Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold89
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: 5168001
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 33045 characters in sequence are not A, C, G, or T
File 9 of 27
Found at i:1221312 original size:6 final size:6
Alignment explanation
Indices: 1221301--1221333 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1221291 GTATATTCTG
*
1221301 ATTGTA ATTGTA ATTGTA AATGTA ATTGTA ATT
1 ATTGTA ATTGTA ATTGTA ATTGTA ATTGTA ATT
1221334 CTGACTCTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.48
Consensus pattern (6 bp):
ATTGTA
Found at i:1221494 original size:2 final size:2
Alignment explanation
Indices: 1221487--1221528 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1221477 TATGAAGAAA
1221487 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1221529 GGAGTTGGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1221928 original size:2 final size:2
Alignment explanation
Indices: 1221877--1221908 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1221867 TTTCATTTCA
1221877 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
1221909 AATCCCTCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1221934 original size:10 final size:10
Alignment explanation
Indices: 1221880--1221934 Score: 65
Period size: 10 Copynumber: 5.5 Consensus size: 10
1221870 CATTTCATCT
*
1221880 CTCTCTCTCT
1 CTCTCTCTCA
*
1221890 CTCTCTCTCT
1 CTCTCTCTCA
1221900 CTCTCTCTCA
1 CTCTCTCTCA
* *
1221910 ATCCCTCTCA
1 CTCTCTCTCA
*
1221920 GTCTCTCTCA
1 CTCTCTCTCA
1221930 CTCTC
1 CTCTC
1221935 ATAATTCTCT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 39 1.00
ACGTcount: A:0.07, C:0.49, G:0.02, T:0.42
Consensus pattern (10 bp):
CTCTCTCTCA
Found at i:1222396 original size:3 final size:3
Alignment explanation
Indices: 1222388--1222413 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1222378 CTCTTTTTTC
1222388 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1222414 GTTGTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1229938 original size:22 final size:21
Alignment explanation
Indices: 1229908--1229948 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1229898 TAAAAAATTA
* *
1229908 TTTATTTATTTAATATAATATT
1 TTTAATTATTAAATA-AATATT
1229930 TTTAATTATTAAATAAATA
1 TTTAATTATTAAATAAATA
1229949 ATAAAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTAATTATTAAATAAATATT
Found at i:1229988 original size:22 final size:21
Alignment explanation
Indices: 1229937--1229988 Score: 52
Period size: 24 Copynumber: 2.4 Consensus size: 21
1229927 ATTTTTAATT
*
1229937 ATTAAA-TAAATAATAAAAAT
1 ATTAAATTAAATAATAAAAAC
*
1229957 ATTTTTAATTAATATAATAAAAAC
1 A--TTAAATTAA-ATAATAAAAAC
1229981 ATTAAATT
1 ATTAAATT
1229989 GATTTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
20 1 0.04
22 10 0.40
23 3 0.12
24 11 0.44
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
ATTAAATTAAATAATAAAAAC
Found at i:1234152 original size:26 final size:26
Alignment explanation
Indices: 1234109--1234164 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
1234099 ATAGAAATAC
1234109 GATTGATAACGTTCAACTTTATCTAA
1 GATTGATAACGTTCAACTTTATCTAA
* *
1234135 GATTGATAATGTTTAACTTTATCTAA
1 GATTGATAACGTTCAACTTTATCTAA
1234161 GATT
1 GATT
1234165 TTAAAGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.43
Consensus pattern (26 bp):
GATTGATAACGTTCAACTTTATCTAA
Found at i:1238294 original size:23 final size:23
Alignment explanation
Indices: 1238268--1238314 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1238258 TAGCACTTAG
*
1238268 AAAGAATAAAACTATAAATAGTT
1 AAAGAAAAAAACTATAAATAGTT
*
1238291 AAAGAAAAAAATTATAAATAGTT
1 AAAGAAAAAAACTATAAATAGTT
1238314 A
1 A
1238315 CATTTCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.26
Consensus pattern (23 bp):
AAAGAAAAAAACTATAAATAGTT
Found at i:1239788 original size:18 final size:19
Alignment explanation
Indices: 1239767--1239802 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1239757 TTATCTATTA
1239767 AATAT-TAAAAATATTTTT
1 AATATGTAAAAATATTTTT
*
1239785 AATATGTAAAATTATTTT
1 AATATGTAAAAATATTTT
1239803 AATGTAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
AATATGTAAAAATATTTTT
Found at i:1245498 original size:2 final size:2
Alignment explanation
Indices: 1245491--1245523 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1245481 TAAAGTGCAA
1245491 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1245524 CTATAAAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1250206 original size:21 final size:22
Alignment explanation
Indices: 1250167--1250213 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
1250157 ATAATTTTTT
*
1250167 AAATTTAATTTAATCTAATCTA
1 AAATTTAATTAAATCTAATCTA
* *
1250189 AAATTTAA-TAAATTTAATTTA
1 AAATTTAATTAAATCTAATCTA
1250210 AAAT
1 AAAT
1250214 AATTTAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (22 bp):
AAATTTAATTAAATCTAATCTA
Found at i:1250219 original size:15 final size:15
Alignment explanation
Indices: 1250190--1250237 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
1250180 TCTAATCTAA
*
1250190 AATTTAATA-AATTT
1 AATTTAAAATAATTT
1250204 AATTTAAAATAATTT
1 AATTTAAAATAATTT
1250219 AAATTT-AAATAATCTT
1 -AATTTAAAATAAT-TT
1250235 AAT
1 AAT
1250238 AACCTTGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 8 0.27
15 15 0.50
16 7 0.23
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATTTAAAATAATTT
Found at i:1250223 original size:16 final size:16
Alignment explanation
Indices: 1250189--1250293 Score: 60
Period size: 16 Copynumber: 6.6 Consensus size: 16
1250179 ATCTAATCTA
*
1250189 AAATTTAATA-AATTT
1 AAATTTAAAATAATTT
1250204 -AATTTAAAATAATTT
1 AAATTTAAAATAATTT
1250219 AAATTT-AAATAATCTT
1 AAATTTAAAATAAT-TT
* * *
1250235 AATAACCTT-GAATTATTGT
1 -A-AA-TTTAAAATAATT-T
*
1250254 -AATTTAAAATAATATA
1 AAATTTAAAATAAT-TT
*
1250270 AAATTT-AAATTATTT
1 AAATTTAAAATAATTT
1250285 AAATTTAAA
1 AAATTTAAA
1250294 TTGATTCAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 21
0.69 0.10 0.21
Matches are distributed among these distances:
14 8 0.12
15 21 0.30
16 22 0.32
17 7 0.10
18 3 0.04
19 8 0.12
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (16 bp):
AAATTTAAAATAATTT
Found at i:1250237 original size:31 final size:31
Alignment explanation
Indices: 1250166--1250226 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
1250156 AATAATTTTT
**
1250166 TAAATTTAATTTAATCTAATCTAAAATTTAA
1 TAAATTTAATTTAAAATAATCTAAAATTTAA
*
1250197 TAAATTTAATTTAAAATAAT-TTAAATTTAA
1 TAAATTTAATTTAAAATAATCTAAAATTTAA
1250227 ATAATCTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (31 bp):
TAAATTTAATTTAAAATAATCTAAAATTTAA
Found at i:1255504 original size:2 final size:2
Alignment explanation
Indices: 1255492--1255526 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1255482 TTCACAACTG
* *
1255492 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1255527 GGTGCTGCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1258593 original size:23 final size:22
Alignment explanation
Indices: 1258562--1258607 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
1258552 TCTCAAATCA
1258562 AAATACTCAA-CAAAATTTCAAT
1 AAATACTCAATC-AAATTTCAAT
*
1258584 AAATAACTCAATCAAGTTTCAAT
1 AAAT-ACTCAATCAAATTTCAAT
1258607 A
1 A
1258608 TCAATTATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
23 16 0.76
24 1 0.05
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.28
Consensus pattern (22 bp):
AAATACTCAATCAAATTTCAAT
Found at i:1258657 original size:2 final size:2
Alignment explanation
