Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold415
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: 1242643
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 8 of 8
Found at i:1197890 original size:2 final size:2
Alignment explanation
Indices: 1197883--1197926 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
1197873 TATACTTTGT
*
1197883 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1197924 TA T
1 TA T
1197927 GATGACTTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1201070 original size:15 final size:15
Alignment explanation
Indices: 1201050--1201094 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 15
1201040 ATTTTTTTAC
1201050 GAATTTAAATATTAT
1 GAATTTAAATATTAT
1201065 GAATTTAAATAATTTAT
1 GAATTTAAAT-A-TTAT
*
1201082 AAATTTAAATATT
1 GAATTTAAATATT
1201095 GAATATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 12 0.44
16 2 0.07
17 13 0.48
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (15 bp):
GAATTTAAATATTAT
Found at i:1201416 original size:18 final size:17
Alignment explanation
Indices: 1201393--1201445 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
1201383 GTCCAAACAT
1201393 AATTTTTTATTTTATTTA
1 AATTTTTTATTTT-TTTA
*
1201411 AA--TTTTATTTTTTAA
1 AATTTTTTATTTTTTTA
*
1201426 AATTTTTATATATTTTTA
1 AATTTTT-TATTTTTTTA
1201444 AA
1 AA
1201446 AAAATAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 5 0.17
16 9 0.31
17 3 0.10
18 12 0.41
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
AATTTTTTATTTTTTTA
Found at i:1201430 original size:15 final size:16
Alignment explanation
Indices: 1201397--1201431 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1201387 AAACATAATT
*
1201397 TTTTATTTTATTTAAA
1 TTTTATTTTATTAAAA
1201413 TTTTATTTT-TTAAAA
1 TTTTATTTTATTAAAA
1201428 TTTT
1 TTTT
1201432 TATATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTATTTTATTAAAA
Found at i:1201432 original size:16 final size:17
Alignment explanation
Indices: 1201396--1201434 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1201386 CAAACATAAT
*
1201396 TTTTTATTTTATTTAAA
1 TTTTTATTTTATTAAAA
1201413 -TTTTATTTT-TTAAAA
1 TTTTTATTTTATTAAAA
1201428 TTTTTAT
1 TTTTTAT
1201435 ATATTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTATTTTATTAAAA
Found at i:1201583 original size:7 final size:7
Alignment explanation
Indices: 1201573--1201606 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
1201563 ATATATAAAA
1201573 TATTTTT
1 TATTTTT
1201580 TA--TTT
1 TATTTTT
1201585 TATTTTT
1 TATTTTT
1201592 TATTTTT
1 TATTTTT
1201599 TATTTTT
1 TATTTTT
1201606 T
1 T
1201607 CAAACTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
7 20 0.80
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TATTTTT
Found at i:1201604 original size:12 final size:12
Alignment explanation
Indices: 1201573--1201597 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1201563 ATATATAAAA
1201573 TATTTTTTATTT
1 TATTTTTTATTT
1201585 TATTTTTTATTT
1 TATTTTTTATTT
1201597 T
1 T
1201598 TTATTTTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TATTTTTTATTT
Found at i:1201760 original size:20 final size:22
Alignment explanation
Indices: 1201733--1201788 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 22
1201723 GGGCCCAAAC
1201733 ATAAATTTTTTATTTTTA-TTT
1 ATAAATTTTTTATTTTTATTTT
*
1201754 A-AAATTTTATA-TTTTATTTT
1 ATAAATTTTTTATTTTTATTTT
*
1201774 ATTAATTTTTTATTT
1 ATAAATTTTTTATTT
1201789 AAAAGCTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 5 0.17
20 13 0.45
21 9 0.31
22 2 0.07
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
ATAAATTTTTTATTTTTATTTT
