Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, whole genome shotgun sequence
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: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 18 of 129
Found at i:3504252 original size:25 final size:26
Alignment explanation
Indices: 3504219--3504277 Score: 86
Period size: 25 Copynumber: 2.3 Consensus size: 26
3504209 TATTAATATA
3504219 ATTATTAAAATAT-TCATAATT-ATTT
1 ATTATTAAAATATATCA-AATTCATTT
*
3504244 ATTATTAAAATATATTAAATTCATTT
1 ATTATTAAAATATATCAAATTCATTT
3504270 ATTATTAA
1 ATTATTAA
3504278 TATTATTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 17 0.55
26 14 0.45
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (26 bp):
ATTATTAAAATATATCAAATTCATTT
Found at i:3504284 original size:25 final size:23
Alignment explanation
Indices: 3504219--3504291 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 23
3504209 TATTAATATA
*
3504219 ATTATTAAAATATTCATAATTATTT
1 ATTATTAAATTATT-A-AATTATTT
3504244 ATTATTAAAATATATTAAATTCATTT
1 ATTATT-AAAT-TATTAAATT-ATTT
3504270 ATTATTAATATTATTAATATTA
1 ATTATTAA-ATTATTAA-ATTA
3504292 AAAATAATTA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
25 19 0.45
26 19 0.45
27 4 0.10
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTATTAAATTATTAAATTATTT
Found at i:3504292 original size:15 final size:15
Alignment explanation
Indices: 3504272--3504582 Score: 55
Period size: 13 Copynumber: 21.9 Consensus size: 15
3504262 ATTCATTTAT
3504272 TATTAATATTATTAA
1 TATTAATATTATTAA
* *
3504287 TATTAAAAATAATT-A
1 TATT-AATATTATTAA
3504302 TATTTAATA--A-TAA
1 TA-TTAATATTATTAA
**
3504315 TATTTAATATTAAAAA
1 TA-TTAATATTATTAA
*
3504331 TATT-ATGTTA--AA
1 TATTAATATTATTAA
* *
3504343 TA-TAAAAATACTTAA
1 TATTAATATTA-TTAA
* * *
3504358 -AATAAAATTATTTAT
1 TATTAATATTA-TTAA
3504373 TATTAATATTATT--
1 TATTAATATTATTAA
3504386 TATTATATATTA-TAA
1 TATTA-ATATTATTAA
3504401 TATT-AT-TTATTAA
1 TATTAATATTATTAA
*
3504414 TA--AAT-TAATTAA
1 TATTAATATTATTAA
*
3504426 TAGT-ATATTATT--
1 TATTAATATTATTAA
3504438 TATTAATA-TA-T--
1 TATTAATATTATTAA
*
3504449 TA-TAATATCATT--
1 TATTAATATTATTAA
3504461 TATTAATAGTTCTATT--
1 TATTAATA--T-TATTAA
3504477 TATTAAATATTATT-A
1 TATT-AATATTATTAA
*
3504492 TATT-GT-TTATTAA
1 TATTAATATTATTAA
*
3504505 TA-TAATATTATTTTTA
1 TATTAATATTA--TTAA
3504521 TATATAATATTTTTATTAA
1 TAT-TAATA---TTATTAA
*
3504540 AATTAATATATAGTATAA
1 TATTAATAT-TA-T-TAA
3504558 TATT-AT-TTATTAA
1 TATTAATATTATTAA
3504571 TA-TAATATTATT
1 TATTAATATTATT
3504583 TTATAAGTAA
Statistics
Matches: 228, Mismatches: 24, Indels: 89
0.67 0.07 0.26
Matches are distributed among these distances:
10 5 0.02
11 5 0.02
12 36 0.16
13 46 0.20
14 29 0.13
15 40 0.18
16 36 0.16
17 7 0.03
18 16 0.07
19 5 0.02
21 3 0.01
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.52
Consensus pattern (15 bp):
TATTAATATTATTAA
Found at i:3504332 original size:16 final size:16
Alignment explanation
Indices: 3504283--3504334 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
3504273 ATTAATATTA
*
3504283 TTAATATTAAAAATAA
1 TTAATATTAAAAATAT
3504299 TT-ATATTTAATAATAATAT
1 TTAATA-TT-A-AA-AATAT
3504318 TTAATATTAAAAATAT
1 TTAATATTAAAAATAT
3504334 T
1 T
3504335 ATGTTAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
15 3 0.10
16 10 0.33
17 3 0.10
18 3 0.10
19 8 0.27
20 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAATATTAAAAATAT
Found at i:3504341 original size:20 final size:18
Alignment explanation
Indices: 3504283--3504352 Score: 54
Period size: 19 Copynumber: 3.8 Consensus size: 18
3504273 ATTAATATTA
3504283 TTAATATTAAAAATAAT-T
1 TTAA-ATTAAAAATAATAT
* * *
3504301 AT-ATTTAATAATAATAT
1 TTAAATTAAAAATAATAT
*
3504318 TTAATATTAAAAATATTAT
1 TTAA-ATTAAAAATAATAT
3504337 GTTAAATATAAAAATA
1 -TTAAAT-TAAAAATA
3504353 CTTAAAATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
16 10 0.25
17 3 0.08
18 2 0.05
19 13 0.32
20 12 0.30
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (18 bp):
TTAAATTAAAAATAATAT
Found at i:3504376 original size:7 final size:7
Alignment explanation
Indices: 3504364--3504412 Score: 53
Period size: 7 Copynumber: 6.6 Consensus size: 7
3504354 TTAAAATAAA
3504364 ATTATTT
1 ATTATTT
3504371 ATTATTAAT
1 ATTATT--T
3504380 ATTATTT
1 ATTATTT
*
3504387 ATTATAT
1 ATTATTT
*
3504394 ATTATAAT
1 ATTAT-TT
3504402 ATTATTT
1 ATTATTT
3504409 ATTA
1 ATTA
3504413 ATAAATTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
7 23 0.62
8 7 0.19
9 7 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
ATTATTT
Found at i:3504407 original size:38 final size:37
Alignment explanation
Indices: 3504364--3504582 Score: 158
Period size: 38 Copynumber: 6.1 Consensus size: 37
3504354 TTAAAATAAA
*
3504364 ATTATTTATTATTAATATTATTTATTATATATTATAAT
1 ATTATTTATTATTAATATTATTTATTA-ATATTATATT
* * *
3504402 ATTATTTATTAATAA-ATTAATTAATAGTATATTAT-TT
1 ATTATTTATTATTAATATTATTTATTA--ATATTATATT
* * *
3504439 ATTAATATATTA-TAATATCATTTATTAATAGTTCTATTT
1 ATT-ATTTATTATTAATATTATTTATTAATA-TTATA-TT
** * *
3504478 ATTAAATATTATT-ATATTGTTTATTAATATAATATT
1 ATTATTTATTATTAATATTATTTATTAATATTATATT
*
3504514 ATT-TTTA-TATATAATATT-TTTATTAAAATTA-A-T
1 ATTATTTATTAT-TAATATTATTTATTAATATTATATT
* *
3504547 A-TA--TAGTA-TAATATTATTTATTAATATAATATT
1 ATTATTTATTATTAATATTATTTATTAATATTATATT
3504580 ATT
1 ATT
3504583 TTATAAGTAA
Statistics
Matches: 146, Mismatches: 20, Indels: 34
0.73 0.10 0.17
Matches are distributed among these distances:
30 7 0.05
31 13 0.09
32 4 0.03
33 4 0.03
34 5 0.03
35 14 0.10
36 13 0.09
37 22 0.15
38 58 0.40
39 6 0.04
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.56
Consensus pattern (37 bp):
ATTATTTATTATTAATATTATTTATTAATATTATATT
Found at i:3504503 original size:53 final size:52
Alignment explanation
Indices: 3504362--3504495 Score: 164
Period size: 53 Copynumber: 2.5 Consensus size: 52
3504352 ACTTAAAATA
*
3504362 AAATTATTTATTATTAATATTATTTATTATATATTATAATATTATTTATTAAT
1 AAATTATTTATTA-TAATATTATTTATTATATATTATAATATCATTTATTAAT
* *
3504415 AAATTAATTAATAGT-ATATTATTTATTAATATATTATAATATCATTTATTAAT
1 AAATTATTTATTA-TAATATTATTTATT-ATATATTATAATATCATTTATTAAT
**
3504468 AGTTCTATTTATTA-AATATTATTATATT
1 AAAT-TATTTATTATAATATTATT-TATT
3504496 GTTTATTAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
52 12 0.17
53 46 0.67
54 11 0.16
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (52 bp):
AAATTATTTATTATAATATTATTTATTATATATTATAATATCATTTATTAAT
Found at i:3504529 original size:61 final size:62
Alignment explanation
Indices: 3504414--3504584 Score: 172
Period size: 61 Copynumber: 2.7 Consensus size: 62
3504404 TATTTATTAA
* * **
3504414 TAAATTAAT-TA-ATAGTATATTATTTATTAATATATTATAATATCATTTATTAATAGTTCTAT
1 TAAATTAATATATATATTATATTATTTATTAATATA--ATATTATTTTTTATTAATAGTTCTAT
* * * *
3504476 T-TATTAA-ATAT-TATTATATTGTTTATTAATATAATATTATTTTTATATATAATATTTTTAT
1 TAAATTAATATATATATTATATTATTTATTAATATAATATTATTTTT-TAT-TAATAGTTCTAT
*
3504537 TAAAATTAATATATAGTATAATATTATTTATTAATATAATATTATTTT
1 T-AAATTAATATATA-TATTATATTATTTATTAATATAATATTATTTT
3504585 ATAAGTAAAA
Statistics
Matches: 89, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
59 8 0.09
60 3 0.03
61 38 0.43
62 1 0.01
63 5 0.06
64 4 0.04
66 30 0.34
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (62 bp):
TAAATTAATATATATATTATATTATTTATTAATATAATATTATTTTTTATTAATAGTTCTAT
Found at i:3505475 original size:15 final size:14
Alignment explanation
Indices: 3505452--3505495 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
3505442 AACAAGAAGA
3505452 TAATATAATATAATT
1 TAATATAAT-TAATT
*
3505467 TAATTTAATTAATT
1 TAATATAATTAATT
3505481 T-ATATAATTATATT
1 TAATATAATTA-ATT
3505495 T
1 T
3505496 TAAAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 8 0.31
14 10 0.38
15 8 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TAATATAATTAATT
Found at i:3505661 original size:1 final size:1
Alignment explanation
Indices: 3505657--3505682 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
3505647 AACAAAATAG
3505657 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
3505683 CTAATTTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3506059 original size:32 final size:31
Alignment explanation
Indices: 3506018--3506098 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
3506008 TTTATAAAAT
* * ***
3506018 ATTTAAAATTTACTTTTATGTACTGGTACAAA
1 ATTTAAAATTTAATTTT-TGTAATCACACAAA
*
3506050 ATTTGAAATTTAATTTTTGTAATCACACAAA
1 ATTTAAAATTTAATTTTTGTAATCACACAAA
*
3506081 ATTTAAAATTTAGTTTTT
1 ATTTAAAATTTAATTTTT
3506099 CTATTATAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 26 0.63
32 15 0.37
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (31 bp):
ATTTAAAATTTAATTTTTGTAATCACACAAA
Found at i:3506609 original size:18 final size:19
Alignment explanation
Indices: 3506572--3506617 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
3506562 GTAAAAGAAA
* *
3506572 AAATCTAAATAATTATGTT
1 AAATCTAAATAATAACGTT
3506591 AAAT-TAAATAATAACGTT
1 AAATCTAAATAATAACGTT
*
3506609 AATTCTAAA
1 AAATCTAAA
3506618 ATGAATATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (19 bp):
AAATCTAAATAATAACGTT
Found at i:3507359 original size:21 final size:20
Alignment explanation
Indices: 3507305--3507359 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
3507295 CATCAGTAAG
* *
3507305 TCAATACCACATTAGCAAAA
1 TCAATACTACGTTAGCAAAA
*
3507325 TCAATACTACGTTAGTAAAA
1 TCAATACTACGTTAGCAAAA
* *
3507345 TTAATGCTCACGTTA
1 TCAATACT-ACGTTA
3507360 TCGAGTTAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 23 0.79
21 6 0.21
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (20 bp):