Indices: 1258650--1258680 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1258640 GTTTAACATA
1258650 AT AT 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 AT AT A
1258681 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1269665 original size:21 final size:22
Alignment explanation
Indices: 1269624--1269666 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1269614 CTTTTTTTTT
*
1269624 AATAAAAAAATCATAATTTAAA
1 AATAAAAAAATCATAAATTAAA
*
1269646 AATAAAAAAAT-TTAAATTAAA
1 AATAAAAAAATCATAAATTAAA
1269667 TTAAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (22 bp):
AATAAAAAAATCATAAATTAAA
Found at i:1271202 original size:17 final size:17
Alignment explanation
Indices: 1271180--1271212 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1271170 GATTATATTA
1271180 GTTTTTTATATTAATAC
1 GTTTTTTATATTAATAC
*
1271197 GTTTTTTATTTTAATA
1 GTTTTTTATATTAATA
1271213 AGATATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (17 bp):
GTTTTTTATATTAATAC
Found at i:1271272 original size:20 final size:18
Alignment explanation
Indices: 1271223--1271288 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 18
1271213 AGATATATAT
1271223 TATATAAATATAATTTTA
1 TATATAAATATAATTTTA
* *
1271241 T-TTTATAGTATATATATTTA
1 TATATA-AATATA-AT-TTTA
1271261 TATATAAATATAAATTTTTA
1 TATATAAATAT-AA-TTTTA
*
1271281 AATATAAA
1 TATATAAA
1271289 AAATAAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
17 3 0.08
18 6 0.16
19 2 0.05
20 21 0.57
21 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TATATAAATATAATTTTA
Found at i:1272173 original size:24 final size:24
Alignment explanation
Indices: 1272116--1272175 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
1272106 ATTAAAATTT
**
1272116 TATAATATAAATTATTTTTTAAAA
1 TATAATATAAATTATTTAATAAAA
1272140 TATTAA-ATAAATTATTATAATAAAA
1 TA-TAATATAAATTATT-TAATAAAA
1272165 -ATAATATAAAT
1 TATAATATAAAT
1272176 ATATAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
23 3 0.10
24 19 0.61
25 9 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TATAATATAAATTATTTAATAAAA
Found at i:1274356 original size:42 final size:42
Alignment explanation
Indices: 1274270--1274394 Score: 205
Period size: 42 Copynumber: 2.9 Consensus size: 42
1274260 TCCCATATTA
*
1274270 AGCCTAGAGTCTTCTAGTGATTATAAGCTCTTGACGGATCGTC
1 AGCCTAGGGTCTTCTAGTGATTATAAG-TCTTGACGGATCGTC
* *
1274313 AGCCTAGGGTCTACTAGTGATTAAAAGTCTTGACGGATCGTC
1 AGCCTAGGGTCTTCTAGTGATTATAAGTCTTGACGGATCGTC
1274355 AGCCTAGGGTCTTCTAGTGATTATAAGTCCTTGACGGATC
1 AGCCTAGGGTCTTCTAGTGATTATAAGT-CTTGACGGATC
1274395 TCTCCATCTA
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
42 41 0.54
43 35 0.46
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (42 bp):
AGCCTAGGGTCTTCTAGTGATTATAAGTCTTGACGGATCGTC
Found at i:1278470 original size:21 final size:20
Alignment explanation
Indices: 1278447--1278486 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1278437 TAATAATTAT
*
1278447 TTTTTAAAATTAAAAAAATA
1 TTTTAAAAATTAAAAAAATA
*
1278467 TTTTAAAAATTTAAAAAATA
1 TTTTAAAAATTAAAAAAATA
1278487 AAAAATCATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TTTTAAAAATTAAAAAAATA
Found at i:1278566 original size:26 final size:26
Alignment explanation
Indices: 1278510--1278565 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
1278500 AACATTCATC
*
1278510 TTTTAAAATTATATATTTAAAAAATA
1 TTTTAAAATTATATATTAAAAAAATA
*
1278536 TTTTAATATTAT-TAATTAAAAATAATA
1 TTTTAAAATTATAT-ATTAAAAA-AATA
1278563 TTT
1 TTT
1278566 ATTTCTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 1 0.04
26 18 0.69
27 7 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTTAAAATTATATATTAAAAAAATA
Found at i:1281189 original size:5 final size:5
Alignment explanation
Indices: 1281160--1281230 Score: 58
Period size: 5 Copynumber: 14.2 Consensus size: 5
1281150 AATTTCAAAA
* * *
1281160 ATAAT ATAAT -T-AT ATAAC ATAAAT ATAAT ATAAA ATAAT -TAAA ATACGAT
1 ATAAT ATAAT ATAAT ATAAT AT-AAT ATAAT ATAAT ATAAT ATAAT ATA--AT
*
1281210 ATAAT ATAAT ATAAT AAAAT A
1 ATAAT ATAAT ATAAT ATAAT A
1281231 AACATTATAT
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
3 2 0.04
4 5 0.09
5 38 0.72
6 4 0.08
7 4 0.08
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (5 bp):
ATAAT
Found at i:1281204 original size:21 final size:21
Alignment explanation
Indices: 1281180--1281219 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1281170 TATATAACAT
*
1281180 AAATATAATATAAAATAATTA
1 AAATACAATATAAAATAATTA
* *
1281201 AAATACGATATAATATAAT
1 AAATACAATATAAAATAAT
1281220 ATAATAAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (21 bp):
AAATACAATATAAAATAATTA
Found at i:1281297 original size:10 final size:10
Alignment explanation
Indices: 1281246--1281303 Score: 53
Period size: 11 Copynumber: 5.4 Consensus size: 10
1281236 TATATAAAAA
1281246 TAAAACTATAT
1 TAAAA-TATAT
*
1281257 TAAAATTTAT
1 TAAAATATAT
* *
1281267 GTAAATTAAAT
1 -TAAAATATAT
1281278 TAATAATATAT
1 TAA-AATATAT
1281289 TAAAATATAT
1 TAAAATATAT
1281299 ATAAA
1 -TAAA
1281304 TATTTAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
10 14 0.37
11 24 0.63
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (10 bp):
TAAAATATAT
Found at i:1281350 original size:11 final size:11
Alignment explanation
Indices: 1281326--1281361 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
1281316 TAAATTTAAT
1281326 TATAATA-AAA
1 TATAATATAAA
1281336 -ATAATATAAA
1 TATAATATAAA
1281346 TATAATATAAA
1 TATAATATAAA
1281357 TATAA
1 TATAA
1281362 AAAAATTACG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 6 0.25
10 3 0.12
11 15 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TATAATATAAA
Found at i:1281358 original size:26 final size:26
Alignment explanation
Indices: 1281156--1281363 Score: 82
Period size: 26 Copynumber: 8.2 Consensus size: 26
1281146 TGACAATTTC
1281156 AAAAATAATAT-AAT-T-ATATAACAT
1 AAAAATAATATAAATATAATATAA-AT
*
1281180 AAATATAATATAAA-ATAAT-TAAAAT
1 AAAAATAATATAAATATAATAT-AAAT
* *
1281205 ACGATATAATAT-AATATAATA-AAAT
1 A-AAAATAATATAAATATAATATAAAT
* * * * *
1281230 AAACATTATATAAAAATAAAACTATATT
1 AAAAATAATATAAATATAATA-TA-AAT
* * * *
1281258 AAAATTTATGTAAAT-TAA-ATTAAT
1 AAAAATAATATAAATATAATATAAAT
* *
1281282 -AATATATTA-AAATAT-ATATAAAT
1 AAAAATAATATAAATATAATATAAAT
** * * *
1281305 ATTTAATATTTTAAATTTAAT-TATAAT
1 A-AAAATAATATAAATATAATATA-AAT
1281332 AAAAATAATATAAATATAATATAAAT
1 AAAAATAATATAAATATAATATAAAT
1281358 ATAAAA
1 A-AAAA
1281364 AAATTACGTA
Statistics
Matches: 134, Mismatches: 30, Indels: 37
0.67 0.15 0.18
Matches are distributed among these distances:
22 5 0.04
23 10 0.07
24 19 0.14
25 27 0.20
26 44 0.33
27 16 0.12
28 13 0.10
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.37
Consensus pattern (26 bp):
AAAAATAATATAAATATAATATAAAT
Found at i:1281653 original size:20 final size:18
Alignment explanation
Indices: 1281625--1281670 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 18
1281615 TCATATATAT
1281625 ATATATATAATTTATTTATAA
1 ATATATAT-A-TTATTT-TAA
1281646 ATTATATATATTATTTTAA
1 A-TATATATATTATTTTAA
1281665 ATATAT
1 ATATAT
1281671 TTATCAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 5 0.21
19 4 0.17
20 6 0.25
21 2 0.08
22 7 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATATATATTATTTTAA
Found at i:1282110 original size:23 final size:25
Alignment explanation
Indices: 1282064--1282116 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 25
1282054 AACGTGAATT
**
1282064 TAATTAATTTATAATTATTTTTTAA
1 TAATTAATTTATAATTATAATTTAA
*
1282089 -AATT-ATTTTTAATTATAATTTAA
1 TAATTAATTTATAATTATAATTTAA
1282112 TAATT
1 TAATT
