Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 97 of 120
Found at i:28696658 original size:23 final size:23
Alignment explanation
Indices: 28696627--28696702 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
28696617 AGTGTTATTG
28696627 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * *
28696650 TTCAGTGGTAGCTACAGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
28696673 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
28696696 ATCAGTG
1 ATCAGTG
28696703 TGGCACTTAT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:28700466 original size:44 final size:44
Alignment explanation
Indices: 28700416--28700507 Score: 175
Period size: 44 Copynumber: 2.1 Consensus size: 44
28700406 TGACGTTGAG
28700416 GATTAATTTTAAAAGAGGGAGAAAACAAAAAAATTATTATTTTA
1 GATTAATTTTAAAAGAGGGAGAAAACAAAAAAATTATTATTTTA
*
28700460 GATTAATTTTAAAAGAGTGAGAAAACAAAAAAATTATTATTTTA
1 GATTAATTTTAAAAGAGGGAGAAAACAAAAAAATTATTATTTTA
28700504 GATT
1 GATT
28700508 TTTTAGTGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.51, C:0.02, G:0.13, T:0.34
Consensus pattern (44 bp):
GATTAATTTTAAAAGAGGGAGAAAACAAAAAAATTATTATTTTA
Found at i:28705165 original size:44 final size:44
Alignment explanation
Indices: 28705095--28705565 Score: 232
Period size: 44 Copynumber: 10.9 Consensus size: 44
28705085 GAAGATGGCG
*
28705095 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCAAT
* * * *
28705139 AATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCACAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCA-AT
* * * * * *
28705184 -ATCTTATCTCTCTGAAGTTGTAG-AGAGCAGATCGCATCC---
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCAAT
* * * *****
28705223 AGTCTTATCTCCTTGAAGTTGCAGTGG-GCAGACTGAAGATGGCG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-CCAAT
* * * *
28705267 AATCTTATTTCCCTAAAGTTGCAGAGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCAAT
* ** * * ***
28705311 AATCCTATCTCCCTGAAGTTGCAACGGAGCGGGTT-AAAATAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCAAT
* * * * *
28705354 AGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCGCA-TC--T
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCAAT
* * * * * *
28705395 AGTCTTATCTCCCTGAAGTTGCAGCGGAGCAAACT-AAG-AAAGC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCAA-T
* * * * *****
28705438 AAGTCTTATCCCCCTGAAGTTGTAGTGGGGCAGACTGAAGATGGCG
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-CCAAT
* * * * * **
28705484 AATCTTATTTCCCTAAAGTTACAGTGGAGCAAACTGAA-TAAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCAAT
* * *
28705527 CAATCTTATCTCTCTGAAGTTGCATTGGGGCAGATTGAA
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA
28705566 ATTACAAATC
Statistics
Matches: 312, Mismatches: 95, Indels: 40
0.70 0.21 0.09
Matches are distributed among these distances:
40 48 0.15
41 9 0.03
43 25 0.08
44 185 0.59
45 43 0.14
46 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCAAT
Found at i:28705362 original size:172 final size:172
Alignment explanation
Indices: 28705055--28705418 Score: 523
Period size: 172 Copynumber: 2.1 Consensus size: 172
28705045 CCACAAATCC
* * * * *
28705055 TATCTCCTTGAAGTTGTAGTGGAATGGATTGAAGATGGCGAATCTTATCTCCCTGAAGTTGTAGT
1 TATCTCCTTGAAGTTGCAGTGGAA-GGACTGAAGATGGCGAATCTTATCTCCCTAAAGTTGCAGA
* ** * *
28705120 GGAGCAGATTGAAGCCAATAATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCACATA
65 GGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTACAACGGAGCAGATTAAAACAACAGA
*
28705185 TCTTATCTCTCTGAAGTTGTAGAGAGCAGATCGCATCCAGTCT
130 TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCCAGTCT
* *
28705228 TATCTCCTTGAAGTTGCAGTGGGCA-GACTGAAGATGGCGAATCTTATTTCCCTAAAGTTGCAGA
1 TATCTCCTTGAAGTTGCAGT-GGAAGGACTGAAGATGGCGAATCTTATCTCCCTAAAGTTGCAGA
* * * * *
28705292 GGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAACGGAGCGGGTTAAAATAATAGA
65 GGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTACAACGGAGCAGATTAAAACAACAGA
*
28705357 TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCT
130 TCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCCAGTCT
*
28705400 TATCTCCCTGAAGTTGCAG
1 TATCTCCTTGAAGTTGCAG
28705419 CGGAGCAAAC
Statistics
Matches: 170, Mismatches: 20, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
172 148 0.87
173 19 0.11
174 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (172 bp):
TATCTCCTTGAAGTTGCAGTGGAAGGACTGAAGATGGCGAATCTTATCTCCCTAAAGTTGCAGAG
GAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTACAACGGAGCAGATTAAAACAACAGAT
CTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCCAGTCT
Found at i:28705548 original size:89 final size:88
Alignment explanation
Indices: 28705397--28705583 Score: 223
Period size: 89 Copynumber: 2.1 Consensus size: 88
28705387 TCGCATCTAG
* * * *
28705397 TCTTATCTCCCTGAAGTTGCAGCGGAGCAAACTAAGAAAGCAAGTCTTATCCCCCTGAAGTTGTA
1 TCTTATTTCCCTAAAGTTACAGCGGAGCAAACTAAGAAAGCAAGTCTTATCCCCCTGAAGTTGCA
* *
28705462 GTGGGGCAGACTGAAGATGGCGAA
66 GTGGGGCAGACTGAA-ATGACAAA
* * * * *
28705486 TCTTATTTCCCTAAAGTTACAGTGGAGCAAACTGAATAAATCAA-TCTTATCTCTCTGAAGTTGC
1 TCTTATTTCCCTAAAGTTACAGCGGAGCAAACT-AAGAAAGCAAGTCTTATCCCCCTGAAGTTGC
* * *
28705550 ATTGGGGCAGATTGAAATTACAAA
65 AGTGGGGCAGACTGAAATGACAAA
28705574 TCTTATTTCC
1 TCTTATTTCC
28705584 TTGGCGTTGC
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
88 15 0.18
89 60 0.72
90 8 0.10
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (88 bp):
TCTTATTTCCCTAAAGTTACAGCGGAGCAAACTAAGAAAGCAAGTCTTATCCCCCTGAAGTTGCA
GTGGGGCAGACTGAAATGACAAA
Found at i:28719390 original size:32 final size:31
Alignment explanation
Indices: 28719327--28719395 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
28719317 TTGATTAATC
*
28719327 TTAGTCCTTGTATTTTTCGAGTTGGTCAATT
1 TTAGTCCTTGTATTTTTCGAGTTGGTAAATT
* *
28719358 TTAGTCCTTTTTATTTTTCGAGTT-TTGAAATT
1 TTAGTCC-TTGTATTTTTCGAGTTGGT-AAATT
28719390 TTAGTC
1 TTAGTC
28719396 TTGATCCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 8 0.24
32 25 0.76
ACGTcount: A:0.17, C:0.12, G:0.16, T:0.55
Consensus pattern (31 bp):
TTAGTCCTTGTATTTTTCGAGTTGGTAAATT
Found at i:28721863 original size:46 final size:46
Alignment explanation
Indices: 28721806--28721990 Score: 291
Period size: 46 Copynumber: 4.0 Consensus size: 46
28721796 ACATTGCTAT
*
28721806 AACTCAGTATGGTTTTCTTCAC-GAAAATACCATACCTACTTTTCAC
1 AACTCAATATGGTTTTCTTCACTG-AAATACCATACCTACTTTTCAC
*
28721852 AACTCAATATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAATATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* *
28721898 AACTCAATATGGTTTTCTTCACTGAAACATCATACCTACTTTTCAC
1 AACTCAATATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* * *
28721944 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACGTTTCAC
1 AACTCAATATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
28721990 A
1 A
28721991 CTTTGCCATG
Statistics
Matches: 130, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
46 129 0.99
47 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.36
Consensus pattern (46 bp):
AACTCAATATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
Found at i:28723261 original size:16 final size:17
Alignment explanation
Indices: 28723215--28723261 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
28723205 TAAATTTTTT
28723215 TAAATCACAAAATTCAA
1 TAAATCACAAAATTCAA
*
28723232 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAA
*
28723249 TAATTCA-AAAATT
1 TAAATCACAAAATT
28723262 ATTCTAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 6 0.21
17 22 0.79
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:28726938 original size:19 final size:19
Alignment explanation
Indices: 28726910--28726949 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
28726900 ACAACAAAAT
*
28726910 AATAGCAACATAATAGTGA
1 AATAGCAACAAAATAGTGA
*
28726929 AATAGTAACAAAATAGTGA
1 AATAGCAACAAAATAGTGA
28726948 AA
1 AA
28726950 ACAAAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.57, C:0.07, G:0.15, T:0.20
Consensus pattern (19 bp):
AATAGCAACAAAATAGTGA
Found at i:28727556 original size:5 final size:5
Alignment explanation
Indices: 28727536--28727573 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
28727526 GAAAAATTAA
*
28727536 TATAT GTATGT TATAT TATAT TATAT TATAT TA-AT TAT
1 TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TAT
28727574 TATAAGAGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
4 4 0.14
5 21 0.72
6 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:28737974 original size:2 final size:2
Alignment explanation
Indices: 28737967--28737994 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28737957 TTGCTTATTC
28737967 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
28737995 TATTAATGGA
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:28743960 original size:18 final size:18
Alignment explanation
Indices: 28743937--28743972 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28743927 TTTTAAATAA
28743937 AAAAATAAAAAATAAAAT
1 AAAAATAAAAAATAAAAT
* *
28743955 AAAAATACAAAATCAAAT
1 AAAAATAAAAAATAAAAT
28743973 TCGCATATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (18 bp):
AAAAATAAAAAATAAAAT
Found at i:28757757 original size:13 final size:13
Alignment explanation
Indices: 28757718--28757770 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
28757708 AGTTTGGCAA
28757718 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
28757731 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
*
