Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 189 of 206
Found at i:57422288 original size:9 final size:9
Alignment explanation
Indices: 57422271--57422307 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
57422261 TATAGTTTGA
*
57422271 TATTAGAAT
1 TATTCGAAT
57422280 TATTCGAAT
1 TATTCGAAT
*
57422289 TATTCGAGT
1 TATTCGAAT
57422298 TATTCGAAT
1 TATTCGAAT
57422307 T
1 T
57422308 TGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:57422510 original size:18 final size:18
Alignment explanation
Indices: 57422483--57422517 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
57422473 GGAAAAGGTA
* *
57422483 ACATATAAGGGTTAGGAT
1 ACATAAAAGGGCTAGGAT
57422501 ACATAAAAGGGCTAGGA
1 ACATAAAAGGGCTAGGA
57422518 AACGTACCTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.09, G:0.29, T:0.20
Consensus pattern (18 bp):
ACATAAAAGGGCTAGGAT
Found at i:57424387 original size:51 final size:51
Alignment explanation
Indices: 57424332--57424431 Score: 141
Period size: 51 Copynumber: 2.0 Consensus size: 51
57424322 AATTATTTAA
57424332 AAATA-GGAATTTAAGAGAAATTTA-AGAGGAACTTGAGAGCAAATTGAGATT
1 AAATATGG-ATTTAAGAGAAATTTAGA-AGGAACTTGAGAGCAAATTGAGATT
* * *
57424383 AAATATGGATTTGAGAGAAATTTGGAAGGAATTTGAGAGCAAATTGAGA
1 AAATATGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGAGA
57424432 GGAAATTGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
51 41 0.93
52 3 0.07
ACGTcount: A:0.45, C:0.03, G:0.26, T:0.26
Consensus pattern (51 bp):
AAATATGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGAGATT
Found at i:57424405 original size:11 final size:11
Alignment explanation
Indices: 57424391--57424452 Score: 58
Period size: 11 Copynumber: 5.5 Consensus size: 11
57424381 TTAAATATGG
57424391 ATTTGAGAGAA
1 ATTTGAGAGAA
*
57424402 ATTTG-GAAGGA
1 ATTTGAG-AGAA
57424413 ATTTGAGAGCAA
1 ATTTGAGAG-AA
57424425 A-TTGAGAGGAA
1 ATTTGAGA-GAA
57424436 A-TTGAGAGGAA
1 ATTTGAGA-GAA
57424447 ATTTGA
1 ATTTGA
57424453 AAGAGGATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
10 1 0.02
11 35 0.80
12 8 0.18
ACGTcount: A:0.42, C:0.02, G:0.31, T:0.26
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:57424416 original size:22 final size:23
Alignment explanation
Indices: 57424391--57424451 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
57424381 TTAAATATGG
57424391 ATTTGAGAGAAATTTGGA-AGGA
1 ATTTGAGAGAAATTTGGAGAGGA
57424413 ATTTGAGAGCAAA-TT-GAGAGGA
1 ATTTGAGAG-AAATTTGGAGAGGA
*
57424435 AATTGAGAGGAAATTTG
1 ATTTGAGA-GAAATTTG
57424452 AAAGAGGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
21 2 0.06
22 25 0.76
23 6 0.18
ACGTcount: A:0.41, C:0.02, G:0.31, T:0.26
Consensus pattern (23 bp):
ATTTGAGAGAAATTTGGAGAGGA
Found at i:57424459 original size:14 final size:11
Alignment explanation
Indices: 57424409--57424449 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
57424399 GAAATTTGGA
*
57424409 AGGAATTTGAG
1 AGGAAATTGAG
*
57424420 AGCAAATTGAG
1 AGGAAATTGAG
57424431 AGGAAATTGAG
1 AGGAAATTGAG
57424442 AGGAAATT
1 AGGAAATT
57424450 TGAAAGAGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.44, C:0.02, G:0.32, T:0.22