1282117 TTATATATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TAATTAATTTATAATTATAATTTAA
Found at i:1282401 original size:21 final size:20
Alignment explanation
Indices: 1282371--1282425 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
1282361 AATATATAAT
1282371 AAAT-ATAATTATATTATTA
1 AAATAATAATTATATTATTA
*
1282390 AATTTAATAATTA-ATTTATTA
1 AA-ATAATAATTATA-TTATTA
*
1282411 AAATATTAATTATAT
1 AAATAATAATTATAT
1282426 AAAAAATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 2 0.07
20 11 0.38
21 16 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATAATAATTATATTATTA
Found at i:1298203 original size:2 final size:2
Alignment explanation
Indices: 1298196--1298249 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1298186 GCATGAACAC
1298196 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1298238 AG AG AG AG AG AG
1 AG AG AG AG AG AG
1298250 GTCTATAACT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1300880 original size:24 final size:24
Alignment explanation
Indices: 1300802--1300881 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 24
1300792 AGGTGCAGAA
*
1300802 GATGCTCCAAAAGCA-GA-AG-TT
1 GATGCTCCAAAAGCAGGAGTGCTT
* **
1300823 GAAGCTCCAAAAGCAGGAGTGCCA
1 GATGCTCCAAAAGCAGGAGTGCTT
*
1300847 GATG-TACCAAAAGCAGGTGTGCTT
1 GATGCT-CCAAAAGCAGGAGTGCTT
1300871 GATGCTCCAAA
1 GATGCTCCAAA
1300882 TGTGCCTCCT
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
21 14 0.30
22 2 0.04
23 2 0.04
24 27 0.59
25 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.26, T:0.17
Consensus pattern (24 bp):
GATGCTCCAAAAGCAGGAGTGCTT
Found at i:1300991 original size:24 final size:24
Alignment explanation
Indices: 1300964--1301148 Score: 178
Period size: 24 Copynumber: 7.7 Consensus size: 24
1300954 TCCAGTTGAG
* *
1300964 CCAAAGGCAGGTGTGCTCGTGGCA
1 CCAAAGGCAGGGGTGCTTGTGGCA
* *
1300988 CCAAAGGCAGCGGTGCTAGTGGCA
1 CCAAAGGCAGGGGTGCTTGTGGCA
* ** *
1301012 CCAAACGCAGCAGTAG-TTGTAGCA
1 CCAAAGGCAGGGGT-GCTTGTGGCA
* *
1301036 CCGAAA-GCTGGGGTGCTAGTGGCA
1 CC-AAAGGCAGGGGTGCTTGTGGCA
* *
1301060 CCAAATGCAGGGGTTG-TTGTTGCA
1 CCAAAGGCAGGGG-TGCTTGTGGCA
* * *
1301084 CCAAAAGCTGGGGTGGTTGTGGCA
1 CCAAAGGCAGGGGTGCTTGTGGCA
*
1301108 CCAAATGCAGGGGTGCTTGTGGCA
1 CCAAAGGCAGGGGTGCTTGTGGCA
1301132 CCAAAGGCAGGGGTGCT
1 CCAAAGGCAGGGGTGCT
1301149 GGAACCAAAT
Statistics
Matches: 133, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
23 6 0.05
24 121 0.91
25 6 0.05
ACGTcount: A:0.23, C:0.22, G:0.37, T:0.18
Consensus pattern (24 bp):
CCAAAGGCAGGGGTGCTTGTGGCA
Found at i:1301058 original size:72 final size:72
Alignment explanation
Indices: 1300964--1301148 Score: 203
Period size: 72 Copynumber: 2.6 Consensus size: 72
1300954 TCCAGTTGAG
* * * * *
1300964 CCAAAGGCAGGTGTGCTCGTGGCACCAAAGGCAGCGGTGCTAGTGGCACCAAACGCAGCAGTAGT
1 CCAAATGCAGGGGTGCTAGTGGCACCAAAGGCAGGGGTGCTAGTGGCACCAAAAGCAGCAGTAGT
1301029 TGTAGCA
66 TGTAGCA
* * * * * ** *
1301036 CCGAAA-GCTGGGGTGCTAGTGGCACCAAATGCAGGGGTTG-TTGTTGCACCAAAAGCTGGGGTG
1 CC-AAATGCAGGGGTGCTAGTGGCACCAAAGGCAGGGG-TGCTAGTGGCACCAAAAGCAGCAGTA
*
1301099 GTTGTGGCA
64 GTTGTAGCA
*
1301108 CCAAATGCAGGGGTGCTTGTGGCACCAAAGGCAGGGGTGCT
1 CCAAATGCAGGGGTGCTAGTGGCACCAAAGGCAGGGGTGCT
1301149 GGAACCAAAT
Statistics
Matches: 93, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
71 5 0.05
72 83 0.89
73 5 0.05
ACGTcount: A:0.23, C:0.22, G:0.37, T:0.18
Consensus pattern (72 bp):
CCAAATGCAGGGGTGCTAGTGGCACCAAAGGCAGGGGTGCTAGTGGCACCAAAAGCAGCAGTAGT
TGTAGCA
Found at i:1301157 original size:21 final size:22
Alignment explanation
Indices: 1301045--1301162 Score: 69
Period size: 24 Copynumber: 5.0 Consensus size: 22
1301035 ACCGAAAGCT
*
1301045 GGGGTGCTAGTGGCACCAAATGCA
1 GGGGTGCT--TGGAACCAAATGCA
* * *
1301069 GGGGTTG-TTGTTGCACCAAAAGCT
1 GGGG-TGCTTG--GAACCAAATGCA
* *
1301093 GGGGTGGTTGTGGCACCAAATGCA
1 GGGGT-GCT-TGGAACCAAATGCA
* *
1301117 GGGGTGCTTGTGGCACCAAAGGCA
1 GGGGTGC-T-TGGAACCAAATGCA
1301141 GGGGTGC-TGGAACCAAATGCA
1 GGGGTGCTTGGAACCAAATGCA
1301162 G
1 G
1301163 ACTGAGTTGA
Statistics
Matches: 79, Mismatches: 8, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
21 13 0.16
22 2 0.03
23 2 0.03
24 57 0.72
25 3 0.04
26 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.39, T:0.19
Consensus pattern (22 bp):
GGGGTGCTTGGAACCAAATGCA
Found at i:1301797 original size:2 final size:2
Alignment explanation
Indices: 1301790--1301825 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1301780 GATAGAAAAT
1301790 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
1301826 GAAATACTGA
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:1303329 original size:2 final size:2
Alignment explanation
Indices: 1303322--1303346 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1303312 AGGGTTTGTA
1303322 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1303347 ACAAGGGAGA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1304426 original size:16 final size:16
Alignment explanation
Indices: 1304405--1304436 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1304395 TTTATAAAAC
1304405 TATTTTTAATTTAATT
1 TATTTTTAATTTAATT
*
1304421 TATTTTTGATTTAATT
1 TATTTTTAATTTAATT
1304437 GTTTTCTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (16 bp):
TATTTTTAATTTAATT
Found at i:1305994 original size:18 final size:19
Alignment explanation
Indices: 1305961--1305996 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1305951 ATTAAATGAA
*
1305961 TATTTATATTTTTATAAAT
1 TATTTATATATTTATAAAT
1305980 TATTTA-ATATTTATAAA
1 TATTTATATATTTATAAA
1305997 ATTAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTTATATATTTATAAAT
Found at i:1306004 original size:20 final size:19
Alignment explanation
Indices: 1305961--1306000 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1305951 ATTAAATGAA
*
1305961 TATTTATATTTTTATAAAT
1 TATTTATATTTATATAAAT
1305980 TATTTAATATTTATA-AAAT
1 TATTT-ATATTTATATAAAT
1305999 TA
1 TA
1306001 ATTTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTATATTTATATAAAT
Found at i:1306080 original size:141 final size:140
Alignment explanation
Indices: 1305825--1306090 Score: 308
Period size: 141 Copynumber: 1.9 Consensus size: 140
1305815 ATGTTGATAA
* * * *
1305825 ATATTCTTGTAAATTATTTAATTTTTATAAAATTAATTGAAATTATAATATTATAATTGTTTATT
1 ATATTCTTATAAATTATTTAATATTTATAAAATTAATTGAAATTATAATATTATAAATGTTTAAT
* * * * *
1305890 TTTGTATTAATTTATAAGGAGAAAAAATATAATACAAAAAGAAATAAAAATACAAAATTAAATTA
66 TATGTATTAATTTATAAGAAGAAAAAATATAAAAAAAAAAGAAA-AAAAAAACAAAATTAAATTA
1305955 AATGAATATTT
130 AATGAATATTT
* **
1305966 ATATTTTTATAAATTATTTAATATTTATAAAATTAATTTTAATTATAATA-TA-AAAT-TTTAAT
1 ATATTCTTATAAATTATTTAATATTTATAAAATTAATTGAAATTATAATATTATAAATGTTTAAT
* * *
1306028 TATGT-TTTATTTATCAAGAAGATAAAATGGA-AAAAAAAGAAAGAAACAAAAAAATAAAATTAA
66 TATGTATTAATTTAT-AAGAAGAAAAAAT--ATAAAAAAA-AAAGAAA-AAAAAAACAAAATTAA
1306091 TTTATACAAA
Statistics
Matches: 105, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
137 8 0.08
138 20 0.19
139 8 0.08
140 24 0.23
141 45 0.43
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (140 bp):
ATATTCTTATAAATTATTTAATATTTATAAAATTAATTGAAATTATAATATTATAAATGTTTAAT
TATGTATTAATTTATAAGAAGAAAAAATATAAAAAAAAAAGAAAAAAAAAACAAAATTAAATTAA
ATGAATATTT
Found at i:1306220 original size:19 final size:20
Alignment explanation
Indices: 1306196--1306236 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1306186 CTTATTTGTT
1306196 TATAAAAAAT-AAAAGAAAA
1 TATAAAAAATAAAAAGAAAA
**
1306215 TATAAAATTTAAAAAGAAAA
1 TATAAAAAATAAAAAGAAAA
1306235 TA
1 TA
1306237 AAGGACTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (20 bp):
TATAAAAAATAAAAAGAAAA
