Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, 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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 17 of 195
Found at i:3904447 original size:11 final size:11
Alignment explanation
Indices: 3904433--3904468 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
3904423 AAAAAACAAA
3904433 AAAAAATTTAT
1 AAAAAATTTAT
3904444 AAAAAGATTTAT
1 AAAAA-ATTTAT
*
3904456 AAAAAATTAAT
1 AAAAAATTTAT
3904467 AA
1 AA
3904469 TATTATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (11 bp):
AAAAAATTTAT
Found at i:3904447 original size:12 final size:12
Alignment explanation
Indices: 3904432--3904461 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3904422 CAAAAAACAA
3904432 AAAAAAATTTAT
1 AAAAAAATTTAT
*
3904444 AAAAAGATTTAT
1 AAAAAAATTTAT
3904456 AAAAAA
1 AAAAAA
3904462 TTAATAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (12 bp):
AAAAAAATTTAT
Found at i:3907116 original size:21 final size:19
Alignment explanation
Indices: 3907090--3907138 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
3907080 CGATTTTTAA
*
3907090 ATTTTAAATTTTTTATATATT
1 ATTTTAAATATTTTA-ATA-T
3907111 ATTTTAATAATATTTTAATAT
1 ATTTT-A-AATATTTTAATAT
3907132 ATTTTAA
1 ATTTTAA
3907139 TAAATTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 1 0.04
20 1 0.04
21 11 0.44
22 4 0.16
23 8 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTAAATATTTTAATAT
Found at i:3907135 original size:10 final size:10
Alignment explanation
Indices: 3907090--3907145 Score: 60
Period size: 10 Copynumber: 5.4 Consensus size: 10
3907080 CGATTTTTAA
3907090 ATTTTAA-AT
1 ATTTTAATAT
*
3907099 TTTTTATATATT
1 ATTTTA-ATA-T
3907111 ATTTTAATAAT
1 ATTTTAAT-AT
3907122 ATTTTAATAT
1 ATTTTAATAT
*
3907132 ATTTTAATAA
1 ATTTTAATAT
3907142 ATTT
1 ATTT
3907146 ATATATAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
9 5 0.12
10 16 0.40
11 12 0.30
12 7 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
ATTTTAATAT
Found at i:3907139 original size:21 final size:22
Alignment explanation
Indices: 3907100--3907152 Score: 74
Period size: 21 Copynumber: 2.4 Consensus size: 22
3907090 ATTTTAAATT
3907100 TTTTATATATTATTTTAATAATA
1 TTTTATATATTATTTTAATAA-A
3907123 TTTTA-ATA-TATTTTAATAAA
1 TTTTATATATTATTTTAATAAA
3907143 TTTATATATA
1 TTT-TATATA
3907153 AAATAATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.14
21 13 0.46
22 6 0.21
23 5 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTATATATTATTTTAATAAA
Found at i:3908032 original size:2 final size:2
Alignment explanation
Indices: 3908025--3908060 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3908015 ATATCTAACA
3908025 AC AC AC AC AC AC AC AC AC AC AC AC -C AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3908061 TATATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3908290 original size:10 final size:10
Alignment explanation
Indices: 3908257--3908296 Score: 53
Period size: 10 Copynumber: 3.7 Consensus size: 10
3908247 ATTTTAAGTG
3908257 TTAAAATATT
1 TTAAAATATT
3908267 TTACAATATAATT
1 TTA-AA-AT-ATT
3908280 TTAAAATATT
1 TTAAAATATT
3908290 TTAAAAT
1 TTAAAAT
3908297 GCAACAATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 13 0.48
11 4 0.15
12 4 0.15
13 6 0.22
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (10 bp):
TTAAAATATT
Found at i:3908921 original size:21 final size:21
Alignment explanation
Indices: 3908901--3908939 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3908891 ATTTCTTTTA
*
3908901 AATT-TTCCTTTGTTTTGTTT
1 AATTGTTCCTTTGATTTGTTT
*
3908921 AATTGTTTCTTTGATTTGT
1 AATTGTTCCTTTGATTTGT
3908940 AATTAATTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.13, C:0.08, G:0.13, T:0.67
Consensus pattern (21 bp):
AATTGTTCCTTTGATTTGTTT
Found at i:3911743 original size:23 final size:23
Alignment explanation
Indices: 3911712--3911764 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
3911702 TAAAATTTTT
*
3911712 AATATTTTTTTAATCATAATAAC
1 AATAATTTTTTAATCATAATAAC
* * *
3911735 AATAATTTTTTAATTATAATTAT
1 AATAATTTTTTAATCATAATAAC
3911758 AATAATT
1 AATAATT
3911765 ATTATTATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
AATAATTTTTTAATCATAATAAC
Found at i:3916468 original size:21 final size:21
Alignment explanation
Indices: 3916444--3916483 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3916434 GAACTGCTGT
* *
3916444 TGCTGCAGTTATTGTTGCTCC
1 TGCTCCAGTTACTGTTGCTCC
*
3916465 TGCTCCAGTTGCTGTTGCT
1 TGCTCCAGTTACTGTTGCT
3916484 GCAATATCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.07, C:0.25, G:0.25, T:0.42
Consensus pattern (21 bp):
TGCTCCAGTTACTGTTGCTCC
Found at i:3917313 original size:23 final size:22
Alignment explanation
Indices: 3917273--3917337 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 22
3917263 CTATTACAAC
*
3917273 ATAATCAATATTATAATTATTAA-
1 ATAATCAATAATA-AATTA-TAAT
3917296 ATAATCAATTAATAAATTATAAT
1 ATAATCAA-TAATAAATTATAAT
*
3917319 ATAATTAAATAATTAAATT
1 ATAA-TCAATAA-TAAATT
3917338 TATATACAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
22 3 0.08
23 20 0.56
24 13 0.36
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (22 bp):
ATAATCAATAATAAATTATAAT
Found at i:3922206 original size:19 final size:17
Alignment explanation
Indices: 3922170--3922235 Score: 75
Period size: 19 Copynumber: 3.9 Consensus size: 17
3922160 ATTTGAATTT
3922170 ATTTAAATATTAATTTAA
1 ATTTAAATATT-ATTTAA
3922188 ATTTAATATTATTATTTAA
1 ATTTAA-A-TATTATTTAA
3922207 ATTTAAATA-TATTTAA
1 ATTTAAATATTATTTAA
*
3922223 A--GAAATATTATTT
1 ATTTAAATATTATTT
3922236 GTTTAAATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
14 5 0.11
15 5 0.11
16 8 0.18
17 2 0.05
18 7 0.16
19 13 0.30
20 4 0.09
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:3922272 original size:20 final size:18
Alignment explanation
Indices: 3922227--3922273 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
3922217 ATTTAAAGAA
*
3922227 ATATT-ATTTGTTTAAAT
1 ATATTAATTTGTTAAAAT
3922244 ATATTAATTTGTTAAAAT
1 ATATTAATTTGTTAAAAT
3922262 ATCAGTTAATTT
1 AT-A-TTAATTT
3922274 AAAATTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 5 0.19
18 13 0.50
19 1 0.04
20 7 0.27
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.53
Consensus pattern (18 bp):
ATATTAATTTGTTAAAAT
Found at i:3927154 original size:25 final size:27
Alignment explanation
Indices: 3927098--3927157 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 27
3927088 AATTAGATTT
* *
3927098 AATATATTTTTATTAAAAAAATATTTA
1 AATATATATTTATTAAAAAAATATCTA
* *
3927125 TATATATATTTA-T-AAAAATTATCTA
1 AATATATATTTATTAAAAAAATATCTA
3927150 AATATATA
1 AATATATA
3927158 AAATAAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 17 0.61
26 1 0.04
27 10 0.36
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
AATATATATTTATTAAAAAAATATCTA
Found at i:3927436 original size:2 final size:2
Alignment explanation
Indices: 3927429--3927460 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3927419 TTTAAAAATA
3927429 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3927461 CATGATTACC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3928435 original size:2 final size:2
Alignment explanation
Indices: 3928428--3928454 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3928418 GTCTTTAACT
3928428 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 T
3928455 GCATTACAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3930640 original size:25 final size:24
Alignment explanation
Indices: 3930612--3930658 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
3930602 TTTCAGTTAC
3930612 AATTGAAAAAT-AATTAATTAAAAAA
1 AATT-AAAAATAAATTAA-TAAAAAA
*
3930637 AATTAAAAGTAAATTAATAAAA
1 AATTAAAAATAAATTAATAAAA
3930659 TAAGATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (24 bp):
AATTAAAAATAAATTAATAAAAAA
Found at i:3931365 original size:60 final size:60
Alignment explanation
Indices: 3931240--3931515 Score: 314
Period size: 59 Copynumber: 4.6 Consensus size: 60
3931230 AAATATCATT
* * ** *
3931240 ATATTTTTGAA-AAAAAATTGAAAGTATCAATTTTTTTTTTAAATAAAAATGTC-AAAAAA
1 ATATTTTT-AAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTTCAAAAAAA
*
3931299 ATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTT-TTAAAAAATAAAAATTTCAAAAAAA
1 ATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTT-AAAAATAAAAATTTCAAAAAAA
* * * * *
3931359 ATA-TTTTAAGAAAAAGTTGAAACTGTTAGTTTTTCTTAAAAAT-AAAA-TTAAAAAAATA
1 ATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTTCAAAAAA-A
* * * * *
3931417 TATATTTTTGAGAAAAAGTTGAGAGTATCAATTTTTCTTGAAAATAAAATTTTCAAGAAAA
1 -ATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTTCAAAAAAA
3931478 ATATTTTTAAGGAAAAA-TTGAAAGTATCAATTTTTCTT
1 ATATTTTTAA-GAAAAAGTTGAAAGTATCAATTTTTCTT
3931516 GTATAAAAGC
Statistics
Matches: 184, Mismatches: 23, Indels: 19
0.81 0.10 0.08
Matches are distributed among these distances:
57 8 0.04
58 9 0.05
59 77 0.42
60 73 0.40
61 10 0.05
62 7 0.04
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (60 bp):
ATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTTCAAAAAAA
Found at i:3931516 original size:60 final size:59
Alignment explanation
Indices: 3931240--3931515 Score: 301
Period size: 60 Copynumber: 4.6 Consensus size: 59
3931230 AAATATCATT
* * ** *
3931240 ATATTTTTGAAAAAAAATTGAAAGTATCAATTTTTTTTTTAAATAAAAATGTC-AAAAAA
1 ATATTTTT-AAGAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAAATTTCAAAAAAA
*
3931299 ATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTT-TTAAAAAATAAAAATTTCAAAAAAA
1 ATATTTTTAA-GAAAAATTGAAAGTATCAATTTTTCTT-AAAAATAAAAATTTCAAAAAAA
* * * * *
3931359 ATA-TTTTAAGAAAAAGTTGAAACTGTTAGTTTTTCTTAAAAAT-AAAA-TTAAAAAAATA
1 ATATTTTTAAGAAAAA-TTGAAAGTATCAATTTTTCTTAAAAATAAAAATTTCAAAAAA-A
* * * * *
3931417 TATATTTTTGAGAAAAAGTTGAGAGTATCAATTTTTCTTGAAAATAAAATTTTCAAGAAAA
1 -ATATTTTTAAGAAAAA-TTGAAAGTATCAATTTTTCTTAAAAATAAAAATTTCAAAAAAA
3931478 ATATTTTTAAGGAAAAATTGAAAGTATCAATTTTTCTT
1 ATATTTTTAA-GAAAAATTGAAAGTATCAATTTTTCTT
3931516 GTATAAAAGC
Statistics