28757744 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
28757757 TGTTTTTGAAAAG
1 TGCTTTTGAAAAG
28757770 T
1 T
28757771 TTGGTTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
12 3 0.09
13 27 0.82
14 3 0.09
ACGTcount: A:0.30, C:0.06, G:0.26, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:28775232 original size:6 final size:6
Alignment explanation
Indices: 28775221--28775246 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
28775211 CAATATCTCC
28775221 AAAGCA AAAGCA AAAGCA AAAGCA AA
1 AAAGCA AAAGCA AAAGCA AAAGCA AA
28775247 CACACACATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.15, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGCA
Found at i:28775266 original size:2 final size:2
Alignment explanation
Indices: 28775261--28775299 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
28775251 CACATGTATG
28775261 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28775300 TAGTAGCCCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28779250 original size:3 final size:3
Alignment explanation
Indices: 28779236--28779295 Score: 86
Period size: 3 Copynumber: 19.7 Consensus size: 3
28779226 TCGTTGCTAC
28779236 TAT TACT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
28779281 CAT TATT TAT TAT TA
1 TAT TA-T TAT TAT TA
28779296 CTATACCTAC
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 1 0.02
3 45 0.87
4 6 0.12
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:28779485 original size:28 final size:28
Alignment explanation
Indices: 28779454--28779511 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
28779444 AGTTTTTCAT
*
28779454 ATTTTATA-ATCCAAATATATATATATAC
1 ATTTTATATATAC-AATATATATATATAC
*
28779482 ATTTTTTATATACAATATATATATATAC
1 ATTTTATATATACAATATATATATATAC
28779510 AT
1 AT
28779512 ACACTATTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTTTATATATACAATATATATATATAC
Found at i:28779593 original size:18 final size:18
Alignment explanation
Indices: 28779572--28779611 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28779562 ATATATGTTC
28779572 ATAATTTATTAATATATT
1 ATAATTTATTAATATATT
* * *
28779590 ATAATTTTTTTATATTTT
1 ATAATTTATTAATATATT
28779608 ATAA
1 ATAA
28779612 ATACATGTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATAATTTATTAATATATT
Found at i:28784978 original size:2 final size:2
Alignment explanation
Indices: 28784971--28785018 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
28784961 ATAGAAAAGG
28784971 AT AT AT AT 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 AT AT AT AT
28785013 AT AT AT
1 AT AT AT
28785019 TAGTAGTAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28785404 original size:19 final size:18
Alignment explanation
Indices: 28785382--28785435 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
28785372 AATACGAAAT
*
28785382 AATTCAAAATAATTTTTAA
1 AATTCAAAAT-ATTTATAA
*
28785401 AATTCAATATATTTATAAA
1 AATTCAAAATATTTAT-AA
*
28785420 AATTCCAAAT-TTTATA
1 AATTCAAAATATTTATA
28785436 TATTTTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 1 0.03
18 10 0.33
19 19 0.63
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTCAAAATATTTATAA
Found at i:28785419 original size:18 final size:19
Alignment explanation
Indices: 28785382--28785420 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
28785372 AATACGAAAT
*
28785382 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTATAA
*
28785401 AATTCAATAT-ATTTATAA
1 AATTCAAAATAATTTATAA
28785419 AA
1 AA
28785421 ATTCCAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTCAAAATAATTTATAA
Found at i:28785465 original size:20 final size:20
Alignment explanation
Indices: 28785437--28785474 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28785427 AATTTTATAT
*
28785437 ATTTTAAAAAATTATAAAAA
1 ATTTAAAAAAATTATAAAAA
*
28785457 ATTTAAAAAAATTCTAAA
1 ATTTAAAAAAATTATAAA
28785475 TAATATATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (20 bp):
ATTTAAAAAAATTATAAAAA
Found at i:28785627 original size:16 final size:16
Alignment explanation
Indices: 28785606--28785636 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28785596 TGAAAAAGGT
28785606 TTTCAAATATATATGA
1 TTTCAAATATATATGA
*
28785622 TTTCAAATTTATATG
1 TTTCAAATATATATG
28785637 TTGTAATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGA
Found at i:28799975 original size:41 final size:41
Alignment explanation
Indices: 28799958--28800111 Score: 290
Period size: 41 Copynumber: 3.8 Consensus size: 41
28799948 ACTTATAGCA
28799958 TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
1 TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
* *
28799999 TGATTCAAATCACCGGCACGTAGCCTACTAGGTTTATAACC
1 TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
28800040 TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
1 TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
28800081 TGATTCAGATCACCGGCACGTAGCCTGCTAG
1 TGATTCAGATCACCGGCACGTAGCCTGCTAG
28800112 ACTTAAAGTC
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 109 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (41 bp):
TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
Found at i:28802129 original size:13 final size:13
Alignment explanation
Indices: 28802111--28802135 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28802101 CAATCAAATG
28802111 CACACAAAATAAA
1 CACACAAAATAAA
28802124 CACACAAAATAA
1 CACACAAAATAA
28802136 TATTAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:28819553 original size:27 final size:27
Alignment explanation
Indices: 28819523--28819585 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
28819513 GAGAATAAAA
28819523 AGGCAGCACCAATGGTGCCTTTTCCAT
1 AGGCAGCACCAATGGTGCCTTTTCCAT
*
28819550 AGGCAACACCAATGGTGCCTTTTCCAT
1 AGGCAGCACCAATGGTGCCTTTTCCAT
*
28819577 AGGCGGCAC
1 AGGCAGCAC
28819586 AGGACTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.22
Consensus pattern (27 bp):
AGGCAGCACCAATGGTGCCTTTTCCAT
Found at i:28820310 original size:30 final size:30
Alignment explanation
Indices: 28820274--28820335 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
28820264 CTGATAAAAA
28820274 TATCCTTTATTGTTAATTATATTACTAAAC
1 TATCCTTTATTGTTAATTATATTACTAAAC
28820304 TATCCTTTATTGTTAATTATATTACTAAAC
1 TATCCTTTATTGTTAATTATATTACTAAAC
28820334 TA
1 TA
28820336 CATTAGAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.34, C:0.13, G:0.03, T:0.50
Consensus pattern (30 bp):
TATCCTTTATTGTTAATTATATTACTAAAC
Found at i:28821398 original size:27 final size:27
Alignment explanation
Indices: 28821360--28821422 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
28821350 TTTTAATCAT
28821360 GTGCCGCCTATGAGAAAGGCACCATTG
1 GTGCCGCCTATGAGAAAGGCACCATTG
* *
28821387 GTGCCGCCTATGGGAAATGCACCATTG
1 GTGCCGCCTATGAGAAAGGCACCATTG
28821414 GTGCCGCCT
1 GTGCCGCCT
28821423 TTTTATTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.21, C:0.29, G:0.30, T:0.21
Consensus pattern (27 bp):
GTGCCGCCTATGAGAAAGGCACCATTG
Found at i:28821880 original size:39 final size:39
Alignment explanation
Indices: 28821811--28821885 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
28821801 ATACTTTAAA
* *
28821811 TTTATATATATCATTTATCACAATACTAATGAATTTGAG
1 TTTAAATATATCATATATCACAATACTAATGAATTTGAG
* * *
28821850 TTTAAATATTTCATATATCATAATATTAATGAATTT
1 TTTAAATATATCATATATCACAATACTAATGAATTT
28821886 AAATACATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (39 bp):
TTTAAATATATCATATATCACAATACTAATGAATTTGAG
Found at i:28828316 original size:4 final size:4
Alignment explanation
Indices: 28828309--28828335 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
28828299 AAAATATTTG
28828309 TAAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAA
28828336 TAGACGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:28831201 original size:15 final size:14
Alignment explanation
Indices: 28831181--28831223 Score: 56
Period size: 12 Copynumber: 3.2 Consensus size: 14
28831171 TTATTTTATT
28831181 TTATTCATTGATTTC
1 TTATTCATT-ATTTC
28831196 TTATTC-TTATTT-
1 TTATTCATTATTTC
28831208 TT-TTCATTATTTC
1 TTATTCATTATTTC
28831221 TTA
1 TTA
28831224 GATAATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
11 3 0.12
12 8 0.32
13 6 0.24
14 2 0.08
15 6 0.24
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.67
Consensus pattern (14 bp):
TTATTCATTATTTC
Found at i:28831219 original size:25 final size:24
Alignment explanation
Indices: 28831165--28831223 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 24
28831155 TTAAAATATG
28831165 TTATTT-TTATTTTATTTTATTCA
1 TTATTTCTTATTTTATTTTATTCA
*
28831188 TTGATTTCTTATTCTTATTTTTTTCA
1 TT-ATTTCTTATT-TTATTTTATTCA
28831214 TTATTTCTTA
1 TTATTTCTTA
28831224 GATAATTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 2 0.06
24 4 0.12
25 13 0.41
26 13 0.41
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (24 bp):
TTATTTCTTATTTTATTTTATTCA
Found at i:28831421 original size:29 final size:30
Alignment explanation
Indices: 28831360--28831431 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
28831350 GTAATTTTTT
*
28831360 ATAGTT-AGGTGACCAAAAAGAAATTTGCTA
1 ATAGTTGA-GTGACCAAAAAGAAATTTACTA
* * *
28831390 ATATTTGAGTGACCAAAAA-AATTTTATTA
1 ATAGTTGAGTGACCAAAAAGAAATTTACTA
*
28831419 ATAGTTGGGTGAC
1 ATAGTTGAGTGAC
28831432 TATTAATGTC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
29 18 0.51
30 16 0.46
31 1 0.03
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.32
Consensus pattern (30 bp):
ATAGTTGAGTGACCAAAAAGAAATTTACTA