Found at i:1307224 original size:21 final size:20
Alignment explanation
Indices: 1307192--1307232 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
1307182 GCCCTAAGGT
*
1307192 TTAAAAAGAAAAGATAAAGA
1 TTAAAAAGAAAAGAAAAAGA
1307212 TTAAAAAGAAAAAGAAAAAGA
1 TTAAAAAG-AAAAGAAAAAGA
1307233 GGTGATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (20 bp):
TTAAAAAGAAAAGAAAAAGA
Found at i:1309389 original size:3 final size:3
Alignment explanation
Indices: 1309371--1309413 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
1309361 ATAGATATCT
1309371 TTA TTA TT- TT- TCTA TTA TTA TTA TTA TTA TTA TTA TATA TTA T
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA T-TA TTA T
1309414 CTATCTAGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 3 0.08
3 30 0.81
4 4 0.11
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1310252 original size:21 final size:22
Alignment explanation
Indices: 1310222--1310262 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1310212 TACTGCCGAG
1310222 GATGCAGCTCGAG-CTTACGAC
1 GATGCAGCTCGAGCCTTACGAC
* *
1310243 GATGCTGCTCGGGCCTTACG
1 GATGCAGCTCGAGCCTTACG
1310263 TGGAGCTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.17, C:0.29, G:0.32, T:0.22
Consensus pattern (22 bp):
GATGCAGCTCGAGCCTTACGAC
Found at i:1312343 original size:18 final size:17
Alignment explanation
Indices: 1312303--1312343 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
1312293 TTATAGCTTT
*
1312303 TTAAAAATTTTTAAATA
1 TTAAAAATTTTTAAAAA
1312320 TATAAAAATATTTTAAAAA
1 T-TAAAAAT-TTTTAAAAA
1312339 TTAAA
1 TTAAA
1312344 TATACAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 11 0.52
19 9 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAAAATTTTTAAAAA
Found at i:1313468 original size:19 final size:19
Alignment explanation
Indices: 1313441--1313500 Score: 50
Period size: 19 Copynumber: 3.0 Consensus size: 19
1313431 ATTAAATCAG
*
1313441 TTTAATTAAGAATCAAAAA
1 TTTATTTAAGAATCAAAAA
*
1313460 TTTATTTAATG-ATAAAAAA
1 TTTATTTAA-GAATCAAAAA
*
1313479 TTATCATTTAATAACTCAAAAA
1 TT-T-ATTTAAGAA-TCAAAAA
1313501 AGTCAATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
19 17 0.53
20 2 0.06
21 7 0.22
22 6 0.19
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (19 bp):
TTTATTTAAGAATCAAAAA
Found at i:1314007 original size:23 final size:22
Alignment explanation
Indices: 1313980--1314024 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1313970 ACATGAACTT
1313980 TCATC-ATGATAATTGATAGATAA
1 TCATCAAT-ATAATT-ATAGATAA
1314003 TCATCTAATATAATTATAGATA
1 TCATC-AATATAATTATAGATA
1314025 TTACTTAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 12 0.60
24 6 0.30
25 2 0.10
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (22 bp):
TCATCAATATAATTATAGATAA
Found at i:1315502 original size:2 final size:2
Alignment explanation
Indices: 1315489--1315519 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1315479 CATACTCTTT
*
1315489 AG AG AT AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1315520 TAACAGAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.45, T:0.03
Consensus pattern (2 bp):
AG
Found at i:1318172 original size:8 final size:8
Alignment explanation
Indices: 1318159--1318239 Score: 53
Period size: 8 Copynumber: 10.4 Consensus size: 8
1318149 TAAAATATAT
1318159 TATATAAA
1 TATATAAA
1318167 TATATAAA
1 TATATAAA
*
1318175 TATATCAA
1 TATATAAA
* *
1318183 CAT-TACA
1 TATATAAA
*
1318190 TATATATA
1 TATATAAA
**
1318198 TATATATT
1 TATATAAA
1318206 TATATACAA
1 TATATA-AA
1318215 -ATATAAA
1 TATATAAA
*
1318222 T-TTTAAA
1 TATATAAA
1318229 -ATTATAAA
1 TA-TATAAA
1318237 TAT
1 TAT
1318240 TTAATATCAA
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
7 11 0.20
8 44 0.79
9 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (8 bp):
TATATAAA
Found at i:1318178 original size:51 final size:50
Alignment explanation
Indices: 1318083--1318178 Score: 122
Period size: 51 Copynumber: 1.9 Consensus size: 50
1318073 TACCATGATA
* * * * *
1318083 TTTTAAAAATCTTTTTGTAAGTGTATATATATATATATATATATAATGTT
1 TTTTAAAAATCTTTTAGTAAATATATATATAAATATATAAATATAATGTT
1318133 TTTTAAAAATC-TTTAGTAAAATATATTATATAAATATATAAATATA
1 TTTTAAAAATCTTTTAGT-AAATATA-TATATAAATATATAAATATA
1318179 TCAACATTAC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
49 5 0.13
50 16 0.41
51 18 0.46
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (50 bp):
TTTTAAAAATCTTTTAGTAAATATATATATAAATATATAAATATAATGTT
Found at i:1318391 original size:22 final size:23
Alignment explanation
Indices: 1318366--1318419 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
1318356 TAAATGTAAT
* *
1318366 TATAAAAAAAT-TAACTTAAAAA
1 TATAAAAAAATGAAAATTAAAAA
* *
1318388 TATAAATAAGTGAAAATTAAAAA
1 TATAAAAAAATGAAAATTAAAAA
1318411 -ATAAAAAAA
1 TATAAAAAAA
1318420 ATTTATATAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (23 bp):
TATAAAAAAATGAAAATTAAAAA
Found at i:1318810 original size:31 final size:30
Alignment explanation
Indices: 1318767--1318825 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
1318757 TTTAAATTAT
*
1318767 TTATTGTTTTT-AAATAATAAATAATTTTCA
1 TTATTATTTTTAAAATAA-AAATAATTTTCA
*
1318797 TTATTATTATTTAAAATAAATATAATTTT
1 TTATTATT-TTTAAAATAAAAATAATTTT
1318826 TATAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.28
31 12 0.48
32 6 0.24
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (30 bp):
TTATTATTTTTAAAATAAAAATAATTTTCA
Found at i:1318881 original size:42 final size:44
Alignment explanation
Indices: 1318808--1318901 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 44
1318798 TATTATTATT
1318808 TAAA-ATAAATATAATTTTTATAATTTAATTTTTATT-CTAAATA
1 TAAATATAAATATAATTTTTATAATTTAA-TTTTATTGCTAAATA
* *
1318851 TAAATATAAATATAATTTTTAT-ATTT-ATTTTATTGTTTAATA
1 TAAATATAAATATAATTTTTATAATTTAATTTTATTGCTAAATA
1318893 TAAATATAA
1 TAAATATAA
1318902 TTTTAATAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
41 7 0.15
42 15 0.32
43 8 0.17
44 17 0.36
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (44 bp):
TAAATATAAATATAATTTTTATAATTTAATTTTATTGCTAAATA
Found at i:1318925 original size:42 final size:40
Alignment explanation
Indices: 1318789--1318926 Score: 108
Period size: 42 Copynumber: 3.4 Consensus size: 40
1318779 AATAATAAAT
* *
1318789 AATTTTCATTA-TTATTATTTAAAATAAATATAATTTT-TA
1 AATTTTAATTATTTATT-TTTAATATAAATATAATTTTATA
* * *
1318828 TAA-TTTAATT-TTTATTCTAAATATAAATATAA--ATATA
1 -AATTTTAATTATTTATTTTTAATATAAATATAATTTTATA
*
1318865 ATTTTTATATTTATTTTATTGTTTAATATAAATATAATTTTAATA
1 AATTTTA-A-TTA-TTTATT-TTTAATATAAATATAATTTT-ATA
*
1318910 AATTTTGATTATTTATT
1 AATTTTAATTATTTATT
1318927 AATTTTATAA
Statistics
Matches: 76, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
36 2 0.03
37 6 0.08
38 14 0.18
39 13 0.17
40 2 0.03
41 6 0.08
42 20 0.26
43 3 0.04
44 2 0.03
45 8 0.11
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (40 bp):
AATTTTAATTATTTATTTTTAATATAAATATAATTTTATA
Found at i:1319520 original size:35 final size:33
Alignment explanation
Indices: 1319471--1319537 Score: 116
Period size: 35 Copynumber: 2.0 Consensus size: 33
1319461 TATATGTTAT
1319471 TATTAAATTTTATTATATTTATTATTTATTCAG
1 TATTAAATTTTATTATATTTATTATTTATTCAG
1319504 TATTAAAATATTTATTATATTTATTATTTATTCA
1 TATT-AAAT-TTTATTATATTTATTATTTATTCA
1319538 ATCAAATCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 4 0.12
34 4 0.12
35 24 0.75
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (33 bp):
TATTAAATTTTATTATATTTATTATTTATTCAG
Found at i:1322249 original size:23 final size:24
Alignment explanation
Indices: 1322221--1322267 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1322211 TTTTTATTTT