Matches: 183, Mismatches: 23, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
57 8 0.04
58 14 0.08
59 71 0.39
60 73 0.40
61 10 0.05
62 7 0.04
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (59 bp):
ATATTTTTAAGAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAAATTTCAAAAAAA
Found at i:3932295 original size:4 final size:4
Alignment explanation
Indices: 3932278--3932309 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
3932268 AGGGTTTTTC
*
3932278 TATT TATT TGTT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT
3932310 ATTATTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:3932313 original size:3 final size:3
Alignment explanation
Indices: 3932305--3932336 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3932295 ATTTATTTAT
3932305 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3932337 TTGCTTATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3932520 original size:57 final size:57
Alignment explanation
Indices: 3932408--3932707 Score: 327
Period size: 57 Copynumber: 5.1 Consensus size: 57
3932398 TTTTCAATGA
* * *
3932408 TTTCTTGAAAATAAAA-TTAAAAAATATATATTTTTGAAAAAAAGTTGAAAATATCAATT
1 TTTCTTAAAAATAAAATTTTAAAAA-A-ATA-TTTTGAGAAAAAGTTGAAAATATCAATT
* *
3932467 TTTCTCAAAAATAAAAATTTT-AAAAAATATTTTGAGAAAAAGTTGAAAGTATCAATT
1 TTTCTTAAAAAT-AAAATTTTAAAAAAATATTTTGAGAAAAAGTTGAAAATATCAATT
* * * * * *
3932524 TTTCTTAAAAATAAGATTTCAAAAAAACATTTTAAGAAAAAGTTGAAAATGTTAATT
1 TTTCTTAAAAATAAAATTTTAAAAAAATATTTTGAGAAAAAGTTGAAAATATCAATT
* * *
3932581 TTCCTTGAAAATAAAATTTTCAAAAAAAAGTATTTTTGAGAAAAAGTTGAAAGTATCAATT
1 TTTCTTAAAAATAAAATTTT--AAAAAAA-TA-TTTTGAGAAAAAGTTGAAAATATCAATT
* *
3932642 TTT-TTAAAAAATAAAATTTTTAAAAAAAATATTTTTAAAGAAAAGTTGAAAATATCAATT
1 TTTCTT-AAAAATAAAA-TTTT-AAAAAAATATTTTGAGA-AAAAGTTGAAAATATCAATT
3932702 TTTCTT
1 TTTCTT
3932708 GTACAAAAAC
Statistics
Matches: 203, Mismatches: 27, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
56 6 0.03
57 84 0.41
58 3 0.01
59 24 0.12
60 35 0.17
61 47 0.23
62 4 0.02
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (57 bp):
TTTCTTAAAAATAAAATTTTAAAAAAATATTTTGAGAAAAAGTTGAAAATATCAATT
Found at i:3932642 original size:118 final size:115
Alignment explanation
Indices: 3932415--3932708 Score: 357
Period size: 118 Copynumber: 2.5 Consensus size: 115
3932405 TGATTTCTTG
* **
3932415 AAAATAAAA--TTAAAAAATATATATTTTTGAAAAAAAGTTGAAAATATCAATTTTTCTCAAAAA
1 AAAATAAAATTTTAAAAAA-A-ACATTTTT-AAAAAAAGTTGAAAATATCAATTTTTCTTGAAAA
3932478 TAAAAATTTTAAAAAATATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT-A
63 TAAAAATTTTAAAAAATATTTTGAGAAAAAGTTGAAAGTATCAATTTTT-TTAA
* * * * *
3932531 AAAATAAGA-TTTCAAAAAAACA-TTTTAAGAAAAAGTTGAAAATGTTAATTTTCCTTGAAAAT-
1 AAAATAAAATTTTAAAAAAAACATTTTTAA-AAAAAGTTGAAAATATCAATTTTTCTTGAAAATA
3932593 AAAATTTTCAAAAAAAAGTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTTTAA
65 AAAATTTT---AAAAAA-TA-TTTTGAGAAAAAGTTGAAAGTATCAATTTTTTTAA
*
3932649 AAAATAAAATTTTTAAAAAAAATATTTTTAAAGAAAAGTTGAAAATATCAATTTTTCTTG
1 AAAATAAAA-TTTTAAAAAAAACATTTTTAAA-AAAAGTTGAAAATATCAATTTTTCTTG
3932709 TACAAAAACA
Statistics
Matches: 152, Mismatches: 14, Indels: 19
0.82 0.08 0.10
Matches are distributed among these distances:
113 10 0.07
114 32 0.21
115 2 0.01
116 15 0.10
117 11 0.07
118 40 0.26
120 12 0.08
121 30 0.20
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.36
Consensus pattern (115 bp):
AAAATAAAATTTTAAAAAAAACATTTTTAAAAAAAGTTGAAAATATCAATTTTTCTTGAAAATAA
AAATTTTAAAAAATATTTTGAGAAAAAGTTGAAAGTATCAATTTTTTTAA
Found at i:3932666 original size:15 final size:15
Alignment explanation
Indices: 3932642--3932685 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
3932632 AGTATCAATT
*
3932642 TTTTTAAAAAATAAAA
1 TTTTTAAAAAA-AATA
3932658 TTTTTAAAAAAAATA
1 TTTTTAAAAAAAATA
3932673 TTTTTAAAGAAAA
1 TTTTTAAA-AAAA
3932686 GTTGAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (15 bp):
TTTTTAAAAAAAATA
Found at i:3933555 original size:23 final size:24
Alignment explanation
Indices: 3933529--3933577 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
3933519 ATTTTATAAT
*
3933529 ATTAAATATATTTTAAAT-TAAAA
1 ATTAAATAAATTTTAAATATAAAA
*
3933552 ATTAAATAAATTTTTAATATAAAA
1 ATTAAATAAATTTTAAATATAAAA
3933576 AT
1 AT
3933578 ATTTTTAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATTAAATAAATTTTAAATATAAAA
Found at i:3934948 original size:18 final size:17
Alignment explanation
Indices: 3934921--3934965 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
3934911 AAGGAGTCAA
*
3934921 ATAAACAAATAACTAAT
1 ATAAAAAAATAACTAAT
3934938 ATTAAAAAAAT-ACTAAT
1 A-TAAAAAAATAACTAAT
*
3934955 ATAAAACAATA
1 ATAAAAAAATA
3934966 TTTATGTGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 8 0.33
17 8 0.33
18 8 0.33
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (17 bp):
ATAAAAAAATAACTAAT
Found at i:3935747 original size:18 final size:18
Alignment explanation
Indices: 3935717--3935762 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
3935707 TTATTTTATA
* *
3935717 AAAATTTTA-AAAAATTT
1 AAAATTTAATAAAAATAT
3935734 AAAATTTAATAAAAATAT
1 AAAATTTAATAAAAATAT
*
3935752 ATAATTTAATA
1 AAAATTTAATA
3935763 CGATTCAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAATTTAATAAAAATAT
Found at i:3939788 original size:13 final size:14
Alignment explanation
Indices: 3939764--3939798 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
3939754 TTATTCCAGT
*
3939764 AAGAACAAAACAAA
1 AAGAAAAAAACAAA
3939778 AA-AAAAAAACAAA
1 AAGAAAAAAACAAA
3939791 AAGAAAAA
1 AAGAAAAA
3939799 TATTCCCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.86, C:0.09, G:0.06, T:0.00
Consensus pattern (14 bp):
AAGAAAAAAACAAA
Found at i:3943761 original size:23 final size:23
Alignment explanation
Indices: 3943734--3943784 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
3943724 TATATATTTG
3943734 ATATATTATTAATGTATAAAATT
1 ATATATTATTAATGTATAAAATT
* * *
3943757 ATATATTATTAGTTTATAACATT
1 ATATATTATTAATGTATAAAATT
3943780 ATATA
1 ATATA
3943785 CGGTTAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (23 bp):
ATATATTATTAATGTATAAAATT
Found at i:3957505 original size:17 final size:17
Alignment explanation
Indices: 3957464--3957505 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
3957454 ATATTTATTT
* *
3957464 TATAATAAATTAAAATA
1 TATAATTAATAAAAATA
3957481 TATAAATTAATAAAAATA
1 TAT-AATTAATAAAAATA
3957499 TATAATT
1 TATAATT
3957506 CAAATCCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TATAATTAATAAAAATA
Found at i:3958025 original size:22 final size:23
Alignment explanation
Indices: 3957975--3958027 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
3957965 CAAAATTATA
3957975 TATATTTTTTAACATCTAAAACT
1 TATATTTTTTAACATCTAAAACT
* *
3957998 TTTATTTTTTATATAT-TAAAA-T
1 TATATTTTTTA-ACATCTAAAACT
3958020 TATATTTT
1 TATATTTT
3958028 ATTTTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 8 0.31
23 15 0.58
24 3 0.12
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (23 bp):
TATATTTTTTAACATCTAAAACT
Found at i:3969269 original size:3 final size:3
Alignment explanation
Indices: 3969261--3969307 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
3969251 TTCAACGTCC
* * *
3969261 TCA TCA TCA TCC TCA TCA TCA TCC TCA TCA TCA TCT TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
3969308 CTCTTCTTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.26, C:0.38, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:3969273 original size:12 final size:12
Alignment explanation
Indices: 3969258--3969310 Score: 97
Period size: 12 Copynumber: 4.4 Consensus size: 12
3969248 CTCTTCAACG
3969258 TCCTCATCATCA
1 TCCTCATCATCA
3969270 TCCTCATCATCA
1 TCCTCATCATCA
3969282 TCCTCATCATCA
1 TCCTCATCATCA
*
3969294 TCTTCATCATCA
1 TCCTCATCATCA
3969306 TCCTC
1 TCCTC
3969311 TTCTTCACTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.36
Consensus pattern (12 bp):
TCCTCATCATCA
Found at i:3973122 original size:18 final size:17
Alignment explanation
Indices: 3973099--3973164 Score: 64
Period size: 16 Copynumber: 3.9 Consensus size: 17
3973089 ATAATTTTGA
3973099 TTTTTTATGTATTCATAT
1 TTTTTTATGTATT-ATAT
3973117 TTTTTTAT-TATTATAT
1 TTTTTTATGTATTATAT
* * *
3973133 ATTTTTATG-ATTTTAA
1 TTTTTTATGTATTATAT
* *
3973149 TCTTTTATTTATTATA
1 TTTTTTATGTATTATA
3973165 AATAATAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
16 22 0.56
17 9 0.23
18 8 0.21
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTTTATGTATTATAT
Found at i:3974166 original size:12 final size:13
Alignment explanation
Indices: 3974149--3974177 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3974139 ATTATATAAA
3974149 ATATAAAAAT-TT
1 ATATAAAAATATT
3974161 ATATAAAAATATT
1 ATATAAAAATATT
3974174 ATAT
1 ATAT
3974178 TTTTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATAAAAATATT
Found at i:3974302 original size:10 final size:11
Alignment explanation
Indices: 3974282--3974345 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 11
3974272 TTTTAAATCG
3974282 TATTATTTTTA
1 TATTATTTTTA
3974293 TATT-TTTTTA
1 TATTATTTTTA
* *
3974303 TATCATATTTA
1 TATTATTTTTA
*
3974314 TAATATATTATTA
1 T-AT-TATTTTTA
3974327 TATCGTATTTTTA
1 TAT--TATTTTTA
3974340 -ATTATT
1 TATTATT
3974346 AAATTTATAT
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
10 13 0.31
11 10 0.24
12 6 0.14
13 13 0.31
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (11 bp):
TATTATTTTTA
Found at i:3974319 original size:24 final size:24
Alignment explanation
Indices: 3974300--3974346 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3974290 TTATATTTTT
3974300 TTATATCATATTTATAATATATTA
1 TTATATCATATTTATAATATATTA
* *
3974324 TTATATCGTATTTTTAAT-TATTA
1 TTATATCATATTTATAATATATTA
3974347 AATTTATATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.57
Consensus pattern (24 bp):
TTATATCATATTTATAATATATTA
Found at i:3974353 original size:26 final size:25
Alignment explanation
Indices: 3974299--3974357 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
3974289 TTTATATTTT
3974299 TTTATATCATATTTATAATATATTA
1 TTTATATCATATTTATAATATATTA
* *