Found at i:28835905 original size:41 final size:41
Alignment explanation
Indices: 28835855--28835934 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
28835845 CCGAATAATT
* *
28835855 TCACTGGCATTAAGCCTGCTAGACAATAAGTCTGAATTATA
1 TCACCGGCATCAAGCCTGCTAGACAATAAGTCTGAATTATA
28835896 TCACCGGCATCAAGCCTGCTAGACAATAAGTCTGAATTA
1 TCACCGGCATCAAGCCTGCTAGACAATAAGTCTGAATTA
28835935 CATTCGATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (41 bp):
TCACCGGCATCAAGCCTGCTAGACAATAAGTCTGAATTATA
Found at i:28837381 original size:23 final size:23
Alignment explanation
Indices: 28837354--28837399 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
28837344 TAATTTGTTA
28837354 TATTAA-ACATATATTAACCTTAT
1 TATTAATAC-TATATTAACCTTAT
28837377 TATTAATTTACTATATTAACCTT
1 TATTAA--TACTATATTAACCTT
28837400 TACTAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
25 12 0.60
26 2 0.10
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTAATACTATATTAACCTTAT
Found at i:28843618 original size:3 final size:3
Alignment explanation
Indices: 28843610--28843638 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28843600 TTTACGCTTA
28843610 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
28843639 AAGATTCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28850269 original size:13 final size:13
Alignment explanation
Indices: 28850251--28850276 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28850241 AAAGAGATTT
28850251 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
28850264 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
28850277 AAATTTGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
GTTTTCTAGTAAA
Found at i:28850347 original size:19 final size:19
Alignment explanation
Indices: 28850307--28850349 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
28850297 GTCTCTTTTC
* *
28850307 GCATTCATTTCATGCATTT
1 GCATTCATTACATGCATAT
28850326 GCATTGCATTACAT-CATAT
1 GCATT-CATTACATGCATAT
28850345 GCATT
1 GCATT
28850350 AAACATAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.42
Consensus pattern (19 bp):
GCATTCATTACATGCATAT
Found at i:28853170 original size:7 final size:7
Alignment explanation
Indices: 28853158--28853200 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
28853148 AAATGACGAG
28853158 ATGAAAA
1 ATGAAAA
28853165 ATGAAAA
1 ATGAAAA
28853172 AGTG-AAA
1 A-TGAAAA
28853179 ATGAAAA
1 ATGAAAA
*
28853186 CTGAAAA
1 ATGAAAA
28853193 ATGGAAAA
1 AT-GAAAA
28853201 GTAAAATGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 2 0.06
7 22 0.71
8 7 0.23
ACGTcount: A:0.65, C:0.02, G:0.19, T:0.14
Consensus pattern (7 bp):
ATGAAAA
Found at i:28853179 original size:14 final size:13
Alignment explanation
Indices: 28853162--28853208 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
28853152 GACGAGATGA
28853162 AAAATGAAAAAGTG
1 AAAATG-AAAAGTG
*
28853176 AAAATGAAAACTG
1 AAAATGAAAAGTG
28853189 AAAAATGGAAAAGT-
1 -AAAAT-GAAAAGTG
28853203 AAAATG
1 AAAATG
28853209 GAGAGGCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 1 0.03
13 11 0.38
14 11 0.38
15 6 0.21
ACGTcount: A:0.64, C:0.02, G:0.19, T:0.15
Consensus pattern (13 bp):
AAAATGAAAAGTG
Found at i:28854649 original size:89 final size:89
Alignment explanation
Indices: 28854493--28855653 Score: 1779
Period size: 89 Copynumber: 13.0 Consensus size: 89
28854483 AGGTTAAAAA
* *
28854493 AAAGTAGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCA
1 AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCA
28854558 TACTGGTGGCGAAACAGATCGAAG
66 TACTGGTGGCGAAACAGATCGAAG
* * *
28854582 AAAGCAGATCTTGTCTTTATAG-ACTGGCGTGAAGTAGATCAAAGATAATAGATCTTGTCTTCTC
1 AAAGCAGATCTTGTCTTCAT-GTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCC
*
28854646 ATACTGGTGGCAAAACAGATCGAAG
65 ATACTGGTGGCGAAACAGATCGAAG
28854671 AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGAT-AAAGATAACAGATCTTGTCTTCCCA
1 AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCA
28854735 TACTGGTGGCGAAACAGATCGAAG
66 TACTGGTGGCGAAACAGATCGAAG
*
28854759 AAAGCGGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCA
1 AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCA
28854824 TACTGGTGGCGAAACAGATCGAAG
66 TACTGGTGGCGAAACAGATCGAAG
* * *
28854848 AAAACAGATCTTGTCTTCATAG-ACTAGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCTC
1 AAAGCAGATCTTGTCTTCAT-GTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCC
28854912 ATACTGGTGGCGAAACAGATCGAAG
65 ATACTGGTGGCGAAACAGATCGAAG
28854937 AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCA
1 AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCA
28855002 TACTGGTGGCGAAACAGATCGAAG
66 TACTGGTGGCGAAACAGATCGAAG
**
28855026 AAAGTGGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCA
1 AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCA
** **
28855091 TACTGGTGGCGAAGTAGATTAAAG
66 TACTGGTGGCGAAACAGATCGAAG
* * *
28855115 AAAGCAGATCTTGTCTTCATGTACTAGCGTGAAGTGGATCAAAGATAACAGATCTTGCCTTCCCA
1 AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCA
* * ** *
28855180 TACTAGTGGCGAAGCAGATTAAAA
66 TACTGGTGGCGAAACAGATCGAAG
* * * *
28855204 AAAGCAGGTCTTGTCTTCATGTACTGGCATGAAGTAGATCAGAGATACCAGATCTTGTCTTCCCA
1 AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCA
* *
28855269 TACTGGTGGCGAAGCAGATCAAAG
66 TACTGGTGGCGAAACAGATCGAAG
* * * *
28855293 AAAGCAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTTCCA
1 AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCA
*
28855358 TACTGGTGGCGAAATAGATCGAAGAAG
66 TACTGGTGGCGAAACAGATC---GAAG
* * *
28855385 AAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTTCCCA
1 AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCA
** *
28855450 TACTGGTGGCGAAGTAGATTGAAG
66 TACTGGTGGCGAAACAGATCGAAG
* * * * *
28855474 AAAACAGATCTTGTCTTCATGTACTGGCATGGAGTAGATTCAAAGATAACAAATCTTGCCTTCCC
1 AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGA-TCAAAGATAACAGATCTTGTCTTCCC
* *
28855539 ATACTGGTGGTGAAGCAGATCGAAG
65 ATACTGGTGGCGAAACAGATCGAAG
* * *
28855564 AAAGCGGATATTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTTCCCA
1 AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCA
*
28855629 TACTGGTGGTGAAACAGATCGAAG
66 TACTGGTGGCGAAACAGATCGAAG
28855653 A
1 A
28855654 TGGCAGATTT
Statistics
Matches: 986, Mismatches: 77, Indels: 18
0.91 0.07 0.02
Matches are distributed among these distances:
88 86 0.09
89 739 0.75
90 82 0.08
92 79 0.08
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (89 bp):
AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCA
TACTGGTGGCGAAACAGATCGAAG
Found at i:28859451 original size:6 final size:7
Alignment explanation
Indices: 28859426--28859450 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28859416 AAAAAACTGT
28859426 AAAAAGA
1 AAAAAGA
28859433 AAAAAGA
1 AAAAAGA
28859440 AAAAAGA
1 AAAAAGA
28859447 AAAA
1 AAAA
28859451 GCAAACCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:28863170 original size:5 final size:5
Alignment explanation
Indices: 28863160--28863186 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
28863150 ACAGATATAA
28863160 GGGAT GGGAT GGGAT GGGAT GGGAT GG
1 GGGAT GGGAT GGGAT GGGAT GGGAT GG
28863187 TGAGGCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.63, T:0.19
Consensus pattern (5 bp):
GGGAT
Found at i:28863996 original size:22 final size:22
Alignment explanation
Indices: 28863968--28864009 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
28863958 ATATCTAGTA
*
28863968 ATAAATATTTTATCAATAAAAT
1 ATAAATATTTTAACAATAAAAT
28863990 ATAAATATTTTAACAATAAA
1 ATAAATATTTTAACAATAAA
28864010 TAGTTCATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAAATATTTTAACAATAAAAT
Found at i:28865546 original size:177 final size:177
Alignment explanation
Indices: 28865246--28865607 Score: 715
Period size: 177 Copynumber: 2.0 Consensus size: 177
28865236 GTCGAAGATG
28865246 GGTCGATCCATCAGCATTGGTGAACTTAACGTATAACTCAATAACAACATTTTCGCTTGAGATGT
1 GGTCGATCCATCAGCATTGGTGAACTTAACGTATAACTCAATAACAACATTTTCGCTTGAGATGT
28865311 GCGATAATATGATCGTCTTAAGATACATTTCACTAATCACATCGAATAGCTCATACTTGTAGGGG
66 GCGATAATATGATCGTCTTAAGATACATTTCACTAATCACATCGAATAGCTCATACTTGTAGGGG
28865376 TCAATGGAAGCAAGAAATCTGCATTGCAACCTCATAATTTTTCCTTA
131 TCAATGGAAGCAAGAAATCTGCATTGCAACCTCATAATTTTTCCTTA
*
28865423 GGTTGATCCATCAGCATTGGTGAACTTAACGTATAACTCAATAACAACATTTTCGCTTGAGATGT
1 GGTCGATCCATCAGCATTGGTGAACTTAACGTATAACTCAATAACAACATTTTCGCTTGAGATGT
28865488 GCGATAATATGATCGTCTTAAGATACATTTCACTAATCACATCGAATAGCTCATACTTGTAGGGG
66 GCGATAATATGATCGTCTTAAGATACATTTCACTAATCACATCGAATAGCTCATACTTGTAGGGG
28865553 TCAATGGAAGCAAGAAATCTGCATTGCAACCTCATAATTTTTCCTTA
131 TCAATGGAAGCAAGAAATCTGCATTGCAACCTCATAATTTTTCCTTA
28865600 GGTCGATC
1 GGTCGATC
28865608 TTTCGATTTT
Statistics
Matches: 183, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
177 183 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (177 bp):
GGTCGATCCATCAGCATTGGTGAACTTAACGTATAACTCAATAACAACATTTTCGCTTGAGATGT
GCGATAATATGATCGTCTTAAGATACATTTCACTAATCACATCGAATAGCTCATACTTGTAGGGG
TCAATGGAAGCAAGAAATCTGCATTGCAACCTCATAATTTTTCCTTA
Found at i:28871670 original size:16 final size:15
Alignment explanation
Indices: 28871628--28871680 Score: 63
Period size: 16 Copynumber: 3.5 Consensus size: 15
28871618 ATAGGTTTTT
*
28871628 TTAAAAAAAATAAAAA
1 TTAAAAAAAAT-AATA
*
28871644 TTATAAAAAATAATA
1 TTAAAAAAAATAATA
28871659 TTAAAAATAAATAATA
1 TTAAAAA-AAATAATA
28871675 -TAAAAA
1 TTAAAAA
28871681 CTATGCAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
15 15 0.45