1322221 AAAATAAA-ATTTAAAAA-GAAATA
1 AAAATAAATA-TTAAAAATGAAATA
*
1322244 AAAATAGATATTAAAAATGAAATA
1 AAAATAAATATTAAAAATGAAATA
1322268 TGAAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.23
Consensus pattern (24 bp):
AAAATAAATATTAAAAATGAAATA
Found at i:1322464 original size:21 final size:21
Alignment explanation
Indices: 1322440--1322479 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1322430 ATTTTTAAAT
*
1322440 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TAAAAAATATA
1322461 TAAATATTAATAAAAAATA
1 TAAATATTAATAAAAAATA
1322480 ATTTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATATTAATAAAAAATATA
Found at i:1322653 original size:14 final size:14
Alignment explanation
Indices: 1322631--1322673 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
1322621 CTCTCTTTTT
*
1322631 AATTTATTTTTTAA
1 AATTAATTTTTTAA
* *
1322645 AATTAATTTAATAAA
1 AATTAATTT-TTTAA
1322660 AATTAATTTTTTAA
1 AATTAATTTTTTAA
1322674 TTTTTAATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATTAATTTTTTAA
Found at i:1325129 original size:3 final size:3
Alignment explanation
Indices: 1325121--1325151 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1325111 TATCGTCATT
1325121 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1325152 TAAGTTAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1325557 original size:5 final size:5
Alignment explanation
Indices: 1325524--1325553 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1325514 AAAAAATGGT
*
1325524 CCATC CCATC CCATC CCATC CCATC TCATC
1 CCATC CCATC CCATC CCATC CCATC CCATC
1325554 TCATAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.20, C:0.57, G:0.00, T:0.23
Consensus pattern (5 bp):
CCATC
Found at i:1326030 original size:15 final size:16
Alignment explanation
Indices: 1326010--1326041 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1326000 TGGGTTAAGA
1326010 TTTTATTTATTA-TTT
1 TTTTATTTATTACTTT
1326025 TTTTATTTATTACTTT
1 TTTTATTTATTACTTT
1326041 T
1 T
1326042 CAATACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTATTTATTACTTT
Found at i:1326108 original size:20 final size:20
Alignment explanation
Indices: 1326070--1326108 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1326060 TACTTATATA
* *
1326070 TATAAAATTCATCTGTGAAT
1 TATAAAAATCATATGTGAAT
*
1326090 TATAAAAATCATATTTGAA
1 TATAAAAATCATATGTGAA
1326109 GATGATGAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (20 bp):
TATAAAAATCATATGTGAAT
Found at i:1326826 original size:26 final size:25
Alignment explanation
Indices: 1326775--1326826 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
1326765 TAATAATTAA
**
1326775 ATTTAAATAAAAATAAAATTTTATT
1 ATTTAAATAAAAATAAAATTAAATT
* *
1326800 ATTTAAATATTAAATTAAATTAAATT
1 ATTTAAATA-AAAATAAAATTAAATT
1326826 A
1 A
1326827 AATTATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
ATTTAAATAAAAATAAAATTAAATT
Found at i:1326832 original size:31 final size:31
Alignment explanation
Indices: 1326771--1326832 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
1326761 TTTATAATAA
**
1326771 TTAAATTTAAATAAAAATAAAATTTTATTAT
1 TTAAATTTAAATAAAAATAAAATTAAATTAT
* *
1326802 TTAAATATTAAAT-TAAATTAAATTAAATTAT
1 TTAAAT-TTAAATAAAAATAAAATTAAATTAT
1326833 AAAATTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 20 0.77
32 6 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
TTAAATTTAAATAAAAATAAAATTAAATTAT
Found at i:1326844 original size:42 final size:41
Alignment explanation
Indices: 1326768--1326866 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 41
1326758 ATATTTATAA
1326768 TAATTAAATTTAAA-TAAAAATAAAATTTTATTATTTAAATAT
1 TAATTAAA-TTAAATTAAAAATAAAATTTTATTATTTAAAT-T
*
1326810 TAAATTAAATTAAATTAAATTATAAAA-TTT-TTATTTAAATT
1 T-AATTAAATTAAATTAAA-AATAAAATTTTATTATTTAAATT
*
1326851 TAATTATAAATAAATT
1 TAATTA-AATTAAATT
1326867 TATCATCATA
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
40 5 0.10
41 10 0.20
42 16 0.31
43 14 0.27
44 6 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (41 bp):
TAATTAAATTAAATTAAAAATAAAATTTTATTATTTAAATT
Found at i:1328010 original size:2 final size:2
Alignment explanation
Indices: 1328003--1328041 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1327993 GAAGTTTTAT
*
1328003 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1328042 CAGATAAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1330934 original size:15 final size:16
Alignment explanation
Indices: 1330907--1330936 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1330897 GTAATTAATT
1330907 TAATTATTTGATATAA
1 TAATTATTTGATATAA
1330923 TAATTA-TTGATATA
1 TAATTATTTGATATA
1330937 CATTATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAATTATTTGATATAA
Found at i:1330963 original size:21 final size:21
Alignment explanation
Indices: 1330938--1330988 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
1330928 ATTGATATAC
*
1330938 ATTATATTTTACATTA-AAATT
1 ATTATATTTTA-ATTAGAAATA
*
1330959 ATTATTTTATTAATTAGAAATA
1 ATTATATT-TTAATTAGAAATA
1330981 ATT-TATTT
1 ATTATATTT
1330989 ATTTAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.04
21 14 0.56
22 10 0.40
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTATATTTTAATTAGAAATA
Found at i:1331545 original size:13 final size:13
Alignment explanation
Indices: 1331527--1331553 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1331517 GTGTTCAATC
1331527 TAAATTTGAATTT
1 TAAATTTGAATTT
1331540 TAAATTTGAATTT
1 TAAATTTGAATTT
1331553 T
1 T
1331554 TTTATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (13 bp):
TAAATTTGAATTT
Found at i:1336718 original size:6 final size:6
Alignment explanation
Indices: 1336709--1336736 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1336699 GCCACTGCAT
1336709 CATTCC CATTCC CATTCC CATTCC CATT
1 CATTCC CATTCC CATTCC CATTCC CATT
1336737 TGTGGGGCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.00, T:0.36
Consensus pattern (6 bp):
CATTCC
Found at i:1338606 original size:3 final size:3
Alignment explanation
Indices: 1338600--1338637 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1338590 TTGAAAGAAG
1338600 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1338638 GGGTCAGCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1338869 original size:3 final size:3
Alignment explanation
Indices: 1338861--1338897 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1338851 ATCCTTAATC
1338861 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1338898 GAAACACAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1339239 original size:22 final size:22
Alignment explanation
Indices: 1339185--1339256 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
1339175 CTGCTAAAAT
* *
1339185 TTTAAATATAGTATAATATAATA
1 TTTAAATATA-TATTATATTATA
* *
1339208 ATAAATATATTATATTA-ATTATA
1 TTTAA-ATA-TATATTATATTATA
* *
1339231 TTTAAATATATTTTATTTTATA
1 TTTAAATATATATTATATTATA
1339253 TTTA
1 TTTA
1339257 TTGAATATAT
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
21 6 0.16
22 12 0.32
23 11 0.29
24 7 0.18
25 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (22 bp):
TTTAAATATATATTATATTATA
Found at i:1339283 original size:25 final size:25
Alignment explanation
Indices: 1339211--1339283 Score: 82
Period size: 24 Copynumber: 3.0 Consensus size: 25
1339201 TATAATAATA
1339211 AATATATTATATTAATTATATTTA---
1 AATATATTATATT--TTATATTTATTG
*
1339235 AATATATTTTATTTTATATTTATTG
1 AATATATTATATTTTATATTTATTG
1339260 AATATATTAT-TTTTATATTGTATT
1 AATATATTATATTTTATATT-TATT
1339284 TTCATTATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