3974324 -TTATATCGTATTTTTAAT-TATTAAA
1 TTTATATCATATTTATAATATATT--A
3974349 TTTATATCA
1 TTTATATCA
3974358 AAATGTCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 4 0.14
24 16 0.57
25 1 0.04
26 7 0.25
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (25 bp):
TTTATATCATATTTATAATATATTA
Found at i:3987393 original size:18 final size:18
Alignment explanation
Indices: 3987372--3987407 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3987362 GAATAAATTT
3987372 GGATTTGAGAAAATGCTG
1 GGATTTGAGAAAATGCTG
*
3987390 GGATTTGAGAAGATGCTG
1 GGATTTGAGAAAATGCTG
3987408 CGAGAACCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.36, T:0.28
Consensus pattern (18 bp):
GGATTTGAGAAAATGCTG
Found at i:3988632 original size:2 final size:2
Alignment explanation
Indices: 3988627--3988663 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3988617 TGCAATTTTT
*
3988627 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC AC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3988664 GTTTTTACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.03, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:3988679 original size:3 final size:3
Alignment explanation
Indices: 3988671--3988696 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3988661 TCTGTTTTTA
3988671 CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT
3988697 AATTAACCGA
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:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:4003131 original size:4 final size:4
Alignment explanation
Indices: 4003124--4003185 Score: 124
Period size: 4 Copynumber: 15.5 Consensus size: 4
4003114 ATATATATAT
4003124 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
4003172 ATAG ATAG ATAG AT
1 ATAG ATAG ATAG AT
4003186 GTGGGAATTG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:4003539 original size:212 final size:203
Alignment explanation
Indices: 4003172--4003775 Score: 970
Period size: 212 Copynumber: 3.0 Consensus size: 203
4003162 AGATAGATAG
**
4003172 ATAGATAGATAGATGTGGGAATTGGAAGCATTCAAGGCCCCGTTGCTTTCCCTGCAAGGATTTGG
1 ATAGATAGATAGATGTGGGGCTTGGAAGCATTCAAGGCCCCGTTGCTTTCCCTGCAAGGATTTGG
* * *
4003237 TCTTCCTTGTCCTACCAGGATTACAGCTTTTCCTTCTAATTAAAAAGTTACATAAAGAGTGGAGA
66 TTTTCCTTGTCCTACCAGGATTACAGCTTTTCCTTCTAATTAAAAAGTTATATAAAGAGTTGAGA
* *
4003302 GTTAGCTTGCTTCGTATTCCAATGTTAAATAATCGATATAACAAACAACTTTGCCTAGAGATCAA
131 GTTAGCTCGCTTTGTATTCCAATGTTAAATAATCGATATAACAAACAACTTTGCCTAGAGATC--
4003367 TATATATAAATATATAT
194 ---A-AT--A-ATATAT
*
4003384 ATAGATAGATAGATGTGGGGCTTGGAAGCATTCAAGGCCTCGTTGCTTTCCCTGCAAGGATTTGG
1 ATAGATAGATAGATGTGGGGCTTGGAAGCATTCAAGGCCCCGTTGCTTTCCCTGCAAGGATTTGG
4003449 TTTTCCTTGTCCTACCAGGATTACAGCTTTTCCTTCTAATTAAAAAGTTATATAAAGAGTTGAGA
66 TTTTCCTTGTCCTACCAGGATTACAGCTTTTCCTTCTAATTAAAAAGTTATATAAAGAGTTGAGA
*
4003514 GTTAGCTCGCTTTGTATTCCAATGTTAAATAATCGATATAACAGACAACTTTGCCTAGAGATC--
131 GTTAGCTCGCTTTGTATTCCAATGTTAAATAATCGATATAACAAACAACTTTGCCTAGAGATCAA
4003577 -AATATAT
196 TAATATAT
4003584 AT--AT--ATAGATGTGGGGCTTGGAAGCATTCAAGGCCCCGTTGCTTTCCCTGCAAGGATTTGG
1 ATAGATAGATAGATGTGGGGCTTGGAAGCATTCAAGGCCCCGTTGCTTTCCCTGCAAGGATTTGG
*
4003645 TTTTCCTTGTCCTACCAGGATTACAGCTTTTCCTTCTAATTAAAATGTTATATAAAGAGTTGAGA
66 TTTTCCTTGTCCTACCAGGATTACAGCTTTTCCTTCTAATTAAAAAGTTATATAAAGAGTTGAGA
* *
4003710 GTTAGCTCGCTTTGTATTCCAATGTTAAATAATCGATATAACAAACAACTTGGCCTAGGGATCAA
131 GTTAGCTCGCTTTGTATTCCAATGTTAAATAATCGATATAACAAACAACTTTGCCTAGAGATCAA
4003775 T
196 T
4003776 TAAGAATTTC
Statistics
Matches: 375, Mismatches: 14, Indels: 19
0.92 0.03 0.05
Matches are distributed among these distances:
196 180 0.48
198 2 0.01
200 8 0.02
201 1 0.00
212 184 0.49
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (203 bp):
ATAGATAGATAGATGTGGGGCTTGGAAGCATTCAAGGCCCCGTTGCTTTCCCTGCAAGGATTTGG
TTTTCCTTGTCCTACCAGGATTACAGCTTTTCCTTCTAATTAAAAAGTTATATAAAGAGTTGAGA
GTTAGCTCGCTTTGTATTCCAATGTTAAATAATCGATATAACAAACAACTTTGCCTAGAGATCAA
TAATATAT
Found at i:4003726 original size:196 final size:196
Alignment explanation
Indices: 4003382--4003775 Score: 725
Period size: 196 Copynumber: 2.0 Consensus size: 196
4003372 ATAAATATAT
*
4003382 ATATAGATAGATAGATGTGGGGCTTGGAAGCATTCAAGGCCTCGTTGCTTTCCCTGCAAGGATTT
1 ATATAGATAGATAGATGTGGGGCTTGGAAGCATTCAAGGCCCCGTTGCTTTCCCTGCAAGGATTT
4003447 GGTTTTCCTTGTCCTACCAGGATTACAGCTTTTCCTTCTAATTAAAAAGTTATATAAAGAGTTGA
66 GGTTTTCCTTGTCCTACCAGGATTACAGCTTTTCCTTCTAATTAAAAAGTTATATAAAGAGTTGA
* *
4003512 GAGTTAGCTCGCTTTGTATTCCAATGTTAAATAATCGATATAACAGACAACTTTGCCTAGAGATC
131 GAGTTAGCTCGCTTTGTATTCCAATGTTAAATAATCGATATAACAAACAACTTGGCCTAGAGATC
4003577 A
196 A
* *
4003578 ATATATATATATAGATGTGGGGCTTGGAAGCATTCAAGGCCCCGTTGCTTTCCCTGCAAGGATTT
1 ATATAGATAGATAGATGTGGGGCTTGGAAGCATTCAAGGCCCCGTTGCTTTCCCTGCAAGGATTT
*
4003643 GGTTTTCCTTGTCCTACCAGGATTACAGCTTTTCCTTCTAATTAAAATGTTATATAAAGAGTTGA
66 GGTTTTCCTTGTCCTACCAGGATTACAGCTTTTCCTTCTAATTAAAAAGTTATATAAAGAGTTGA
*
4003708 GAGTTAGCTCGCTTTGTATTCCAATGTTAAATAATCGATATAACAAACAACTTGGCCTAGGGATC
131 GAGTTAGCTCGCTTTGTATTCCAATGTTAAATAATCGATATAACAAACAACTTGGCCTAGAGATC
4003773 A
196 A
4003774 AT
1 AT
4003776 TAAGAATTTC
Statistics
Matches: 191, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
196 191 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (196 bp):
ATATAGATAGATAGATGTGGGGCTTGGAAGCATTCAAGGCCCCGTTGCTTTCCCTGCAAGGATTT
GGTTTTCCTTGTCCTACCAGGATTACAGCTTTTCCTTCTAATTAAAAAGTTATATAAAGAGTTGA
GAGTTAGCTCGCTTTGTATTCCAATGTTAAATAATCGATATAACAAACAACTTGGCCTAGAGATC
A
Found at i:4008211 original size:3 final size:3
Alignment explanation
Indices: 4008203--4008237 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4008193 GCTTTTCAGA
4008203 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
4008238 AGACCGGCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:4009543 original size:70 final size:72
Alignment explanation
Indices: 4009463--4009611 Score: 203
Period size: 77 Copynumber: 2.0 Consensus size: 72
4009453 GTAAGTTGAC
* *
4009463 CTATCTCTATAAATTTTGCT-C-AGAACATTAGGTGTTAGTGCAAATGTCTAATTTAATTACAGA
1 CTATCCCTATAAATTTTGCTACTAGAACATTAGGTGTTAGTGCAAATATCTAATTTAATTACAGA
4009526 TTAAAAG
66 TTAAAAG
* *
4009533 CTATCCCTATAAATTTTGCTAAGGACTTAGAGCATTAGGTGTTAGTTCAAATATCTAATTTAATT
1 CTATCCCTATAAATTTTGCT----AC-TAGAACATTAGGTGTTAGTGCAAATATCTAATTTAATT
4009598 ACAGATTAAAAG
61 ACAGATTAAAAG
4009610 CT
1 CT
4009612 TAAAAACAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
70 19 0.28
75 1 0.01
77 48 0.71
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (72 bp):
CTATCCCTATAAATTTTGCTACTAGAACATTAGGTGTTAGTGCAAATATCTAATTTAATTACAGA
TTAAAAG
Found at i:4009669 original size:85 final size:85
Alignment explanation
Indices: 4009559--4009731 Score: 292
Period size: 85 Copynumber: 2.0 Consensus size: 85
4009549 TGCTAAGGAC
* * *
4009559 TTAGAGCATTAGGTGTTAGTTCAAATATCTAATTTAATTACAGATTAAAAGCTTAAAAACAAATG
1 TTAGAACATTAGGTGTTAGTTCAAATATCTAATTTAATTACAAATTAAAAGCTAAAAAACAAATG
4009624 TCCTCTTCTTTACAGATTAA
66 TCCTCTTCTTTACAGATTAA
*
4009644 TTAGAACATTAGGTGTTAGTTCAAATGTCTAATTTAATTACAAATTAAAAGCTAAAAAACAAATG
1 TTAGAACATTAGGTGTTAGTTCAAATATCTAATTTAATTACAAATTAAAAGCTAAAAAACAAATG
* *
4009709 TCCTCTTGTTTACGGATTAA
66 TCCTCTTCTTTACAGATTAA
4009729 TTA
1 TTA
4009732 TTATTTTTTC
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (85 bp):
TTAGAACATTAGGTGTTAGTTCAAATATCTAATTTAATTACAAATTAAAAGCTAAAAAACAAATG
TCCTCTTCTTTACAGATTAA
Found at i:4010741 original size:25 final size:26
Alignment explanation
Indices: 4010689--4010741 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
4010679 TGACTGTACA
**
4010689 TTTTGAATAGCTAAAAACTATTTGTT
1 TTTTGAATAGCTAAAAACTATTCATT
* *
4010715 TTTTGAATAG-TTAAAATTATTCATT
1 TTTTGAATAGCTAAAAACTATTCATT
4010740 TT
1 TT
4010742 GACCAGACTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (26 bp):
TTTTGAATAGCTAAAAACTATTCATT
Found at i:4017856 original size:20 final size:20
Alignment explanation
Indices: 4017818--4017861 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
4017808 AAACAATGAG
*
4017818 ATTATTATTGTTATTATATT
1 ATTATTATTGTTATGATATT
4017838 ATTATTATT-TTGATGATATT
1 ATTATTATTGTT-ATGATATT
4017858 -TTAT
1 ATTAT
4017862 CATCAAAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (20 bp):
ATTATTATTGTTATGATATT
Found at i:4019298 original size:30 final size:30
Alignment explanation
Indices: 4019261--4019326 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
4019251 AATTAAGTTA
4019261 AATTTAAATATTTTTATACTCAATTTAAAT
1 AATTTAAATATTTTTATACTCAATTTAAAT
* * *
4019291 AGTTTAAATATTTTTATATTTAATTTAAAT
1 AATTTAAATATTTTTATACTCAATTTAAAT
4019321 AATTTA
1 AATTTA
4019327 TGAGTTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (30 bp):
AATTTAAATATTTTTATACTCAATTTAAAT
Found at i:4019334 original size:22 final size:21
Alignment explanation
Indices: 4019293--4019351 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
4019283 ATTTAAATAG
*
4019293 TTTAAATATTTTTATATTTAA
1 TTTAAATATATTTATATTTAA
4019314 TTTAAATA-ATTTATGAGTTTAA
1 TTTAAATATATTTAT-A-TTTAA
*
4019336 -TCAAA-AT-TTTATATTT
1 TTTAAATATATTTATATTT
4019352 TAATATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
18 3 0.09
19 1 0.03
20 11 0.33
21 13 0.39
22 5 0.15
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (21 bp):
TTTAAATATATTTATATTTAA
Found at i:4019394 original size:18 final size:17
Alignment explanation
Indices: 4019356--4019390 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
4019346 ATATTTTAAT
*
4019356 ATATTTTAATTAATAAA
1 ATATCTTAATTAATAAA
4019373 ATATCTTAATTAATAAA
1 ATATCTTAATTAATAAA
4019390 A
1 A
4019391 ATATAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATCTTAATTAATAAA
Found at i:4019518 original size:18 final size:18
Alignment explanation
Indices: 4019463--4019520 Score: 82
Period size: 18 Copynumber: 3.2 Consensus size: 18
4019453 TAATTTTTTT
4019463 ATTTTAAATCAAATTTAA
1 ATTTTAAATCAAATTTAA
*
4019481 A-TTCAAATCAAATTTTAA
1 ATTTTAAATCAAA-TTTAA
*
4019499 ATTTTAAATCAAATTCAA
1 ATTTTAAATCAAATTTAA
4019517 ATTT
1 ATTT
4019521 AAACTTAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 10 0.29
