-TT
445267 ACATAACTT
1 ACATAACTT
445276 ACATAA--T
1 ACATAACTT
*
445283 ACAAAAAACTT
1 AC--ATAACTT
445294 ACATAACTT
1 ACATAACTT
* * *
445303 AAATATCTA
1 ACATAACTT
*
445312 ACACAACTT
1 ACATAACTT
*
445321 ACATAACCT
1 ACATAACTT
445330 ACATAA--T
1 ACATAACTT
445337 ACATTTAACTT
1 ACA--TAACTT
445348 ACATAACTT
1 ACATAACTT
*
445357 ACATAATACAT
1 ACAT-A-ACTT
445368 A-ATAACTT
1 ACATAACTT
445376 AC--AACTT
1 ACATAACTT
*
445383 ACATAACAT
1 ACATAACTT
*
445392 ACATTACTT
1 ACATAACTT
**
445401 TTATAACTT
1 ACATAACTT
445410 ACATAA--T
1 ACATAACTT
*
445417 ACACAACTT
1 ACATAACTT
445426 ACATAACTT
1 ACATAACTT
*
445435 --ATACACGT
1 ACATA-ACTT
445443 ACATAACTT
1 ACATAACTT
*
445452 ACATAATTT
1 ACATAACTT
445461 AC
1 AC
445463 TTAATACATA
Statistics
Matches: 166, Mismatches: 30, Indels: 44
0.69 0.12 0.18
Matches are distributed among these distances:
7 23 0.14
8 7 0.04
9 106 0.64
10 11 0.07
11 11 0.07
12 5 0.03
13 3 0.02
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.31
Consensus pattern (9 bp):
ACATAACTT
Found at i:445346 original size:27 final size:26
Alignment explanation
Indices: 445267--445471 Score: 161
Period size: 27 Copynumber: 7.8 Consensus size: 26
445257 TAATAACATA
**
445267 ACATAACTTACATAATACAAAAAACTT
1 ACATAACTTACATAATAC-ATTAACTT
* * *
445294 ACATAACTTAAATATCTAACA-CAACTT
1 ACATAACTTACATA-AT-ACATTAACTT
*
445321 ACATAACCTACATAATACATTTAACTT
1 ACATAACTTACATAATACA-TTAACTT
445348 ACATAACTTACATAATACATAATAACTT
1 ACATAACTTACATAATACAT--TAACTT
445376 AC--AACTTACATAACATACATT-ACTT
1 ACATAACTTACAT-A-ATACATTAACTT
** *
445401 TTATAACTTACATAATACA-CAACTT
1 ACATAACTTACATAATACATTAACTT
* * *
445426 ACATAACTTATACACGTACA-TAACTT
1 ACATAACTTACATA-ATACATTAACTT
* *
445452 ACATAATTTACTTAATACAT
1 ACATAACTTACATAATACAT
445472 AGATATATAT
Statistics
Matches: 143, Mismatches: 22, Indels: 27
0.74 0.11 0.14
Matches are distributed among these distances:
25 30 0.21
26 32 0.22
27 63 0.44
28 16 0.11
29 2 0.01
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.32
Consensus pattern (26 bp):
ACATAACTTACATAATACATTAACTT
Found at i:445429 original size:34 final size:34
Alignment explanation
Indices: 445369--445434 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
445359 ATAATACATA
* * *
445369 ATAACTTACAACTTACATAACATACATTACTTTT
1 ATAACTTACAACATACACAACATACATAACTTTT
*
445403 ATAACTTACATA-ATACACAACTTACATAACTT
1 ATAACTTACA-ACATACACAACATACATAACTT
445435 ATACACGTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 26 0.96
35 1 0.04
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (34 bp):
ATAACTTACAACATACACAACATACATAACTTTT
Found at i:445429 original size:62 final size:60
Alignment explanation
Indices: 445314--445456 Score: 141
Period size: 62 Copynumber: 2.4 Consensus size: 60
445304 AATATCTAAC
* *
445314 ACAACTTACATAACCTACATAATACATTTAACTTACATAACTTACATAATACATAATAACTT
1 ACAACTTACATAACATACAT-ATACATTTAACTTACATAAC-TACACAATACATAATAACTT
* *
445376 ACAACTTACATAACATACAT-TACTTTTATAACTTACATAA-TACAC-A-ACTTACATAACTT
1 ACAACTTACATAACATACATATAC-ATT-TAACTTACATAACTACACAATACATA-ATAACTT
* * *
445435 ATACACGTACATAACTTACATA
1 ACA-ACTTACATAACATACATA
445457 ATTTACTTAA
Statistics
Matches: 69, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
58 4 0.06
59 10 0.14
60 22 0.32
61 2 0.03
62 31 0.45
ACGTcount: A:0.45, C:0.22, G:0.01, T:0.32
Consensus pattern (60 bp):
ACAACTTACATAACATACATATACATTTAACTTACATAACTACACAATACATAATAACTT
Done.