TCAATACTACGTTAGCAAAA
Found at i:3508241 original size:20 final size:19
Alignment explanation
Indices: 3508206--3508243 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
3508196 TTTTTTGTAA
3508206 ATTAAATAAAATTATTTTT
1 ATTAAATAAAATTATTTTT
3508225 ATTAATATAATAA-TATTTT
1 ATTAA-ATAA-AATTATTTT
3508244 AAGTTAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 10 0.59
21 2 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTAAATAAAATTATTTTT
Found at i:3508457 original size:20 final size:20
Alignment explanation
Indices: 3508432--3508490 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
3508422 CAGGTCCGGG
3508432 CCCGGATCAATTGGGCCTGA
1 CCCGGATCAATTGGGCCTGA
3508452 CCCGGATCAATTGGGCCTGA
1 CCCGGATCAATTGGGCCTGA
* *
3508472 CCCAGATCATTTGGGCCTG
1 CCCGGATCAATTGGGCCTG
3508491 GCCCAAATGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.19, C:0.31, G:0.29, T:0.22
Consensus pattern (20 bp):
CCCGGATCAATTGGGCCTGA
Found at i:3508662 original size:3 final size:3
Alignment explanation
Indices: 3508654--3508682 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3508644 AGTTATATAT
3508654 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3508683 TTTGTAAGAT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3509331 original size:19 final size:19
Alignment explanation
Indices: 3509307--3509353 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
3509297 TTCCGGCCAT
3509307 ATTCCGGCAAAAATTCCAG
1 ATTCCGGCAAAAATTCCAG
* * *
3509326 ATTCCGGCGACATTTCCAG
1 ATTCCGGCAAAAATTCCAG
*
3509345 AATCCGGCA
1 ATTCCGGCA
3509354 CCGGTGTTCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (19 bp):
ATTCCGGCAAAAATTCCAG
Found at i:3509717 original size:25 final size:24
Alignment explanation
Indices: 3509678--3509761 Score: 65
Period size: 26 Copynumber: 3.6 Consensus size: 24
3509668 CGCTCCAGGT
3509678 TTTTTTTTTTTTTT---TTTTTTT
1 TTTTTTTTTTTTTTCGATTTTTTT
3509699 TTTTT---TTTTTTCGAATTTTTTT
1 TTTTTTTTTTTTTTCG-ATTTTTTT
*
3509721 TTTTTTTTTTATTTT-GATCTTGATTT
1 TTTTTTTTTT-TTTTCGAT-TT-TTTT
*
3509747 TTTTTTTCTTTTTTC
1 TTTTTTTTTTTTTTC
3509762 TTTAATTAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
18 6 0.12
21 5 0.10
22 12 0.24
24 2 0.04
25 9 0.18
26 16 0.32
ACGTcount: A:0.06, C:0.05, G:0.04, T:0.86
Consensus pattern (24 bp):
TTTTTTTTTTTTTTCGATTTTTTT
Found at i:3509717 original size:26 final size:25
Alignment explanation
Indices: 3509678--3509761 Score: 65
Period size: 25 Copynumber: 3.6 Consensus size: 25
3509668 CGCTCCAGGT
3509678 TTTTTTTTTTTTT---TTTTTTTTT
1 TTTTTTTTTTTTTCGATTTTTTTTT
3509700 TTT---TTTTTTTCGAATTTTTTTTT
1 TTTTTTTTTTTTTCG-ATTTTTTTTT
* **
3509723 TTTTTTTTATTTT-GATCTTGATTTT
1 TTTTTTTTTTTTTCGAT-TTTTTTTT
*
3509748 TTTTTTCTTTTTTC
1 TTTTTTTTTTTTTC
3509762 TTTAATTAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
19 7 0.15
22 3 0.06
23 12 0.25
24 2 0.04
25 18 0.38
26 6 0.12
ACGTcount: A:0.06, C:0.05, G:0.04, T:0.86
Consensus pattern (25 bp):
TTTTTTTTTTTTTCGATTTTTTTTT
Found at i:3509721 original size:31 final size:30
Alignment explanation
Indices: 3509684--3509760 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
3509674 AGGTTTTTTT
* *
3509684 TTTTTTTTTTTTTTTTT-TTTT-TTTTTCGAA
1 TTTTTTTTTTTTTTTTTATTTTGATCTT-G-A
3509714 TTTTTTTTTTTTTTTTTATTTTGATCTTGA
1 TTTTTTTTTTTTTTTTTATTTTGATCTTGA
*
3509744 TTTTTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTT
3509761 CTTTAATTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 34 0.81
31 5 0.12
32 3 0.07
ACGTcount: A:0.06, C:0.04, G:0.04, T:0.86
Consensus pattern (30 bp):
TTTTTTTTTTTTTTTTTATTTTGATCTTGA
Found at i:3509753 original size:1 final size:1
Alignment explanation
Indices: 3509677--3509735 Score: 73
Period size: 1 Copynumber: 59.0 Consensus size: 1
3509667 CCGCTCCAGG
**** *
3509677 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCGAATTTTTTTTTTTTTTTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3509736 GATCTTGATT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.05, C:0.02, G:0.02, T:0.92
Consensus pattern (1 bp):
T
Found at i:3510041 original size:156 final size:157
Alignment explanation
Indices: 3509756--3510041 Score: 520
Period size: 156 Copynumber: 1.8 Consensus size: 157
3509746 TTTTTTTTCT
*
3509756 TTTTTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACT
1 TTTTTCTTTAAATAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACT
*
3509821 CCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
66 CCTGAGGTGAGAGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
3509886 GATAATTAATTAATTGGTTGATCTTGA
131 GATAATTAATTAATTGGTTGATCTTGA
* *
3509913 TTTTTCTTTAAATAATCCGACGACGGAGCCTCTGCAAGT-GAAACAGTAGTTTTTCTTGCATACT
1 TTTTTCTTTAAATAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACT
*
3509977 CTTGAGGTGAGAGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
66 CCTGAGGTGAGAGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
3510042 AACAACTAAC
Statistics
Matches: 124, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
156 87 0.70
157 37 0.30
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (157 bp):
TTTTTCTTTAAATAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACT
CCTGAGGTGAGAGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
GATAATTAATTAATTGGTTGATCTTGA
Found at i:3515343 original size:15 final size:14
Alignment explanation
Indices: 3515323--3515352 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3515313 CAGAAATGCT
3515323 AGAGAAGGCTAGAAG
1 AGAGAAGGCTA-AAG
3515338 AGAGAAGGCTAAAG
1 AGAGAAGGCTAAAG
3515352 A
1 A
3515353 AGGAGAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.50, C:0.07, G:0.37, T:0.07
Consensus pattern (14 bp):
AGAGAAGGCTAAAG
Found at i:3520265 original size:7 final size:8
Alignment explanation
Indices: 3520244--3520301 Score: 53
Period size: 8 Copynumber: 6.8 Consensus size: 8
3520234 ACTATGCTTG
3520244 AAAAAAAT
1 AAAAAAAT
3520252 ACAAAAAAAT
1 --AAAAAAAT
3520262 AAAAAAAT
1 AAAAAAAT
3520270 AAAAAAAAT
1 -AAAAAAAT
*
3520279 GAAAAAAT
1 AAAAAAAT
*
3520287 GGAAAAAAT
1 -AAAAAAAT
*
3520296 GAAAAA
1 AAAAAA
3520302 TGATGAAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
8 21 0.47
9 16 0.36
10 8 0.18
ACGTcount: A:0.81, C:0.02, G:0.07, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:3520265 original size:8 final size:9
Alignment explanation
Indices: 3520244--3520285 Score: 59
Period size: 10 Copynumber: 4.6 Consensus size: 9
3520234 ACTATGCTTG
3520244 AAAAAAATA
1 AAAAAAATA
3520253 CAAAAAAAT-
1 -AAAAAAATA
3520262 AAAAAAATA
1 AAAAAAATA
3520271 AAAAAAATGA
1 AAAAAAAT-A
3520281 AAAAA
1 AAAAA
3520286 TGGAAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.27
9 8 0.27
10 14 0.47
ACGTcount: A:0.86, C:0.02, G:0.02, T:0.10
Consensus pattern (9 bp):
AAAAAAATA
Found at i:3520267 original size:17 final size:17
Alignment explanation
Indices: 3520244--3520301 Score: 71
Period size: 17 Copynumber: 3.3 Consensus size: 17
3520234 ACTATGCTTG
3520244 AAAAAAATACAAAAAAAT
1 AAAAAAATA-AAAAAAAT
3520262 AAAAAAATAAAAAAAAT
1 AAAAAAATAAAAAAAAT
* **
3520279 GAAAAAATGGAAAAAAT
1 AAAAAAATAAAAAAAAT
3520296 GAAAAA
1 -AAAAA
3520302 TGATGAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 22 0.63
18 13 0.37
ACGTcount: A:0.81, C:0.02, G:0.07, T:0.10
Consensus pattern (17 bp):
AAAAAAATAAAAAAAAT
Found at i:3520319 original size:9 final size:9
Alignment explanation
Indices: 3520242--3520345 Score: 92
Period size: 9 Copynumber: 11.8 Consensus size: 9
3520232 ATACTATGCT
3520242 TGAAAAAAA
1 TGAAAAAAA
*
3520251 TACAAAAAAA
1 T-GAAAAAAA
3520261 T-AAAAAAA
1 TGAAAAAAA
*
3520269 TAAAAAAAA
1 TGAAAAAAA
3520278 TG-AAAAAA
1 TGAAAAAAA
*
3520286 TGGAAAAAA
1 TGAAAAAAA
3520295 TG--AAAAA
1 TGAAAAAAA
*
3520302 TGATGAAAAA
1 TGA-AAAAAA
3520312 TGAAAAAAAA
1 TG-AAAAAAA
*
3520322 TGGAAAAAA
1 TGAAAAAAA
*
3520331 TGGAAAAAA
1 TGAAAAAAA
3520340 -GAAAAA
1 TGAAAAA
3520346 GTGAATGAAA
Statistics
Matches: 83, Mismatches: 5, Indels: 15
0.81 0.05 0.15
Matches are distributed among these distances:
7 7 0.08
8 21 0.25
9 32 0.39
10 22 0.27
11 1 0.01
ACGTcount: A:0.75, C:0.01, G:0.12, T:0.12
Consensus pattern (9 bp):
TGAAAAAAA
Found at i:3520345 original size:17 final size:18
Alignment explanation
Indices: 3520255--3520339 Score: 88
Period size: 17 Copynumber: 4.8 Consensus size: 18
3520245 AAAAAATACA
**
3520255 AAAAAAT-AAAAAAATAA
1 AAAAAATGAAAAAAATGG
3520272 AAAAAATG-AAAAAATGG
1 AAAAAATGAAAAAAATGG
*
3520289 AAAAAATGAAAAATGAT-G
1 AAAAAATGAAAAA-AATGG
3520307 -AAAAATGAAAAAAAATGG
1 AAAAAATG-AAAAAAATGG
3520325 AAAAAATGGAAAAAA
1 AAAAAAT-GAAAAAA
3520340 GAAAAAGTGA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
17 31 0.54
18 11 0.19
19 14 0.25
20 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.12
Consensus pattern (18 bp):
AAAAAATGAAAAAAATGG
Found at i:3521481 original size:42 final size:39
Alignment explanation
Indices: 3521356--3521935 Score: 763
Period size: 42 Copynumber: 14.2 Consensus size: 39
3521346 ATGATCGTCT
3521356 AGGAG-AATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAG-TCGTTGCCTCTGTTTAG
*
3521395 AGGAGCAATTTATTTTTC-AAGTTCCGTTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAG-T-CGTTGCCTCTGTTTAG
3521435 AGGAGCAATTTACTTTTCAAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTC-AAAGTCGT--TGCCTCTGTTTAG
*
3521477 AGGAGCAATTTATTTTTCCAAAGTTCCGTTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAG-T-CGTTGCCTCTGTTTAG
3521519 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGT--TGCCTCTGTTTAG
*
3521560 AGGAGCAA-TTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAGTCGT--TGCCTCTGTTTAG
*