Found at i:1203391 original size:3 final size:3
Alignment explanation
Indices: 1203383--1203431 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1203373 CATTTTTGTG
1203383 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1203431 T
1 T
1203432 ATACGTGTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1203647 original size:3 final size:3
Alignment explanation
Indices: 1203641--1203674 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
1203631 TAATATTATT
*
1203641 ATA ATA ATA ATA A-A TTA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1203675 TGTTAGTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 1 0.04
3 27 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1204052 original size:21 final size:21
Alignment explanation
Indices: 1204008--1204052 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1203998 TATAAATTAT
* *
1204008 TTTTATATTAATATTTATATA
1 TTTTATATTAATATTTAAAAA
1204029 TTTTATAATTAA-ATTTAAAAA
1 TTTTAT-ATTAATATTTAAAAA
1204050 TTT
1 TTT
1204053 ATTCAATGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTTATATTAATATTTAAAAA
Found at i:1204715 original size:16 final size:14
Alignment explanation
Indices: 1204696--1204732 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 14
1204686 TAATCGAAAC
1204696 TTAAAATAATTTAAAT
1 TTAAAATAATTT--AT
1204712 TTAAAATAATTTAT
1 TTAAAATAATTTAT
1204726 TTAAAAT
1 TTAAAAT
1204733 CATAATATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 9 0.43
16 12 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TTAAAATAATTTAT
Found at i:1205289 original size:21 final size:24
Alignment explanation
Indices: 1205242--1205290 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 24
1205232 AAAAACCTAT
*
1205242 TTTACTATTATTTTAATCTTAATA
1 TTTACTATTATTTTAATATTAATA
*
1205266 TTTA-TATT-TTTTACTATTAA-A
1 TTTACTATTATTTTAATATTAATA
1205287 TTTA
1 TTTA
1205291 AATAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 5 0.22
22 10 0.43
23 4 0.17
24 4 0.17
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTACTATTATTTTAATATTAATA
Found at i:1211995 original size:28 final size:28
Alignment explanation
Indices: 1211950--1212047 Score: 164
Period size: 27 Copynumber: 3.6 Consensus size: 28
1211940 ATATAATAAC
1211950 AAAAAATATATTA-TTTTTAATTTTTTT
1 AAAAAATATATTATTTTTTAATTTTTTT
1211977 AAAAAATATATTATTTTTTAATTTTTTT
1 AAAAAATATATTATTTTTTAATTTTTTT
1212005 AAAAAATATATTATTTTTT-ATTTTTTT
1 AAAAAATATATTATTTTTTAATTTTTTT
* *
1212032 AACAAATATATAATTT
1 AAAAAATATATTATTT
1212048 AAATTTACTT
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
27 35 0.51
28 33 0.49
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (28 bp):
AAAAAATATATTATTTTTTAATTTTTTT
Found at i:1212066 original size:30 final size:27
Alignment explanation
Indices: 1211953--1212066 Score: 88
Period size: 27 Copynumber: 4.1 Consensus size: 27
1211943 TAATAACAAA
* * *
1211953 AAATATATTATTTTTAATTTTTTTAAA-
1 AAATATATAATTTTTTA-CTTTTTAAAC
* *
1211980 AAATATATTATTTTTTAATTTTTTTAAA-
1 AAATATATAATTTTTT-A-CTTTTTAAAC
* * *
1212008 AAATATATTATTTTTTATTTTTTTAAC
1 AAATATATAATTTTTTACTTTTTAAAC
1212035 AAATATATAATTTAAATTTACTTTTTAAAC
1 AAATATATAATTT---TTTACTTTTTAAAC
1212065 AA
1 AA
1212067 CTTTTTAAAT
Statistics
Matches: 77, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
26 8 0.10
27 28 0.36
28 27 0.35
30 14 0.18
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (27 bp):
AAATATATAATTTTTTACTTTTTAAAC
Found at i:1213541 original size:20 final size:19
Alignment explanation
Indices: 1213497--1213545 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
1213487 TCTCCCCTTT