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:57424998 original size:94 final size:94
Alignment explanation
Indices: 57424891--57425085 Score: 259
Period size: 94 Copynumber: 2.1 Consensus size: 94
57424881 TTTTTAATTT
* * * * *
57424891 ATATATTTAATTAATAATTCTTTTATTTATATAAATAAAATAATAAATATGGAATTGTACAAT-A
1 ATATTTTTAATTAATAATTATTTTATTGATATAAACAAAATAATAAATATGGAATTATACAATGA
* * *
57424955 -AAAATATATCTATCTTTCATTATGTTAAAA
66 GAAAATATAT-TATATAT-ATTATGCTAAAA
* *
57424985 ATATTTTTAATTAATAATTATTTTATTGATATAAACAAAATAATAAATATGGAGTTATATAATGA
1 ATATTTTTAATTAATAATTATTTTATTGATATAAACAAAATAATAAATATGGAATTATACAATGA
*
57425050 GAATATATATTATATATATTATGCTAAAA
66 GAAAATATATTATATATATTATGCTAAAA
57425079 ATATTTT
1 ATATTTT
57425086 ATTTTTTTGA
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
94 74 0.84
95 6 0.07
96 8 0.09
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.44
Consensus pattern (94 bp):
ATATTTTTAATTAATAATTATTTTATTGATATAAACAAAATAATAAATATGGAATTATACAATGA
GAAAATATATTATATATATTATGCTAAAA
Found at i:57437219 original size:20 final size:20
Alignment explanation
Indices: 57437182--57437234 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 20
57437172 CCGGCCCATT
*
57437182 TTTTAATAAATACCAAAAATTTA
1 TTTTAA-AAATA-CAAAAA-ATA
57437205 TTTTAAAAATA-AAAAAATA
1 TTTTAAAAATACAAAAAATA
57437224 TTTTAAAAATA
1 TTTTAAAAATA
57437235 TTTTAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 13 0.45
20 5 0.17
22 5 0.17
23 6 0.21
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTTAAAAATACAAAAAATA
Found at i:57437233 original size:11 final size:11
Alignment explanation
Indices: 57437217--57437282 Score: 61
Period size: 11 Copynumber: 6.4 Consensus size: 11
57437207 TTAAAAATAA
57437217 AAAAATATTTT
1 AAAAATATTTT
57437228 AAAAATATTTT
1 AAAAATATTTT
*
57437239 --AAA-A-TTA
1 AAAAATATTTT
* *
57437246 AAAAATA-ATA
1 AAAAATATTTT
57437256 AAAAAGTATTTT
1 AAAAA-TATTTT
57437268 AAAAATATTTT
1 AAAAATATTTT
57437279 AAAA
1 AAAA
57437283 TTAAAAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
7 2 0.04
8 1 0.02
9 6 0.13
10 8 0.17
11 23 0.50
12 6 0.13
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:57437237 original size:30 final size:30
Alignment explanation
Indices: 57437203--57437274 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
57437193 ACCAAAAATT
* *
57437203 TATTTTAAAAATAAAAAAATATTTTAAAAA-
1 TATTTTAAAAATAAAAAAATA-ATAAAAAAG
*
57437233 TATTTT-AAAATTAAAAAATAATAAAAAAG
1 TATTTTAAAAATAAAAAAATAATAAAAAAG
57437262 TATTTTAAAAATA
1 TATTTTAAAAATA
57437275 TTTTAAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.17
29 19 0.53
30 11 0.31
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (30 bp):
TATTTTAAAAATAAAAAAATAATAAAAAAG
Found at i:57437266 original size:40 final size:40
Alignment explanation
Indices: 57437212--57437303 Score: 150
Period size: 40 Copynumber: 2.3 Consensus size: 40
57437202 TTATTTTAAA
57437212 AATAAAAAAATATTTTAAAAATATTTTAAAATTAAAAAAT
1 AATAAAAAAATATTTTAAAAATATTTTAAAATTAAAAAAT
*