18 15 0.43
19 10 0.29
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTTTAAATCAAATTTAA
Found at i:4019523 original size:17 final size:17
Alignment explanation
Indices: 4019465--4019523 Score: 82
Period size: 17 Copynumber: 3.4 Consensus size: 17
4019455 ATTTTTTTAT
4019465 TTTAAATCAAATTTAAA
1 TTTAAATCAAATTTAAA
*
4019482 TTCAAATCAAATTTTAAA
1 TTTAAATCAAA-TTTAAA
*
4019500 TTTTAAATCAAATTCAAA
1 -TTTAAATCAAATTTAAA
4019518 TTTAAA
1 TTTAAA
4019524 CTTAATATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 16 0.43
18 11 0.30
19 10 0.27
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTAAATCAAATTTAAA
Found at i:4020647 original size:9 final size:9
Alignment explanation
Indices: 4020633--4020660 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
4020623 CATTGTAGTA
4020633 TCCTTTGCT
1 TCCTTTGCT
4020642 TCCTTTGCT
1 TCCTTTGCT
4020651 TCCTTTGCT
1 TCCTTTGCT
4020660 T
1 T
4020661 TCTATGCCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.11, T:0.57
Consensus pattern (9 bp):
TCCTTTGCT
Found at i:4020883 original size:66 final size:66
Alignment explanation
Indices: 4020804--4020964 Score: 270
Period size: 66 Copynumber: 2.4 Consensus size: 66
4020794 CTGGGCAGCA
*
4020804 GAGTCTTTCGTTTCCTTTGCCTTCTGTGCTGCATAATCTGTATACTCAGAAGCTTTACCTGTTAC
1 GAGTCTTTCGTTTCCTTTGCCTTCTGGGCTGCATAATCTGTATACTCAGAAGCTTTACCTGTTAC
4020869 T
66 T
* *
4020870 GTGTCTTTTGTTTCCTTTGCCTTCTGGGCTGCATAATCTGTATACTCAGAAGCTTTACCTGTTAC
1 GAGTCTTTCGTTTCCTTTGCCTTCTGGGCTGCATAATCTGTATACTCAGAAGCTTTACCTGTTAC
4020935 T
66 T
*
4020936 GAGTCCTTCGTTT-CTTTCGCCTTCTGGGC
1 GAGTCTTTCGTTTCCTTT-GCCTTCTGGGC
4020965 GGTAGAGTCT
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
65 4 0.05
66 84 0.95
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.43
Consensus pattern (66 bp):
GAGTCTTTCGTTTCCTTTGCCTTCTGGGCTGCATAATCTGTATACTCAGAAGCTTTACCTGTTAC
T
Found at i:4021056 original size:165 final size:164
Alignment explanation
Indices: 4020745--4021057 Score: 369
Period size: 165 Copynumber: 1.9 Consensus size: 164
4020735 CCATAGTCAT
* * * *
4020745 TATACTCAGCAGCTTTGCCTGTTACTTAGTCCTTCGCTTCTTTAGCTTTCTGGGCAGCAGAGTCT
1 TATACTCAGAAGCTTTACCTGTTACTGAGTCCTTCGCTTCTTTAGCCTTCTGGGCAGCAGAGTCT
* * * *
4020810 TTCGTTTCCTTTGCCTTCTGTGCTGCATAATCTGTATACTCAGAAGCTTTACCTGTTACTGTGTC
66 TTCGTCTCCTTTGCCTTCTGTGCTG-ATAATCTGTACACTCAGAAGCTTTACCTGTTACAGTATC
* ***
4020875 TTTTGTTTCCTTTGCCTTCTGGGCTGCATAATCTG
130 CTTTACCTCCTTTGCCTTCTGGGCTGCATAATCTG
* * * *
4020910 TATACTCAGAAGCTTTACCTGTTACTGAGTCCTTCGTTTCTTTCGCCTTCTGGGCGGTAGAGTCT
1 TATACTCAGAAGCTTTACCTGTTACTGAGTCCTTCGCTTCTTTAGCCTTCTGGGCAGCAGAGTCT
* * * * * *
4020975 TTCGTCTCCTTTGCCTTCTTATTGGTG-TAATCTGTACACTTAGCAGCCTTTAGCTTTTA-AGTA
66 TTCGTCTCCTTTGCCTTC-T-GTGCTGATAATCTGTACACTCAGAAG-CTTTACCTGTTACAGTA
*
4021038 TCCTTTACCTCTTTTGCCTT
128 TCCTTTACCTCCTTTGCCTT
4021058 ATCTGCAGCC
Statistics
Matches: 122, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
165 107 0.88
166 11 0.09
167 4 0.03
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (164 bp):
TATACTCAGAAGCTTTACCTGTTACTGAGTCCTTCGCTTCTTTAGCCTTCTGGGCAGCAGAGTCT
TTCGTCTCCTTTGCCTTCTGTGCTGATAATCTGTACACTCAGAAGCTTTACCTGTTACAGTATCC
TTTACCTCCTTTGCCTTCTGGGCTGCATAATCTG
Found at i:4021609 original size:51 final size:51
Alignment explanation
Indices: 4021541--4021641 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 51
4021531 CATGACTCTG
*
4021541 TTGCTGTTGCTGCGGGGATTGATCCCACTGCTCCTTATAGACAACTCTTTT
1 TTGCTGTTGCTGCGGGGATTGATCCCACTCCTCCTTATAGACAACTCTTTT
* *
4021592 TTGCTGTTGCTGTGGGGATTGATCGCACTCCTCCTTATAGACAACTCTTT
1 TTGCTGTTGCTGCGGGGATTGATCCCACTCCTCCTTATAGACAACTCTTT
4021642 CTTCATGTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.38
Consensus pattern (51 bp):
TTGCTGTTGCTGCGGGGATTGATCCCACTCCTCCTTATAGACAACTCTTTT
Found at i:4039947 original size:16 final size:17
Alignment explanation
Indices: 4039926--4039958 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4039916 TTTGCACACT
4039926 TCTAATC-TAATGTCCC
1 TCTAATCTTAATGTCCC
4039942 TCTAATCTTAATGTCCC
1 TCTAATCTTAATGTCCC
4039959 AAGTTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.24, C:0.30, G:0.06, T:0.39
Consensus pattern (17 bp):
TCTAATCTTAATGTCCC
Found at i:4042511 original size:18 final size:18
Alignment explanation
Indices: 4042473--4042508 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
4042463 AAATCGAATA
4042473 ATATTTTTTAAAATTTTT
1 ATATTTTTTAAAATTTTT
4042491 ATATATTTTTAAAATTTT
1 ATAT-TTTTTAAAATTTT
4042509 ATAAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATATTTTTTAAAATTTTT
Found at i:4044338 original size:23 final size:22
Alignment explanation
Indices: 4044297--4044339 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
4044287 AATTAACTAA
*
4044297 TCAATGAAAAATAATTTATTAG
1 TCAATGAAAAATAAATTATTAG
4044319 TCAATGAAAAATAAAATTATT
1 TCAATGAAAAAT-AAATTATT
4044340 TTTTAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (22 bp):
TCAATGAAAAATAAATTATTAG
Found at i:4044498 original size:18 final size:18
Alignment explanation
Indices: 4044437--4044604 Score: 141
Period size: 18 Copynumber: 9.2 Consensus size: 18
4044427 TAGCATAATT
*
4044437 TTATTTATAAATAATATA
1 TTATTAATAAATAATATA
** *
4044455 TTAAAAATAATATATTA-A
1 TTATTAATAA-ATAATATA
*
4044473 TATATTAATAAATAATGTA
1 T-TATTAATAAATAATATA
4044492 TTATTAATAAATAATATA
1 TTATTAATAAATAATATA
*
4044510 CTATTAAT--ATAATATA
1 TTATTAATAAATAATATA
*
4044526 TTACTAAT-AAT-A-ATA
1 TTATTAATAAATAATATA
4044541 TTATTAATAAATATATACTA
1 TTATTAATAAATA-ATA-TA
*
4044561 TTAATATAATATATTAATAAATA
1 TT-AT-TAATA-AATAAT--ATA
4044584 TTATTAATAAATAATATA
1 TTATTAATAAATAATATA
4044602 TTA
1 TTA
4044605 ATATATTAAT
Statistics
Matches: 121, Mismatches: 15, Indels: 28
0.74 0.09 0.17
Matches are distributed among these distances:
15 10 0.08
16 18 0.15
17 2 0.02
18 43 0.36
19 15 0.12
20 9 0.07
21 7 0.06
22 9 0.07
23 7 0.06
24 1 0.01
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.44
Consensus pattern (18 bp):
TTATTAATAAATAATATA
Found at i:4044566 original size:13 final size:12
Alignment explanation
Indices: 4044446--4044610 Score: 71
Period size: 13 Copynumber: 13.6 Consensus size: 12
4044436 TTTATTTATA
4044446 AATA-ATATATT
1 AATATATATATT
*
4044457 AAAAATAATATATT
1 -AATAT-ATATATT
*
4044471 AATATAT-TAAT
1 AATATATATATT
*
4044482 AA-ATAATGTATT
1 AATAT-ATATATT
* *
4044494 ATTA-ATA-AAT
1 AATATATATATT
*
4044504 AATATA-CTATT
1 AATATATATATT
4044515 AATATAATATATT
1 AATAT-ATATATT
*
4044528 ACTA-ATA-A-T
1 AATATATATATT
*
4044537 AATAT-TATTAATA
1 AATATATA-T-ATT
4044550 AATATATACTATT
1 AATATATA-TATT
4044563 AATATAATATATT
1 AATAT-ATATATT
*
4044576 AATAAATATTATT
1 AATATATA-TATT
4044589 AATAAATAATATATT
1 AAT--AT-ATATATT
4044604 AATATAT
1 AATATAT
4044611 TAATAAAAGA
Statistics
Matches: 115, Mismatches: 18, Indels: 40
0.66 0.10 0.23
Matches are distributed among these distances:
9 6 0.05
10 8 0.07
11 20 0.17
12 16 0.14
13 41 0.36
14 13 0.11
15 8 0.07
16 3 0.03
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.43
Consensus pattern (12 bp):
AATATATATATT
Found at i:4044615 original size:92 final size:88
Alignment explanation
Indices: 4044446--4044615 Score: 227
Period size: 92 Copynumber: 1.9 Consensus size: 88
4044436 TTTATTTATA
* *
4044446 AATAATATATTAAAAATAATATATTAATATATTAATAAATAATGTATTATTAATAAATAATATAC
1 AATAATATATTAAAAATAATATATTAATATAATAATAAATAATATATTATTAATAAATAATATAC
*
4044511 TATTAATATAATATATTACTAAT
66 TAATAATATAATATATTACTAAT
*
4044534 AATAATATTATTAATAAATATATACTATTAATATAATATATTAATAA-ATATTATTAATAAATAA
1 AATAATA-TATTAA-AAATA-ATA-TATTAATATAATA-ATAAATAATATATTATTAATAAATAA
*
4044598 TATATTAAT-ATATTAATA
61 TATACTAATAATA-TAATA
4044616 AAAGATATAA
Statistics
Matches: 71, Mismatches: 5, Indels: 8
0.85 0.06 0.10
Matches are distributed among these distances:
88 7 0.10
89 6 0.08
90 5 0.07
91 6 0.08
92 40 0.56
93 7 0.10
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.43
Consensus pattern (88 bp):
AATAATATATTAAAAATAATATATTAATATAATAATAAATAATATATTATTAATAAATAATATAC
TAATAATATAATATATTACTAAT
Found at i:4044625 original size:28 final size:28
Alignment explanation
Indices: 4044493--4044625 Score: 78
Period size: 28 Copynumber: 4.6 Consensus size: 28
4044483 AATAATGTAT
*
4044493 TATTAATAAATAATATACTATTAATATAAT-A
1 TATTAATAAA-AATATAATA-T-AT-TAATAA
* *
4044524 TATTACT-AATA-ATAATATTATTAATAAA
1 TATTAATAAAAATATAATA-TATTAAT-AA
* **
4044552 TATATACTATTAATATAATATATTAATAAA
1 TAT-TAATAAAAATATAATATATTAAT-AA
* *
4044582 TATTATTAATAA-ATAATATATTAAT-A
1 TATTAATAAAAATATAATATATTAATAA
4044608 TATTAATAAAAGATATAA
1 TATTAATAAAA-ATATAA
4044626 AGAATAATAA
Statistics
Matches: 85, Mismatches: 10, Indels: 17
0.76 0.09 0.15
Matches are distributed among these distances:
26 14 0.16
27 3 0.04
28 28 0.33
29 12 0.14
30 16 0.19
31 12 0.14
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (28 bp):
TATTAATAAAAATATAATATATTAATAA
Found at i:4044681 original size:19 final size:18
Alignment explanation
Indices: 4044654--4044741 Score: 58
Period size: 19 Copynumber: 4.9 Consensus size: 18
4044644 ATTTTAGTAT
*
4044654 TTTTTATATTAACATAATA
1 TTTTAATATTAA-ATAATA
*
4044673 TTTTAATATTAAATATTA
1 TTTTAATATTAAATAATA
* ** * *
4044691 TTATTAA-AATATGTTTATT
1 TT-TTAATATTA-AATAATA
4044710 TTTTAATATT-AAT-A-A
1 TTTTAATATTAAATAATA
4044725 TTTTAATATTAAATAAT
1 TTTTAATATTAAATAAT
4044742 TCCAATATAT
Statistics
Matches: 51, Mismatches: 12, Indels: 13
0.67 0.16 0.17
Matches are distributed among these distances:
15 10 0.20
16 4 0.08
17 2 0.04
18 14 0.27
19 21 0.41
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (18 bp):
TTTTAATATTAAATAATA
Found at i:4044730 original size:15 final size:16
Alignment explanation
Indices: 4044710--4044742 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
4044700 TATGTTTATT
4044710 TTTTAATATT-AATAA
1 TTTTAATATTAAATAA
4044725 TTTTAATATTAAATAA
1 TTTTAATATTAAATAA
4044741 TT
1 TT
4044743 CCAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTTAATATTAAATAA
Found at i:4044741 original size:25 final size:25
Alignment explanation