16 18 0.55
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
TTAAAAAAAATAATA
Found at i:28871678 original size:15 final size:15
Alignment explanation
Indices: 28871633--28871680 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
28871623 TTTTTTTAAA
28871633 AAAAATAAA-AAT-T
1 AAAAATAAATAATAT
*
28871646 ATAAA-AAATAATATT
1 AAAAATAAATAATA-T
28871661 AAAAATAAATAATAT
1 AAAAATAAATAATAT
28871676 AAAAA
1 AAAAA
28871681 CTATGCAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 3 0.10
13 7 0.24
15 11 0.38
16 8 0.28
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAAATAAATAATAT
Found at i:28881293 original size:37 final size:37
Alignment explanation
Indices: 28881243--28881316 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
28881233 TACTCCGATT
*
28881243 TGCTCAATCACCCCAACCTATTCGTTTGGCTACCATC
1 TGCTCAATCACCCCAACCTATTCGGTTGGCTACCATC
*
28881280 TGCTCAATCACCCCAACCTATTTGGTTGGCTACCATC
1 TGCTCAATCACCCCAACCTATTCGGTTGGCTACCATC
28881317 AAGCTCTCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.22, C:0.36, G:0.12, T:0.30
Consensus pattern (37 bp):
TGCTCAATCACCCCAACCTATTCGGTTGGCTACCATC
Found at i:28888165 original size:32 final size:32
Alignment explanation
Indices: 28888119--28888181 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
28888109 AGAAACTAGA
* * *
28888119 GAATAAGTTGTATTATTATGAGAGTATTTTTT
1 GAATAAGTTATATTATTATGAAAATATTTTTT
28888151 GAATAAGTTATATTATTATGAAAATATTTTT
1 GAATAAGTTATATTATTATGAAAATATTTTT
28888182 ATCTCTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (32 bp):
GAATAAGTTATATTATTATGAAAATATTTTTT
Found at i:28893446 original size:27 final size:27
Alignment explanation
Indices: 28893408--28893477 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
28893398 TGATCATCTG
28893408 CTGCATCGCCGTTGACTGTCCCCTCTA
1 CTGCATCGCCGTTGACTGTCCCCTCTA
* * * *
28893435 CTGCATCGCCGTCGACTGTCCCTTTTG
1 CTGCATCGCCGTTGACTGTCCCCTCTA
*
28893462 CTGCATAGCCGTTGAC
1 CTGCATCGCCGTTGAC
28893478 ATTTCTCTGC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.11, C:0.37, G:0.21, T:0.30
Consensus pattern (27 bp):
CTGCATCGCCGTTGACTGTCCCCTCTA
Found at i:28894487 original size:22 final size:22
Alignment explanation
Indices: 28894462--28894505 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
28894452 TGTGCTGCTG
*
28894462 TTTGTAATTTTTGGATTA-TTTA
1 TTTGTAAATTTT-GATTAGTTTA
28894484 TTTGTAAATTTTGATTAGTTTA
1 TTTGTAAATTTTGATTAGTTTA
28894506 ATTATATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.25, C:0.00, G:0.14, T:0.61
Consensus pattern (22 bp):
TTTGTAAATTTTGATTAGTTTA
Found at i:28895960 original size:117 final size:117
Alignment explanation
Indices: 28895816--28896048 Score: 423
Period size: 117 Copynumber: 2.0 Consensus size: 117
28895806 AGTTACTGAG
28895816 CTCCAAATTATCTATTTCTTTCTCTTTTTTGGTCAGA-CAGTATTAAGCAGGCCAAAGTTTGTAA
1 CTCCAAATTATCTATTTCTTTCTCTTTTTTGGTCAGATC-GTATTAAGCAGGCCAAAGTTTGTAA
* *
28895880 AGGTAATAGCAGTGAATTTCACCCTTATATTTAAAACTGTTGCTTACTCTTCA
65 AGGTAATAGCAGTGAATTTCACCATTATATTTAAAACTGTGGCTTACTCTTCA
28895933 CTCCAAATTATCTATTTCTTTCTCTTTTTTGGTCAGATCGTATTAAGCAGGCCAAAGTTTGTAAA
1 CTCCAAATTATCTATTTCTTTCTCTTTTTTGGTCAGATCGTATTAAGCAGGCCAAAGTTTGTAAA
*
28895998 GGTAATAGCAGTGAATTTCACCATTATATTTAAAACTGTGGCTTTCTCTTC
66 GGTAATAGCAGTGAATTTCACCATTATATTTAAAACTGTGGCTTACTCTTC
28896049 GCTTGGTATT
Statistics
Matches: 112, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
117 111 0.99
118 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.40
Consensus pattern (117 bp):
CTCCAAATTATCTATTTCTTTCTCTTTTTTGGTCAGATCGTATTAAGCAGGCCAAAGTTTGTAAA
GGTAATAGCAGTGAATTTCACCATTATATTTAAAACTGTGGCTTACTCTTCA
Found at i:28896737 original size:71 final size:72
Alignment explanation
Indices: 28896626--28896859 Score: 222
Period size: 72 Copynumber: 3.2 Consensus size: 72
28896616 TAAGTAAATT
* *** *
28896626 CGTTTATTTAATTATGTGTTTTTAAAAAAGGTTAATTTAGTTCAATTTATTAAGTTTTGATATTA
1 CGTTTATTTAGTTATACATTTTT-AAAAAGCTTAATTTAGTTCAATTTATTAAGTTTTGATATTA
*
28896691 AGCGAAAC
65 AGTGAAAC
* * ** **
28896699 CGTTTATTTAGTTATACA-TTTTCAGAAGCTTAATTTAGTTTGATTTATTAAAATTTGATATTAA
1 CGTTTATTTAGTTATACATTTTTAAAAAGCTTAATTTAGTTCAATTTATTAAGTTTTGATATTAA
* *
28896763 GTAAAAA
66 GTGAAAC
* * * * * *
28896770 CGTTTGTTCAATTATGA-ATTTTTAAAAAGGTTAATTTAGTTCAACTTATTGAGTTTTGATATTA
1 CGTTTATTTAGTTAT-ACATTTTTAAAAAGCTTAATTTAGTTCAATTTATTAAGTTTTGATATTA
*
28896834 AGTGGAAC
65 AGTGAAAC
*
28896842 CATTTATTCT-GTTATACA
1 CGTTTATT-TAGTTATACA
28896860 AAGTAAAACC
Statistics
Matches: 124, Mismatches: 33, Indels: 9
0.75 0.20 0.05
Matches are distributed among these distances:
71 53 0.43
72 57 0.46
73 14 0.11
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.46
Consensus pattern (72 bp):
CGTTTATTTAGTTATACATTTTTAAAAAGCTTAATTTAGTTCAATTTATTAAGTTTTGATATTAA
GTGAAAC
Found at i:28896829 original size:72 final size:72
Alignment explanation
Indices: 28896616--28896836 Score: 239
Period size: 71 Copynumber: 3.1 Consensus size: 72
28896606 ATTAATTATC
** **
28896616 TAAGTAAATTCGTTTATTTAATTATGTGTTTTTAAAAAAGGTTAATTTAGTTCAATTTATTAAGT
1 TAAGTAAAAACGTTTATTTAATTATGAATTTTT-AAAAAGGTTAATTTAGTTCAATTTATTAAGT
28896681 TTTGATAT
65 TTTGATAT
** * * * * * ** **
28896689 TAAGCGAAACCGTTTATTTAGTTAT-ACA-TTTTCAGAAGCTTAATTTAGTTTGATTTATTAAAA
1 TAAGTAAAAACGTTTATTTAATTATGA-ATTTTTAAAAAGGTTAATTTAGTTCAATTTATTAAGT
28896752 TTTGATAT
65 TTTGATAT
* * * *
28896760 TAAGTAAAAACGTTTGTTCAATTATGAATTTTTAAAAAGGTTAATTTAGTTCAACTTATTGAGTT
1 TAAGTAAAAACGTTTATTTAATTATGAATTTTTAAAAAGGTTAATTTAGTTCAATTTATTAAGTT
28896825 TTGATAT
66 TTGATAT
28896832 TAAGT
1 TAAGT
28896837 GGAACCATTT
Statistics
Matches: 116, Mismatches: 29, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
71 52 0.45
72 44 0.38
73 20 0.17
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (72 bp):
TAAGTAAAAACGTTTATTTAATTATGAATTTTTAAAAAGGTTAATTTAGTTCAATTTATTAAGTT
TTGATAT
Found at i:28896896 original size:28 final size:28
Alignment explanation
Indices: 28896865--28896919 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
28896855 ATACAAAGTA
*
28896865 AAACCGCTTGTTCATTTATGCCTTTTTT
1 AAACCGCTTGTTCAATTATGCCTTTTTT
*
28896893 AAACCGCTTGTTCAATTATGCGTTTTT
1 AAACCGCTTGTTCAATTATGCCTTTTT
28896920 ATTTATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (28 bp):
AAACCGCTTGTTCAATTATGCCTTTTTT
Found at i:28897045 original size:19 final size:17
Alignment explanation
Indices: 28897013--28897052 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
28897003 ATTTTAGTAT
28897013 TGAAAAAATAAACAAAA
1 TGAAAAAATAAACAAAA
28897030 TGAAAAGAAGTAAACAAAA
1 TGAAAA-AA-TAAACAAAA
28897049 -GAAA
1 TGAAA
28897053 TAACAAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.29
18 6 0.29
19 9 0.43
ACGTcount: A:0.72, C:0.05, G:0.12, T:0.10
Consensus pattern (17 bp):
TGAAAAAATAAACAAAA
Found at i:28897829 original size:13 final size:13
Alignment explanation
Indices: 28897813--28897839 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28897803 ATAATTAAGG
28897813 GTTAAAATTTAAA
1 GTTAAAATTTAAA
28897826 GTTAAAATTTAAA
1 GTTAAAATTTAAA
28897839 G
1 G
28897840 ATGATAATCA
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:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (13 bp):
GTTAAAATTTAAA
Found at i:28897933 original size:18 final size:17
Alignment explanation
Indices: 28897907--28898047 Score: 75
Period size: 18 Copynumber: 7.5 Consensus size: 17
28897897 AACTTACATA
28897907 ATACATAAATATATATC
1 ATACATAAATATATATC
* *
28897924 ATACCATAAATTACATAAC
1 ATA-CATAAA-TATATATC
*
28897943 TTACATAAATATATATC
1 ATACATAAATATATATC
* *
28897960 ATATCATAACTTACATAGCTTACATA
1 ATA-CAT-A---A-ATA---TATATC
28897986 ATACATAAATATATATC
1 ATACATAAATATATATC
* * *
28898003 ATATCATAACTTACATAAC
1 ATA-CATAA-ATATATATC
*
28898022 TTACATAAATATATATC
1 ATACATAAATATATATC
28898039 ATATCATAA
1 ATA-CATAA
28898048 CTTACATAAA
Statistics
Matches: 92, Mismatches: 18, Indels: 27
0.67 0.13 0.20
Matches are distributed among these distances:
17 26 0.28
18 30 0.33
19 17 0.18
20 3 0.03
21 1 0.01
22 1 0.01
23 3 0.03
24 1 0.01
25 3 0.03
26 7 0.08
ACGTcount: A:0.49, C:0.16, G:0.01, T:0.35
Consensus pattern (17 bp):
ATACATAAATATATATC
Found at i:28897955 original size:36 final size:36
Alignment explanation
Indices: 28897887--28898056 Score: 227
Period size: 36 Copynumber: 4.6 Consensus size: 36
28897877 AAAAAATTGG
* *
28897887 ATCATAACTTAACTTACATAA--TACATAAATATAT
1 ATCATATCATAACTTACATAACTTACATAAATATAT
* *
28897921 ATCATACCATAAATTACATAACTTACATAAATATAT
1 ATCATATCATAACTTACATAACTTACATAAATATAT
28897957 ATCATATCATAACTTACATAGCTTACATAATACATAAATATAT
1 ATCATATCATAACTTACATA----AC-T--TACATAAATATAT
28898000 ATCATATCATAACTTACATAACTTACATAAATATAT
1 ATCATATCATAACTTACATAACTTACATAAATATAT
28898036 ATCATATCATAACTTACATAA
1 ATCATATCATAACTTACATAA
28898057 AACTTTGGAT
Statistics
Matches: 122, Mismatches: 5, Indels: 16
0.85 0.03 0.11
Matches are distributed among these distances:
34 18 0.15
36 65 0.53
38 1 0.01
39 2 0.02
40 2 0.02
41 1 0.01
43 33 0.27
ACGTcount: A:0.48, C:0.16, G:0.01, T:0.35
Consensus pattern (36 bp):
ATCATATCATAACTTACATAACTTACATAAATATAT
Found at i:28897994 original size:79 final size:79
Alignment explanation
Indices: 28897899--28898055 Score: 296
Period size: 79 Copynumber: 2.0 Consensus size: 79
28897889 CATAACTTAA
28897899 CTTACATAATACATAAATATATATCATACCATAAATTACATAACTTACATAAATATATATCATAT
1 CTTACATAATACATAAATATATATCATACCATAAATTACATAACTTACATAAATATATATCATAT
28897964 CATAACTTACATAG
66 CATAACTTACATAG