**
1213497 CTTTTCCTTTTTCTCTCTT
1 CTTTTCCTTTTTCTCTCCC
*
1213516 CATTTCCTTTTTCTTCTCCC
1 CTTTTCCTTTTTC-TCTCCC
1213536 CTTTTCCTTT
1 CTTTTCCTTT
1213546 CTTTAGCCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (19 bp):
CTTTTCCTTTTTCTCTCCC
Found at i:1214294 original size:16 final size:17
Alignment explanation
Indices: 1214265--1214301 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
1214255 AAAATTTTTC
1214265 AATCATTTTCAAATTCA
1 AATCATTTTCAAATTCA
*
1214282 AATCATTTT-AAATTTA
1 AATCATTTTCAAATTCA
1214298 AATC
1 AATC
1214302 GATCAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (17 bp):
AATCATTTTCAAATTCA
Found at i:1214449 original size:22 final size:26
Alignment explanation
Indices: 1214414--1214464 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 26
1214404 ATTATTTTAA
1214414 ATTCAAATTAATTTT-AATT-A-ATT
1 ATTCAAATTAATTTTGAATTCATATT
*
1214437 ATTC-AATTCATTTTGAATTCATATT
1 ATTCAAATTAATTTTGAATTCATATT
1214462 ATT
1 ATT
1214465 TTAAATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 9 0.38
23 8 0.33
24 1 0.04
25 6 0.25
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (26 bp):
ATTCAAATTAATTTTGAATTCATATT
Found at i:1214465 original size:16 final size:16
Alignment explanation
Indices: 1214437--1214507 Score: 63
Period size: 16 Copynumber: 4.4 Consensus size: 16
1214427 TTAATTAATT
*
1214437 ATTCAATTCATTTTGA
1 ATTCAATTCATTTTAA
1214453 ATTCATATT-ATTTTAA
1 ATTCA-ATTCATTTTAA
* *
1214469 ATTTAAATCATTTTAA
1 ATTCAATTCATTTTAA
* * *
1214485 ATTTAAATAATTTTCAA
1 ATTCAATTCATTTT-AA
1214502 ATTCAA
1 ATTCAA
1214508 CTTAATCGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
15 2 0.04
16 35 0.74
17 10 0.21
ACGTcount: A:0.41, C:0.08, G:0.01, T:0.49
Consensus pattern (16 bp):
ATTCAATTCATTTTAA
Found at i:1218403 original size:13 final size:13
Alignment explanation
Indices: 1218387--1218417 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1218377 TTATTCATAT
*
1218387 ATATTAAATATAA
1 ATATTAAATAAAA
1218400 ATATTAAATAAAA
1 ATATTAAATAAAA
1218413 ATATT
1 ATATT
1218418 TTTAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATTAAATAAAA
Found at i:1218504 original size:7 final size:7
Alignment explanation
Indices: 1218492--1218519 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1218482 TTGTCGATAA
1218492 ATTTAAT
1 ATTTAAT
1218499 ATTTAAT
1 ATTTAAT
1218506 ATTTAAT
1 ATTTAAT
1218513 ATTTAAT
1 ATTTAAT
1218520 TATGCCTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTTAAT
Found at i:1220923 original size:22 final size:23
Alignment explanation
Indices: 1220898--1220940 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1220888 ATAATTTTAT
* *
1220898 TTAAAAGATAATAT-TTAATAAA
1 TTAAAAAATAAAATCTTAATAAA
1220920 TTAAAAAATAAAATCTTAATA
1 TTAAAAAATAAAATCTTAATA
1220941 TCTGTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
TTAAAAAATAAAATCTTAATAAA
Found at i:1225042 original size:11 final size:11
Alignment explanation
Indices: 1225026--1225058 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1225016 TATTTAAAAA
*
1225026 ATTTGTTCATT
1 ATTTGTGCATT
1225037 ATTTGTGCATT
1 ATTTGTGCATT
1225048 ATTTGTGCATT
1 ATTTGTGCATT
1225059 TTTATATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.18, C:0.09, G:0.15, T:0.58
Consensus pattern (11 bp):
ATTTGTGCATT
Found at i:1226798 original size:22 final size:23
Alignment explanation
Indices: 1226768--1226833 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 23
1226758 ATAATATGCT
*
1226768 ATTATTTTTTAAAAGAT-TTAAA-
1 ATTAATTTTTAAAA-ATATTAAAG
*
1226790 ATTAA-TTTTACAAATATTAAAG
1 ATTAATTTTTAAAAATATTAAAG
*
1226812 ATTAATTTTATAAAAAAATTAA