Indices: 4044713--4044798 Score: 77
Period size: 26 Copynumber: 3.3 Consensus size: 25
4044703 GTTTATTTTT
4044713 TAATATTAATAATTTTAATATTAAA
1 TAATATTAATAATTTTAATATTAAA
* *
4044738 TAAT-TCCAATATATTTTAATAATAAA
1 TAATAT-TAATA-ATTTTAATATTAAA
* *
4044764 TAATTTTTAAT-ATTTTAATAATTATAT
1 TAA-TATTAATAATTTTAAT-ATTA-AA
4044791 TAATATTA
1 TAATATTA
4044799 TTTTTTAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
24 1 0.02
25 16 0.33
26 23 0.47
27 8 0.16
28 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
TAATATTAATAATTTTAATATTAAA
Found at i:4044763 original size:26 final size:26
Alignment explanation
Indices: 4044720--4044785 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 26
4044710 TTTTAATATT
*
4044720 AATA-ATTTTAATATTAAATAATTCC
1 AATATATTTTAATAATAAATAATTCC
**
4044745 AATATATTTTAATAATAAATAATTTT
1 AATATATTTTAATAATAAATAATTCC
*
4044771 TA-ATATTTTAATAAT
1 AATATATTTTAATAAT
4044786 TATATTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
25 17 0.47
26 19 0.53
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (26 bp):
AATATATTTTAATAATAAATAATTCC
Found at i:4045077 original size:19 final size:21
Alignment explanation
Indices: 4045049--4045087 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
4045039 TTTTATATGC
4045049 TTTTTAATTAT-TTTTTAAAA
1 TTTTTAATTATATTTTTAAAA
4045069 TTTTT-ATTATATTTTTAAA
1 TTTTTAATTATATTTTTAAA
4045088 TCGTATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTTAATTATATTTTTAAAA
Found at i:4051727 original size:12 final size:11
Alignment explanation
Indices: 4051710--4051742 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
4051700 CACAACAAAC
4051710 AAAAGAAGGAAA
1 AAAAGAA-GAAA
4051722 AAAAGAAGAAA
1 AAAAGAAGAAA
4051733 AAAA-AAGAAA
1 AAAAGAAGAAA
4051743 TTCCCAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 6 0.29
11 8 0.38
12 7 0.33
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAAA
Found at i:4056815 original size:14 final size:14
Alignment explanation
Indices: 4056798--4056824 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4056788 GCTTAAAGTG
4056798 AAAAAAAAAAGAAA
1 AAAAAAAAAAGAAA
4056812 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
4056825 CCCTACCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGAAA
Found at i:4062385 original size:203 final size:191
Alignment explanation
Indices: 4061806--4062385 Score: 546
Period size: 203 Copynumber: 3.0 Consensus size: 191
4061796 TGGGAAAATG
* *
4061806 ACTACAAAGTTAGGCCAAATTAACAAAGACTATTGTCAAAGTTTAATTATATAAAATTAAGGC-C
1 ACTACAAAGTTAGGCCAAATTAAGAAAGA-TATTGTCAAAGCTTAATTATATAAAATTAAGGCAC
* * *
4061870 AAACAAAGATTAGCTCAAT--CTATGCCT-AAGAT-TAAAAATCTTTCATTAGTGGCTGAGAAAA
65 AAACAAAGATTAGCTCAATCCCTAAGCCTAAAAATCTAAAAAT-TTTCATTAGTGGCT-A-AAAT
* * *
4061931 TATGAAACATTACTCGAACACTACTAAATCATCATCTT-AA-TCAAGAGAGGACATTCTAAAATC
127 TAT-AAACGTTACTCGAACACTACTAAATCATCATCTTAAACTAAAAAGA-GACA-TCTAAAATC
4061994 TTT
189 TTT
* * * * *
4061997 ACTATAAAATTAGGCC--A--ACG--AG-TATTGTCAAATCTTAATTATATAAAATTAAGAC-CA
1 ACTACAAAGTTAGGCCAAATTAAGAAAGATATTGTCAAAGCTTAATTATATAAAATTAAGGCACA
* *
4062054 AACAAAGATTAGCTCAATCTATGCCTAAACTTAAAAATCTATAAAA-TTTCATTAGTGGCTAAGA
66 AACAAAGATTAGCTCAATC----CCTAAGCCTAAAAATCTA-AAAATTTTCATTAGTGGCT-A-A
** * * * * *
4062118 AATTACGAACGTTCCTCGAACACTAATAAATCGTCATCTTAATCTGAAAAA-TGACATACTAAAA
124 AATTATAAACGTTACTCGAACACTACTAAATCATCATCTTAAACT-AAAAAGAGACAT-CTAAAA
4062182 TCTTT
187 TCTTT
*
4062187 ACTACAAAGTTAGGCCAAATTAAGAAAGATTATCGTCAAAGCTTAATTATATAAAATTAAGGCTA
1 ACTACAAAGTTAGGCCAAATTAAGAAAGA-TATTGTCAAAGCTTAATTATATAAAATTAAGGC--
* *
4062252 AACAAACAATGATTAGCTCAATCCCCACCTAAGCCTAAAATATCTAGAAATTTTCATTAGTGGCT
63 -ACAAACAAAGATTAGCTCAAT---C-CCTAAGCCTAAAA-ATCTAAAAATTTTCATTAGTGGCT
* *
4062317 AAAACTTAATAAATGTTACTCGAACACTACTAAATCATCGTCTTAAACTAAAAAGAGACACTCTA
122 AAAA-TT-ATAAACGTTACTCGAACACTACTAAATCATCATCTTAAACTAAAAAGAGACA-TCTA
4062382 AAAT
184 AAAT
4062386 TCTTAAATTT
Statistics
Matches: 312, Mismatches: 43, Indels: 56
0.76 0.10 0.14
Matches are distributed among these distances:
183 50 0.16
185 2 0.01
187 1 0.00
189 36 0.12
190 55 0.18
191 17 0.05
192 8 0.03
194 2 0.01
196 2 0.01
198 30 0.10
201 3 0.01
202 41 0.13
203 63 0.20
204 1 0.00
205 1 0.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (191 bp):
ACTACAAAGTTAGGCCAAATTAAGAAAGATATTGTCAAAGCTTAATTATATAAAATTAAGGCACA
AACAAAGATTAGCTCAATCCCTAAGCCTAAAAATCTAAAAATTTTCATTAGTGGCTAAAATTATA
AACGTTACTCGAACACTACTAAATCATCATCTTAAACTAAAAAGAGACATCTAAAATCTTT
Found at i:4066021 original size:23 final size:23
Alignment explanation
Indices: 4065959--4066021 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 23
4065949 TAAAAAATAA
4065959 ATATTTTAATACTATAAATATTTTG
1 ATATTTTAATA-TATAAATA-TTTG
*
4065984 ATATTTTAA-AAATAAATA-TT-
1 ATATTTTAATATATAAATATTTG
4066004 ACTATTTTAATATTATAA
1 A-TATTTTAATA-TATAA
4066022 TAATTATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
20 1 0.03
21 10 0.30
22 1 0.03
23 11 0.33
24 1 0.03
25 9 0.27
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (23 bp):
ATATTTTAATATATAAATATTTG
Found at i:4066183 original size:15 final size:16
Alignment explanation
Indices: 4066165--4066198 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4066155 ATATAATTAT
*
4066165 TTTTAATA-TTAATAA
1 TTTTAATAGTAAATAA
4066180 TTTTAATAGTAAATAA
1 TTTTAATAGTAAATAA
4066196 TTT
1 TTT
4066199 CAAAATACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTTAATAGTAAATAA
Found at i:4066809 original size:29 final size:29
Alignment explanation
Indices: 4066757--4066856 Score: 89
Period size: 29 Copynumber: 3.5 Consensus size: 29
4066747 ACATGATAAA
* * **
4066757 AATAAATACGAATAACACGAATATATATG
1 AATAAATATGACTAACTTGAATATATATG
* * *
4066786 AATAGATATGACTAA-TATGTATATATACG
1 AATAAATATGACTAACT-TGAATATATATG
* *
4066815 AATAAACACGACTAACTTGAATATATAT-
1 AATAAATATGACTAACTTGAATATATATG
4066843 AA-AAATATGACTAA
1 AATAAATATGACTAA
4066857 AATAATAAAT
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
27 10 0.18
28 2 0.04
29 42 0.76
30 1 0.02
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (29 bp):
AATAAATATGACTAACTTGAATATATATG
Found at i:4071957 original size:198 final size:196
Alignment explanation
Indices: 4071495--4072003 Score: 591
Period size: 183 Copynumber: 2.6 Consensus size: 196
4071485 TGCGAAAATG
*
4071495 ACTACAAAGTTAGGCCAAATTAACAAAGATTATCGTCAAAGCTTAATTATATAAAATTAAGGCCA
1 ACTACAAAGTTAGGCCAAATTAAGAAAGATTATCGTCAAAGCTTAATTATATAAAATTAAGGCCA
* *
4071560 AACAAAGATTAGCTCAATCTATGCCTAAGA-TTAAAAATC-----TTTCATCAGTGGCTGAGAAA
66 AACAAAGATTAGCTCAATCTATGCCTAA-ACTTAAAAATCTAAAATTTCATTAGTGGCTAAGAAA
* * * *
4071619 ATATGAAACATTACTCGAACACTACTAAATCATCATCTTAATCAAGAGAGGACATTCTAAAATCT
130 ATACGAAACATTACTCGAACACTAATAAATCATCATCTTAATCAAGAAAGGACATACTAAAATCT
4071684 TT
195 TT
* * * * * *
4071686 ACTATAAAATTAGGCC--A--ACG--AG--TATTGTCAAATCTTAATTATATAAAATTAAGACCA
1 ACTACAAAGTTAGGCCAAATTAAGAAAGATTATCGTCAAAGCTTAATTATATAAAATTAAGGCCA
4071743 AACAAAGATTAGCTCAATCTATGCCTAAACTTAAAAATCTATAAAATTTCATTAGTGGCTAAGAA
66 AACAAAGATTAGCTCAATCTATGCCTAAACTTAAAAATC--TAAAATTTCATTAGTGGCTAAGAA
* * * * * *
4071808 ATTACG-AACGTTCCTCGAACACTAATAAATCGTCATCTTAATTTGAA-AAATGACATACTAAAA
129 AATACGAAACATTACTCGAACACTAATAAATCATCATCTTAA--TCAAGAAAGGACATACTAAAA
4071871 TCTTT
192 TCTTT
*
4071876 ACTACAAAGTTAGGCCAAATTAAGAAAGATTATCGTCAAAGCTTAATTATATAAAATTAAGGCTA
1 ACTACAAAGTTAGGCCAAATTAAGAAAGATTATCGTCAAAGCTTAATTATATAAAATTAAGGCCA
* ** * * * *
4071941 AACAATGATTAGCTCAATCCCTACCTAAGCCTAAAATATCTAGAAATTTTCTTTAGTGGCTAA
66 AACAAAGATTAGCTCAATCTATGCCTAAACTTAAAA-ATCTA-AAA-TTTCATTAGTGGCTAA
4072004 AACTTTATAA
Statistics
Matches: 264, Mismatches: 33, Indels: 34
0.80 0.10 0.10
Matches are distributed among these distances:
182 1 0.00
183 69 0.26
185 2 0.01
187 1 0.00
189 32 0.12
190 53 0.20
191 17 0.06
192 1 0.00
194 2 0.01
196 2 0.01
197 2 0.01
198 64 0.24
199 18 0.07
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (196 bp):
ACTACAAAGTTAGGCCAAATTAAGAAAGATTATCGTCAAAGCTTAATTATATAAAATTAAGGCCA
AACAAAGATTAGCTCAATCTATGCCTAAACTTAAAAATCTAAAATTTCATTAGTGGCTAAGAAAA
TACGAAACATTACTCGAACACTAATAAATCATCATCTTAATCAAGAAAGGACATACTAAAATCTT
T
Found at i:4072536 original size:12 final size:12
Alignment explanation
Indices: 4072519--4072560 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
4072509 TGATATAGTA
*
4072519 TTAAATTTAAGT
1 TTAAATTTGAGT
*
4072531 TTAAATTTGACT
1 TTAAATTTGAGT
4072543 TTAAATTTGAGAT
1 TTAAATTTGAG-T
4072556 TTAAA
1 TTAAA
4072561 ATTCGGTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 20 0.77
13 6 0.23
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (12 bp):
TTAAATTTGAGT
Found at i:4073600 original size:4 final size:4
Alignment explanation
Indices: 4073591--4073620 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
4073581 ATCATGTGTA
4073591 AAAT AAAT AAAT AAAT AAAT AAAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT -AAAT AAAT A
4073621 GAAGACGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:4073608 original size:12 final size:13
Alignment explanation
Indices: 4073591--4073620 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4073581 ATCATGTGTA
4073591 AAATAAAT-AAAT
1 AAATAAATAAAAT
4073603 AAATAAATAAAAT
1 AAATAAATAAAAT
4073616 AAATA
1 AAATA
4073621 GAAGACGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:4074513 original size:13 final size:13
Alignment explanation
Indices: 4074495--4074523 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
4074485 ATTTTATGTT
4074495 AATATATCAAATA
1 AATATATCAAATA
4074508 AATATATCAAATA
1 AATATATCAAATA
4074521 AAT
1 AAT
4074524 GGTTAGAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (13 bp):
AATATATCAAATA
Found at i:4074861 original size:136 final size:134
Alignment explanation
Indices: 4074700--4074970 Score: 488
Period size: 136 Copynumber: 2.0 Consensus size: 134
4074690 AAAGAAACAA
4074700 ATTTAGTTTCTTTTTTTTTTAAATAAAAACTCGTTTAAGGAAATGATAAGTATAAAAAAATAAAT
1 ATTTAGTTTCTTTTTTTTTTAAATAAAAACTCGTTTAAGGAAATGATAAGTATAAAAAAATAAAT
*
4074765 AAATAATGGGATAAAAGGTTCCAGATGGTCCATTGGACCCTTAAAGCTCCAGCCCTAAGCTGGTG