3521601 AGGAGCAATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAGTCGT--TGCCTCTGTTTAG
3521643 AGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAG-TCGTTGCCTCTGTTTAG
*
3521683 AGGAGCAATTTATTTTTCAAAGTTCCGTTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAG-T-CGTTGCCTCTGTTTAG
3521724 AGGAGCAATTTACTTTTCAAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTC-AAAGTCGT--TGCCTCTGTTTAG
*
3521766 AGGAGCAATTTATTTTTCAAAGTTCCGTTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAG-T-CGTTGCCTCTGTTTAG
*
3521807 AGGAGCAATTTATTTTTCCAAAGTCGTGTTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAGTC--GTTGCCTCTGTTTAG
*
3521849 AGGAGCAATTTACTTTCCAAAGTCCGTTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGT-CGTTGCCTCTGTTTAG
*
3521889 AGGAGCAATTTAC-TTTCAAAAGTCGTTGAGTCTCTGTTTAG
1 AGGAGCAATTTACTTTTC-AAAGTCGTT--GCCTCTGTTTAG
3521930 AGGAGC
1 AGGAGC
3521936 TTCGGCCAAA
Statistics
Matches: 501, Mismatches: 13, Indels: 52
0.89 0.02 0.09
Matches are distributed among these distances:
39 20 0.04
40 128 0.26
41 156 0.31
42 189 0.38
43 5 0.01
44 3 0.01
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (39 bp):
AGGAGCAATTTACTTTTCAAAGTCGTTGCCTCTGTTTAG
Found at i:3521623 original size:83 final size:79
Alignment explanation
Indices: 3521356--3521935 Score: 785
Period size: 83 Copynumber: 7.1 Consensus size: 79
3521346 ATGATCGTCT
3521356 AGGAG-AATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTT-C-AAGTT
1 AGGAGCAATTTACTTTTCAAAG-TCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAG-T
3521418 CCGTTGCCTCTGTTTAG
64 -CGTTGCCTCTGTTTAG
3521435 AGGAGCAATTTACTTTTCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAG
1 AGGAGCAATTTACTTTTC-AAAGTCGT--TGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAG
3521500 TTCCGTTGCCTCTGTTTAG
63 -T-CGTTGCCTCTGTTTAG
3521519 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAA-TTATTTTTCCAAAGT
1 AGGAGCAATTTACTTTTCAAAGTCGT--TGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGT
3521583 CGTGGTGCCTCTGTTTAG
64 CGT--TGCCTCTGTTTAG
* *
3521601 AGGAGCAATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAG
1 AGGAGCAATTTACTTTT-CAAAGTCGT--TGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAG
3521665 TTCGTTGCCTCTGTTTAG
63 -TCGTTGCCTCTGTTTAG
* * *
3521683 AGGAGCAATTTATTTTTCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAAGT
1 AGGAGCAATTTACTTTTCAAAG-T-CGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGT
3521748 CGTGGTGCCTCTGTTTAG
64 CGT--TGCCTCTGTTTAG
*
3521766 AGGAGCAATTTATTTTTCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGT
1 AGGAGCAATTTACTTTTCAAAG-T-CGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGT
3521831 CGTGTTGCCTCTGTTTAG
64 C--GTTGCCTCTGTTTAG
* * *
3521849 AGGAGCAATTTACTTTCCAAAGTCCGTTGCCTCTGTTTAGAGGAGCAATTTA-CTTTCAAAAGTC
1 AGGAGCAATTTACTTTTCAAAGT-CGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTC
*
3521913 GTTGAGTCTCTGTTTAG
65 GTT--GCCTCTGTTTAG
3521930 AGGAGC
1 AGGAGC
3521936 TTCGGCCAAA
Statistics
Matches: 471, Mismatches: 10, Indels: 38
0.91 0.02 0.07
Matches are distributed among these distances:
79 8 0.02
80 19 0.04
81 71 0.15
82 138 0.29
83 182 0.39
84 51 0.11
85 2 0.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (79 bp):
AGGAGCAATTTACTTTTCAAAGTCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCG
TTGCCTCTGTTTAG
Found at i:3521749 original size:206 final size:204
Alignment explanation
Indices: 3521356--3521935 Score: 896
Period size: 206 Copynumber: 2.8 Consensus size: 204
3521346 ATGATCGTCT
*
3521356 AGGAG-AATTTACTTTTCAAAGTT-CGTTGCCTCTGTTTAGAGGAGCAATTTATTTTT-C-AAGT
1 AGGAGCAATTTATTTTTCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAG-
3521417 TCCGT-TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAAG-TCGTGGTGCCTCTGTTTAGAGG
65 T-CGTGTGCCTCTGTTTAGAGGAGCAATTTACTTTTC-AAAGTTCGT--TGCCTCTGTTTAGAGG
3521480 AGCAATTTATTTTTCCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGT
126 AGCAATTTATTTTT-CAAAGTTCCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGT
3521545 GGTGCCTCTGTTTAG
190 GGTGCCTCTGTTTAG
3521560 AGGAGCAA-TTATTTTTCCAAAG-T-CGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAA
1 AGGAGCAATTTATTTTT-CAAAGTTCCGT--TGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAA
3521622 AGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGA
63 AGTCGT-GTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGA
3521687 GCAATTTATTTTTCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAAGTCGTG
127 GCAATTTATTTTTCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTC-AAAGTCGTG
3521752 GTGCCTCTGTTTAG
191 GTGCCTCTGTTTAG
3521766 AGGAGCAATTTATTTTTCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGT
1 AGGAGCAATTTATTTTTCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGT
* *
3521831 CGTGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCCGTTGCCTCTGTTTAGAGGAGCA
66 CGTG-TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
* *
3521896 ATTTA-CTTTCAAAAG-T-CGTTGAGTCTCTGTTTAGAGGAGC
130 ATTTATTTTTC-AAAGTTCCGTT--GCCTCTGTTTAGAGGAGC
3521936 TTCGGCCAAA
Statistics
Matches: 354, Mismatches: 5, Indels: 32
0.91 0.01 0.08
Matches are distributed among these distances:
204 20 0.06
205 55 0.16
206 223 0.63
207 15 0.04
208 41 0.12
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (204 bp):
AGGAGCAATTTATTTTTCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGT
CGTGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAA
TTTATTTTTCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCC
TCTGTTTAG
Found at i:3521963 original size:15 final size:15
Alignment explanation
Indices: 3521943--3522059 Score: 121
Period size: 15 Copynumber: 7.5 Consensus size: 15
3521933 AGCTTCGGCC
3521943 AAAAAAAAAACAAAA
1 AAAAAAAAAACAAAA
*
3521958 AAAAAACAAAAAAACAA
1 AAAAAA-AAAACAA-AA
3521975 AAAACAAAAAAC-AAA
1 AAAA-AAAAAACAAAA
*
3521990 AAAACAAAAACAAAA
1 AAAAAAAAAACAAAA
3522005 AAATCAAAAAAA-ATAAA
1 AAA--AAAAAAACA-AAA
3522022 AAAAATAAAAACAAAA
1 AAAAA-AAAAACAAAA
*
3522038 AAAAAAAAATCAAAA
1 AAAAAAAAAACAAAA
*
3522053 ATAAAAA
1 AAAAAAA
3522060 TGTTGAGTTG
Statistics
Matches: 87, Mismatches: 6, Indels: 18
0.78 0.05 0.16
Matches are distributed among these distances:
14 6 0.07
15 35 0.40
16 21 0.24
17 23 0.26
18 2 0.02
ACGTcount: A:0.87, C:0.09, G:0.00, T:0.04
Consensus pattern (15 bp):
AAAAAAAAAACAAAA
Found at i:3522006 original size:54 final size:52
Alignment explanation
Indices: 3521943--3522060 Score: 150
Period size: 54 Copynumber: 2.2 Consensus size: 52
3521933 AGCTTCGGCC
3521943 AAAAAAAAAA-CAAAAAAAAAACAAAAAAACAAAAAACAAAAAACAAAAAAA-CAA
1 AAAAAAAAAATCAAAAAAAAAA-AAAAAAA-AAAAAACAAAAAA-AAAAAAATC-A
* *
3521997 AAACAAAAAAATCAAAAAAAATAAAAAAAATAAAAACAAAAAAAAAAAAATCA
1 AAA-AAAAAAATCAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAATCA
*
3522050 AAAATAAAAAT
1 AAAAAAAAAAT
3522061 GTTGAGTTGA
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
52 7 0.12
53 11 0.19
54 16 0.28
55 14 0.24
56 10 0.17
ACGTcount: A:0.86, C:0.08, G:0.00, T:0.05
Consensus pattern (52 bp):
AAAAAAAAAATCAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAATCA
Found at i:3522059 original size:1 final size:1
Alignment explanation
Indices: 3521943--3522046 Score: 100
Period size: 1 Copynumber: 104.0 Consensus size: 1
3521933 AGCTTCGGCC
* * * * * * *
3521943 AAAAAAAAAACAAAAAAAAAACAAAAAAACAAAAAACAAAAAACAAAAAAACAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * * *
3522008 TCAAAAAAAATAAAAAAAATAAAAACAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3522047 TCAAAAATAA
Statistics
Matches: 80, Mismatches: 23, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 80 1.00
ACGTcount: A:0.88, C:0.09, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:3522187 original size:20 final size:20
Alignment explanation
Indices: 3522162--3522220 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
3522152 CAGGTCCGGG
3522162 CCCGGATCAATTGGGCCTGA
1 CCCGGATCAATTGGGCCTGA
3522182 CCCGGATCAATTGGGCCTGA
1 CCCGGATCAATTGGGCCTGA
* *
3522202 CCCAGATCATTTGGGCCTG
1 CCCGGATCAATTGGGCCTG
3522221 GCCCAAATGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.19, C:0.31, G:0.29, T:0.22
Consensus pattern (20 bp):
CCCGGATCAATTGGGCCTGA
Found at i:3522282 original size:14 final size:13
Alignment explanation
Indices: 3522263--3522297 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
3522253 ATTATTATTA
*
3522263 TTTTTTTTTTTCC
1 TTTTTTTTTTTTC
3522276 TTTTTTTTTTTTC
1 TTTTTTTTTTTTC
3522289 TTTTCTTTT
1 TTTT-TTTT
3522298 GTATTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTTTTC
Found at i:3522304 original size:18 final size:19
Alignment explanation
Indices: 3522264--3522305 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
3522254 TTATTATTAT
* * *
3522264 TTTTTTTTTTCCTTTTTTT
1 TTTTTCTTTTCCTTTTGTA
3522283 TTTTTCTTTT-CTTTTGTA
1 TTTTTCTTTTCCTTTTGTA
3522301 TTTTT
1 TTTTT
3522306 ATATTTATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.02, C:0.10, G:0.02, T:0.86
Consensus pattern (19 bp):
TTTTTCTTTTCCTTTTGTA
Found at i:3522398 original size:3 final size:3
Alignment explanation
Indices: 3522390--3522418 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3522380 AGTTATATAT
3522390 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3522419 TTTGTAAGAT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3522983 original size:31 final size:31
Alignment explanation
Indices: 3522914--3522984 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
3522904 GGAAATTTCC
* *
3522914 AGATTCCGGCGAAAATTCCGGCGACATTTGA
1 AGATTCCGGCGAAAATTCCGGCGAAACTTGA