22 9 0.21
24 21 0.49
25 13 0.30
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (25 bp):
AATATATTATATTTTATATTTATTG
Found at i:1342209 original size:3 final size:3
Alignment explanation
Indices: 1342201--1342239 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1342191 TGTTTGTTTT
1342201 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
1342240 AGTTAACCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1349234 original size:20 final size:19
Alignment explanation
Indices: 1349199--1349240 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1349189 ACATTTTTTG
* *
1349199 TATTAATATAATAATTATT
1 TATTAATATAAAAATTAAT
1349218 TATTAATTATAAAAATTAAT
1 TATTAA-TATAAAAATTAAT
1349238 TAT
1 TAT
1349241 GTTATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTAATATAAAAATTAAT
Found at i:1349513 original size:30 final size:31
Alignment explanation
Indices: 1349477--1349536 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
1349467 ACATAATAAG
*
1349477 AATATAAAGAT-ATGTCAAAATTTAT-TAAAA
1 AATATAAA-ATCATATCAAAATTTATATAAAA
*
1349507 AATATAAATTCATATCAAAATTTATATAAA
1 AATATAAAATCATATCAAAATTTATATAAA
1349537 TATATAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 1 0.04
30 21 0.81
31 4 0.15
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (31 bp):
AATATAAAATCATATCAAAATTTATATAAAA
Found at i:1352599 original size:15 final size:16
Alignment explanation
Indices: 1352579--1352620 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
1352569 ATTCAATAAC
**
1352579 TTAAATTATTTAA-AT
1 TTAAATTAAATAATAT
1352594 TTAAATTAAATAATAT
1 TTAAATTAAATAATAT
*
1352610 TTAAATCAAAT
1 TTAAATTAAAT
1352621 TTTTTTAGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAATTAAATAATAT
Found at i:1352806 original size:18 final size:18
Alignment explanation
Indices: 1352788--1352822 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1352778 TATTTATATA
1352788 AATTT-TAATATATTAAT
1 AATTTATAATATATTAAT
*
1352805 AATTTATATTATATTAAT
1 AATTTATAATATATTAAT
1352823 TTAAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATTTATAATATATTAAT
Found at i:1352824 original size:32 final size:32
Alignment explanation
Indices: 1352781--1352859 Score: 82
Period size: 26 Copynumber: 2.7 Consensus size: 32
1352771 TTAAAAATAT
*
1352781 TTATATAAATTTTAATATATTAATAATTTATA
1 TTATATTAATTTTAATATATTAATAATTTATA
*
1352813 TTATATTAA-TTT-A-A-A--AATATTTTATA
1 TTATATTAATTTTAATATATTAATAATTTATA
1352839 TTATATTATATTTTAAT-TATT
1 TTATATTA-ATTTTAATATATT
1352860 TTTATATTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
26 18 0.47
27 1 0.03
28 4 0.11
29 2 0.05
30 2 0.05
31 3 0.08
32 8 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
TTATATTAATTTTAATATATTAATAATTTATA
Found at i:1352861 original size:26 final size:25
Alignment explanation
Indices: 1352739--1352867 Score: 98
Period size: 27 Copynumber: 4.8 Consensus size: 25
1352729 TAATTTATGC
*
1352739 TATATTTTTATATTTTATATTTATAAT
1 TATATTTTAATATTTTATA-TTAT-AT
* * * *
1352766 TATATTTAAAAATATTTATATAAATTT
1 TATATTTTAATAT-TTTATAT-TATAT
* *
1352793 TAATATATTAATAATTTATATTATAT
1 T-ATATTTTAATATTTTATATTATAT
*
1352819 TA-ATTTAAAAATATTTTATATTATAT
1 TATATTT--TAATATTTTATATTATAT
1352845 TATATTTTAATTATTTTTATATT
1 TATATTTTAA-TA-TTTTATATT
1352868 CTAATTATGT
Statistics
Matches: 79, Mismatches: 15, Indels: 16
0.72 0.14 0.15
Matches are distributed among these distances:
24 3 0.04
25 3 0.04
26 24 0.30
27 33 0.42
28 16 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TATATTTTAATATTTTATATTATAT
Found at i:1352864 original size:17 final size:17
Alignment explanation
Indices: 1352829--1352875 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
1352819 TAATTTAAAA
1352829 ATATTTTATATTA-TATT
1 ATATTTTA-ATTATTATT
*
1352846 ATATTTTAATTATTTTT
1 ATATTTTAATTATTATT
*
1352863 ATATTCTAATTAT
1 ATATTTTAATTAT
1352876 GTCATTGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 4 0.15
17 23 0.85
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTTTAATTATTATT
Found at i:1353688 original size:23 final size:22
Alignment explanation
Indices: 1353640--1353692 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
1353630 TTTATGTTAT
*
1353640 TATTTAAAAATAATATTTTTAAA
1 TATTT-AAAATAATATTTATAAA
* *
1353663 TATTTAAATTAATATTTATAGTA
1 TATTTAAAATAATATTTATA-AA
1353686 TATTTAA
1 TATTTAA
1353693 TTTTAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 13 0.50
23 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TATTTAAAATAATATTTATAAA
Found at i:1353980 original size:25 final size:26
Alignment explanation
Indices: 1353952--1354007 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
1353942 ATTTATTCAT
* * *
1353952 TAATTATAAAAT-TATATTTTATAAA
1 TAATAATAAAATATATATTTAAAAAA
*
1353977 TAATAATTAAATATATATTTAAAAAA
1 TAATAATAAAATATATATTTAAAAAA
1354003 TAATA
1 TAATA
1354008 CAAAAAAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
TAATAATAAAATATATATTTAAAAAA
Found at i:1354322 original size:2 final size:2
Alignment explanation
Indices: 1354315--1354345 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1354305 TTGGAAGTGG
1354315 AT AT 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 AT AT A
1354346 ATTATTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1354688 original size:20 final size:19
Alignment explanation
Indices: 1354665--1354708 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1354655 TCTTGCTATG
1354665 TTTTT-CTTTTAAAATTAT
1 TTTTTACTTTTAAAATTAT
*
1354683 TATTTTACTTTTTAAATTAT
1 T-TTTTACTTTTAAAATTAT
1354703 TTTTTA
1 TTTTTA
1354709 TATATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 1 0.04
19 9 0.39
20 13 0.57
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTACTTTTAAAATTAT
Found at i:1354747 original size:17 final size:17
Alignment explanation
Indices: 1354727--1354821 Score: 56
Period size: 17 Copynumber: 5.5 Consensus size: 17
1354717 TTTATAATTT
1354727 ATATATATATATATTAG
1 ATATATATATATATTAG
1354744 ATATATGCATATATATACTA-
1 ATATAT--ATATATAT--TAG
*
1354764 A-A-ATCATATAT-TTTG
1 ATATAT-ATATATATTAG
* *
1354779 AGTATATATGTATAATAG
1 A-TATATATATATATTAG
*
1354797 ATATAGTATATATA-TAT
1 ATATA-TATATATATTAG
1354814 ATATATAT
1 ATATATAT
1354822 TATGGCATTA
Statistics
Matches: 62, Mismatches: 6, Indels: 21
0.70 0.07 0.24
Matches are distributed among these distances:
14 1 0.02
15 1 0.02
16 4 0.06
17 30 0.48
18 14 0.23
19 9 0.15
20 1 0.02
21 2 0.03
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.44
Consensus pattern (17 bp):
ATATATATATATATTAG
Found at i:1354836 original size:2 final size:2
Alignment explanation
Indices: 1354726--1354821 Score: 56
Period size: 2 Copynumber: 47.5 Consensus size: 2
1354716 TTTTATAATT
* * * *
1354726 TA TA TA TA TA TA TA T- TA GA TA TA TG CA TA TA TA TA CTA -A AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * *
1354767 TCA TA TA T- TT TGA GTA TA TA TG TA TA -A TA GA TA TA GTA TA TA
1 T-A TA TA TA TA T-A -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
1354809 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1354822 TATGGCATTA
Statistics
Matches: 73, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
1 4 0.05
2 61 0.84
3 7 0.10
4 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1355493 original size:30 final size:31
Alignment explanation
Indices: 1355447--1355516 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 31
1355437 TATGTATTGA
*
1355447 AATAT-AAAACTTTTAAA-ATT-ATAAATAAT
1 AATATAAAAAATTTTAAACATTAATAAAT-AT
1355476 AATATAAAAAATTTTAAACATTAAATAAATAT
1 AATATAAAAAATTTTAAACATT-AATAAATAT
1355508 AATATAAAA
1 AATATAAAA