66 AAATAATGGGATAAAAGGTTCCAGATGATCCATTGGACCCTTAAAGCTCCAGCCCTAAGCTGGTG
4074830 TGTT
131 TGTT
* *
4074834 ATTTAGTTTCTTTTTTTTTTTTTAATAAAAACTCGTTTAAGGGAATGATAAGTATAAAAAAATAA
1 ATTTAGTTTC--TTTTTTTTTTAAATAAAAACTCGTTTAAGGAAATGATAAGTATAAAAAAATAA
*
4074899 ATAAATAATGGGATAAAAGGTTCCAGATGATCCATTGGACCCTTAAAGCTCCAGCCCTTAGCTGG
64 ATAAATAATGGGATAAAAGGTTCCAGATGATCCATTGGACCCTTAAAGCTCCAGCCCTAAGCTGG
4074964 TGTGTT
129 TGTGTT
4074970 A
1 A
4074971 GTGTGGTCCA
Statistics
Matches: 131, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
134 10 0.08
136 121 0.92
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.35
Consensus pattern (134 bp):
ATTTAGTTTCTTTTTTTTTTAAATAAAAACTCGTTTAAGGAAATGATAAGTATAAAAAAATAAAT
AAATAATGGGATAAAAGGTTCCAGATGATCCATTGGACCCTTAAAGCTCCAGCCCTAAGCTGGTG
TGTT
Found at i:4075853 original size:23 final size:23
Alignment explanation
Indices: 4075791--4075853 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 23
4075781 TAAAAAATAA
4075791 ATATTTTAATACTATAAATATTTTG
1 ATATTTTAATA-TATAAATA-TTTG
*
4075816 ATATTTTAA-AAATAAATA-TT-
1 ATATTTTAATATATAAATATTTG
4075836 ACTATTTTAATATTATAA
1 A-TATTTTAATA-TATAA
4075854 TAATTATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
20 1 0.03
21 10 0.30
22 1 0.03
23 11 0.33
24 1 0.03
25 9 0.27
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (23 bp):
ATATTTTAATATATAAATATTTG
Found at i:4076018 original size:15 final size:16
Alignment explanation
Indices: 4076000--4076033 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4075990 ATATAATTAT
*
4076000 TTTTAATA-TTAATAA
1 TTTTAATAGTAAATAA
4076015 TTTTAATAGTAAATAA
1 TTTTAATAGTAAATAA
4076031 TTT
1 TTT
4076034 CAAAATACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTTAATAGTAAATAA
Found at i:4076657 original size:31 final size:31
Alignment explanation
Indices: 4076616--4076684 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
4076606 AATAATACGG
* * *
4076616 ATATACACGAATAGATACGACTAATA-TATAT
1 ATATATACGAATAAACACGACTAATATTA-AT
4076647 ATATATACGAATAAACACGACTAATATTAAT
1 ATATATACGAATAAACACGACTAATATTAAT
4076678 ATATATA
1 ATATATA
4076685 AAAATATGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 32 0.94
32 2 0.06
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.30
Consensus pattern (31 bp):
ATATATACGAATAAACACGACTAATATTAAT
Found at i:4081022 original size:29 final size:29
Alignment explanation
Indices: 4080989--4081048 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
4080979 TCACTGCGGG
4080989 TGACGGATGGTAAGTGTTCTATTTTAAAA
1 TGACGGATGGTAAGTGTTCTATTTTAAAA
4081018 TGACGGATGGTAAGTGTTCTATTTTAAAA
1 TGACGGATGGTAAGTGTTCTATTTTAAAA
4081047 TG
1 TG
4081049 CAAAAGGAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.38
Consensus pattern (29 bp):
TGACGGATGGTAAGTGTTCTATTTTAAAA
Found at i:4081240 original size:281 final size:281
Alignment explanation
Indices: 4080737--4081300 Score: 1065
Period size: 281 Copynumber: 2.0 Consensus size: 281
4080727 TTACTGCGGG
*
4080737 TGACGGATGGTAAGTGTTCTATATTAAAATGCACAAGGAAGGAGTGCGCTCCTTGGACTCGAAAC
1 TGACGGATGGTAAGTGTTCTATATTAAAATGCAAAAGGAAGGAGTGCGCTCCTTGGACTCGAAAC
* *
4080802 TCTATACCGTGAGACAATAGACCAGACACGCTGTGTGGAAAGAAAGATGGAGCGAGTTTCATTCA
66 TCTACACCGTGAGACAACAGACCAGACACGCTGTGTGGAAAGAAAGATGGAGCGAGTTTCATTCA
4080867 ATTTCAAGTAAGTTTTCGGTTGCAATTTTTGGAGTGAACAAATGGAGGCTATGAAAGATTGACAC
131 ATTTCAAGTAAGTTTTCGGTTGCAATTTTTGGAGTGAACAAATGGAGGCTATGAAAGATTGACAC
4080932 CTGATGAAAATGACGTAAGCATATCACTGTAACTGACGGGTTTCGTGTCACTGCGGGTGACGGAT
196 CTGATGAAAATGACGTAAGCATATCACTGTAACTGACGGGTTTCGTGTCACTGCGGGTGACGGAT
*
4080997 GGTAAGTGTTCTATTTTAAAA
261 GGTAAGTGTTCTATATTAAAA
*
4081018 TGACGGATGGTAAGTGTTCTATTTTAAAATGCAAAAGGAAGGAGTGCGCTCCTTGGACTCGAAAC
1 TGACGGATGGTAAGTGTTCTATATTAAAATGCAAAAGGAAGGAGTGCGCTCCTTGGACTCGAAAC
4081083 TCTACACCGTGAGACAACAGACCAGACACGCTGTGTGGAAAGAAAGATGGAGCGAGTTTCATTCA
66 TCTACACCGTGAGACAACAGACCAGACACGCTGTGTGGAAAGAAAGATGGAGCGAGTTTCATTCA
4081148 ATTTCAAGTAAGTTTTCGGTTGCAATTTTTGGAGTGAACAAATGGAGGCTATGAAAGATTGACAC
131 ATTTCAAGTAAGTTTTCGGTTGCAATTTTTGGAGTGAACAAATGGAGGCTATGAAAGATTGACAC
* *
4081213 CTGGTGAAAATGACGTAAGCATATCACTGTACCTGACGGGTTTCGTGTCACTGCGGGTGACGGAT
196 CTGATGAAAATGACGTAAGCATATCACTGTAACTGACGGGTTTCGTGTCACTGCGGGTGACGGAT
4081278 GGTAAGTGTTCTATATTAAAA
261 GGTAAGTGTTCTATATTAAAA
4081299 TG
1 TG
4081301 CACAAGGAAG
Statistics
Matches: 276, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
281 276 1.00
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.27
Consensus pattern (281 bp):
TGACGGATGGTAAGTGTTCTATATTAAAATGCAAAAGGAAGGAGTGCGCTCCTTGGACTCGAAAC
TCTACACCGTGAGACAACAGACCAGACACGCTGTGTGGAAAGAAAGATGGAGCGAGTTTCATTCA
ATTTCAAGTAAGTTTTCGGTTGCAATTTTTGGAGTGAACAAATGGAGGCTATGAAAGATTGACAC
CTGATGAAAATGACGTAAGCATATCACTGTAACTGACGGGTTTCGTGTCACTGCGGGTGACGGAT
GGTAAGTGTTCTATATTAAAA
Found at i:4082906 original size:12 final size:12
Alignment explanation
Indices: 4082886--4082933 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
4082876 CGATATAATA
4082886 TTAAATTTGAGT
1 TTAAATTTGAGT
* *
4082898 TTGAATTTGATT
1 TTAAATTTGAGT
4082910 TTAAATTTGAGAT
1 TTAAATTTGAG-T
4082923 TTAAAATTTGA
1 TT-AAATTTGA
4082934 TTCGAATTCG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 19 0.63
13 3 0.10
14 8 0.27
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (12 bp):
TTAAATTTGAGT
Found at i:4082916 original size:24 final size:26
Alignment explanation
Indices: 4082886--4082935 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
4082876 CGATATAATA
*
4082886 TTAAATTTGAG-TTT-GAATTTGATT
1 TTAAATTTGAGATTTAAAATTTGATT
4082910 TTAAATTTGAGATTTAAAATTTGATT
1 TTAAATTTGAGATTTAAAATTTGATT
4082936 CGAATTCGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.48
25 3 0.13
26 9 0.39
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (26 bp):
TTAAATTTGAGATTTAAAATTTGATT
Found at i:4085829 original size:46 final size:46
Alignment explanation
Indices: 4085762--4085855 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
4085752 CTATTACATA
*
4085762 AAGGCAATCTGCCTTTTCAACATCTTGTAAAGAAAGATCACAAACC
1 AAGGCAATCTGCCTTGTCAACATCTTGTAAAGAAAGATCACAAACC
*
4085808 AAGGCAATCTGCCTTGTCAACATCTTGTTAAGAAAGATCACAAACC
1 AAGGCAATCTGCCTTGTCAACATCTTGTAAAGAAAGATCACAAACC
4085854 AA
1 AA
4085856 AACTATTACT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.23
Consensus pattern (46 bp):
AAGGCAATCTGCCTTGTCAACATCTTGTAAAGAAAGATCACAAACC
Found at i:4089242 original size:30 final size:30
Alignment explanation
Indices: 4089192--4089248 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
4089182 TAATAAAATA
*
4089192 TAAATATAAATATAAATTTTTATAAATAAT
1 TAAATATAAATACAAATTTTTATAAATAAT
*
4089222 TAAA-ATAAATACACAATTTTTTTAAAT
1 TAAATATAAATACA-AATTTTTATAAAT
4089249 TTTTTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (30 bp):
TAAATATAAATACAAATTTTTATAAATAAT
Found at i:4090834 original size:15 final size:14
Alignment explanation
Indices: 4090814--4090844 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
4090804 GTTTAATTAA
4090814 AATTAAAAATTAATT
1 AATTAAAAATT-ATT
4090829 AATTAAAAATTATT
1 AATTAAAAATTATT
4090843 AA
1 AA
4090845 AAAAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTAAAAATTATT
Found at i:4091001 original size:11 final size:11
Alignment explanation
Indices: 4090985--4091034 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
4090975 CCACGCTCCT
4090985 ACCCTATAGCC
1 ACCCTATAGCC
*
4090996 ACCCTACAGCC
1 ACCCTATAGCC
4091007 TA-CCT-TAGCC
1 -ACCCTATAGCC
4091017 ATCCCTATAGCC
1 A-CCCTATAGCC
4091029 ACCCTA
1 ACCCTA
4091035 CTCCACTCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
9 1 0.03
10 4 0.12
11 21 0.64
12 7 0.21
ACGTcount: A:0.26, C:0.46, G:0.08, T:0.20
Consensus pattern (11 bp):
ACCCTATAGCC
Found at i:4091028 original size:22 final size:23
Alignment explanation
Indices: 4090982--4091034 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
4090972 CGTCCACGCT
4090982 CCTACCCTATAGCCACCCTACAG
1 CCTACCCTATAGCCACCCTACAG
*
4091005 CCTA-CCT-TAGCCATCCCTATAG
1 CCTACCCTATAGCCA-CCCTACAG
4091027 CC-ACCCTA
1 CCTACCCTA
4091035 CTCCACTCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 7 0.27
22 15 0.58
23 4 0.15
ACGTcount: A:0.25, C:0.47, G:0.08, T:0.21
Consensus pattern (23 bp):
CCTACCCTATAGCCACCCTACAG
Found at i:4100273 original size:33 final size:33
Alignment explanation
Indices: 4100235--4100512 Score: 222
Period size: 33 Copynumber: 8.5 Consensus size: 33
4100225 AAAAATAAAA
*
4100235 TTTAAGCCCAGTTTATCTAACC-TCAAATAAGGT
1 TTTAAGCCCAGTTTATCTAACCATC-AATAAAGT
*
4100268 TTTAAGCCCAGTTTATCTGACCATCAATAAAGT
1 TTTAAGCCCAGTTTATCTAACCATCAATAAAGT
* *** * * *
4100301 TTTAAGCCCAATTTATCTGGTCATTAATGAAGC
1 TTTAAGCCCAGTTTATCTAACCATCAATAAAGT
**
4100334 TTTAAGCCCAG-TTATCTGGCCATCAATAAAGT
1 TTTAAGCCCAGTTTATCTAACCATCAATAAAGT
* * ** * *
4100366 TTTAAGCCTAGTTTATTTGGCCATTAATAAAGC
1 TTTAAGCCCAGTTTATCTAACCATCAATAAAGT
** ** *
4100399 TTTAAGCTTAGTTTATCTTGCCATTAATGAAA--
1 TTTAAGCCCAGTTTATCTAACCATCAAT-AAAGT
* *
4100431 TTTAAGCTCAGTTTATCTGACCATCAATAAAGT
1 TTTAAGCCCAGTTTATCTAACCATCAATAAAGT
* * * ** * * *
4100464 TTTAAGTCCAGTTTATTTGACTTTAAATGAGGT
1 TTTAAGCCCAGTTTATCTAACCATCAATAAAGT
4100497 TTTAAGCCCAGTTTAT
1 TTTAAGCCCAGTTTAT
4100513 TTGGCCCTAA
Statistics
Matches: 207, Mismatches: 33, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
31 3 0.01
32 51 0.25
33 148 0.71
34 5 0.02
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (33 bp):
TTTAAGCCCAGTTTATCTAACCATCAATAAAGT
Found at i:4100361 original size:65 final size:66
Alignment explanation
Indices: 4100235--4100518 Score: 270
Period size: 65 Copynumber: 4.3 Consensus size: 66
4100225 AAAAATAAAA
** * * * *
4100235 TTTAAGCCCAGTTTATCTAACC-TCAAATAAGGTTTTAAGCCCAGTTTATCTGACCATCAATAAA
1 TTTAAGCCCAGTTTATCTGGCCAT-TAATAAAGCTTTAAGCCCAGTTTATCTGGCCATCAATAAA
4100299 GT
65 GT
* * *
4100301 TTTAAGCCCAATTTATCTGGTCATTAATGAAGCTTTAAGCCCAG-TTATCTGGCCATCAATAAAG
1 TTTAAGCCCAGTTTATCTGGCCATTAATAAAGCTTTAAGCCCAGTTTATCTGGCCATCAATAAAG
4100365 T
66 T
* * ** * *
4100366 TTTAAGCCTAGTTTATTTGGCCATTAATAAAGCTTTAAGCTTAGTTTATCTTGCCATTAATGAAA