**
3522945 ATTTTCCGGC-ACAAATTCCGGCGAAACTTGA
1 AGATTCCGGCGA-AAATTCCGGCGAAACTTGA
3522976 AGATTCCGG
1 AGATTCCGG
3522985 TGACCAACCC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 1 0.03
31 32 0.97
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (31 bp):
AGATTCCGGCGAAAATTCCGGCGAAACTTGA
Found at i:3523063 original size:19 final size:19
Alignment explanation
Indices: 3523039--3523085 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
3523029 TTCCGGCCAT
3523039 ATTCCGGCAAAAATTCCAG
1 ATTCCGGCAAAAATTCCAG
* * *
3523058 ATTCCGGCGACATTTCCAG
1 ATTCCGGCAAAAATTCCAG
*
3523077 AATCCGGCA
1 ATTCCGGCA
3523086 CCGGTGTTCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (19 bp):
ATTCCGGCAAAAATTCCAG
Found at i:3523415 original size:1 final size:1
Alignment explanation
Indices: 3523409--3523444 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
3523399 CCGCTCCAGG
3523409 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3523445 GACTTTGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3523727 original size:160 final size:160
Alignment explanation
Indices: 3523462--3523920 Score: 768
Period size: 156 Copynumber: 2.9 Consensus size: 160
3523452 ATTTTGATCT
* * *
3523462 TGATTTT-TTTTTCTTTTTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGT
1 TGATTTTGATTTT-TTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGT-GAAACAGTAGT
3523526 TTTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAAT
64 TTTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAAT
*
3523591 TGAGAATAA-TTTCTGATAATTAATTACTTGGC
129 TGAGAATAATTTTC-GATAATTAATTAATTGGC
3523623 TGATTTTGATTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTT
1 TGATTTTGATTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTT
3523688 TTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTG
66 TTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTG
*
3523753 AGAATAATTTTCGATAATTAATTAATTGGT
131 AGAATAATTTTCGATAATTAATTAATTGGC
* *
3523783 TGATCTTGA----TTTTTCTTTAAATAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTT
1 TGATTTTGATTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTT
* *
3523844 TTCTTGCATACTCTTGAGGTGAGAGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTG
66 TTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTG
3523909 AGAATAATTTTC
131 AGAATAATTTTC
3523921 AACAACTAAC
Statistics
Matches: 287, Mismatches: 9, Indels: 9
0.94 0.03 0.03
Matches are distributed among these distances:
156 126 0.44
160 108 0.38
161 49 0.17
162 4 0.01
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (160 bp):
TGATTTTGATTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTT
TTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTG
AGAATAATTTTCGATAATTAATTAATTGGC
Found at i:3524938 original size:36 final size:37
Alignment explanation
Indices: 3524868--3524938 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
3524858 CTCATTTTTT
* **
3524868 TCTTCTTTCTTTCTTTTTTTTTATTTTTTTTCCATCA
1 TCTTCTTTCTTTCTTTTTTTTCATTTTTCATCCATCA
*
3524905 TCTT-TTTTTTTCTTTTTTTTCATTTTTCATCCAT
1 TCTTCTTTCTTTCTTTTTTTTCATTTTTCATCCAT
3524939 TGTTGATATC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 26 0.87
37 4 0.13
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.73
Consensus pattern (37 bp):
TCTTCTTTCTTTCTTTTTTTTCATTTTTCATCCATCA
Found at i:3527690 original size:160 final size:162
Alignment explanation
Indices: 3527443--3527746 Score: 558
Period size: 160 Copynumber: 1.9 Consensus size: 162
3527433 GTTAGTTGTT
3527443 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAG
1 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAG
3527508 AGTATGCAAGAAAAACTACTG-TTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAG-AAAA
66 AGTATGCAAGAAAAACTACTGTTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAA
3527571 AAAAATCAAAATCAGCCAAGTAATTAATTATC
131 AAAAATCAAAATCAGCCAAGTAATTAATTATC
*
3527603 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAGG
1 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAG
* *
3527668 AGTATGCAAGAAAAACTACTGTTTTTACTTGTAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAA
66 AGTATGCAAGAAAAACTACTGTTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAA
*
3527733 AAAAATCAAGATCA
131 AAAAATCAAAATCA
3527747 AAATCAAAGT
Statistics
Matches: 138, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
160 85 0.62
161 36 0.26
162 17 0.12
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.28
Consensus pattern (162 bp):
GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAG
AGTATGCAAGAAAAACTACTGTTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAA
AAAAATCAAAATCAGCCAAGTAATTAATTATC
Found at i:3528087 original size:19 final size:19
Alignment explanation
Indices: 3528058--3528102 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
3528048 GAACGCCGGT
*
3528058 GCCGGATTCTGGAAATTTC
1 GCCGGAATCTGGAAATTTC
* *
3528077 GTCGGAATCTGGGAATTTC
1 GCCGGAATCTGGAAATTTC
3528096 GCCGGAA
1 GCCGGAA
3528103 ATTGGCCGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.27
Consensus pattern (19 bp):
GCCGGAATCTGGAAATTTC
Found at i:3528191 original size:31 final size:31
Alignment explanation
Indices: 3528153--3528225 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
3528143 AAACTGGGTC
* *
3528153 TGTCGCCGGAAACTTC-AAAGTTCGTCGGAAT
1 TGTCGCCGGAAAATTCAAAAG-TCGCCGGAAT
3528184 TGTCGCCGGAAAATTCAAAAGTCGCCGGAAT
1 TGTCGCCGGAAAATTCAAAAGTCGCCGGAAT
*
3528215 TTTCGCCGGAA
1 TGTCGCCGGAA
3528226 TCTGGAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 34 0.89
32 4 0.11
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.23
Consensus pattern (31 bp):
TGTCGCCGGAAAATTCAAAAGTCGCCGGAAT
Found at i:3528880 original size:20 final size:20
Alignment explanation
Indices: 3528857--3528898 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3528847 GGCCTTGCCC
3528857 ATTTGGGGCAGGCCCAAATG
1 ATTTGGGGCAGGCCCAAATG
* *
3528877 ATTTGGGTCAGGCCCAATTG
1 ATTTGGGGCAGGCCCAAATG
3528897 AT
1 AT
3528899 CCGGGCCCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (20 bp):
ATTTGGGGCAGGCCCAAATG
Found at i:3529023 original size:1 final size:1
Alignment explanation
Indices: 3529019--3529094 Score: 71
Period size: 1 Copynumber: 76.0 Consensus size: 1
3529009 TCATTTTTGA
* * ** ** * * *
3529019 TTTTTTTTTTTTGTTTTTATTTTTTTTGATTTTTTTGATTTTTTTGTTTTTTTGTTTTTTTGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3529084 TTTTTTTTTTT
1 TTTTTTTTTTT
3529095 GGCCGAAGCT
Statistics
Matches: 59, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.04, C:0.00, G:0.08, T:0.88
Consensus pattern (1 bp):
T
Found at i:3529035 original size:9 final size:9
Alignment explanation
Indices: 3529012--3529094 Score: 91
Period size: 9 Copynumber: 9.3 Consensus size: 9
3529002 GACATTTTCA
3529012 TTTTTGATTT
1 TTTTTG-TTT
*
3529022 TTTTTTTTT
1 TTTTTGTTT
*
3529031 GTTTTTATTT
1 -TTTTTGTTT
*
3529041 TTTTTGATT
1 TTTTTGTTT
*
3529050 TTTTTGATT
1 TTTTTGTTT
3529059 TTTTTG-TT
1 TTTTTGTTT
3529067 TTTTTG-TT
1 TTTTTGTTT
3529075 TTTTTGTTT
1 TTTTTGTTT
3529084 TTTTT-TTT
1 TTTTTGTTT
3529092 TTT
1 TTT
3529095 GGCCGAAGCT
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
8 22 0.33
9 32 0.48
10 13 0.19
ACGTcount: A:0.05, C:0.00, G:0.08, T:0.87
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:3529228 original size:42 final size:42
Alignment explanation
Indices: 3529102--3529716 Score: 849
Period size: 42 Copynumber: 15.0 Consensus size: 42
3529092 TTTGGCCGAA
* * * *
3529102 GCTCCTCTAAACAGAGACTCAACGACTTTTG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
3529143 GCTCCTCTAAACAGAGGCA--ACGGAC-TTGG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCAC-GACTTTGGAAAAGTAAATT
* *
3529182 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
*
3529224 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAA-TAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
**
3529265 GCTCCTCTTCACAGAGGCACCACGACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
3529306 GCTCCTCTAAACAGAGGCA--ACGAACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGGAAAAGTAAATT
** *
3529346 GCTCCTCTAAACAGAGGCACCACGACTTTAAAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
3529388 GCTCCTCTAAACAGAGGCA--ACGAAC-TTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGGAAAAGTAAATT
*
3529428 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
*
3529470 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
*
3529512 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
* *
3529554 GCTCCTCTAAACAGAGGCAACA-GAACTTT-GAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGGAAAAGTAAATT
*
3529595 GCTCCTCTAAACAGAGGCA--ACGGAACTTT-GAAAAGCAAATT
1 GCTCCTCTAAACAGAGGCACCAC-G-ACTTTGGAAAAGTAAATT
*
3529636 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
3529678 GCTCCTCTAAACAGAGGCA--ACGAAC-TTGGAAAAGTAAAT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGGAAAAGTAAAT
3529717 ACTCCTAGAC
Statistics
Matches: 530, Mismatches: 23, Indels: 43
0.89 0.04 0.07
Matches are distributed among these distances:
39 37 0.07
40 97 0.18
41 162 0.31
42 232 0.44
43 2 0.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (42 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
Found at i:3529320 original size:82 final size:81
Alignment explanation
Indices: 3529102--3529716 Score: 822
Period size: 82 Copynumber: 7.5 Consensus size: 81
3529092 TTTGGCCGAA
* * *
3529102 GCTCCTCTAAACAGAGACTCAACGACTTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCA-ACG
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACAC-
*
3529165 GAC-TTGGAAAGTAAATT
64 GACTTTGGAAAATAAATT