1355517 GTATTATAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 5 0.14
30 11 0.31
31 3 0.08
32 11 0.31
33 6 0.17
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (31 bp):
AATATAAAAAATTTTAAACATTAATAAATAT
Found at i:1359241 original size:21 final size:22
Alignment explanation
Indices: 1359214--1359268 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
1359204 CATTTCATAT
*
1359214 GTAATTAAAGTATAATATAATA
1 GTAATTAAAATATAATATAATA
* *
1359236 -TAATTAAAATTTAATTTAATA
1 GTAATTAAAATATAATATAATA
1359257 GTAATTAAAATA
1 GTAATTAAAATA
1359269 ATTTTAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (22 bp):
GTAATTAAAATATAATATAATA
Found at i:1359274 original size:21 final size:20
Alignment explanation
Indices: 1359214--1359286 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 20
1359204 CATTTCATAT
*
1359214 GTAATTAAAGTATAATATAATA
1 GTAATTAAA--ATAATTTAATA
1359236 -TAATTAAAATTTAATTTAATA
1 GTAATTAAAA--TAATTTAATA
*
1359257 GTAATTAAAATAATTTTAAAA
1 GTAATTAAAATAA-TTTAATA
*
1359278 TTAATTAAA
1 GTAATTAAA
1359287 TTTTTATGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
19 1 0.02
20 3 0.07
21 31 0.70
22 9 0.20
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (20 bp):
GTAATTAAAATAATTTAATA
Found at i:1359283 original size:43 final size:43
Alignment explanation
Indices: 1359195--1359286 Score: 107
Period size: 43 Copynumber: 2.1 Consensus size: 43
1359185 AACTAAGTTT
* * *
1359195 TTAAAATTTCATTTCATATGTAATTAAAGTATAATATAATATAA
1 TTAAAATTTAATTTAATATGTAATTAAAG-ATAATATAAAATAA
*
1359239 TTAAAATTTAATTTAATA-GTAATTAAA-ATAATTTTAAAATTAA
1 TTAAAATTTAATTTAATATGTAATTAAAGATAA-TATAAAA-TAA
1359282 TTAAA
1 TTAAA
1359287 TTTTTATGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
41 4 0.10
42 5 0.12
43 17 0.40
44 16 0.38
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.43
Consensus pattern (43 bp):
TTAAAATTTAATTTAATATGTAATTAAAGATAATATAAAATAA
Found at i:1362603 original size:3 final size:3
Alignment explanation
Indices: 1362597--1362637 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
1362587 ATGCTGATGA
*
1362597 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGA TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
1362638 AGAAGTTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.02, C:0.00, G:0.63, T:0.34
Consensus pattern (3 bp):
TGG
Found at i:1364206 original size:2 final size:2
Alignment explanation
Indices: 1364199--1364228 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1364189 TCATGTATGC
1364199 AT 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 AT
1364229 GTTTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1366280 original size:9 final size:9
Alignment explanation
Indices: 1366197--1366280 Score: 52
Period size: 8 Copynumber: 9.4 Consensus size: 9
1366187 TTTTATTTTG
*
1366197 TATTAATTA
1 TATTAAATA
1366206 -ATTAAATA
1 TATTAAATA
*
1366214 TAAATAAA-A
1 T-ATTAAATA
1366223 TA-TAAAT-
1 TATTAAATA
1366230 TATTAAATA
1 TATTAAATA
*
1366239 T-TTTAATA
1 TATTAAATA
*
1366247 TTTTAAATAA
1 TATTAAAT-A
*
1366257 GATATAATATA
1 TAT-TAA-ATA
1366268 TATTAAATA
1 TATTAAATA
1366277 TATT
1 TATT
1366281 TTATTAATTA
Statistics
Matches: 59, Mismatches: 7, Indels: 18
0.70 0.08 0.21
Matches are distributed among these distances:
7 6 0.10
8 20 0.34
9 15 0.25
10 10 0.17
11 6 0.10
12 2 0.03
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (9 bp):
TATTAAATA
Found at i:1366299 original size:14 final size:13
Alignment explanation
Indices: 1366263--1366335 Score: 53
Period size: 14 Copynumber: 5.7 Consensus size: 13
1366253 ATAAGATATA
*
1366263 ATATATATTAAAT
1 ATATATATTAATT
*
1366276 ATATTTTATTAATT
1 ATA-TATATTAATT
*
1366290 ATATGATATTTATT
1 ATAT-ATATTAATT
*
1366304 ATAT-TATT-TTT
1 ATATATATTAATT
* *
1366315 ATATTTATTAAAT
1 ATATATATTAATT
1366328 ATAT-TATT
1 ATATATATT
1366336 TTTATATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
11 6 0.12
12 12 0.24
13 9 0.18
14 22 0.45
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (13 bp):
ATATATATTAATT
Found at i:1366316 original size:11 final size:11
Alignment explanation
Indices: 1366296--1366343 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
1366286 AATTATATGA
1366296 TATTTATTATAT
1 TATTT-TTATAT
1366308 TATTTTTATATT
1 TATTTTTATA-T
**
1366320 TATTAAATATAT
1 TATT-TTTATAT
1366332 TATTTTTATAT
1 TATTTTTATAT
1366343 T
1 T
1366344 TTTATATTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
11 11 0.37
12 15 0.50
13 4 0.13
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTTTTATAT
Found at i:1369663 original size:2 final size:2
Alignment explanation
Indices: 1369658--1369688 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1369648 AAAAACCCCA
1369658 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1369689 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1369924 original size:16 final size:17
Alignment explanation
Indices: 1369905--1369976 Score: 64
Period size: 15 Copynumber: 4.4 Consensus size: 17
1369895 TATTATAATT
1369905 TATTTA-AAATATTATA
1 TATTTATAAATATTATA
*
1369921 TATTTATATAATTTTA-A
1 TATTTATA-AATATTATA
1369938 TATTTTATAAATATTAT-
1 TA-TTTATAAATATTATA
* *
1369955 TTTTTAT-TATATTATA
1 TATTTATAAATATTATA
1369971 T-TTTAT
1 TATTTAT
1369977 CATATTCGAC
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
15 12 0.26
16 12 0.26
17 11 0.23
18 12 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTTATAAATATTATA
Found at i:1369966 original size:15 final size:15
Alignment explanation
Indices: 1369937--1369982 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
1369927 TATAATTTTA
*
1369937 ATATTTTATAAATATT
1 ATATTTTAT-CATATT
* *
1369953 ATTTTTTATTATATT
1 ATATTTTATCATATT
1369968 ATATTTTATCATATT
1 ATATTTTATCATATT
1369983 CGACATTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 18 0.69
16 8 0.31
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (15 bp):
ATATTTTATCATATT
Found at i:1374406 original size:12 final size:12
Alignment explanation
Indices: 1374382--1374423 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1374372 ATATGTGAAA
*
1374382 AAATATATTTTT
1 AAATATATATTT
* *
1374394 ATATTTATATTT
1 AAATATATATTT
1374406 AAATATATA-TT
1 AAATATATATTT
1374417 AAATATA
1 AAATATA
1374424 AATATTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
AAATATATATTT
Found at i:1375720 original size:20 final size:20
Alignment explanation
Indices: 1375684--1375759 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
1375674 ATAATTTTTT
* *
1375684 ATATAAGTTTCATAATAATTG
1 ATATAA-TTTTATAATAATTA
*
1375705 ATATAATTTTATAATAATTT
1 ATATAATTTTATAATAATTA
*
1375725 A-ATAATAGTTATAATAATTTTA
1 ATATAAT-TTTATAATAA--TTA
1375747 ATATAATTTTATA
1 ATATAATTTTATA
1375760 TCCAAATATT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
19 5 0.11
20 22 0.48
21 6 0.13
22 8 0.17
23 5 0.11
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (20 bp):
ATATAATTTTATAATAATTA
Found at i:1375723 original size:11 final size:11
Alignment explanation
Indices: 1375674--1375759 Score: 65
Period size: 11 Copynumber: 8.0 Consensus size: 11
1375664 GTACGTAACG
*
1375674 ATAATTTTTTA
1 ATAATTTTATA
*
1375685 TATAAGTTTCATA
1 -ATAA-TTTTATA
*
1375698 ATAA-TTGAT-
1 ATAATTTTATA
1375707 ATAATTTTATA
1 ATAATTTTATA
*
1375718 ATAATTTAATA
1 ATAATTTTATA
*
1375729 AT-A-GTTATA
1 ATAATTTTATA
1375738 ATAATTTTA-A
1 ATAATTTTATA
1375748 TATAATTTTATA
1 -ATAATTTTATA
1375760 TCCAAATATT
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
9 10 0.17
10 11 0.19
11 24 0.41
12 9 0.15
13 5 0.08
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (11 bp):
ATAATTTTATA
Found at i:1375730 original size:31 final size:32