57437252 AATAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAA-
1 AATAAAAAAATATTTTAAAAATATTTTAAAATTAAAAAAT
*
57437291 AATTTAAAAAATA
1 AA-TAAAAAAATA
57437304 AATATATTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
39 2 0.04
40 46 0.96
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (40 bp):
AATAAAAAAATATTTTAAAAATATTTTAAAATTAAAAAAT
Found at i:57439077 original size:23 final size:23
Alignment explanation
Indices: 57439051--57439241 Score: 346
Period size: 23 Copynumber: 8.3 Consensus size: 23
57439041 ATAAGTGCCA
57439051 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
57439074 CACTGATACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
57439097 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
57439120 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
57439143 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
57439166 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
57439189 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
57439212 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
57439235 CACTGAT
1 CACTGAT
57439242 CAATAACACT
Statistics
Matches: 160, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 160 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:57441218 original size:33 final size:33
Alignment explanation
Indices: 57441180--57441242 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
57441170 TTGTTTTCTT
* *
57441180 GAAATTG-TTGATATAACTTTGATTGAATTGTTA
1 GAAATTGTTTGAAATAA-TGTGATTGAATTGTTA
57441213 GAAATTGTTTGAAATAATGTGATTGAATTG
1 GAAATTGTTTGAAATAATGTGATTGAATTG
57441243 CATGTGGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 19 0.70
34 8 0.30
ACGTcount: A:0.35, C:0.02, G:0.21, T:0.43
Consensus pattern (33 bp):
GAAATTGTTTGAAATAATGTGATTGAATTGTTA
Found at i:57446130 original size:11 final size:11
Alignment explanation
Indices: 57446114--57446140 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
57446104 ATTTCGGGCT
57446114 GGGCCGGGCCC
1 GGGCCGGGCCC
57446125 GGGCCGGGCCC
1 GGGCCGGGCCC
57446136 GGGCC
1 GGGCC
57446141 TAAGAGTCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.44, G:0.56, T:0.00
Consensus pattern (11 bp):
GGGCCGGGCCC
Found at i:57456812 original size:29 final size:25
Alignment explanation
Indices: 57456743--57456812 Score: 61
Period size: 29 Copynumber: 2.7 Consensus size: 25
57456733 CTTTCAATTT
57456743 CATCTGAAAAATTC-TTTGATTACC
1 CATCTGAAAAATTCTTTTGATTACC
** **
57456767 CATCTGAGGAACCCTTTTGATTACGCAAC
1 CATCTGAAAAATTCTTTTGATTA--C--C
57456796 CATCTGAAAAATTCTTT
1 CATCTGAAAAATTCTTT
57456813 ACCATCTCAT
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
24 10 0.30
25 8 0.24
27 1 0.03
29 14 0.42
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (25 bp):
CATCTGAAAAATTCTTTTGATTACC
Found at i:57457356 original size:9 final size:9
Alignment explanation
Indices: 57457344--57457479 Score: 75
Period size: 9 Copynumber: 14.7 Consensus size: 9
57457334 GTCTGTTATG
57457344 TATGTATAT
1 TATGTATAT
*
57457353 TATGTATGT
1 TATGTATAT
57457362 TATGTATAT
1 TATGTATAT
*
57457371 TACTGTTTAT