* * *
3529182 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCA-CAC
3529247 GACTTTGGAAAATAAATT
64 GACTTTGGAAAATAAATT
**
3529265 GCTCCTCTTCACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA-ACGA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACACG-
3529329 ACTTT-GAAAAGTAAATT
65 ACTTTGGAAAA-TAAATT
* *
3529346 GCTCCTCTAAACAGAGGCACCACGACTTTAAAAAAATAAATTGCTCCTCTAAACAGAGGCA-ACG
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCACACG
3529410 AAC-TTGGAAAAGTAAATT
65 -ACTTTGGAAAA-TAAATT
*
3529428 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCA-CAC
3529493 GACTTTGGAAAAATAAATT
64 GACTTTGG-AAAATAAATT
3529512 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA-ACA
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACAC-
*
3529576 GAACTTTGAAAAATAAATT
64 G-ACTTTGGAAAATAAATT
*
3529595 GCTCCTCTAAACAGAGGCA--ACGGAACTTTGAAAAGCAAATTGCTCCTCTAAACAGAGGCACCA
1 GCTCCTCTAAACAGAGGCACCAC-G-ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA-CA
*
3529658 CGACTTTTGAAAAGTAAATT
63 CGACTTTGGAAAA-TAAATT
*
3529678 GCTCCTCTAAACAGAGGCA--ACGAACTTGGAAAAGTAAAT
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGAAAAGTAAAT
3529717 ACTCCTAGAC
Statistics
Matches: 490, Mismatches: 24, Indels: 40
0.88 0.04 0.07
Matches are distributed among these distances:
79 3 0.01
80 31 0.06
81 69 0.14
82 199 0.41
83 104 0.21
84 77 0.16
85 7 0.01
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (81 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACACGA
CTTTGGAAAATAAATT
Found at i:3529496 original size:124 final size:123
Alignment explanation
Indices: 3529102--3529716 Score: 853
Period size: 124 Copynumber: 5.0 Consensus size: 123
3529092 TTTGGCCGAA
* * * *
3529102 GCTCCTCTAAACAGAGACTCAACGACTTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCA-ACG
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACAC-
* *
3529165 GAC-TTGGAAAGTAAATTGCTCCTCTCAACAGAGGCACCACG-ACTTTGGAAAAATAAATT
64 GACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA-CACGAACTTTGGAAAAATAAATT
* * **
3529224 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAATAAATTGCTCCTCTTCACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCA-CACG
*
3529289 ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA-ACGAACTTT-GAAAAGTAAATT
65 ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACACGAACTTTGGAAAAATAAATT
*
3529346 GCTCCTCTAAACAGAGGCACCACGACTTTAAAAAAATAAATTGCTCCTCTAAACAGAGGCA-ACG
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAATAAATTGCTCCTCTAAACAGAGGCACACG
*
3529410 AACTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG-ACTTTGGAAAAATAAATT
65 -ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA-CACGAACTTTGGAAAAATAAATT
3529470 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAATAAATTGCTCCTCTAAACAGAGGCA-CAC
3529535 GACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA-ACAGAACTTT-GAAAAATAAATT
64 GAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACAC-GAACTTTGGAAAAATAAATT
**
3529595 GCTCCTCTAAACAGAGGCA--ACGGAACTTTGAAAAGCAAATTGCTCCTCTAAACAGAGGCACCA
1 GCTCCTCTAAACAGAGGCACCAC-G-ACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCA-CA
*
3529658 CGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA-ACGAAC-TTGGAAAAGTAAAT
63 CGAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACACGAACTTTGGAAAAATAAAT
3529717 ACTCCTAGAC
Statistics
Matches: 452, Mismatches: 23, Indels: 35
0.89 0.05 0.07
Matches are distributed among these distances:
121 7 0.02
122 127 0.28
123 56 0.12
124 182 0.40
125 39 0.09
126 41 0.09
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (123 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACACGA
CTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACACGAACTTTGGAAAAATAAATT
Found at i:3530918 original size:8 final size:8
Alignment explanation
Indices: 3530905--3530943 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
3530895 TTCGGATCTC
3530905 TTTTTTCA
1 TTTTTTCA
3530913 TTTTTTCA
1 TTTTTTCA
3530921 TTTTTTCA
1 TTTTTTCA
*
3530929 TTTTCTCA
1 TTTTTTCA
3530937 TTTTTTC
1 TTTTTTC
3530944 TTCTTTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTTCA
Found at i:3532367 original size:9 final size:8
Alignment explanation
Indices: 3532259--3532368 Score: 100
Period size: 8 Copynumber: 13.2 Consensus size: 8
3532249 NNNNNNNNNN
3532259 AAAACAAA
1 AAAACAAA
*
3532267 AAAAAAAA
1 AAAACAAA
3532275 AAAACAAAA
1 AAAAC-AAA
3532284 AAAACAAA
1 AAAACAAA
*
3532292 AAAAC--C
1 AAAACAAA
3532298 AAAACAAA
1 AAAACAAA
3532306 AAAATCAAAA
1 AAAA-C-AAA
3532316 AAAATCAAA
1 AAAA-CAAA
3532325 AAAA-ATAA
1 AAAACA-AA
*
3532333 AAAAAAATA
1 AAAACAA-A
3532342 AAAACAAA
1 AAAACAAA
*
3532350 AAAAAAAA
1 AAAACAAA
3532358 AAAATCAAA
1 AAAA-CAAA
3532367 AA
1 AA
3532369 TAAAAATGTT
Statistics
Matches: 86, Mismatches: 7, Indels: 17
0.78 0.06 0.15
Matches are distributed among these distances:
6 5 0.06
7 1 0.01
8 42 0.49
9 29 0.34
10 9 0.10
ACGTcount: A:0.86, C:0.09, G:0.00, T:0.05
Consensus pattern (8 bp):
AAAACAAA
Found at i:3532373 original size:6 final size:6
Alignment explanation
Indices: 3532325--3532375 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 6
3532315 AAAAATCAAA
*
3532325 AAAAAT -AAAA- AAAAAT AAAAAC AAAAA- AAAAA- AAAAAT CAAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT -AAAAAT
3532370 AAAAAT
1 AAAAAT
3532376 GTTGAGTTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
5 18 0.45
6 16 0.40
7 6 0.15
ACGTcount: A:0.86, C:0.04, G:0.00, T:0.10
Consensus pattern (6 bp):
AAAAAT
Found at i:3532374 original size:1 final size:1
Alignment explanation
Indices: 3532259--3532361 Score: 89
Period size: 1 Copynumber: 103.0 Consensus size: 1
3532249 NNNNNNNNNN
* * * ** * ** **
3532259 AAAACAAAAAAAAAAAAAAACAAAAAAAACAAAAAAACCAAAACAAAAAAATCAAAAAAAATCAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
3532324 AAAAAATAAAAAAAAATAAAAACAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3532362 TCAAAAATAA
Statistics
Matches: 80, Mismatches: 22, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 80 1.00
ACGTcount: A:0.87, C:0.09, G:0.00, T:0.04
Consensus pattern (1 bp):
A
Found at i:3532510 original size:20 final size:20
Alignment explanation
Indices: 3532481--3532520 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3532471 TCCGGGCCCG
3532481 GATCAATTGGGCCTGACCCA
1 GATCAATTGGGCCTGACCCA
* *
3532501 GATCATTTGGGCCTGGCCCA
1 GATCAATTGGGCCTGACCCA
3532521 AATGGGTAAG
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:0.20, C:0.30, G:0.28, T:0.23
Consensus pattern (20 bp):
GATCAATTGGGCCTGACCCA
Found at i:3532690 original size:3 final size:3
Alignment explanation
Indices: 3532682--3532710 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3532672 AGTTATATAT
3532682 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3532711 TTTGTAAGAT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3533272 original size:31 final size:31
Alignment explanation
Indices: 3533215--3533273 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
3533205 GATTCCGCGA
* * **
3533215 AAATTCCGGCGACATTTGAATTTTCCGGCAC
1 AAATTCCGGCGAAACTTGAAGATTCCGGCAC
3533246 AAATTCCGGCGAAACTTGAAGATTCCGG
1 AAATTCCGGCGAAACTTGAAGATTCCGG
3533274 TGACCAACCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (31 bp):
AAATTCCGGCGAAACTTGAAGATTCCGGCAC
Found at i:3533352 original size:19 final size:19
Alignment explanation
Indices: 3533328--3533374 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
3533318 TTCCGGCCAT
3533328 ATTCCGGCAAAAATTCCAG
1 ATTCCGGCAAAAATTCCAG
* * *
3533347 ATTCCGGCGACATTTCCAG
1 ATTCCGGCAAAAATTCCAG
*
3533366 AATCCGGCA
1 ATTCCGGCA
3533375 CCGGTGTTCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (19 bp):
ATTCCGGCAAAAATTCCAG
Found at i:3533703 original size:1 final size:1
Alignment explanation
Indices: 3533697--3533741 Score: 90
Period size: 1 Copynumber: 45.0 Consensus size: 1
3533687 CCGCTCCAGG
3533697 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3533742 CTTTGATTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3534043 original size:157 final size:159
Alignment explanation
Indices: 3533771--3534058 Score: 544
Period size: 157 Copynumber: 1.8 Consensus size: 159
3533761 TTTTTTTTTC
3533771 TTTTTTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATAC
1 TTTTTTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATAC
3533836 TCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTT
66 TCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTT
3533901 CGATAATTAATTACTTGGCTGATTTTGAT
131 CGATAATTAATTACTTGGCTGATTTTGAT
* *
3533930 TTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGT-GAAACAGTAGTTTTTCTTGCATAC
1 TTTTTTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATAC
3533994 TCCTGAGGTGA-GGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTT
66 TCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTT
3534058 C
131 C
3534059 AACAACTAAC
Statistics
Matches: 127, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
157 54 0.43
158 34 0.27
159 39 0.31
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (159 bp):
TTTTTTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATAC
TCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTT
CGATAATTAATTACTTGGCTGATTTTGAT
Found at i:3534807 original size:19 final size:18
Alignment explanation
Indices: 3534771--3534806 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3534761 ACTGAATCAT
3534771 TGGGTAAAAAACAAAAAA
1 TGGGTAAAAAACAAAAAA
3534789 TGGGTAAAAAACAAAAAA
1 TGGGTAAAAAACAAAAAA
3534807 AAAAAGTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.06, G:0.17, T:0.11