Alignment explanation
Indices: 1375674--1375755 Score: 98
Period size: 31 Copynumber: 2.6 Consensus size: 32
1375664 GTACGTAACG
* *
1375674 ATAATTTTTTATATAAGTTTCATAATAATTGAT-
1 ATAATTTTATATATAA-TTTAATAATAATT-ATA
*
1375707 ATAATTTTATA-ATAATTTAATAATAGTTATA
1 ATAATTTTATATATAATTTAATAATAATTATA
1375738 ATAATTTTA-ATATAATTT
1 ATAATTTTATATATAATTT
1375756 TATATCCAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
30 3 0.07
31 27 0.61
32 4 0.09
33 10 0.23
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (32 bp):
ATAATTTTATATATAATTTAATAATAATTATA
Found at i:1376569 original size:33 final size:33
Alignment explanation
Indices: 1376526--1376597 Score: 135
Period size: 33 Copynumber: 2.2 Consensus size: 33
1376516 GACCCATGAT
1376526 ATCACCAGGATTCTTAGCTACAATCACCCCAAC
1 ATCACCAGGATTCTTAGCTACAATCACCCCAAC
*
1376559 GTCACCAGGATTCTTAGCTACAATCACCCCAAC
1 ATCACCAGGATTCTTAGCTACAATCACCCCAAC
1376592 ATCACC
1 ATCACC
1376598 GGCTGCTCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.32, C:0.38, G:0.10, T:0.21
Consensus pattern (33 bp):
ATCACCAGGATTCTTAGCTACAATCACCCCAAC
Found at i:1377171 original size:2 final size:2
Alignment explanation
Indices: 1377164--1377197 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1377154 TTGAAACGGA
1377164 AT AT AT 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 AT AT AT
1377198 TAGCAGCTCT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1378621 original size:17 final size:16
Alignment explanation
Indices: 1378579--1378624 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1378569 AAAATGATTC
1378579 AATTTTAAAATAATCT
1 AATTTTAAAATAATCT
* * *
1378595 GATCTTAAAATAATTT
1 AATTTTAAAATAATCT
1378611 AAATTTTAAAATAA
1 -AATTTTAAAATAA
1378625 CTCAAAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (16 bp):
AATTTTAAAATAATCT
Found at i:1383324 original size:11 final size:11
Alignment explanation
Indices: 1383310--1383401 Score: 56
Period size: 11 Copynumber: 8.8 Consensus size: 11
1383300 TAATAATTTA
1383310 TATATTTATAT
1 TATATTTATAT
1383321 TATA-TTAT-T
1 TATATTTATAT
* *
1383330 TAT-GTAATAAT
1 TATATTTAT-AT
1383341 ATATATTTATA-
1 -TATATTTATAT
1383352 T-TATTT-T-T
1 TATATTTATAT
* *
1383360 TAAATTTATTT
1 TATATTTATAT
1383371 TATATTTATAT
1 TATATTTATAT
1383382 TATATTT-TAAT
1 TATATTTAT-AT
*
1383393 TATTTTTAT
1 TATATTTAT
1383402 TAAATTATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 21
0.69 0.08 0.23
Matches are distributed among these distances:
8 2 0.03
9 16 0.25
10 7 0.11
11 30 0.48
12 5 0.08
13 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1383328 original size:18 final size:18
Alignment explanation
Indices: 1383307--1383387 Score: 66
Period size: 18 Copynumber: 4.8 Consensus size: 18
1383297 ATATAATAAT
1383307 TTATATATTTATATTATA
1 TTATATATTTATATTATA
* *
1383325 TTATTTATGTA-A-TA-A
1 TTATATATTTATATTATA
*
1383340 -TATATATTTATATTATT
1 TTATATATTTATATTATA
* * *
1383357 TTTTAAATTTATTTTATA
1 TTATATATTTATATTATA
1383375 TT-TATA-TTATATT
1 TTATATATTTATATT
1383388 TTAATTATTT
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
14 8 0.17
15 2 0.04
16 10 0.21
17 4 0.08
18 24 0.50
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (18 bp):
TTATATATTTATATTATA
Found at i:1383338 original size:34 final size:32
Alignment explanation
Indices: 1383295--1383394 Score: 104
Period size: 32 Copynumber: 3.2 Consensus size: 32
1383285 AAAAAATAAA
1383295 TTATATAATAATTTATATATTTATATTATATTAT
1 TTAT-TAATAATTTATATATTTATATTATATT-T
1383329 TTATGTAATAA--TATATATTTATATTAT-TTT
1 TTAT-TAATAATTTATATATTTATATTATATTT
*
1383359 TTA--AATTTATTT-TATATTTATATTATATTT
1 TTATTAA-TAATTTATATATTTATATTATATTT
*
1383389 TAATTA
1 TTATTA
1383395 TTTTTATTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
27 2 0.04
28 2 0.04
29 14 0.25
30 10 0.18
31 2 0.04
32 17 0.30
34 10 0.18
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (32 bp):
TTATTAATAATTTATATATTTATATTATATTT
Found at i:1383369 original size:40 final size:42
Alignment explanation
Indices: 1383312--1383412 Score: 104
Period size: 40 Copynumber: 2.5 Consensus size: 42
1383302 ATAATTTATA
* * *
1383312 TATTTATATTATATTATTTATGTAATAATA-TATA-TTTATAT
1 TATTTTTATTAAATTATTTATATAATAATATTATATTTTA-AT
* *
1383353 TA-TTTT-TTAAATTTATTT-TATATTTATATTATATTTTAAT
1 TATTTTTATTAAA-TTATTTATATAATAATATTATATTTTAAT
1383393 TATTTTTATTAAATTATTTA
1 TATTTTTATTAAATTATTTA
1383413 ATTTATTTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
39 11 0.22
40 17 0.35
41 16 0.33
42 5 0.10
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (42 bp):
TATTTTTATTAAATTATTTATATAATAATATTATATTTTAAT
Found at i:1383384 original size:29 final size:27
Alignment explanation
Indices: 1383314--1383411 Score: 96
Period size: 29 Copynumber: 3.7 Consensus size: 27
1383304 AATTTATATA
* *
1383314 TTTATA-TTATATTATTTATGTAA-TAA
1 TTTATATTTATATTATTT-TTTAATTAT
*
1383340 TATATATTTATATTATTTTTTAAATTTAT
1 TTTATATTTATATTATTTTTT-AA-TTAT
*
1383369 TTTATATTTATATTATATTTTAATTAT
1 TTTATATTTATATTATTTTTTAATTAT
*
1383396 TTT-TA-TTAAATTATTT
1 TTTATATTTATATTATTT
1383412 AATTTATTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
25 9 0.15
26 9 0.15
27 20 0.33
28 2 0.03
29 21 0.34
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (27 bp):
TTTATATTTATATTATTTTTTAATTAT
Found at i:1383390 original size:18 final size:18
Alignment explanation
Indices: 1383295--1383387 Score: 56
Period size: 18 Copynumber: 5.4 Consensus size: 18
1383285 AAAAAATAAA
*
1383295 TTATATAATAATTTATATAT
1 TTATATTAT-ATTT-TATAT
1383315 TTATATTATATTATT-TAT
1 TTATATTATATT-TTATAT
* *
1383333 GTA-A-TA-A-TATATAT
1 TTATATTATATTTTATAT
* *
1383347 TTATATTATTTTTTAAAT
1 TTATATTATATTTTATAT
*
1383365 TTATTTTATA-TTTATA-
1 TTATATTATATTTTATAT
1383381 TTATATT
1 TTATATT
1383388 TTAATTATTT
Statistics
Matches: 56, Mismatches: 11, Indels: 16
0.67 0.13 0.19
Matches are distributed among these distances:
13 1 0.02
14 6 0.11
15 2 0.04
16 10 0.18
17 6 0.11
18 18 0.32
19 4 0.07
20 9 0.16
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (18 bp):
TTATATTATATTTTATAT
Found at i:1383395 original size:22 final size:24
Alignment explanation
Indices: 1383370--1383426 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 24
1383360 TAAATTTATT
*
1383370 TTATATTTATATTATA-T-TTTAA
1 TTATATTTATATTAAATTATTTAA
1383392 TTAT-TTT-TATTAAATTATTTAA
1 TTATATTTATATTAAATTATTTAA
*
1383414 TT-TATTTAAATTA
1 TTATATTTATATTA
1383427 CAAAAGGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
20 6 0.21
21 5 0.17
22 14 0.48
23 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TTATATTTATATTAAATTATTTAA
Found at i:1383410 original size:23 final size:23
Alignment explanation
Indices: 1383346--1383420 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 23
1383336 ATAATATATA
1383346 TTTATATTA-TTTT-TTAAATTTAT
1 TTTA-ATTATTTTTATTAAA-TTAT
*
1383369 TTT-A-TATTTATATT--A-TAT
1 TTTAATTATTTTTATTAAATTAT
1383387 TTTAATTATTTTTATTAAATTA-
1 TTTAATTATTTTTATTAAATTAT
1383409 TTTAATTTATTT
1 TTTAA-TTATTT
1383421 AAATTACAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 16
0.70 0.03 0.27
Matches are distributed among these distances:
18 6 0.14
19 1 0.02
20 12 0.29
21 4 0.10
22 8 0.19
23 11 0.26
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTAATTATTTTTATTAAATTAT
Found at i:1383579 original size:2 final size:2
Alignment explanation
Indices: 1383572--1383608 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1383562 TGATTGGGTT
1383572 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1383609 CTGAGAAGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Done.