1 TTTAAGCCCAGTTTATCTGGCCATTAATAAAGCTTTAAGCCCAGTTTATCTGGCCATCAAT-AAA
4100431 --
65 GT
* * * * * * * ** * * *
4100431 TTTAAGCTCAGTTTATCTGACCATCAATAAAGTTTTAAGTCCAGTTTATTTGACTTTAAATGAGG
1 TTTAAGCCCAGTTTATCTGGCCATTAATAAAGCTTTAAGCCCAGTTTATCTGGCCATCAATAAAG
4100496 T
66 T
*
4100497 TTTAAGCCCAGTTTATTTGGCC
1 TTTAAGCCCAGTTTATCTGGCC
4100519 CTAAAAGAAA
Statistics
Matches: 175, Mismatches: 38, Indels: 10
0.78 0.17 0.04
Matches are distributed among these distances:
64 1 0.01
65 103 0.59
66 67 0.38
67 4 0.02
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (66 bp):
TTTAAGCCCAGTTTATCTGGCCATTAATAAAGCTTTAAGCCCAGTTTATCTGGCCATCAATAAAG
T
Found at i:4100501 original size:98 final size:96
Alignment explanation
Indices: 4100232--4100518 Score: 326
Period size: 98 Copynumber: 2.9 Consensus size: 96
4100222 AAAAAAAATA
* * * *
4100232 AAATTTAAGCCCAGTTTATCTAACC-TCAAATAAGGTTTTAAGCCCAGTTTATCTGACCATCAAT
1 AAATTTAAGCCCAGTTTATCTGACCATC-AATAAAGTTTTAAG-CCAGTTTATTTGA-CATTAAT
* *
4100296 AAAGTTTTAAGCCCAATTTATCTGGTCATTAATG
63 AAAGTTTTAAGCCCAGTTTATCTGGCCATTAATG
* * *
4100330 AAGCTTTAAGCCCAG-TTATCTGGCCATCAATAAAGTTTTAAGCCTAGTTTATTTGGCCATTAAT
1 AA-ATTTAAGCCCAGTTTATCTGACCATCAATAAAGTTTTAAGCC-AGTTTATTT-GACATTAAT
* ** *
4100394 AAAGCTTTAAGCTTAGTTTATCTTGCCATTAATG
63 AAAGTTTTAAGCCCAGTTTATCTGGCCATTAATG
* * *
4100428 AAATTTAAGCTCAGTTTATCTGACCATCAATAAAGTTTTAAGTCCAGTTTATTTGACTTTAAATG
1 AAATTTAAGCCCAGTTTATCTGACCATCAATAAAGTTTTAAG-CCAGTTTATTTGACATT-AATA
* *
4100493 AGGTTTTAAGCCCAGTTTATTTGGCC
64 AAGTTTTAAGCCCAGTTTATCTGGCC
4100519 CTAAAAGAAA
Statistics
Matches: 157, Mismatches: 25, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
97 16 0.10
98 125 0.80
99 16 0.10
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (96 bp):
AAATTTAAGCCCAGTTTATCTGACCATCAATAAAGTTTTAAGCCAGTTTATTTGACATTAATAAA
GTTTTAAGCCCAGTTTATCTGGCCATTAATG
Found at i:4101196 original size:87 final size:87
Alignment explanation
Indices: 4101050--4101245 Score: 279
Period size: 87 Copynumber: 2.3 Consensus size: 87
4101040 TCATAATTTT
* *
4101050 TAAGATCTCT-AGGCATAATTTTGATTCGCGGTGTTGTCCCAATCGATTCATTATTCTTGACTTA
1 TAAGATCTCTGA-GCATAATTTTGATTCGCAGTGTTATCCCAATCGATTCATTATTCTTGACTTA
*
4101114 TGATGTTATCCCAGTCGATTCTG
65 CGATGTTATCCCAGTCGATTCTG
* *
4101137 TAAGATCTCTGAGCATAATTTTGATTCGCAGTGTTATCCCGATCGATTCATTATTCTTGATTTAC
1 TAAGATCTCTGAGCATAATTTTGATTCGCAGTGTTATCCCAATCGATTCATTATTCTTGACTTAC
* * *
4101202 GGTGTTATCCTAGTTGATTCTG
66 GATGTTATCCCAGTCGATTCTG
*
4101224 TAAGACCTCTG-GACATAATTTT
1 TAAGATCTCTGAG-CATAATTTT
4101246 TGTAAGACTT
Statistics
Matches: 98, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
86 1 0.01
87 96 0.98
88 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (87 bp):
TAAGATCTCTGAGCATAATTTTGATTCGCAGTGTTATCCCAATCGATTCATTATTCTTGACTTAC
GATGTTATCCCAGTCGATTCTG
Found at i:4101355 original size:87 final size:87
Alignment explanation
Indices: 4101243--4101429 Score: 277
Period size: 87 Copynumber: 2.1 Consensus size: 87
4101233 TGGACATAAT
* * *
4101243 TTTTGTAAGACTTTCGAGCATGATTTCGATTCGTAG-TGTTATCCCGATCGATTCTTTAATTTTG
1 TTTTGTAAGACCTCCGAGCATGATTTCGATTCG-AGATATTATCCCGATCGATTCTTTAATTTTG
4101307 ACTTACGATGTTATCTCAGTCGA
65 ACTTACGATGTTATCTCAGTCGA
* * * *
4101330 TTTTGTAAGACCTCCGGGCATGATTTTGATTCGCGATATTATTCCGATCGATTCTTTAATTTTGA
1 TTTTGTAAGACCTCCGAGCATGATTTCGATTCGAGATATTATCCCGATCGATTCTTTAATTTTGA
*
4101395 CTTACGGTGTTATCTCAGTCGA
66 CTTACGATGTTATCTCAGTCGA
*
4101417 TTCTGTAAGACCT
1 TTTTGTAAGACCT
4101430 TTGGATATGA
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
86 1 0.01
87 89 0.99
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (87 bp):
TTTTGTAAGACCTCCGAGCATGATTTCGATTCGAGATATTATCCCGATCGATTCTTTAATTTTGA
CTTACGATGTTATCTCAGTCGA
Found at i:4101356 original size:111 final size:111
Alignment explanation
Indices: 4101147--4101356 Score: 289
Period size: 111 Copynumber: 1.9 Consensus size: 111
4101137 TAAGATCTCT
* * *
4101147 GAGCATAATTTTGATTCGCAGTGTTATCCCGATCGATTCATTATTCTTGATTTACGGTGTTATCC
1 GAGCATAATTTCGATTCGCAGTGTTATCCCGATCGATTCATTATTCTTGACTTACGATGTTATCC
* *
4101212 TAGTTGATTCTGTAAGACCTCTGGACATAATTTTTGTAAGACTTTC
66 TAGTCGATTCTGTAAGACCTCCGGACATAATTTTTGTAAGACTTTC
* * *
4101258 GAGCATGATTTCGATTCGTAGTGTTATCCCGATCGATTCTTTAATT-TTGACTTACGATGTTAT-
1 GAGCATAATTTCGATTCGCAGTGTTATCCCGATCGATTCATT-ATTCTTGACTTACGATGTTATC
* * *
4101321 CTCAGTCGATTTTGTAAGACCTCCGGGCATGATTTT
65 CT-AGTCGATTCTGTAAGACCTCCGGACATAATTTT
4101357 GATTCGCGAT
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
110 2 0.02
111 81 0.94
112 3 0.03
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (111 bp):
GAGCATAATTTCGATTCGCAGTGTTATCCCGATCGATTCATTATTCTTGACTTACGATGTTATCC
TAGTCGATTCTGTAAGACCTCCGGACATAATTTTTGTAAGACTTTC
Found at i:4101429 original size:198 final size:198
Alignment explanation
Indices: 4101041--4101554 Score: 644
Period size: 198 Copynumber: 2.6 Consensus size: 198
4101031 ATTTAAATAT
* * * * * * *
4101041 CATAA-TTTT-TAAGATCTCTAGGCATAATTTTGATTCGCGGTGTTGTCCCAATCGATTCATTAT
1 CATAATTTTTGTAAGACCTCCAAGCATGATTTCGATTCGCGGTGTTATCCCGATCGATTCATTAT
* * * * *
4101104 TCTTGACTTATGATGTTATCCCAGTCGATTCTGTAAGATCTCTGAGCATAATTTTGATTCGCAGT
66 TCTTGACTTACGATGTTATCTCAGTCGATTCTGTAAGACCTCTGGGCATGATTTTGATTCGCAGT
* * *
4101169 GTTATCCCGATCGATTCATTATTCTTGATTTACGGTGTTATCCTAGTTGATTCTGTAAGACCTCT
131 ATTATCCCGATCGATTCATTATTCTTGACTTACGGTGTTATCCTAGTCGATTCTGTAAGACCTCT
4101234 GGA
196 GGA
* * * ** *
4101237 CATAATTTTTGTAAGACTTTCGAGCATGATTTCGATTCGTAGTGTTATCCCGATCGATTCTTTAA
1 CATAATTTTTGTAAGACCTCCAAGCATGATTTCGATTCGCGGTGTTATCCCGATCGATTCATT-A
* *
4101302 TT-TTGACTTACGATGTTATCTCAGTCGATTTTGTAAGACCTCCGGGCATGATTTTGATTCGC-G
65 TTCTTGACTTACGATGTTATCTCAGTCGATTCTGTAAGACCTCTGGGCATGATTTTGATTCGCAG
* *
4101365 ATATTATTCCGATCGATTCTTTAATT-TTGACTTACGGTGTTAT-CTCAGTCGATTCTGTAAGAC
130 -TATTATCCCGATCGATTCATT-ATTCTTGACTTACGGTGTTATCCT-AGTCGATTCTGTAAGAC
*
4101428 CTTTGGA
192 CTCTGGA
* *
4101435 TATGATTTTTGTAAGACCTCCAAGCATGATTTCGATTCGCGGTGTTATCCCGATCGATTCATTAT
1 CATAATTTTTGTAAGACCTCCAAGCATGATTTCGATTCGCGGTGTTATCCCGATCGATTCATTAT
* * * * * *
4101500 TCTTGACTTGCGATATTGTCTCAGTTGATTCTATAAGACCTCTAGGCATGATTTT
66 TCTTGACTTACGATGTTATCTCAGTCGATTCTGTAAGACCTCTGGGCATGATTTT
4101555 TGTAAGACTT
Statistics
Matches: 269, Mismatches: 42, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
196 5 0.02
197 10 0.04
198 248 0.92
199 6 0.02
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (198 bp):
CATAATTTTTGTAAGACCTCCAAGCATGATTTCGATTCGCGGTGTTATCCCGATCGATTCATTAT
TCTTGACTTACGATGTTATCTCAGTCGATTCTGTAAGACCTCTGGGCATGATTTTGATTCGCAGT
ATTATCCCGATCGATTCATTATTCTTGACTTACGGTGTTATCCTAGTCGATTCTGTAAGACCTCT
GGA
Found at i:4101675 original size:24 final size:24
Alignment explanation
Indices: 4101639--4101689 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
4101629 TCTCAATCAA
* * * *
4101639 TTCTTTAATACCTTCGGACCTGAT
1 TTCTGTAAGACCTCCGGACATGAT
*
4101663 TTCTGTAAGACCTCCGGGCATGAT
1 TTCTGTAAGACCTCCGGACATGAT
4101687 TTC
1 TTC
4101690 GATTCGCGAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (24 bp):
TTCTGTAAGACCTCCGGACATGAT
Found at i:4101764 original size:111 final size:111
Alignment explanation
Indices: 4101330--4101776 Score: 454
Period size: 111 Copynumber: 4.0 Consensus size: 111
4101320 TCTCAGTCGA
* * *
4101330 TTTTGTAAGACCTCCGGGCATGATTTTGATTCGCGATATTATTCCGATCGATTCTTTAATT-TTG
1 TTTTGTAAGACCTCCGAGCATGATTTCGATTCGCGATATTATCCCGATCGATTCTTT-ATTCTTG
* * *
4101394 ACTTACGGTGTTATCTCAGTCGATTCTGTAAGACCTTTGGATATGAT
65 ACTTACGGTGTTATCTCAATCGATTCTGTAAGACCTTCGGACATGAT
* * * *
4101441 TTTTGTAAGACCTCCAAGCATGATTTCGATTCGCGGTGTTATCCCGATCGATTCATTATTCTTGA
1 TTTTGTAAGACCTCCGAGCATGATTTCGATTCGCGATATTATCCCGATCGATTCTTTATTCTTGA
* * * * * * * *
4101506 CTTGCGATATTGTCTCAGTTGATTCTATAAGACCTCTAGG-CATGAT
66 CTTACGGTGTTATCTCAATCGATTCTGTAAGACCT-TCGGACATGAT
* ** * * ** * *
4101552 TTTTGTAAGACTTCCGAATATAATTTTGATTTACGGTGTTATCCCGATCGATT-TATTATTCTTG
1 TTTTGTAAGACCTCCGAGCATGATTTCGATTCGCGATATTATCCCGATCGATTCT-TTATTCTTG
* * * * *
4101616 ACTTGCGGTGTTATCTCAATCAATTCTTTAATACCTTCGGACCTGAT
65 ACTTACGGTGTTATCTCAATCGATTCTGTAAGACCTTCGGACATGAT
* * * * *
4101663 TTCTGTAAGACCTCCGGGCATGATTTCGATTCGCGATATTATCCCTATCAATT-TTTCAATT-TC
1 TTTTGTAAGACCTCCGAGCATGATTTCGATTCGCGATATTATCCCGATCGATTCTTT--ATTCTT
* * *
4101726 GACTTACGGTGTTATCCCAATCGATTCTGTAAGACCTTCGGGCATAAT
64 GACTTACGGTGTTATCTCAATCGATTCTGTAAGACCTTCGGACATGAT
4101774 TTT
1 TTT
4101777 GATTTGTGAT
Statistics
Matches: 273, Mismatches: 57, Indels: 12
0.80 0.17 0.04
Matches are distributed among these distances:
110 8 0.03
111 259 0.95
112 6 0.02
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.40
Consensus pattern (111 bp):
TTTTGTAAGACCTCCGAGCATGATTTCGATTCGCGATATTATCCCGATCGATTCTTTATTCTTGA
CTTACGGTGTTATCTCAATCGATTCTGTAAGACCTTCGGACATGAT
Found at i:4101792 original size:87 final size:87
Alignment explanation
Indices: 4101663--4101850 Score: 209
Period size: 87 Copynumber: 2.2 Consensus size: 87
4101653 CGGACCTGAT
* * * *
4101663 TTCTGTAAGACCTCCGGGCATGATTTCGATTCGCGATATTATCCCTATCAATT-TTTCAATT-TC
1 TTCTGTAAGACCTTCGGGCATAATTTCGATTCGCGATATTATCCCGATCAATTCATT--ATTCTC
*
4101726 GACTTACGGTGTTATCCCAATCGA
64 AACTTACGGTGTTATCCCAATCGA
* * * * * *
4101750 TTCTGTAAGACCTTCGGGCATAATTTTGATTTGTGATGTTATCTCGATCGATTCATTATTCTCAA
1 TTCTGTAAGACCTTCGGGCATAATTTCGATTCGCGATATTATCCCGATCAATTCATTATTCTCAA
* ** *
4101815 CTTATGGTGTTATCTTAGTCGA
66 CTTACGGTGTTATCCCAATCGA
4101837 TTCTGTAAGACCTT
1 TTCTGTAAGACCTT
4101851 TGGACATGAT
Statistics
Matches: 84, Mismatches: 15, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
86 3 0.04
87 79 0.94
88 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.40
Consensus pattern (87 bp):
TTCTGTAAGACCTTCGGGCATAATTTCGATTCGCGATATTATCCCGATCAATTCATTATTCTCAA
CTTACGGTGTTATCCCAATCGA
Found at i:4101899 original size:109 final size:109
Alignment explanation
Indices: 4101768--4101971 Score: 275
Period size: 109 Copynumber: 1.9 Consensus size: 109
4101758 GACCTTCGGG
* * * * **
4101768 CATAATTTTGATTTGTGATGTTAT-CTCGATCGATTCATTATTCTCAACTTATGGTGTTATCTTA
1 CATAATTTTGATTCGCGATGTTATCCT-GATCGATTCATTATTCTCAACTTACGATGTTATCCCA