Consensus pattern (18 bp):
TGGGTAAAAAACAAAAAA
Found at i:3535446 original size:21 final size:21
Alignment explanation
Indices: 3535406--3535489 Score: 71
Period size: 21 Copynumber: 3.9 Consensus size: 21
3535396 TTATTTATCG
*
3535406 AATATATTTGTTTGCATGATT
1 AATATATTTATTTGCATGATT
**
3535427 AATATATTTATTTGTGTGATT
1 AATATATTTATTTGCATGATT
* *
3535448 TAT-TAATATATTTGCATGATTATT
1 AATAT-ATTTATTTGCATG---ATT
*
3535472 AATATATTTAATTGCATG
1 AATATATTTATTTGCATG
3535490 TTTATTTACA
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
20 1 0.02
21 30 0.62
24 16 0.33
25 1 0.02
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.52
Consensus pattern (21 bp):
AATATATTTATTTGCATGATT
Found at i:3535472 original size:20 final size:20
Alignment explanation
Indices: 3535416--3535480 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
3535406 AATATATTTG
* *
3535416 TTTGCATGATTAATATATTTA
1 TTTGCATGATTATTA-ATATA
**
3535437 TTTGTGTGATTTATTAATATA
1 TTTGCATGA-TTATTAATATA
3535458 TTTGCATGATTATTAATATA
1 TTTGCATGATTATTAATATA
3535478 TTT
1 TTT
3535481 AATTGCATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 14 0.38
21 18 0.49
22 5 0.14
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTGCATGATTATTAATATA
Found at i:3535560 original size:31 final size:31
Alignment explanation
Indices: 3535524--3535587 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
3535514 ATTGCATATT
* *
3535524 TTGCATGGTTTATATGTTATTATTTACATGA
1 TTGCATGATTTATATATTATTATTTACATGA
*
3535555 TTGCATGATTTATATATTATTATTTGCATGA
1 TTGCATGATTTATATATTATTATTTACATGA
3535586 TT
1 TT
3535588 ATGTATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.06, G:0.14, T:0.53
Consensus pattern (31 bp):
TTGCATGATTTATATATTATTATTTACATGA
Found at i:3535603 original size:20 final size:23
Alignment explanation
Indices: 3535554--3535608 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 23
3535544 TATTTACATG
3535554 ATTGCATGATTTATATATTATTA
1 ATTGCATGATTTATATATTATTA
* *
3535577 TTTGCATGA-TTATGTA-T-TTA
1 ATTGCATGATTTATATATTATTA
3535597 ATTGCAT-ATTTA
1 ATTGCATGATTTA
3535609 ATTGCATGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 1 0.04
20 12 0.43
21 1 0.04
22 6 0.21
23 8 0.29
ACGTcount: A:0.31, C:0.05, G:0.11, T:0.53
Consensus pattern (23 bp):
ATTGCATGATTTATATATTATTA
Found at i:3535626 original size:15 final size:12
Alignment explanation
Indices: 3535591--3535615 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3535581 CATGATTATG
3535591 TATTTAATTGCA
1 TATTTAATTGCA
3535603 TATTTAATTGCA
1 TATTTAATTGCA
3535615 T
1 T
3535616 GATTATTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (12 bp):
TATTTAATTGCA
Found at i:3535690 original size:21 final size:20
Alignment explanation
Indices: 3535665--3535706 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
3535655 TATTTAATTG
*
3535665 TATATTTATTTGCATGGTTTA
1 TATATTTAATTGCAT-GTTTA
3535686 TATATTTAATTGCATGTTTA
1 TATATTTAATTGCATGTTTA
3535706 T
1 T
3535707 TTGCATGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.26, C:0.05, G:0.12, T:0.57
Consensus pattern (20 bp):
TATATTTAATTGCATGTTTA
Found at i:3535729 original size:33 final size:33
Alignment explanation
Indices: 3535574--3535718 Score: 147
Period size: 32 Copynumber: 4.5 Consensus size: 33
3535564 TTATATATTA
*
3535574 TTATTTGCATGA-TTATGTATTTAATTGCATAT
1 TTATTTGCATGATTTATATATTTAATTGCATAT
* * * * *
3535606 TTAATTGCATGA-TTAT-TAATTTATTTACTTGT
1 TTATTTGCATGATTTATAT-ATTTAATTGCATAT
* *
3535638 GTGA-TTGCATGA-TTATATATTTAATTGTATAT
1 -TTATTTGCATGATTTATATATTTAATTGCATAT
* *
3535670 TTATTTGCATGGTTTATATATTTAATTGCATGT
1 TTATTTGCATGATTTATATATTTAATTGCATAT
3535703 TTATTTGCATGATTTA
1 TTATTTGCATGATTTA
3535719 CATTGTTAAT
Statistics
Matches: 92, Mismatches: 16, Indels: 9
0.79 0.14 0.08
Matches are distributed among these distances:
31 3 0.03
32 53 0.58
33 36 0.39
ACGTcount: A:0.28, C:0.06, G:0.13, T:0.54
Consensus pattern (33 bp):
TTATTTGCATGATTTATATATTTAATTGCATAT
Found at i:3535863 original size:19 final size:19
Alignment explanation
Indices: 3535826--3535864 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3535816 TTATTTATTA
* *
3535826 TTATTGCATGATTTTATAT
1 TTATTGCATGATATGATAT
*
3535845 TTATTGTATGATATGATAT
1 TTATTGCATGATATGATAT
3535864 T
1 T
3535865 ATATGTTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.13, T:0.56
Consensus pattern (19 bp):
TTATTGCATGATATGATAT
Found at i:3535866 original size:24 final size:24
Alignment explanation
Indices: 3535833--3535894 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
3535823 TTATTATTGC
* *
3535833 ATGATTTTATATTTATTGTATGAT
1 ATGATATTATATTTATTGCATGAT
3535857 ATGATATTATATGTTATTGCATGAT
1 ATGATATTATAT-TTATTGCATGAT
*
3535882 -TAATATTATATTT
1 ATGATATTATATTT
3535895 GAATGATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.06
24 21 0.62
25 11 0.32
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (24 bp):
ATGATATTATATTTATTGCATGAT
Found at i:3536069 original size:60 final size:58
Alignment explanation
Indices: 3535957--3536070 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 58
3535947 TTATACATAA
* * * *
3535957 TTATTAATATATTTGTGTGATTTTACTTAATTTCATGATTATATATTTGCATGAATGG
1 TTATTAATATATTTGTGTGATTTTACTTAATTACATGATAATAGATTAGCATGAATGG
*
3536015 TTATTAATATATTTGCATG-GTATTTTA-TATTATTACATGATAATAGATTAGCATGA
1 TTATTAATATATTTG--TGTG-ATTTTACT-TAATTACATGATAATAGATTAGCATGA
3536071 TATTATATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
58 15 0.32
59 2 0.04
60 30 0.64
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.49
Consensus pattern (58 bp):
TTATTAATATATTTGTGTGATTTTACTTAATTACATGATAATAGATTAGCATGAATGG
Found at i:3544554 original size:21 final size:21
Alignment explanation
Indices: 3544513--3544554 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3544503 TTTAAAAATT
* *
3544513 ATTTTGGTGATCTTATCACCA
1 ATTTTAGTGATCTAATCACCA
*
3544534 ATTTTAGTGATCTAATTACCA
1 ATTTTAGTGATCTAATCACCA
3544555 TGGTGATAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (21 bp):
ATTTTAGTGATCTAATCACCA
Found at i:3547629 original size:2 final size:2
Alignment explanation
Indices: 3547624--3547654 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3547614 AAAAAAAAAA
*
3547624 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3547655 CACATTCTTT
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:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3550100 original size:9 final size:9
Alignment explanation
Indices: 3550079--3550108 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3550069 TGTGTGTGTG
3550079 TATATAT-A
1 TATATATAA
3550087 TATATATAA
1 TATATATAA
3550096 TATATATAA
1 TATATATAA
3550105 TATA
1 TATA
3550109 AAAATTTGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TATATATAA
Found at i:3552535 original size:41 final size:42
Alignment explanation
Indices: 3552458--3552536 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 42
3552448 AGATTAAAAA
* **
3552458 TTAAAAAAATAAATTGAATTGATTTATATATTTTTATTAATT
1 TTAAAAAAATAAAATGAATTGATTTATATAAATTTATTAATT
*
3552500 TTAATAAAATAAAAT-AATT-ATTATATATAAATTTATT
1 TTAAAAAAATAAAATGAATTGATT-TATATAAATTTATT
3552537 TAAATATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 3 0.09
41 16 0.50
42 13 0.41
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (42 bp):
TTAAAAAAATAAAATGAATTGATTTATATAAATTTATTAATT
Found at i:3552992 original size:15 final size:16
Alignment explanation
Indices: 3552964--3552998 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
3552954 GGGAAAAAGA
3552964 AAAAATAAAGAAAAAT
1 AAAAATAAAGAAAAAT
*
3552980 AAAATTAAA-AAAAAT
1 AAAAATAAAGAAAAAT
3552995 AAAA
1 AAAA
3552999 GAAATAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (16 bp):
AAAAATAAAGAAAAAT
Found at i:3553120 original size:13 final size:12
Alignment explanation
Indices: 3553099--3553132 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
3553089 ATACTTTAAT
3553099 TTAGAAAAAAAG
1 TTAGAAAAAAAG
3553111 TTAGAGAAAAAAG
1 TTAGA-AAAAAAG
*
3553124 TTACAAAAA
1 TTAGAAAAA
3553133 TTTTTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.65, C:0.03, G:0.15, T:0.18
Consensus pattern (12 bp):
TTAGAAAAAAAG
Found at i:3554603 original size:24 final size:22
Alignment explanation
Indices: 3554575--3554633 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 22
3554565 TTTTTTAAAA
*
3554575 ATTTTAAATTATATTATTTTTT
1 ATTTTAAATTATATTATTTTAT
* *
3554597 AATTTTTTATTTATATTATTTTAT
1 -A-TTTTAAATTATATTATTTTAT
3554621 ATTTTAAATTATA
1 ATTTTAAATTATA
3554634 AGATCTCAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 10 0.33
23 2 0.07
24 18 0.60
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
ATTTTAAATTATATTATTTTAT
Found at i:3555156 original size:13 final size:14
Alignment explanation
Indices: 3555140--3555170 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3555130 TATTATTTAT
3555140 TAAATTT-AATAAA
1 TAAATTTAAATAAA
3555153 TAAATTTAAATAAA
1 TAAATTTAAATAAA
3555167 TAAA
1 TAAA
3555171 AATTAATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAATTTAAATAAA
Found at i:3555853 original size:3 final size:3
Alignment explanation
Indices: 3555845--3555870 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3555835 TCTATACTTG
3555845 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
3555871 TAAACAAAAA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:3556657 original size:22 final size:21
Alignment explanation
Indices: 3556610--3556657 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3556600 AATTTAAAAT
*
3556610 TTTTAAAAAATTATAAATAAA