* *
28897978 CTTACATAATACATAAATATATATCATATCATAACTTACATAACTTACATAAATATATATCATAT
1 CTTACATAATACATAAATATATATCATACCATAAATTACATAACTTACATAAATATATATCATAT
28898043 CATAACTTACATA
66 CATAACTTACATA
28898056 AAACTTTGGA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.48, C:0.17, G:0.01, T:0.35
Consensus pattern (79 bp):
CTTACATAATACATAAATATATATCATACCATAAATTACATAACTTACATAAATATATATCATAT
CATAACTTACATAG
Found at i:28904232 original size:43 final size:43
Alignment explanation
Indices: 28904137--28904242 Score: 124
Period size: 43 Copynumber: 2.5 Consensus size: 43
28904127 TATTAAAAAC
** ** *
28904137 GCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTGGGAAAAGT
1 GCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAAGT
* *
28904180 GTCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGGAAA-T
1 GCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAAGT
*
28904222 CGCCGTTAAAGGTCATGTTCT
1 -GCCGCTAAAGGTCATGTTCT
28904243 ATAACGGTGT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 1 0.02
43 52 0.98
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (43 bp):
GCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAAGT
Found at i:28905375 original size:25 final size:25
Alignment explanation
Indices: 28905347--28905426 Score: 58
Period size: 25 Copynumber: 3.2 Consensus size: 25
28905337 TACATTGTAA
28905347 AAAGGATCCCGAATTCACAATCAAT
1 AAAGGATCCCGAATTCACAATCAAT
* * ** *
28905372 AAA-GA-GCC-ATATTCCGCAAAAAAAA
1 AAAGGATCCCGA-ATT-CAC-AATCAAT
28905397 AAAAGGATCCCGAATTCACAATCAAT
1 A-AAGGATCCCGAATTCACAATCAAT
28905423 AAAG
1 AAAG
28905427 AGCCATATTC
Statistics
Matches: 38, Mismatches: 10, Indels: 14
0.61 0.16 0.23
Matches are distributed among these distances:
22 1 0.03
23 5 0.13
24 4 0.11
25 11 0.29
26 7 0.18
27 4 0.11
28 5 0.13
29 1 0.03
ACGTcount: A:0.50, C:0.21, G:0.12, T:0.16
Consensus pattern (25 bp):
AAAGGATCCCGAATTCACAATCAAT
Found at i:28905448 original size:51 final size:51
Alignment explanation
Indices: 28905345--28905441 Score: 194
Period size: 51 Copynumber: 1.9 Consensus size: 51
28905335 AATACATTGT
28905345 AAAAAGGATCCCGAATTCACAATCAATAAAGAGCCATATTCCGCAAAAAAA
1 AAAAAGGATCCCGAATTCACAATCAATAAAGAGCCATATTCCGCAAAAAAA
28905396 AAAAAGGATCCCGAATTCACAATCAATAAAGAGCCATATTCCGCAA
1 AAAAAGGATCCCGAATTCACAATCAATAAAGAGCCATATTCCGCAA
28905442 TCAAAAATAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.48, C:0.23, G:0.12, T:0.16
Consensus pattern (51 bp):
AAAAAGGATCCCGAATTCACAATCAATAAAGAGCCATATTCCGCAAAAAAA
Found at i:28907035 original size:98 final size:98
Alignment explanation
Indices: 28906914--28907110 Score: 367
Period size: 98 Copynumber: 2.0 Consensus size: 98
28906904 CTAAAAATAA
* *
28906914 TAAAGGAAATATTCCGAGTTTGGGATTTTGGAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
28906979 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
28907012 TAAAGGAAATATTCTGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
28907077 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
28907110 T
1 T
28907111 TTTATTGCAC
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.27, C:0.09, G:0.26, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:28908988 original size:22 final size:21
Alignment explanation
Indices: 28908963--28909005 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
28908953 AAATGATTTT
* *
28908963 AATATAAATAAAATTAAGAAAA
1 AATAAAAATAAAAATAA-AAAA
28908985 AATAAAAATAAAAATAAAAAA
1 AATAAAAATAAAAATAAAAAA
28909006 CCCAACCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (21 bp):
AATAAAAATAAAAATAAAAAA
Found at i:28921940 original size:2 final size:2
Alignment explanation
Indices: 28921928--28921962 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
28921918 GTTGTAACTG
28921928 AT AT A- 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 AT
28921963 CGTCATAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28928443 original size:16 final size:16
Alignment explanation
Indices: 28928422--28928465 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
28928412 TGTATTGGAT
*
28928422 TAGAGGCGTAATGAAA
1 TAGAGGTGTAATGAAA
* *
28928438 TAGAGGTGTAATGGAT
1 TAGAGGTGTAATGAAA
28928454 TAGAGGTGTAAT
1 TAGAGGTGTAAT
28928466 AGCAAATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.36, C:0.02, G:0.34, T:0.27
Consensus pattern (16 bp):
TAGAGGTGTAATGAAA
Found at i:28928722 original size:16 final size:16
Alignment explanation
Indices: 28928685--28928726 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28928675 TTAATCATAT
*
28928685 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
28928701 TT-AAATATATTATAA
1 TTAAAATATATTATAA
28928716 TTAAAATATAT
1 TTAAAATATAT
28928727 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:28928733 original size:14 final size:15
Alignment explanation
Indices: 28928694--28928735 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28928684 TTTAAACATA
*
28928694 ATTATTATTAAATAT
1 ATTATAATTAAATAT
28928709 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
28928723 A-TATAATTTAATA
1 ATTATAATTAAATA
28928736 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:28928853 original size:14 final size:15
Alignment explanation
Indices: 28928804--28928855 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
28928794 ATAAAATTTA
28928804 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
28928819 TATTAAATATATTAT
1 AATTAAATATATTAT
28928834 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
28928847 AATTTAATA
1 AATTAAATA
28928856 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:28928858 original size:59 final size:59
Alignment explanation
Indices: 28928688--28928988 Score: 267
Period size: 59 Copynumber: 5.0 Consensus size: 59
28928678 ATCATATTTA
*
28928688 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTAAAT
* * * * * * * *
28928747 AATCA-ATATTGTTATATGAATTTACTCA-AATCATAATATATGATACT-ATAAAATT-TAAATT
1 AA-CATA-ATTATTAT-TAAATATA-TTATAATTAAAATATATAAT-TTAATAAAATTCTAAA-T
*
28928808 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTAAAT
* * * * * * * *
28928867 AATCA-ATATTCTTATATGAATTTACTCA-AATCATAATATATGATACT-ATAAAATT-TAAATT
1 AA-CATA-ATTATTAT-TAAATATA-TTATAATTAAAATATATAAT-TTAATAAAATTCTAAA-T
*
28928928 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTAAAT
28928987 AA
1 AA
28928989 TTAATATTCT
Statistics
Matches: 186, Mismatches: 36, Indels: 40
0.71 0.14 0.15
Matches are distributed among these distances:
58 6 0.03
59 64 0.34
60 48 0.26
61 62 0.33
62 6 0.03
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.43
Consensus pattern (59 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTAAAT
Found at i:28928973 original size:14 final size:15
Alignment explanation
Indices: 28928924--28928975 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
28928914 ATAAAATTTA
28928924 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
28928939 TATTAAATATATTAT
1 AATTAAATATATTAT
28928954 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
28928967 AATTTAATA
1 AATTAAATA
28928976 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:28929175 original size:120 final size:120
Alignment explanation
Indices: 28928688--28929159 Score: 831
Period size: 120 Copynumber: 3.9 Consensus size: 120
28928678 ATCATATTTA
28928688 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
*
28928753 TATTGTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATT
28928808 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
28928873 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATT
*
28928928 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
* *
28928993 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAATTTTAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATT
* * * * *
28929048 AAAATAATAATTACTACATATAATT-TAA-TAATAATATATAATTTAATAAAATTCTTAATAATT
1 AACATAATTATTATTAAATAT-ATTATAATTAA-AATATATAATTTAATAAAATTCTTAATAATC
28929111 AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAA
64 AATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAA
28929160 GATAATTTGA
Statistics
Matches: 340, Mismatches: 10, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
119 3 0.01
120 334 0.98
121 3 0.01
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATT
Found at i:28930729 original size:11 final size:11
Alignment explanation
Indices: 28930715--28930741 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
28930705 AAAAATCAAT
28930715 ACAAAAGTTTC
1 ACAAAAGTTTC
28930726 ACAAAAGTTTC
1 ACAAAAGTTTC
28930737 ACAAA
1 ACAAA
28930742 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:28932335 original size:15 final size:15
Alignment explanation
Indices: 28932315--28932345 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28932305 ATATTATGTA
28932315 TAATTGACCTAAAAT
1 TAATTGACCTAAAAT
28932330 TAATTGACCTAAAAT
1 TAATTGACCTAAAAT
28932345 T
1 T
28932346 TGAAGGTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (15 bp):
TAATTGACCTAAAAT
Found at i:28937863 original size:13 final size:13
Alignment explanation
Indices: 28937842--28937882 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
28937832 CTCTTGCTTC
28937842 TTCCGTTTTCTTT
1 TTCCGTTTTCTTT
*
28937855 TTCCTTTTTTCTTT
1 TTCC-GTTTTCTTT
*
28937869 TTCGGTTTTCTTT
1 TTCCGTTTTCTTT
28937882 T
1 T
28937883 CGGTTTTGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.00, C:0.20, G:0.07, T:0.73
Consensus pattern (13 bp):
TTCCGTTTTCTTT
Found at i:28937877 original size:14 final size:14