**
4101832 GTCGATTCTGTAAGACCTTTGGACATGATTTCTAAGACCTCCAAA
65 GTCGATTCTGTAAGACCTTCAGACATGATTTCTAAGACCTCCAAA
* * *
4101877 CATAATTTTGATTCGCGGTGTTATCCTGATCGATTCATTATTCTCGACTTACGATGTTGTCCCAG
1 CATAATTTTGATTCGCGATGTTATCCTGATCGATTCATTATTCTCAACTTACGATGTTATCCCAG
* *
4101942 TCGATTTTGTAAGATCTTCAGACATGATTT
66 TCGATTCTGTAAGACCTTCAGACATGATTT
4101972 TGATTCACGG
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
109 79 0.98
110 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (109 bp):
CATAATTTTGATTCGCGATGTTATCCTGATCGATTCATTATTCTCAACTTACGATGTTATCCCAG
TCGATTCTGTAAGACCTTCAGACATGATTTCTAAGACCTCCAAA
Found at i:4102036 original size:86 final size:87
Alignment explanation
Indices: 4101876--4102041 Score: 210
Period size: 86 Copynumber: 1.9 Consensus size: 87
4101866 AGACCTCCAA
* * *
4101876 ACATAATTTTGATTCGCGGTGTTATCCTGATCGATTCATTATTCTCGACTTACGATGTTGTCCCA
1 ACATAATTTTGATTCACGGTGTTATCCTCATCGATTCATTATTCTCGACTTACGATGTTGTCACA
* *
4101941 GTCGATTTTGTAAGATCTTCAG
66 GACAATTTTGTAAGATCTTCAG
* ** * * *
4101963 ACATGATTTTGATTCACGGTGTTAT-CTCATCGATTTTTTAATT-TTGACTTGCGGTGTTGTCAC
1 ACATAATTTTGATTCACGGTGTTATCCTCATCGATTCATT-ATTCTCGACTTACGATGTTGTCAC
4102026 AGACAATTTTGTAAGA
65 AGACAATTTTGTAAGA
4102042 CCCCCGGGTA
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
86 41 0.61
87 26 0.39
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.42
Consensus pattern (87 bp):
ACATAATTTTGATTCACGGTGTTATCCTCATCGATTCATTATTCTCGACTTACGATGTTGTCACA
GACAATTTTGTAAGATCTTCAG
Found at i:4102150 original size:109 final size:109
Alignment explanation
Indices: 4101984--4102229 Score: 293
Period size: 109 Copynumber: 2.3 Consensus size: 109
4101974 ATTCACGGTG
** **
4101984 TTATCTC-ATCGATTTTTTAATTTTGACTTGCGGTGTTGTCACAGACAATTTTGTAAGACCCCCG
1 TTATCTCGATCGATTCATTAATTTTGACTTGCGGTGTTGTCACAGACAATTTAATAAGACCCCCG
*** *
4102048 GGTATGATTTCTAATA-CCTCTGAGCATAATTTTGATTCGTGATA
66 ACCATGATTTCTAAGATCCTC-GAGCATAATTTTGATTCGTGATA
* * * *
4102092 TTATCTCGATCGATTCATT-ATTTTCGACTTGCGTTGTTGTCCCAGTCGAA-TTAATAAGACCTC
1 TTATCTCGATCGATTCATTAATTTT-GACTTGCGGTGTTGTCACAGAC-AATTTAATAAGACCCC
* *
4102155 TGACCATGATTTCTAAGATCCTCGGGCATAATTTTGATTCGTGATA
64 CGACCATGATTTCTAAGATCCTCGAGCATAATTTTGATTCGTGATA
**
4102201 TTATCTCGATCGATTTTTTAATTTTGACT
1 TTATCTCGATCGATTCATTAATTTTGACT
4102230 ACGATGTTGT
Statistics
Matches: 117, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
108 12 0.10
109 94 0.80
110 11 0.09
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (109 bp):
TTATCTCGATCGATTCATTAATTTTGACTTGCGGTGTTGTCACAGACAATTTAATAAGACCCCCG
ACCATGATTTCTAAGATCCTCGAGCATAATTTTGATTCGTGATA
Found at i:4102340 original size:37 final size:37
Alignment explanation
Indices: 4102299--4102372 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
4102289 GTCCCAATTG
* *
4102299 ATTCTTTATTTCTCGACTTGCAGTGTTGTCCCGATCA
1 ATTCTTTACTTCTCGACTCGCAGTGTTGTCCCGATCA
* *
4102336 ATTCTTTACTTCTCGACTCGCGGTGTTGTCCTGATCA
1 ATTCTTTACTTCTCGACTCGCAGTGTTGTCCCGATCA
4102373 TTTTTGTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.15, C:0.26, G:0.18, T:0.42
Consensus pattern (37 bp):
ATTCTTTACTTCTCGACTCGCAGTGTTGTCCCGATCA
Found at i:4102608 original size:15 final size:14
Alignment explanation
Indices: 4102588--4102618 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
4102578 GTTTAATTAA
4102588 AATTAAAAATTAATT
1 AATTAAAAATT-ATT
4102603 AATTAAAAATTATT
1 AATTAAAAATTATT
4102617 AA
1 AA
4102619 AAAATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTAAAAATTATT
Found at i:4104127 original size:15 final size:14
Alignment explanation
Indices: 4104105--4104159 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 14
4104095 AAAAATTTTG
*
4104105 AACCCTAAAACTAA
1 AACCCTAAAACCAA
4104119 AACCTCTAAAATCCAA
1 AACC-CTAAAA-CCAA
*
4104135 AATCCCTCAAACCAA
1 AA-CCCTAAAACCAA
4104150 AACCCTAAAA
1 AACCCTAAAA
4104160 TCCGAATCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
14 11 0.31
15 12 0.34
16 10 0.29
17 2 0.06
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.15
Consensus pattern (14 bp):
AACCCTAAAACCAA
Found at i:4106229 original size:263 final size:262
Alignment explanation
Indices: 4105756--4106240 Score: 751
Period size: 263 Copynumber: 1.8 Consensus size: 262
4105746 ATTACTTAAA
* *
4105756 TAGATATTATATTTAATCAAATATAAATGTATCAAATAATTAATTAGAGAATCAACAATTTTTTA
1 TAGATACTATATTTAATCAAATATAAATGTATCAAATAATTAATTAGAGAATCAACAATTTTATA
* * * *
4105821 ACTGTAATTGTAGTATTTACTAATTTATTAATTATATATTGATTGATTTAATTTATCAAATTAAT
66 ACTGTAATTGTAGTATTTACTAATTTATTAATTAGATATTAATTGATTAAATTAATCAAATTAAT
* *
4105886 AAATTTTTAATACTTTTAATATGAATTGAATTAAGAGTGATTTAAAATCAATAATAAAAATATAA
131 AAAATTTTAATACTTTTAATATGAATTGAATTAAGAGTGATTTAAAATCAATAATAAAAACATAA
4105951 ATATAATCAATTTAGTTTTTTGAATTAAATTTGCTTTATATATTTACACATGAAATACATTAATT
196 ATATAATCAATTTAGTTTTTTGAATTAAATTTGCTTTATATATTTACACATGAAATACATTAATT
4106016 AC
261 AC
* *
4106018 TAGATACTATATTTAATCAAATATAAATGTATCAAATAATTGATTAGAGAATCAACTATTTTATA
1 TAGATACTATATTTAATCAAATATAAATGTATCAAATAATTAATTAGAGAATCAACAATTTTATA
* * *
4106083 ATTGTAATTGTAGTATTTATTTAATTATATATTAATT-GAT-TTAATTTATTAAATTAAT-AAAT
66 ACTGTAATTGTAGTATTTA-CTAA-T-T-TATTAATTAGATATTAATTGATTAAATTAATCAAAT
* * ** *
4106145 TATTAAAATTTTAATACTTTTAATATGAATTGAATTGAGAGTGATTTAAGGTTAATAATAAAAAC
127 TAATAAAATTTTAATACTTTTAATATGAATTGAATTAAGAGTGATTTAAAATCAATAATAAAAAC
4106210 ATAAATATAATCAATTTAGTTTTTTGAATTA
192 ATAAATATAATCAATTTAGTTTTTTGAATTA
4106241 TTTTTAAATT
Statistics
Matches: 201, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
262 79 0.39
263 96 0.48
264 15 0.07
265 3 0.01
266 8 0.04
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (262 bp):
TAGATACTATATTTAATCAAATATAAATGTATCAAATAATTAATTAGAGAATCAACAATTTTATA
ACTGTAATTGTAGTATTTACTAATTTATTAATTAGATATTAATTGATTAAATTAATCAAATTAAT
AAAATTTTAATACTTTTAATATGAATTGAATTAAGAGTGATTTAAAATCAATAATAAAAACATAA
ATATAATCAATTTAGTTTTTTGAATTAAATTTGCTTTATATATTTACACATGAAATACATTAATT
AC
Found at i:4106287 original size:19 final size:20
Alignment explanation
Indices: 4106238--4106287 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 20
4106228 GTTTTTTGAA
*
4106238 TTATTT-TTAAATTAAAAAT
1 TTATTTATTAAAATAAAAAT
* * *
4106257 ATATTAAATAAAAT-AAAAT
1 TTATTTATTAAAATAAAAAT
4106276 TTATTTATTAAA
1 TTATTTATTAAA
4106288 TATCACGTAA
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTATTTATTAAAATAAAAAT
Found at i:4109436 original size:12 final size:13
Alignment explanation
Indices: 4109408--4109436 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4109398 CCGTGGAAGC
4109408 TTAAATCATGTAT
1 TTAAATCATGTAT
4109421 TTAAATCATG-AT
1 TTAAATCATGTAT
4109433 TTAA
1 TTAA
4109437 CGAAAATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (13 bp):
TTAAATCATGTAT
Found at i:4110463 original size:19 final size:22
Alignment explanation
Indices: 4110439--4110485 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 22
4110429 CTTTGAACCC
4110439 AATTATAAATTTT-T-TTTA-A
1 AATTATAAATTTTATATTTATA
*
4110458 AATTATATATTTTATATTTATA
1 AATTATAAATTTTATATTTATA
4110480 AATTAT
1 AATTAT
4110486 TTATTATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 12 0.50
20 1 0.04
21 4 0.17
22 7 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AATTATAAATTTTATATTTATA
Found at i:4110565 original size:16 final size:16
Alignment explanation
Indices: 4110546--4110595 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 16
4110536 GTGATTTTTT
4110546 TTAATTTTTTTATAAG
1 TTAATTTTTTTATAAG
*
4110562 TTAATTTTTATTTATTAAT
1 TTAA-TTTT-TTTA-TAAG
*
4110581 TTAATTTTTTAATAA
1 TTAATTTTTTTATAA
4110596 TATGTATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 7 0.24
17 7 0.24
18 8 0.28
19 7 0.24
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
TTAATTTTTTTATAAG
Found at i:4110586 original size:19 final size:17
Alignment explanation
Indices: 4110545--4110590 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
4110535 TGTGATTTTT
4110545 TTTAA-TTTTTTTATAA
1 TTTAATTTTTTTTATAA
*
4110561 GTTAATTTTTATTTATTAA
1 TTTAATTTTT-TTTA-TAA
4110580 TTTAATTTTTT
1 TTTAATTTTTT
4110591 AATAATATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 4 0.16
17 4 0.16
18 5 0.20
19 12 0.48
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (17 bp):
TTTAATTTTTTTTATAA
Found at i:4110596 original size:16 final size:16
Alignment explanation
Indices: 4110545--4110596 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
4110535 TGTGATTTTT
*
4110545 TTTAATTTTTTTATAA
1 TTTAATTTTTTAATAA
* *
4110561 GTTAATTTTTATTTATTAA
1 TTTAA--TTT-TTTAATAA
4110580 TTTAATTTTTTAATAA
1 TTTAATTTTTTAATAA
4110596 T
1 T
4110597 ATGTATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
16 12 0.43
17 3 0.11
18 3 0.11
19 10 0.36
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
TTTAATTTTTTAATAA
Found at i:4111475 original size:42 final size:42
Alignment explanation
Indices: 4111409--4111492 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
4111399 ACCTCATTCG
* *
4111409 TCATCATAGTTCCTTCGTTAGCTCACCCACCACGTCATCATA
1 TCATCATAGTTCCTGCCTTAGCTCACCCACCACGTCATCATA
* * *
4111451 TCATCATAGTTCCTGCCTTTGCTCACCTACTACGTCATCATA
1 TCATCATAGTTCCTGCCTTAGCTCACCCACCACGTCATCATA
4111493 ATTCATATGC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.23, C:0.35, G:0.10, T:0.33
Consensus pattern (42 bp):
TCATCATAGTTCCTGCCTTAGCTCACCCACCACGTCATCATA
Found at i:4117113 original size:12 final size:12
Alignment explanation
Indices: 4117096--4117120 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4117086 TTTGAGTAAT
4117096 TAATGTATTTCA
1 TAATGTATTTCA
4117108 TAATGTATTTCA
1 TAATGTATTTCA
4117120 T
1 T
4117121 GTGTAAATAT
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):
TAATGTATTTCA
Found at i:4118469 original size:18 final size:17
Alignment explanation
Indices: 4118446--4118480 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
4118436 ATGTATAAAC
4118446 TTATTATAATAATTATAT
1 TTATTATAA-AATTATAT
4118464 TTATTATAAAATTATAT
1 TTATTATAAAATTATAT
4118481 AGTATAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATTATAAAATTATAT
Done.