1 TTTTAAAAAATTAAAAATAAA
* *
3556631 ATTTAAAAAATTAAAAAATATA
1 TTTTAAAAAATT-AAAAATAAA
3556653 TTTTA
1 TTTTA
3556658 TATTTTTATG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTTAAAAAATTAAAAATAAA
Found at i:3563359 original size:27 final size:27
Alignment explanation
Indices: 3563318--3563384 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
3563308 GGCCTGTACT
** *
3563318 TGTAGTGCCCAGAGAAAAAG-TCATAGC
1 TGTAGTGCCTGGAG-AAAAGCTCAGAGC
* *
3563345 TGTAGTGCCTGGAGAAAAGCTCGGAGT
1 TGTAGTGCCTGGAGAAAAGCTCAGAGC
3563372 TGTAGTGCCTGGA
1 TGTAGTGCCTGGA
3563385 CTAAAGCCTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 5 0.15
27 29 0.85
ACGTcount: A:0.28, C:0.16, G:0.33, T:0.22
Consensus pattern (27 bp):
TGTAGTGCCTGGAGAAAAGCTCAGAGC
Found at i:3565223 original size:5 final size:5
Alignment explanation
Indices: 3565187--3565217 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
3565177 CATTGAGAAG
3565187 AATAA AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA AATAA A
3565218 TCAAATTGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:3565916 original size:20 final size:20
Alignment explanation
Indices: 3565888--3565932 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
3565878 ATATATTTTT
* *
3565888 ATTTATTAAATTTATATATA
1 ATTTTTTAAATTCATATATA
3565908 ATTTTTTAAATTCATATATA
1 ATTTTTTAAATTCATATATA
3565928 ATTTT
1 ATTTT
3565933 GCTCAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTTTTAAATTCATATATA
Found at i:3571153 original size:18 final size:17
Alignment explanation
Indices: 3571115--3571169 Score: 65
Period size: 17 Copynumber: 3.0 Consensus size: 17
3571105 TTTATTAAGT
3571115 ATTTAAATTAAAATTAATTA
1 ATTTAAA-TAAAA--AATTA
3571135 ATTATAAATAAAAAATTA
1 ATT-TAAATAAAAAATTA
*
3571153 ATTTAAATATAAAATTA
1 ATTTAAATAAAAAATTA
3571170 TAAATATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
17 13 0.39
18 8 0.24
20 8 0.24
21 4 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTTAAATAAAAAATTA
Found at i:3571354 original size:25 final size:25
Alignment explanation
Indices: 3571310--3571381 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 25
3571300 TATTTATTTT
3571310 AAAA-TTAA-TTAAT-TATAAATAAA
1 AAAATTTAATTTAATATA-AAATAAA
*
3571333 AAAATTTAATTTAATATAAAATTATA
1 AAAATTTAATTTAATATAAAA-TAAA
* *
3571359 AATATTT-ATTAAATATAAAATAA
1 AAAATTTAATTTAATATAAAATAA
3571382 CACCGTGTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
23 4 0.10
24 6 0.15
25 20 0.49
26 11 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
AAAATTTAATTTAATATAAAATAAA
Found at i:3578064 original size:18 final size:18
Alignment explanation
Indices: 3578021--3578066 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
3578011 TTGAATAACC
*
3578021 AAAATATATATATATTTT
1 AAAATTTATATATATTTT
***
3578039 AGTTTTTATATATATTTT
1 AAAATTTATATATATTTT
3578057 AAAATTTATA
1 AAAATTTATA
3578067 AAGTAAAAAT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
AAAATTTATATATATTTT
Found at i:3578097 original size:34 final size:32
Alignment explanation
Indices: 3578055--3578146 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 32
3578045 TATATATATT
3578055 TTAAAATTTATAAAGTAAAAATAATAATTTTATA
1 TTAAAATTTATAAA-TAAAAATAA-AATTTTATA
* *
3578089 TTAAAATTTACTTAAAT-ATATTAAAATTTTATA
1 TTAAAATTTA--TAAATAAAAATAAAATTTTATA
*
3578122 TTAAAA-TAATAAATAAAAATTAAAA
1 TTAAAATTTATAAATAAAAA-TAAAA
3578147 ATCGATAAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
30 5 0.10
31 2 0.04
32 7 0.14
33 15 0.31
34 15 0.31
35 1 0.02
36 4 0.08
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (32 bp):
TTAAAATTTATAAATAAAAATAAAATTTTATA
Found at i:3580111 original size:57 final size:58
Alignment explanation
Indices: 3580037--3580152 Score: 146
Period size: 60 Copynumber: 2.0 Consensus size: 58
3580027 AATAATCAAT
* **
3580037 TAAAAGTTGAGGGTTAAACGCTTTGT-CCCC-TTAATTAAAGAAATTAAAGGCTAAAA
1 TAAAAGTTGAAGGTTAAACGCTTTGTACCCCATTAAAGAAAGAAATTAAAGGCTAAAA
* * *
3580093 TAAAAGGTTGAAGGTTAAATGTTTTGTACCCCAATTAAAGAAAGGAATTAAAGGCTAAAA
1 TAAAA-GTTGAAGGTTAAACGCTTTGTACCCC-ATTAAAGAAAGAAATTAAAGGCTAAAA
3580153 GTTTAAACAG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
56 5 0.10
57 18 0.36
58 4 0.08
60 23 0.46
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.28
Consensus pattern (58 bp):
TAAAAGTTGAAGGTTAAACGCTTTGTACCCCATTAAAGAAAGAAATTAAAGGCTAAAA
Found at i:3583413 original size:33 final size:33
Alignment explanation
Indices: 3583371--3583439 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
3583361 ACTCGAATTA
*
3583371 TGGGATATTGCAACTGTTGCATATACCTGCATT
1 TGGGATATTGCAACAGTTGCATATACCTGCATT
3583404 TGGGATATTGCAACAGTTGCATATACCTGCATT
1 TGGGATATTGCAACAGTTGCATATACCTGCATT
3583437 TGG
1 TGG
3583440 CTTCTATAGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (33 bp):
TGGGATATTGCAACAGTTGCATATACCTGCATT
Found at i:3584758 original size:2 final size:2
Alignment explanation
Indices: 3584751--3584782 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3584741 AAAGTTAAGA
*
3584751 AT AT AT AT AC 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
3584783 GAAGTTGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3585025 original size:17 final size:15
Alignment explanation
Indices: 3585003--3585040 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
3584993 ACGTGTTGAG
3585003 ATTTAAATTATATATAT
1 ATTTAAA-TAT-TATAT
3585020 ATTTAAATATTATAT
1 ATTTAAATATTATAT
3585035 -TTTAAA
1 ATTTAAA
3585041 AATAATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 5 0.24
16 3 0.14
17 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTAAATATTATAT
Found at i:3586014 original size:2 final size:2
Alignment explanation
Indices: 3586007--3586034 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3585997 TTCTTTTGTT
3586007 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
3586035 AGTTAATATC
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):
TA
Found at i:3586249 original size:12 final size:11
Alignment explanation
Indices: 3586228--3586260 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
3586218 TTAATAAATT
3586228 TATTATTTAAA
1 TATTATTTAAA
3586239 TATTATATTAAA
1 TATTAT-TTAAA
3586251 TATT-TTTAAA
1 TATTATTTAAA
3586261 ATTTAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.24
11 7 0.33
12 9 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TATTATTTAAA
Found at i:3586264 original size:29 final size:31
Alignment explanation
Indices: 3586232--3586304 Score: 96
Period size: 29 Copynumber: 2.4 Consensus size: 31
3586222 TAAATTTATT
* *
3586232 ATTTAAATATTATATTAAAT-ATTT-TTAAA
1 ATTTAAAAATCATATTAAATAATTTATTAAA
*
3586261 ATTTAAAAATCATATTAAATAATTTATTATA
1 ATTTAAAAATCATATTAAATAATTTATTAAA
*
3586292 ATTTAAGAATCAT
1 ATTTAAAAATCAT
3586305 TCATAACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 18 0.47
30 4 0.11
31 16 0.42
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (31 bp):
ATTTAAAAATCATATTAAATAATTTATTAAA
Found at i:3588065 original size:17 final size:16
Alignment explanation
Indices: 3588037--3588071 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
3588027 ATACATATAT
*
3588037 ATAAATATAAAATTAA
1 ATAAATATAAAAATAA
3588053 ATAAATAATAAAAATAA
1 ATAAAT-ATAAAAATAA
3588070 AT
1 AT
3588072 TATATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAAATATAAAAATAA
Found at i:3589289 original size:50 final size:50
Alignment explanation
Indices: 3589214--3589313 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
3589204 GCTTGCTCAA
3589214 ATTAATGTTCATTTGGTATCTGACTTTTGCTTTAATGGAATCATGTGCCT
1 ATTAATGTTCATTTGGTATCTGACTTTTGCTTTAATGGAATCATGTGCCT
3589264 ATTAATGTTCATTTGGTATCTGACTTTTGCTTTAATGGAATCATGTGCCT
1 ATTAATGTTCATTTGGTATCTGACTTTTGCTTTAATGGAATCATGTGCCT
3589314 GTTGGTGAGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.46
Consensus pattern (50 bp):
ATTAATGTTCATTTGGTATCTGACTTTTGCTTTAATGGAATCATGTGCCT
Found at i:3608012 original size:199 final size:198
Alignment explanation
Indices: 3607672--3608070 Score: 771
Period size: 199 Copynumber: 2.0 Consensus size: 198
3607662 TTTTTTTAAA
*
3607672 AATTTTAAGTCTTATTATTTCTATATTCTTTATTCGTATTATTTTCATATAACATCATCGTATCA
1 AATTTTAAGTCTTATTATTTCTATATTCTTTATTCGTATTATTTTCATATAACATCACCGTATCA
3607737 TATTTTAAATTATTATTTATATTAAATTTTATGTTAACTATTCATTAAAATGTTAAATTAAAATA
66 TATTTTAAATTATTATTTATATTAAATTTTATGTTAACTATTCATTAAAATGTTAAATTAAAATA
3607802 TTTTATATTTATTCCCACAAATAAAGCAAATATGGTAATTGAATGTTTCAAGAATCAATTATTGA
131 TTTTATATTTATTCCCACAAATAAAGCAAA-ATGGTAATTGAATGTTTCAAGAATCAATTATTGA
*
3607867 TACT
195 CACT
3607871 AATTTTAAGTCTTATTATTTCTATATTCTTTATTCGTATTATTTTCATATAACATCACCGTATCA
1 AATTTTAAGTCTTATTATTTCTATATTCTTTATTCGTATTATTTTCATATAACATCACCGTATCA
3607936 TATTTTAAATTATTATTTATATTAAATTTTATGTTAACTATTCATTAAAATGTTAAATTAAAATA
66 TATTTTAAATTATTATTTATATTAAATTTTATGTTAACTATTCATTAAAATGTTAAATTAAAATA
3608001 TTTTATATTTATTCCCACAAATAAAGCAAAATGGTAATTGAATGTTTCAAGAATCAATTATTGAC
131 TTTTATATTTATTCCCACAAATAAAGCAAAATGGTAATTGAATGTTTCAAGAATCAATTATTGAC
3608066 ACT
196 ACT
3608069 AA
1 AA
3608071 ATCTTGTTCA
Statistics
Matches: 198, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
198 39 0.20
199 159 0.80
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (198 bp):
AATTTTAAGTCTTATTATTTCTATATTCTTTATTCGTATTATTTTCATATAACATCACCGTATCA
TATTTTAAATTATTATTTATATTAAATTTTATGTTAACTATTCATTAAAATGTTAAATTAAAATA
TTTTATATTTATTCCCACAAATAAAGCAAAATGGTAATTGAATGTTTCAAGAATCAATTATTGAC
ACT
Found at i:3609214 original size:15 final size:17
Alignment explanation
Indices: 3609182--3609230 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
3609172 TAAATAAAAT