Alignment explanation
Indices: 28937847--28937889 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
28937837 GCTTCTTCCG
**
28937847 TTTTCTTTTTCCTT
1 TTTTCTTTTTCGGT
28937861 TTTTCTTTTTCGG-
1 TTTTCTTTTTCGGT
28937874 TTTTC-TTTTCGGT
1 TTTTCTTTTTCGGT
28937887 TTT
1 TTT
28937890 GGTTTTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 7 0.27
13 8 0.31
14 11 0.42
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.74
Consensus pattern (14 bp):
TTTTCTTTTTCGGT
Found at i:28937884 original size:12 final size:13
Alignment explanation
Indices: 28937846--28937889 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
28937836 TGCTTCTTCC
*
28937846 GTTTTCTTTTTCCT
1 GTTTTCTTTTT-CG
*
28937860 TTTTTCTTTTTCG
1 GTTTTCTTTTTCG
28937873 GTTTTC-TTTTCG
1 GTTTTCTTTTTCG
28937885 GTTTT
1 GTTTT
28937890 GGTTTTGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 11 0.41
13 6 0.22
14 10 0.37
ACGTcount: A:0.00, C:0.16, G:0.11, T:0.73
Consensus pattern (13 bp):
GTTTTCTTTTTCG
Found at i:28938652 original size:26 final size:25
Alignment explanation
Indices: 28938623--28938677 Score: 58
Period size: 26 Copynumber: 2.1 Consensus size: 25
28938613 TACTATTTAG
*
28938623 TTAAGTCA-TTTATTTTATATGTTATT
1 TTAAATCAGTTTATTTTA-AT-TTATT
*
28938649 TTAAAATTAGTTTATTTTAATTTATT
1 TT-AAATCAGTTTATTTTAATTTATT
28938675 TTA
1 TTA
28938678 TTTAAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
25 1 0.04
26 9 0.36
27 6 0.24
28 9 0.36
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (25 bp):
TTAAATCAGTTTATTTTAATTTATT
Found at i:28938679 original size:15 final size:16
Alignment explanation
Indices: 28938644--28938686 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
28938634 ATTTTATATG
28938644 TTATTTTAAAATTAGT
1 TTATTTTAAAATTAGT
* *
28938660 TTATTTT-AATTTATT
1 TTATTTTAAAATTAGT
28938675 TTA-TTTAAAATT
1 TTATTTTAAAATT
28938687 TCCCGTGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 3 0.13
15 13 0.57
16 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTATTTTAAAATTAGT
Found at i:28940864 original size:4 final size:4
Alignment explanation
Indices: 28940855--28940881 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
28940845 CATAATTGTA
28940855 TTAT TTAT TTAT TTAT TTAT TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTA
28940882 CGTGTTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:28944498 original size:20 final size:22
Alignment explanation
Indices: 28944455--28944505 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
28944445 TGAGATCCTC
*
28944455 CAAACTAAATAAAAATATATAA
1 CAAATTAAATAAAAATATATAA
*
28944477 CAAATTAAAT-AAATTATA-AA
1 CAAATTAAATAAAAATATATAA
*
28944497 CATATTAAA
1 CAAATTAAA
28944506 AATGCCCCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 10 0.38
21 7 0.27
22 9 0.35
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (22 bp):
CAAATTAAATAAAAATATATAA
Found at i:28945647 original size:19 final size:20
Alignment explanation
Indices: 28945608--28945650 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
28945598 TTGAACTTTT
* *
28945608 AAAATTTATATTTTTTGAAA
1 AAAATTAATATTTATTGAAA
28945628 AAAATTAATATTTATT-AAA
1 AAAATTAATATTTATTGAAA
28945647 AAAA
1 AAAA
28945651 GTTAGAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
AAAATTAATATTTATTGAAA
Found at i:28947870 original size:27 final size:27
Alignment explanation
Indices: 28947820--28947872 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
28947810 ATATCCTTTA
*
28947820 GAAATTTTTTTAAAATATATAAATTTT
1 GAAATTTTTTAAAAATATATAAATTTT
*
28947847 GAAATTTTTATAAAAATTTA-AAATTT
1 GAAATTTTT-TAAAAATATATAAATTT
28947873 AAAAAGTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (27 bp):
GAAATTTTTTAAAAATATATAAATTTT
Found at i:28950099 original size:2 final size:2
Alignment explanation
Indices: 28950092--28950116 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28950082 CTTTTTGCTT
28950092 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
28950117 CCCTTTCCTG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:28962005 original size:2 final size:2
Alignment explanation
Indices: 28962000--28962032 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
28961990 ATTCGAGAAA
28962000 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
28962033 ATCCACAAGG
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:28964374 original size:3 final size:3
Alignment explanation
Indices: 28964360--28964391 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
28964350 TCTCATACCC
*
28964360 CTT CTT CCT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
28964392 GACACATCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:28966590 original size:15 final size:17
Alignment explanation
Indices: 28966570--28966612 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
28966560 TTGTTGTGTC
28966570 ATTAAATATTT-AAA-A
1 ATTAAATATTTCAAATA
*
28966585 ATTAAAAATTTCAAATA
1 ATTAAATATTTCAAATA
*
28966602 AATAAATATTT
1 ATTAAATATTT
28966613 TTTAATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 10 0.43
16 3 0.13
17 10 0.43
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTAAATATTTCAAATA
Found at i:28967262 original size:17 final size:19
Alignment explanation
Indices: 28967226--28967264 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
28967216 TTGAATATTG
*
28967226 TTTTAAAATATTTTATTAA
1 TTTTAAAATATTTTAATAA
28967245 TTTT-AAAT-TTTTAATAA
1 TTTTAAAATATTTTAATAA
28967262 TTT
1 TTT
28967265 CTTATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 4 0.21
19 4 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTAAAATATTTTAATAA
Found at i:28967274 original size:28 final size:27
Alignment explanation
Indices: 28967226--28967279 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
28967216 TTGAATATTG
*
28967226 TTTTAAAATATTTTATTAATTTTAAAT
1 TTTTAAAATATTTTATAAATTTTAAAT
28967253 TTTTAATAAT-TTCTTATAAATTTTAAA
1 TTTTAA-AATATT-TTATAAATTTTAAA
28967280 CCGATTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTTAAAATATTTTATAAATTTTAAAT
Found at i:28974747 original size:15 final size:14
Alignment explanation
Indices: 28974727--28974775 Score: 55
Period size: 13 Copynumber: 3.4 Consensus size: 14
28974717 TTAATTTTGG
28974727 TTTTATATTTATTAT
1 TTTTATATTTATT-T
28974742 TTTTATTATTTATTT
1 TTTTA-TATTTATTT
*
28974757 TTTTAT-TTTGTTT
1 TTTTATATTTATTT
*
28974770 ATTTAT
1 TTTTAT
28974776 TTGGACCGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 11 0.35
14 1 0.03
15 11 0.35
16 8 0.26
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (14 bp):
TTTTATATTTATTT
Found at i:28974748 original size:13 final size:12
Alignment explanation
Indices: 28974727--28974777 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
28974717 TTAATTTTGG
*
28974727 TTTTATATTTAT
1 TTTTTTATTTAT
28974739 TATTTTTA-TTAT
1 T-TTTTTATTTAT
28974751 TTATTTT-TTTAT
1 TT-TTTTATTTAT
28974763 TTTGTTTATTTAT
1 TTT-TTTATTTAT
28974776 TT
1 TT
28974778 GGACCGGGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
11 2 0.06
12 19 0.58
13 12 0.36
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTTTATTTAT
Found at i:28974753 original size:16 final size:15
Alignment explanation
Indices: 28974727--28974763 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
28974717 TTAATTTTGG
28974727 TTTTA-TATTTATTAT
1 TTTTATTATTTATT-T
28974742 TTTTATTATTTATTT
1 TTTTATTATTTATTT
28974757 TTTTATT
1 TTTTATT
28974764 TTGTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTATTATTTATTT
Found at i:28974762 original size:21 final size:21
Alignment explanation
Indices: 28974728--28974777 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
28974718 TAATTTTGGT
28974728 TTTATATTTATTATTTT-TATTA
1 TTTAT-TTTATTATTTTGT-TTA
*
28974750 TTTATTTTTTTATTTTGTTTA
1 TTTATTTTATTATTTTGTTTA
28974771 TTTATTT
1 TTTATTT
28974778 GGACCGGGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (21 bp):
TTTATTTTATTATTTTGTTTA
Found at i:28975055 original size:50 final size:50
Alignment explanation
Indices: 28974966--28975266 Score: 164
Period size: 50 Copynumber: 6.0 Consensus size: 50
28974956 GCTTGGATCC
* * * *
28974966 ACTCCACCGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCT
1 ACTCCACTGCAATGTCGAGGAAGCAAGATACACCATTGTGGCTTTAATCT
* * *
28975016 GCTCTACTGCAATGTCGAGGAAGC-AGAGTACGCCATTGTGGCTTTAATCT
1 ACTCCACTGCAATGTCGAGGAAGCAAGA-TACACCATTGTGGCTTTAATCT
* * * * ** *
28975066 ACTCCACTGC-ATCG-CCAGGGAAGTAACACT-CGCCGCTGTGGCTTTAGTCT
1 ACTCCACTGCAAT-GTCGA-GGAAGCAAGA-TACACCATTGTGGCTTTAATCT
** ** * * * *
28975116 TTTTAACCGCAATGTTCG-GGAGGCAAGATTCACCAATGTGGCTTTAATCT
1 ACTCCACTGCAATG-TCGAGGAAGCAAGATACACCATTGTGGCTTTAATCT
** * * * * * ** *
28975166 GTTCCACTGCACTG-CCAGGGAAGTAAGATTCGCTGTTGTAGCTTTAATCT
1 ACTCCACTGCAATGTCGA-GGAAGCAAGATACACCATTGTGGCTTTAATCT
** ** * *
28975216 TTTTAACTGCAATGTCGGGGAAGCAAGATTCACCATTGTGGCTTTAATCT
1 ACTCCACTGCAATGTCGAGGAAGCAAGATACACCATTGTGGCTTTAATCT
28975266 A
1 A
28975267 TTGCACTACA
Statistics
Matches: 186, Mismatches: 54, Indels: 22
0.71 0.21 0.08
Matches are distributed among these distances:
48 1 0.01
49 8 0.04
50 170 0.91
51 6 0.03
52 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (50 bp):
ACTCCACTGCAATGTCGAGGAAGCAAGATACACCATTGTGGCTTTAATCT
Found at i:28975294 original size:100 final size:100
Alignment explanation
Indices: 28974983--28975279 Score: 350
Period size: 100 Copynumber: 3.0 Consensus size: 100
28974973 CGCAATGTCG
* * * * * *
28974983 GGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGCTCT-ACTGCAATGTCGAGGAAGC-AGAGTA