1 ATTAATTTT-TAAAAATATTAA
1226834 CAGAGAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 2 0.06
21 12 0.33
22 9 0.25
23 3 0.08
24 10 0.28
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (23 bp):
ATTAATTTTTAAAAATATTAAAG
Found at i:1227048 original size:2 final size:2
Alignment explanation
Indices: 1227041--1227076 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1227031 AAATTTTGTG
1227041 TA TA TA TA TA TA TA TA TA 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 TA
1227077 AAACTTATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1227561 original size:2 final size:2
Alignment explanation
Indices: 1227554--1227580 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1227544 ATTCAACTAC
1227554 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1227581 ACGATGATAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1227704 original size:16 final size:17
Alignment explanation
Indices: 1227683--1227716 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1227673 ATTTAATTTA
1227683 TTAATAC-CAACTTAAT
1 TTAATACTCAACTTAAT
*
1227699 TTAATACTCAAGTTAAT
1 TTAATACTCAACTTAAT
1227716 T
1 T
1227717 GAAAAATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (17 bp):
TTAATACTCAACTTAAT
Found at i:1227927 original size:2 final size:2
Alignment explanation
Indices: 1227920--1227947 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1227910 AGGAAAATAA
1227920 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1227948 TTACTTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1231104 original size:2 final size:2
Alignment explanation
Indices: 1231097--1231121 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1231087 TATGTATAAG
1231097 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1231122 GTTGATGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1231201 original size:18 final size:18
Alignment explanation
Indices: 1231180--1231215 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1231170 AACAAATCCA
1231180 TTATGTTCTAAATTATTT
1 TTATGTTCTAAATTATTT
1231198 TTATGTTCTAAATTATTT
1 TTATGTTCTAAATTATTT
1231216 GAAATTACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (18 bp):
TTATGTTCTAAATTATTT
Found at i:1234652 original size:18 final size:18
Alignment explanation
Indices: 1234629--1234663 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1234619 ATAAATTATT
*
1234629 TTTATTTTCTTTTACATA
1 TTTATTGTCTTTTACATA
*
1234647 TTTATTGTGTTTTACAT
1 TTTATTGTCTTTTACAT
1234664 TTATTTGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.09, G:0.06, T:0.66
Consensus pattern (18 bp):
TTTATTGTCTTTTACATA
Found at i:1236640 original size:15 final size:15
Alignment explanation
Indices: 1236616--1236649 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1236606 TTTTGTTAGA
* *
1236616 TTTTACTTTTTTTAT
1 TTTTAATTTTTTAAT
1236631 TTTTAATTTTTTAAT
1 TTTTAATTTTTTAAT
1236646 TTTT
1 TTTT
1236650 CTAGTTCTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTAATTTTTTAAT
Found at i:1237688 original size:23 final size:23
Alignment explanation
Indices: 1237662--1237710 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1237652 TTATTCAAAA
* *
1237662 TAATATTAAAAATATATTTATAT
1 TAATATTAAAAATAAATTTAAAT
* *
1237685 TAATATTATAATTAAATTTAAAT
1 TAATATTAAAAATAAATTTAAAT
1237708 TAA
1 TAA
1237711 AAATATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TAATATTAAAAATAAATTTAAAT
Found at i:1238563 original size:23 final size:22
Alignment explanation
Indices: 1238537--1238580 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1238527 ATAATTTTTT
1238537 ATTTAAAATTATTAAAAATTAAC