3609182 TTAAAATATTATATTAA
1 TTAAAATATTATATTAA
*
3609199 TTAATATATTA-A-TAA
1 TTAAAATATTATATTAA
* *
3609214 TTTAAGTATTATATTAA
1 TTAAAATATTATATTAA
3609231 AAATTTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 11 0.42
16 2 0.08
17 13 0.50
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
TTAAAATATTATATTAA
Found at i:3609243 original size:28 final size:28
Alignment explanation
Indices: 3609176--3609266 Score: 92
Period size: 28 Copynumber: 3.1 Consensus size: 28
3609166 GGTGAATAAA
*
3609176 TAAAATTTAAAATATTATATTAATTAATATAT
1 TAAAATTT-AAATATTATATTAA--AA-ATTT
*
3609208 TAATAATTTAAGTATTATATTAAAAATTT
1 TAA-AATTTAAATATTATATTAAAAATTT
* * *
3609237 TAAAATTTAAATGTTACATTAAATATTT
1 TAAAATTTAAATATTATATTAAAAATTT
3609265 TA
1 TA
3609267 TTGTAATTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
28 23 0.44
29 6 0.12
30 2 0.04
32 16 0.31
33 5 0.10
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (28 bp):
TAAAATTTAAATATTATATTAAAAATTT
Found at i:3610191 original size:2 final size:2
Alignment explanation
Indices: 3610184--3610209 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3610174 ACTACCAAAA
3610184 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
3610210 TAACCTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3611086 original size:43 final size:43
Alignment explanation
Indices: 3611031--3611122 Score: 141
Period size: 43 Copynumber: 2.2 Consensus size: 43
3611021 TATTTTATAA
* * *
3611031 TATTAAAGAGTTGGTTATAAAAGTTGGTCGATTTCGGTTTTAT
1 TATTAAAGAGTTGATTATAAAAGTTGGTCGATTCCGGTTTGAT
*
3611074 TATTAAAGAGTTGATTATAAAAGTTGGTTGATTCCGGTTTGAT
1 TATTAAAGAGTTGATTATAAAAGTTGGTCGATTCCGGTTTGAT
3611117 T-TTAAA
1 TATTAAA
3611123 AAAGTCAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 5 0.11
43 40 0.89
ACGTcount: A:0.30, C:0.04, G:0.22, T:0.43
Consensus pattern (43 bp):
TATTAAAGAGTTGATTATAAAAGTTGGTCGATTCCGGTTTGAT
Found at i:3611137 original size:43 final size:43
Alignment explanation
Indices: 3611047--3611138 Score: 105
Period size: 43 Copynumber: 2.1 Consensus size: 43
3611037 AGAGTTGGTT
* * * ** *
3611047 ATAAAAGTTGGTCGATTTCGGTTTTATTATTAAAGAGTTGATT
1 ATAAAAGTTGGTCGATTCCGGTTTGATTATTAAAAAGTCAATA
*
3611090 ATAAAAGTTGGTTGATTCCGGTTTGATT-TTAAAAAAGTCAATA
1 ATAAAAGTTGGTCGATTCCGGTTTGATTATT-AAAAAGTCAATA
3611133 ATAAAA
1 ATAAAA
3611139 TTAATTAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 2 0.05
43 39 0.95
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.39
Consensus pattern (43 bp):
ATAAAAGTTGGTCGATTCCGGTTTGATTATTAAAAAGTCAATA
Found at i:3611309 original size:16 final size:17
Alignment explanation
Indices: 3611254--3611310 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 17
3611244 TTTTTTATTT
3611254 TTTATATTATAAATAATT-A
1 TTTA-ATTATAAAT--TTAA
3611273 TTTAATTATAAATTTAA
1 TTTAATTATAAATTTAA
3611290 TTTAA-TA-AAATTTAAA
1 TTTAATTATAAATTT-AA
3611306 TTTAA
1 TTTAA
3611311 GTATCATTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
15 6 0.17
16 11 0.31
17 6 0.17
18 9 0.25
19 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTAATTATAAATTTAA
Found at i:3621951 original size:79 final size:78
Alignment explanation
Indices: 3621777--3621932 Score: 208
Period size: 79 Copynumber: 2.0 Consensus size: 78
3621767 AATTTTGTAT
* *
3621777 ATTT-TAAATCATAATATATTGTTCAATGTTTATACATTTGTAAAATTTTCAAAGCCAATCACGA
1 ATTTGTAAATCATAATATATTGTTCAATGTTCATACATTTGTAAAATCTTCAAAGCCAATCACGA
** *
3621841 TTTGGCTTTGTAAA
66 TAGGGC-TCGTAAA
* * *
3621855 ATTTGTAAATCATAATATATTGTTCAATGTTCATATATTTGTAAAATCTTCAAAGCCGATCACTA
1 ATTTGTAAATCATAATATATTGTTCAATGTTCATACATTTGTAAAATCTTCAAAGCCAATCACGA
3621920 TCAGGGC-CGTAAA
66 T-AGGGCTCGTAAA
3621933 TTAAGCTGTA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
78 9 0.13
79 56 0.82
80 3 0.04
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (78 bp):
ATTTGTAAATCATAATATATTGTTCAATGTTCATACATTTGTAAAATCTTCAAAGCCAATCACGA
TAGGGCTCGTAAA
Found at i:3623906 original size:18 final size:18
Alignment explanation
Indices: 3623883--3623921 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3623873 AAACATCCTG
3623883 AAAAAATA-AATCGTTGAA
1 AAAAAATATAAT-GTTGAA
*
3623901 AAAAAATATAATTTTGAA
1 AAAAAATATAATGTTGAA
3623919 AAA
1 AAA
3623922 GAGAGATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.26
Consensus pattern (18 bp):
AAAAAATATAATGTTGAA
Found at i:3631782 original size:25 final size:25
Alignment explanation
Indices: 3631718--3631783 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
3631708 GTATTTATTT
*
3631718 TAAAATTTTAT-ATTTAATTATTAA
1 TAAAATATTATAATTTAATTATTAA
* *
3631742 TAAAATATTATTATTTAATTCATTGA
1 TAAAATATTATAATTTAATT-ATTAA
*
3631768 TAATATA-TATAATTTA
1 TAAAATATTATAATTTA
3631784 TGTATAAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 10 0.28
25 16 0.44
26 10 0.28
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (25 bp):
TAAAATATTATAATTTAATTATTAA
Found at i:3633089 original size:27 final size:27
Alignment explanation
Indices: 3633042--3633094 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
3633032 AATATTTTAT
*
3633042 TAATTTCATATTTAATCGAATTAAATA
1 TAATTTCATATTTAATCGAATAAAATA
* *
3633069 TAATTTTATATATT-ATTGAATAAAAT
1 TAATTTCATAT-TTAATCGAATAAAAT
3633095 CAGATTCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (27 bp):
TAATTTCATATTTAATCGAATAAAATA
Found at i:3633793 original size:26 final size:26
Alignment explanation
Indices: 3633738--3633799 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
3633728 TTTTTATATA
* * *
3633738 AAAATAAAATAGTTATTACACTTCAT
1 AAAATAAAAAAATTATTACACTTCAG
*
3633764 AAAATAAAAAAATTA-TATACTCTCAG
1 AAAATAAAAAAATTATTACACT-TCAG
3633790 AAAA-AAAAAA
1 AAAATAAAAAA
3633800 TAGTAGTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 11 0.35
26 20 0.65
ACGTcount: A:0.61, C:0.10, G:0.03, T:0.26
Consensus pattern (26 bp):
AAAATAAAAAAATTATTACACTTCAG
Found at i:3646836 original size:4 final size:4
Alignment explanation
Indices: 3646827--3646872 Score: 51
Period size: 4 Copynumber: 11.5 Consensus size: 4
3646817 AATTCCTCTC
*
3646827 TTAT TTAT TTAT TTAT TGTAT TT-T TTAT TATAT TTAT AT-T TTAT TT
1 TTAT TTAT TTAT TTAT T-TAT TTAT TTAT T-TAT TTAT TTAT TTAT TT
3646873 TTGTGTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
3 5 0.14
4 23 0.64
5 8 0.22
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:3646855 original size:16 final size:16
Alignment explanation
Indices: 3646828--3646883 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
3646818 ATTCCTCTCT
3646828 TATTTATTTATTTATTG
1 TATTT-TTTATTTATTG
3646845 TATTTTTTATTATATT-
1 TATTTTTTATT-TATTG
*
3646861 TATATTTTATTT-TTG
1 TATTTTTTATTTATTG
*
3646876 TGTTTTTT
1 TATTTTTT
3646884 TGTAGTTTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
14 2 0.06
15 7 0.21
16 16 0.47
17 9 0.26
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (16 bp):
TATTTTTTATTTATTG
Found at i:3646866 original size:23 final size:23
Alignment explanation
Indices: 3646827--3646874 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
3646817 AATTCCTCTC
3646827 TTATTTATTTATTTATTGTATTTT
1 TTATTTATTTA-TTATTGTATTTT
*
3646851 TTATTATATTTA-TATTTTATTTT
1 TTATT-TATTTATTATTGTATTTT
3646874 T
1 T
3646875 GTGTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 11 0.50
24 5 0.23
25 6 0.27
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (23 bp):
TTATTTATTTATTATTGTATTTT
Found at i:3647116 original size:21 final size:20
Alignment explanation
Indices: 3647077--3647120 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
3647067 ATTTCTCTTC
3647077 TTTTATTTTTTTAACTTTTAT
1 TTTTATTTTTTTAACTTTT-T
* **
3647098 TTTTTTTTTTTTAGGTTTTT
1 TTTTATTTTTTTAACTTTTT
3647118 TTT
1 TTT
3647121 AACTTTTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.11, C:0.02, G:0.05, T:0.82
Consensus pattern (20 bp):
TTTTATTTTTTTAACTTTTT
Found at i:3647123 original size:32 final size:32
Alignment explanation
Indices: 3647082--3647142 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
3647072 TCTTCTTTTA
** *
3647082 TTTTTTTAACTTTTATTTTTTTTTTTTTAGGT
1 TTTTTTTAACTTTTAACTTTTATTTTTTAGGT
3647114 TTTTTTTAACTTTTAACTTTTATTTTTTA
1 TTTTTTTAACTTTTAACTTTTATTTTTTA
3647143 TTATATAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.75
Consensus pattern (32 bp):
TTTTTTTAACTTTTAACTTTTATTTTTTAGGT
Found at i:3647334 original size:8 final size:8
Alignment explanation
Indices: 3647321--3647349 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
3647311 ATTACGTGTA
3647321 TATATTTT
1 TATATTTT
3647329 TATATTTT
1 TATATTTT
3647337 TATATTTT
1 TATATTTT
3647345 TATAT
1 TATAT
3647350 GTATTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
TATATTTT
Found at i:3650623 original size:26 final size:27
Alignment explanation
Indices: 3650585--3650644 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 27
3650575 TTATAAACAT
* *
3650585 TAAATAAATATATTCATGAAT-ATAAA
1 TAAATAAACATATTCATAAATAATAAA
* *
3650611 TAAATTAACATATTTATAAATAATAAA
1 TAAATAAACATATTCATAAATAATAAA
*
3650638 CAAATAA
1 TAAATAA
3650645 TAATCAAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 17 0.63
27 10 0.37
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (27 bp):
TAAATAAACATATTCATAAATAATAAA
Found at i:3653372 original size:13 final size:13
Alignment explanation
Indices: 3653338--3653374 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
3653328 ATCTTTTTTG
**
3653338 TGTCATGTCACCA
1 TGTCATGTTTCCA
3653351 TGTCATGTTTCCA
1 TGTCATGTTTCCA
3653364 TGTCATGTTTC
1 TGTCATGTTTC
3653375 AGATTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.43
Consensus pattern (13 bp):
TGTCATGTTTCCA
Done.