1 GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCT-TTTTAACTGCAATGTCGGGGAAGCAAGA-TT
* *
28975046 CGCCATTGTGGCTTTAATCTACTCCACTGCATCGCCA
64 CACCATTGTGGCTTTAATCTATTCCACTGCATCGCCA
* * * * * *
28975083 GGGAAGTAACACTCGCCGCTGTGGCTTTAGTCTTTTTAACCGCAATGTTC-GGGAGGCAAGATTC
1 GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATG-TCGGGGAAGCAAGATTC
* *
28975147 ACCAATGTGGCTTTAATCTGTTCCACTGCA-CTGCCA
65 ACCATTGTGGCTTTAATCTATTCCACTGCATC-GCCA
* *
28975183 GGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCA
1 GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCA
* *
28975248 CCATTGTGGCTTTAATCTATTGCACTACATCG
66 CCATTGTGGCTTTAATCTATTCCACTGCATCG
28975280 GTTGGGAGAT
Statistics
Matches: 163, Mismatches: 28, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
99 5 0.03
100 152 0.93
101 6 0.04
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.30
Consensus pattern (100 bp):
GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCA
CCATTGTGGCTTTAATCTATTCCACTGCATCGCCA
Found at i:28975447 original size:44 final size:44
Alignment explanation
Indices: 28975398--28975484 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
28975388 TTTTGATCCG
* *
28975398 CTCCACTACAATCTCAGGGAGATAGGATTACTAGCTTCCATCTA
1 CTCCACTACAATCTCAGGGAGATAAGATTACTAGCTTCAATCTA
** * *
28975442 CTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCT
1 CTCCACTACAATCTCAGGGAGATAAGATTACTAGCTTCAATCT
28975485 GATGCGATCT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (44 bp):
CTCCACTACAATCTCAGGGAGATAAGATTACTAGCTTCAATCTA
Found at i:28975563 original size:44 final size:45
Alignment explanation
Indices: 28975500--28975754 Score: 157
Period size: 44 Copynumber: 5.6 Consensus size: 45
28975490 GATCTACTCT
*
28975500 ACTGTAA-CTTCAGAGAGATAAGATCCT-TTACTTTAATCCGCTCC
1 ACTGTAATC-TCAGGGAGATAAGATCCTATTACTTTAATCCGCTCC
* * * *
28975544 ACTGTAATCTCAGGGAGATAGGAT--TACTAGTTTCAATCTGCTCC
1 ACTGTAATCTCAGGGAGATAAGATCCTATTACTTT-AATCCGCTCC
* * * * * * *
28975588 GCTGTAATATCAGGGAGATAAGATTTCTAGCTTCCATCTGATGCGATCTACTC
1 ACTGTAATCTCAGGGAGATAAGA-TCCTA--TTAC-TTTAATCCG--CT-C-C
* * *
28975641 TACTGTAA-CTTCAGAGAGATAAGATCCT-TTATTTTAATCCGCTCT
1 -ACTGTAATC-TCAGGGAGATAAGATCCTATTACTTTAATCCGCTCC
* * * *
28975686 ACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTGCTCC
1 ACTGTAATCTCAGGGAGATAAGATCCTATTA-CTTTAATCCGCTCC
*
28975730 GCTGTAATCTCAGGGAGATAAGATC
1 ACTGTAATCTCAGGGAGATAAGATC
28975755 TGTAATTTCC
Statistics
Matches: 158, Mismatches: 34, Indels: 37
0.69 0.15 0.16
Matches are distributed among these distances:
42 2 0.01
43 7 0.04
44 101 0.64
45 3 0.02
46 1 0.01
47 4 0.03
49 10 0.06
50 4 0.03
51 2 0.01
52 1 0.01
53 4 0.03
54 19 0.12
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (45 bp):
ACTGTAATCTCAGGGAGATAAGATCCTATTACTTTAATCCGCTCC
Found at i:28975646 original size:98 final size:97
Alignment explanation
Indices: 28975544--28975725 Score: 215
Period size: 98 Copynumber: 1.9 Consensus size: 97
28975534 AATCCGCTCC
* * * *
28975544 ACTGTAA-TCTCAGGGAGATAGGAT-TACTAGTTTCAATCTGCTCCGCTGTAATATCAGGGAGAT
1 ACTGTAACT-TCAGAGAGATAAGATCT-CTA-TTTCAATCCGCTCCACTGTAATATCAGGGAGAT
* *
28975607 AAGATTTCTAGCTTCCATCTGATGCGATCTACTCT
63 AAGATTACTAGCTTCAATCTGATGCGATCTACTCT
* * * * *
28975642 ACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCTACTGTAATCTCAGGGAGATAG
1 ACTGTAACTTCAGAGAGATAAGAT-CTCTATTTCAATCCGCTCCACTGTAATATCAGGGAGATAA
28975707 GATTACTAGCTTCAATCTG
65 GATTACTAGCTTCAATCTG
28975726 CTCCGCTGTA
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
98 66 0.94
99 3 0.04
100 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (97 bp):
ACTGTAACTTCAGAGAGATAAGATCTCTATTTCAATCCGCTCCACTGTAATATCAGGGAGATAAG
ATTACTAGCTTCAATCTGATGCGATCTACTCT
Found at i:28975765 original size:142 final size:142
Alignment explanation
Indices: 28975341--28975753 Score: 709
Period size: 142 Copynumber: 2.9 Consensus size: 142
28975331 GAGATAAGAC
* * *
28975341 CTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTGATCCGCTCCACTA
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* * * *
28975406 CAATCTCAGGGAGATAGGATTACTAGCTTCCATCTACTCCACTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
* *
28975471 TCTGGCTTCAAT
131 TCTAGCTTCCAT
*
28975483 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTACTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* *
28975548 TAATCTCAGGGAGATAGGATTACTAGTTTCAATCTGCTCCGCTGTAATATCAGGGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
28975613 TCTAGCTTCCAT
131 TCTAGCTTCCAT
*
28975625 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCTACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
28975690 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT
28975754 CTGTAATTTC
Statistics
Matches: 255, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 255 1.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (142 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
TCTAGCTTCCAT
Found at i:28977074 original size:7 final size:7
Alignment explanation
Indices: 28977035--28977065 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
28977025 AGCCTCTCAA
28977035 TTTTCA-
1 TTTTCAT
28977041 TTTTCAT
1 TTTTCAT
28977048 TTTTCAT
1 TTTTCAT
28977055 TTTTCAT
1 TTTTCAT
28977062 TTTT
1 TTTT
28977066 TTCATTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTCAT
Found at i:28986132 original size:18 final size:18
Alignment explanation
Indices: 28986109--28986143 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28986099 AAATGAGTAA
*
28986109 TTTTAAAATTTTAAAGAC
1 TTTTAAAATGTTAAAGAC
28986127 TTTTAAAATGTTAAAGA
1 TTTTAAAATGTTAAAGA
28986144 ATTATTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (18 bp):
TTTTAAAATGTTAAAGAC
Found at i:28986490 original size:39 final size:41
Alignment explanation
Indices: 28986374--28986490 Score: 150
Period size: 40 Copynumber: 2.9 Consensus size: 41
28986364 GCGTTTGGAT
* *
28986374 AAAAAACGCCGCTAAAAATCAAGTATTAGAGGCG-CTTTAG
1 AAAAAACGCCGCTAAAAATCAAGTATTAGCGGCGTTTTTAG
* *
28986414 AAAAAACGCCGCTAAAGATCCAGTATTAGCGGCGTTTTTAG
1 AAAAAACGCCGCTAAAAATCAAGTATTAGCGGCGTTTTTAG
* * *
28986455 -GAAAACGCCGCTAAAAAT-GAGCATTAGCGGCGTTTT
1 AAAAAACGCCGCTAAAAATCAAGTATTAGCGGCGTTTT
28986491 CCAAAAAGCG
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
39 16 0.24
40 47 0.69
41 5 0.07
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (41 bp):
AAAAAACGCCGCTAAAAATCAAGTATTAGCGGCGTTTTTAG
Found at i:28986503 original size:39 final size:39
Alignment explanation
Indices: 28986374--28986510 Score: 141
Period size: 40 Copynumber: 3.5 Consensus size: 39
28986364 GCGTTTGGAT
* **
28986374 AAAAAACGCCGCTAAAAATCAAGTATTAGAGGCGCTTTAG
1 AAAAAACGCCGCTAAAAATCAAGTATTAGCGGCG-TTTTC
* * *
28986414 AAAAAACGCCGCTAAAGATCCAGTATTAGCGGCGTTTTT
1 AAAAAACGCCGCTAAAAATCAAGTATTAGCGGCGTTTTC
* * *
28986453 AGGAAAACGCCGCTAAAAAT-GAGCATTAGCGGCGTTTTCC
1 A-AAAAACGCCGCTAAAAATCAAGTATTAGCGGCGTTTT-C
* *
28986493 AAAAAGCGCCGCAAAAAA
1 AAAAAACGCCGCTAAAAA
28986511 CTGAAGCACA
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
39 34 0.41
40 48 0.59
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.19
Consensus pattern (39 bp):
AAAAAACGCCGCTAAAAATCAAGTATTAGCGGCGTTTTC
Found at i:28986613 original size:41 final size:41
Alignment explanation
Indices: 28986542--28986658 Score: 157
Period size: 41 Copynumber: 2.9 Consensus size: 41
28986532 TTTTGAGTTT
* * *
28986542 TCAGGGCGTTAGCGGCATTTTTGAAGAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
*
28986583 TC-GGGTCTTTAGCGGCGCTTTTT-AAAAAGCGCCACTAATGC
1 TCAGGG-CTTTAGCGGCG-TTTTTGAAAAAGCGCCGCTAATGC
*
28986624 TCAGGGCTTTAGCGACGTTTTTGAAAAAGCGCCGC
1 TCAGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGC
28986659 AAATTTTTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
40 8 0.12
41 50 0.76
42 8 0.12
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.26
Consensus pattern (41 bp):
TCAGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
Found at i:28987503 original size:148 final size:148
Alignment explanation
Indices: 28987313--28987761 Score: 766
Period size: 148 Copynumber: 3.1 Consensus size: 148
28987303 TTTAAGAGAT
28987313 AATAATTTTACTTT-AAAAAAAGCCCCCTTTTAGCATAGCATAGCAAAACGGCGTAGTTTTGTTC
1 AATAATTTTACTTTAAAAAAAAGCCCCCTTTTAGCATAGCATAGCAAAACGGCGTAGTTTTGTTC
28987377 AAAATGAATTTTTTTTGCGGCGCTTTTATGAAAAACGCCGCTAAAGGTAAGCAATAGCGGCGTTT
66 AAAATGAATTTTTTTTGCGGCGCTTTTATGAAAAACGCCGCTAAAGGTAAGCAATAGCGGCGTTT
28987442 ATATAAAAAACGCCACAA
131 ATATAAAAAACGCCACAA
28987460 AATAATTTTACTTTAAAAAAAAGCCCCCTTTTAGCATAGCATAGCAAAACGGCGTAGTTTTGTTC
1 AATAATTTTACTTTAAAAAAAAGCCCCCTTTTAGCATAGCATAGCAAAACGGCGTAGTTTTGTTC
*
28987525 AAAATGAATTTTTTTTGCGGCGCTTTTATGAAAAACGCCGCTAAGGGTAAGCAATAGCGGCGTTT
66 AAAATGAATTTTTTTTGCGGCGCTTTTATGAAAAACGCCGCTAAAGGTAAGCAATAGCGGCGTTT
28987590 ATATAAAAAACGCCACAA
131 ATATAAAAAACGCCACAA
*
28987608 AATAATTTTACTTTAAAAAAAAGCCCCATTTTAGCATAGCATAGC-AAACGGCGTAGTTTTGTTC
1 AATAATTTTACTTTAAAAAAAAGCCCCCTTTTAGCATAGCATAGCAAAACGGCGTAGTTTTGTTC
*
28987672 AAAAT-AATTTTTTTTGCGGCG-TTTT-T---------C-ATAAAGGTAAGCAATAGCGGCGTTT
66 AAAATGAATTTTTTTTGCGGCGCTTTTATGAAAAACGCCGCTAAAGGTAAGCAATAGCGGCGTTT
28987724 ATATAAAAAACGCCACAA
131 ATATAAAAAACGCCACAA
28987742 AATAATTTTACTTTAAAAAA
1 AATAATTTTACTTTAAAAAA
28987762 GNNNNNNNNN
Statistics
Matches: 297, Mismatches: 4, Indels: 15
0.94 0.01 0.05
Matches are distributed among these distances:
134 61 0.21
135 1 0.00
144 1 0.00
145 4 0.01
146 16 0.05
147 38 0.13