1 TA-TGTATAT
*
57457381 GCATGTATAT
1 -TATGTATAT
* *
57457391 TACGTATGT
1 TATGTATAT
57457400 TATGTA-AT
1 TATGTATAT
57457408 ATAT-TACCGT-T
1 -TATGTA---TAT
*
57457419 TATGTATTT
1 TATGTATAT
*
57457428 TATGTATGT
1 TATGTATAT
57457437 TATGTAGTA-
1 TATGTA-TAT
57457446 TAT-TACTATT
1 TATGTA-TA-T
*
57457456 TATGTATTT
1 TATGTATAT
*
57457465 TATGTATGT
1 TATGTATAT
57457474 TATGTA
1 TATGTA
57457480 GTGTTTATGT
Statistics
Matches: 99, Mismatches: 15, Indels: 26
0.71 0.11 0.19
Matches are distributed among these distances:
8 8 0.08
9 65 0.66
10 20 0.20
11 6 0.06
ACGTcount: A:0.27, C:0.04, G:0.15, T:0.54
Consensus pattern (9 bp):
TATGTATAT
Found at i:57457435 original size:37 final size:36
Alignment explanation
Indices: 57457344--57457479 Score: 159
Period size: 37 Copynumber: 3.7 Consensus size: 36
57457334 GTCTGTTATG
57457344 TATGTATATTATGTATGTTATG--TATATTACTGTTT
1 TATGTATATTATGTATGTTATGTATATATTACTG-TT
* *
57457379 ATGCATGTATATTACGTATGTTATGTAATATATTACCGTT
1 -T--ATGTATATTATGTATGTTATGT-ATATATTACTGTT
* *
57457419 TATGTATTTTATGTATGTTATGTAGTATATTACTATT
1 TATGTATATTATGTATGTTATGTA-TATATTACTGTT
*
57457456 TATGTATTTTATGTATGTTATGTA
1 TATGTATATTATGTATGTTATGTA
57457480 GTGTTTATGT
Statistics
Matches: 88, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
36 2 0.02
37 54 0.61
38 20 0.23
39 1 0.01
40 2 0.02
41 9 0.10
ACGTcount: A:0.27, C:0.04, G:0.15, T:0.54
Consensus pattern (36 bp):
TATGTATATTATGTATGTTATGTATATATTACTGTT
Found at i:57457494 original size:18 final size:17
Alignment explanation
Indices: 57457418--57457494 Score: 59
Period size: 18 Copynumber: 4.2 Consensus size: 17
57457408 ATATTACCGT
57457418 TTATGTATTTTATGTATG
1 TTATGTATTTTATGTA-G
* *
57457436 TTATGTAGTATATTA-CTAT
1 TTATGTA-T-T-TTATGTAG
57457455 TTATGTATTTTATGTATG
1 TTATGTATTTTATGTA-G
57457473 TTATGTAGTGTTTATGTA-
1 TTATGTA-T-TTTATGTAG
57457491 TTAT
1 TTAT
57457495 AACTGATTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
16 3 0.06
17 3 0.06
18 19 0.40
19 9 0.19
20 11 0.23
21 3 0.06
ACGTcount: A:0.25, C:0.01, G:0.16, T:0.58
Consensus pattern (17 bp):
TTATGTATTTTATGTAG
Found at i:57457511 original size:46 final size:46
Alignment explanation
Indices: 57457417--57457511 Score: 106
Period size: 46 Copynumber: 2.1 Consensus size: 46
57457407 TATATTACCG
* * *
57457417 TTTATGTATTTTATGTATGTTATGTAGTATATTACTATTTATGTAT
1 TTTATGTATGTTATGTATGTTATGTAGTATATAACTATTTATGAAT
*
57457463 TTTATGTATGTTATGTAGTGTTTATGTA-T-TATAACTGATTTCT-AAT
1 TTTATGTATGTTATGTA-TG-TTATGTAGTATATAACT-ATTTATGAAT
57457509 TTT
1 TTT
57457512 TTTGTTGGCA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
46 27 0.64
47 8 0.19
48 7 0.17
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.58
Consensus pattern (46 bp):
TTTATGTATGTTATGTATGTTATGTAGTATATAACTATTTATGAAT
Found at i:57457684 original size:19 final size:18
Alignment explanation
Indices: 57457629--57457742 Score: 61
Period size: 19 Copynumber: 5.9 Consensus size: 18
57457619 GTATGTTATG
* *
57457629 TATATTACTGCTTATGCATA
1 TATATTA-TGTTTATGTA-A
57457649 TATATTATGCATGTTATGTAA