1 ATTTAAAATTA-TAAAAATTAAC
** *
1238560 ATTTTTAATTATGAAAATTAA
1 ATTTAAAATTATAAAAATTAA
1238581 AAATTTAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
ATTTAAAATTATAAAAATTAAC
Found at i:1238615 original size:152 final size:154
Alignment explanation
Indices: 1238308--1238618 Score: 522
Period size: 152 Copynumber: 2.0 Consensus size: 154
1238298 AAATTTAGGG
1238308 TTTGATTCATGAAACCCACTTTGAAGAAATAATTAAAGTAGATGGTGATCTTATATATATAAATA
1 TTTGATTCATGAAACCCACTTTGAAGAAATAATTAAAGTAGATGGTGATCTTATATATATAAATA
*
1238373 TATAGTTTTTTTAGTTAAAATTATTAAAAATTAAATTTTTTAATCATTGAAATTAAAAATTTAAT
66 TATAGATTTTTTAGTTAAAATTATTAAAAATTAAATTTTTTAATCATTGAAATTAAAAATTTAAT
*
1238438 ATATTATTAATAAATCATACAACT
131 ATATTATTAATAAATCAGACAACT
*
1238462 TTTG-TTCATGAAACCCATTTTGAAGAAATAATTAAAGTAGATGGTGATCTTATATATATAAATA
1 TTTGATTCATGAAACCCACTTTGAAGAAATAATTAAAGTAGATGGTGATCTTATATATATAAATA
* *
1238526 TATA-ATTTTTTATTTAAAATTATTAAAAATTAACA-TTTTTAATTA-TGAAAATTAAAAATTTA
66 TATAGATTTTTTAGTTAAAATTATTAAAAATTAA-ATTTTTTAATCATTG-AAATTAAAAATTTA
*
1238588 ATATTTTATTAATAAATCAGACAACT
129 ATATATTATTAATAAATCAGACAACT
1238614 TTTGA
1 TTTGA
1238619 CATTTTTATT
Statistics
Matches: 148, Mismatches: 6, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
151 2 0.01
152 78 0.53
153 64 0.43
154 4 0.03
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (154 bp):
TTTGATTCATGAAACCCACTTTGAAGAAATAATTAAAGTAGATGGTGATCTTATATATATAAATA
TATAGATTTTTTAGTTAAAATTATTAAAAATTAAATTTTTTAATCATTGAAATTAAAAATTTAAT
ATATTATTAATAAATCAGACAACT
Found at i:1239166 original size:10 final size:10
Alignment explanation
Indices: 1239151--1239197 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
1239141 CAACTACATG
* *
1239151 ATATATCTAT
1 ATATATATAC
1239161 ATATATATAC
1 ATATATATAC
*
1239171 ATATACATAC
1 ATATATATAC
*
1239181 ATATATATAT
1 ATATATATAC
1239191 ATATATA
1 ATATATA
1239198 GATAACGATG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATATATAC
Found at i:1239167 original size:4 final size:4
Alignment explanation
Indices: 1239151--1239197 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
1239141 CAACTACATG
* * * *
1239151 ATAT ATCT ATAT ATAT ATAC ATAT ACAT ACAT ATAT ATAT ATAT ATA
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATA
1239198 GATAACGATG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (4 bp):
ATAT
Found at i:1239167 original size:6 final size:6
Alignment explanation
Indices: 1239151--1239197 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
1239141 CAACTACATG
* * * *
1239151 ATATAT CTATAT ATATAT ACATAT ACATAC ATATAT ATATAT ATATA
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATA
1239198 GATAACGATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (6 bp):
ATATAT
Found at i:1239758 original size:15 final size:16
Alignment explanation
Indices: 1239733--1239763 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1239723 AAATTTCTCC
1239733 CCTTCCATTATATTTT
1 CCTTCCATTATATTTT
1239749 CCTT-CATTATATTTT
1 CCTTCCATTATATTTT
1239764 ATTTACTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (16 bp):
CCTTCCATTATATTTT
Found at i:1241402 original size:2 final size:2
Alignment explanation
Indices: 1241395--1241444 Score: 59
Period size: 2 Copynumber: 24.5 Consensus size: 2
1241385 TGAATACGAG
1241395 TA TA TA TA TA TA TA TA -A CTGA TA T- TA TA TGA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -T-A TA TA TA TA T-A TA TA TA TA TA
1241436 TA TA TA TA T
1 TA TA TA TA T
1241445 GGTATTGTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
1 2 0.05
2 37 0.86
3 3 0.07
4 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Done.