148 176 0.59
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (148 bp):
AATAATTTTACTTTAAAAAAAAGCCCCCTTTTAGCATAGCATAGCAAAACGGCGTAGTTTTGTTC
AAAATGAATTTTTTTTGCGGCGCTTTTATGAAAAACGCCGCTAAAGGTAAGCAATAGCGGCGTTT
ATATAAAAAACGCCACAA
Found at i:28990857 original size:42 final size:42
Alignment explanation
Indices: 28990738--28990878 Score: 180
Period size: 42 Copynumber: 3.3 Consensus size: 42
28990728 TTTTAAAAAG
28990738 TTAGCGGCGTTTGTAATCAAAGCGTCGCTAAAAGGTCTTGAGCTT
1 TTAGCGGCGTTTGTAATCAAAGCGTCGCT-AAAGGTCTTGA--TT
*
28990783 TT-GTGGCGTTTGTAATCAAAGCGTCGCTAAAGGT-TGTGATT
1 TTAGCGGCGTTTGTAATCAAAGCGTCGCTAAAGGTCT-TGATT
* *
28990824 TATAGCGGCGTTTGTGA-GAAAGCGTCGCTAAAGGTCTTGATCT
1 T-TAGCGGCGTTTGTAATCAAAGCGTCGCTAAAGGTCTTGAT-T
28990867 TTAGCGGCGTTT
1 TTAGCGGCGTTT
28990879 TTGGGTAACG
Statistics
Matches: 87, Mismatches: 4, Indels: 13
0.84 0.04 0.12
Matches are distributed among these distances:
41 3 0.03
42 34 0.39
43 23 0.26
44 25 0.29
45 2 0.02
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (42 bp):
TTAGCGGCGTTTGTAATCAAAGCGTCGCTAAAGGTCTTGATT
Found at i:28990911 original size:43 final size:43
Alignment explanation
Indices: 28990826--28991009 Score: 246
Period size: 43 Copynumber: 4.3 Consensus size: 43
28990816 TTGTGATTTA
* * * * * *
28990826 TAGCGGCGTTTGTGAG-AAAGCGTCGCTAAAGGTCTTGATCTT
1 TAGCGGCGTTTTTGGGTAAAGCGCCGCTAAAGATCATGTTCTT
* *
28990868 TAGCGGCGTTTTTGGGTAACGTGCCGCTAAAGATCATGTTCTT
1 TAGCGGCGTTTTTGGGTAAAGCGCCGCTAAAGATCATGTTCTT
* *
28990911 TAGCGGCGTTTGAT-GGTAAAGCGCCGCTAAAGACCATGTTCTT
1 TAGCGGCGTTT-TTGGGTAAAGCGCCGCTAAAGATCATGTTCTT
*
28990954 TAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGATCATGTTCTT
1 TAGCGGCGTTTTTGGGTAAAGCGCCGCTAAAGATCATGTTCTT
28990997 TAGCGGCGTTTTT
1 TAGCGGCGTTTTT
28991010 TATCATAAAC
Statistics
Matches: 124, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
42 15 0.12
43 108 0.87
44 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.32
Consensus pattern (43 bp):
TAGCGGCGTTTTTGGGTAAAGCGCCGCTAAAGATCATGTTCTT
Found at i:28991136 original size:22 final size:22
Alignment explanation
Indices: 28991101--28991143 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28991091 TAGCGGCGCT
* *
28991101 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAACGCCGCTAAAAGCCTA
*
28991123 AAAAAACGCTGCTAAAAGCCT
1 AAAAAACGCCGCTAAAAGCCT
28991144 GTTTTGGTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.26, G:0.19, T:0.12
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAAGCCTA
Found at i:28994395 original size:37 final size:37
Alignment explanation
Indices: 28994352--28994422 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
28994342 ATTAACCAAA
28994352 TTGAATCACTACATAATTAAAAACATCACATAAGCCT
1 TTGAATCACTACATAATTAAAAACATCACATAAGCCT
*
28994389 TTGAATCACTACATAATTAAAAACATTACATAAG
1 TTGAATCACTACATAATTAAAAACATCACATAAG
28994423 TCTTGAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.48, C:0.18, G:0.06, T:0.28
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATCACATAAGCCT
Found at i:28994420 original size:17 final size:17
Alignment explanation
Indices: 28994361--28994421 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
28994351 ATTGAATCAC
28994361 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
* ** * *
28994378 CACATAAGCCTTTGAATCAC
1 TACATAA---TTAAAAACAT
28994398 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
28994415 TACATAA
1 TACATAA
28994422 GTCTTGAAAT
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
17 19 0.61
20 12 0.39
ACGTcount: A:0.51, C:0.18, G:0.03, T:0.28
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:28994440 original size:37 final size:37
Alignment explanation
Indices: 28994352--28994443 Score: 116
Period size: 37 Copynumber: 2.5 Consensus size: 37
28994342 ATTAACCAAA
*
28994352 TTGAATCACTACATAATTAAAAACATCACATAAGCCT
1 TTGAATAACTACATAATTAAAAACATCACATAAGCCT
* * *
28994389 TTGAATCACTACATAATTAAAAACATTACATAAGTC-
1 TTGAATAACTACATAATTAAAAACATCACATAAGCCT
28994425 TTGAAATTAAC-ACATAATT
1 TTG-AA-TAACTACATAATT
28994444 GAAATGTAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
36 3 0.06
37 44 0.88
38 3 0.06
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.30
Consensus pattern (37 bp):
TTGAATAACTACATAATTAAAAACATCACATAAGCCT
Found at i:28994584 original size:24 final size:23
Alignment explanation
Indices: 28994537--28994584 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
28994527 AACATGTGCC
* * *
28994537 TATTTATATATTATTTTTATTTT
1 TATTTATAAATTATTTGTAATTT
28994560 TATTTATTAAATTATTTGTAATTT
1 TATTTA-TAAATTATTTGTAATTT
28994584 T
1 T
28994585 TATGATTGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
TATTTATAAATTATTTGTAATTT
Found at i:28996378 original size:2 final size:2
Alignment explanation
Indices: 28996371--28996410 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
28996361 AGAATTCCAT
28996371 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28996411 TAAGAAGCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:29002507 original size:2 final size:2
Alignment explanation
Indices: 29002500--29002532 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29002490 TTTATGCATT
29002500 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29002533 TTAGAATTAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29008900 original size:43 final size:43
Alignment explanation
Indices: 29008875--29009037 Score: 190
Period size: 43 Copynumber: 3.7 Consensus size: 43
29008865 TCATGGCCTT
29008875 TAGCGGCGCTTTTGCCAAAAACGCCG-TAATAGACCCTGATCTA
1 TAGCGGCGCTTTTGCCAAAAACGCCGCTAA-AGACCCTGATCTA
* *
29008918 TAGCGGCGCTTAT-CCAGAAAACGCCGCTAAATACCCTTTG-TCTATA
1 TAGCGGCGCTTTTGCCA-AAAACGCCGCTAAAGACCC--TGATC--TA
* *
29008964 TAGCGGCGC-TTCGCGCAAAAACGCCGCTAAAGACCCTAATCTA
1 TAGCGGCGCTTTTGC-CAAAAACGCCGCTAAAGACCCTGATCTA
*
29009007 TAGCGGCGCTTTTACCAAAAACGCCGCTAAA
1 TAGCGGCGCTTTTGCCAAAAACGCCGCTAAA
29009038 TTTGGCAGAT
Statistics
Matches: 102, Mismatches: 8, Indels: 20
0.78 0.06 0.15
Matches are distributed among these distances:
42 3 0.03
43 53 0.52
44 9 0.09
45 5 0.05
46 30 0.29
47 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (43 bp):
TAGCGGCGCTTTTGCCAAAAACGCCGCTAAAGACCCTGATCTA
Found at i:29008985 original size:89 final size:89
Alignment explanation
Indices: 29008875--29009038 Score: 253
Period size: 89 Copynumber: 1.8 Consensus size: 89
29008865 TCATGGCCTT
* *
29008875 TAGCGGCGCTTTTGCCAAAAACGCCG-TAATAGACCCTGATCTATAGCGGCGCTTAT-CCAGAAA
1 TAGCGGCGCTTTCGCCAAAAACGCCGCTAA-AGACCCTAATCTATAGCGGCGCTTATACCA-AAA
29008938 ACGCCGCTAAATACCCTTTGTCTATA
64 ACGCCGCTAAATACCCTTTGTCTATA
*
29008964 TAGCGGCGC-TTCGCGCAAAAACGCCGCTAAAGACCCTAATCTATAGCGGCGCTTTTACCAAAAA
1 TAGCGGCGCTTTCGC-CAAAAACGCCGCTAAAGACCCTAATCTATAGCGGCGCTTATACCAAAAA
29009028 CGCCGCTAAAT
65 CGCCGCTAAAT
29009039 TTGGCAGATN
Statistics
Matches: 69, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
88 4 0.06
89 59 0.86
90 6 0.09
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (89 bp):
TAGCGGCGCTTTCGCCAAAAACGCCGCTAAAGACCCTAATCTATAGCGGCGCTTATACCAAAAAC
GCCGCTAAATACCCTTTGTCTATA
Found at i:29009468 original size:21 final size:21
Alignment explanation
Indices: 29009442--29009543 Score: 105
Period size: 21 Copynumber: 4.9 Consensus size: 21
29009432 TTTGACGCTG
29009442 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* **
29009463 CTCTGCTTCCCTCACTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
29009484 CTCTGCTTCCCTTGCTGCAAC
1 CTCTGCTTCCCTCGCTGCAGC
* * * *
29009505 CTGTTCTTCTCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
29009526 CTCTGCTTCTCTTGCTGC
1 CTCTGCTTCCCTCGCTGC
29009544 CGCATCTACT
Statistics
Matches: 64, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 64 1.00
ACGTcount: A:0.05, C:0.43, G:0.16, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:29009602 original size:66 final size:66
Alignment explanation
Indices: 29009525--29009671 Score: 190
Period size: 66 Copynumber: 2.2 Consensus size: 66
29009515 CTCGCTGCCG
* *
29009525 CCTCTGCTTCTCTTGCTGCCGCATCTACTCTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTT
1 CCTCAGCTTCTCTCGCTGCCGCATCTACTCTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-GTT
29009588 GAA
64 GAA
* * * * *
29009591 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCCGCATCTACTCTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
29009656 A
66 A
*
29009657 CATCAGCTTCTCTCG
1 CCTCAGCTTCTCTCG
29009672 ATGTTGCCTC
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
65 1 0.01
66 66 0.93
67 4 0.06
ACGTcount: A:0.14, C:0.29, G:0.18, T:0.39
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCCGCATCTACTCTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
A
Found at i:29009692 original size:66 final size:66
Alignment explanation
Indices: 29009564--29009694 Score: 183
Period size: 66 Copynumber: 2.0 Consensus size: 66
29009554 CTAAGCTGCT
* * * *
29009564 GCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGT
1 GCTGGAGTTCTTCATACTTTCGTTGAACATCAGCTTCTCTCGATGCTGCATCCGCTTCAAGTTGT
29009629 A
66 A
* * *
29009630 GCTGGAGTTCTTCATATCTTT-TTTGAACATCAGCTTCTCTCGATGTTGCCTCCGCTTCAAGTTG
1 GCTGGAGTTCTTCATA-CTTTCGTTGAACATCAGCTTCTCTCGATGCTGCATCCGCTTCAAGTTG
29009694 T
65 T
29009695 GTAATTTGCT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 53 0.93
67 4 0.07
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.40
Consensus pattern (66 bp):
GCTGGAGTTCTTCATACTTTCGTTGAACATCAGCTTCTCTCGATGCTGCATCCGCTTCAAGTTGT
A
Done.