1 TATATTATG--T-TTATGTAA
*
57457670 TATATTATTGTTTATGTAT
1 TATATTA-TGTTTATGTAA
* * *
57457689 TTTATGTATG-TTATGCAG
1 TATAT-TATGTTTATGTAA
*
57457707 TATATTACTGTTTATGTAT
1 TATATTA-TGTTTATGTAA
*
57457726 TTTATGTATG-TTATGTA
1 TATAT-TATGTTTATGTA
57457743 GTGTTTATTT
Statistics
Matches: 76, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
17 2 0.03
18 19 0.25
19 27 0.36
20 12 0.16
21 8 0.11
22 8 0.11
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.54
Consensus pattern (18 bp):
TATATTATGTTTATGTAA
Found at i:57457702 original size:37 final size:36
Alignment explanation
Indices: 57457615--57457942 Score: 161
Period size: 36 Copynumber: 8.9 Consensus size: 36
57457605 AGTATTTCTA
*
57457615 TTATGTATGTTATG--TATATTACTGCTTATGCATATAT
1 TTATGTATGTTATGTATATATTACTGTTTATG--TAT-T
* *
57457652 ATTATGCATGTTATGTAATATATTATTGTTTATGTATT
1 -TTATGTATGTTATGT-ATATATTACTGTTTATGTATT
*
57457690 TTATGTATGTTATGCAGTATATTACTGTTTATGTATT
1 TTATGTATGTTATGTA-TATATTACTGTTTATGTATT
* *
57457727 TTATGTATGTTATGTAGTGTTTATTTA-T-TTTATGTATG
1 TTATGTATGTTATGTA---TATA-TTACTGTTTATGTATT
*
57457765 TTATGTTACTGTTTATGTATGTATGTTA-TGTTTAT-TACTGT
1 TTATG-TA-TG-TTATGTA--TATATTACTGTTTATGTA-T-T
* *
57457806 TTTTGTATG-TATGTATGTATGTA-TGTATGTATGTA-T
1 TTATGTATGTTATGTATATAT-TACTGT-T-TATGTATT
* *
57457842 GTATGTATG-TATGTATGTATGTA-TGTATGTATGTA-T
1 TTATGTATGTTATGTATATAT-TACTGT-T-TATGTATT
* *
57457878 GTATGTATG-TATGTATGTATGTA-TGTTTAT-TACGATT
1 TTATGTATGTTATGTATATAT-TACTGTTTATGT---ATT
*
57457915 TTATG-ATGTTATGT-TATGTTA-TGTTTAT
1 TTATGTATGTTATGTATATATTACTGTTTAT
57457943 TACTATTTAT
Statistics
Matches: 248, Mismatches: 20, Indels: 47
0.79 0.06 0.15
Matches are distributed among these distances:
33 1 0.00
34 3 0.01
35 13 0.05
36 74 0.30
37 64 0.26
38 31 0.12
39 20 0.08
40 17 0.07
41 25 0.10
ACGTcount: A:0.24, C:0.03, G:0.18, T:0.55
Consensus pattern (36 bp):
TTATGTATGTTATGTATATATTACTGTTTATGTATT
Found at i:57457718 original size:18 final size:18
Alignment explanation
Indices: 57457629--57457718 Score: 56
Period size: 18 Copynumber: 4.7 Consensus size: 18
57457619 GTATGTTATG
57457629 TATATTACTGCTTATGCATA
1 TATATTACTG-TTATGCA-A
*
57457649 TATATTATGCATGTTATGTAA
1 TATATTA--C-TGTTATGCAA
* * *
57457670 TATATTATTGTTTATGTAT
1 TATATTACTG-TTATGCAA
* *
57457689 TTTATGTA-TGTTATGCAG
1 TATAT-TACTGTTATGCAA
57457707 TATATTACTGTT
1 TATATTACTGTT
57457719 TATGTATTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
17 2 0.04
18 16 0.28
19 13 0.23
20 9 0.16
21 8 0.14
22 7 0.12
23 2 0.04
ACGTcount: A:0.28, C:0.07, G:0.13, T:0.52
Consensus pattern (18 bp):
TATATTACTGTTATGCAA
Found at i:57457751 original size:25 final size:26
Alignment explanation
Indices: 57457723--57457795 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 26
57457713 ACTGTTTATG
*
57457723 TATTTTATGTATGTTATGTAGTGTTTATT
1 TATTTTATGTATGTTATGTACTG--T-TT
57457752 TATTTTATGTATGTTATGTTACTG-TT
1 TATTTTATGTATGTTATG-TACTGTTT
*
57457778 TA-TGTATGTATGTTATGT
1 TATTTTATGTATGTTATGT
57457796 TTATTACTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
24 1 0.02
25 14 0.34
26 4 0.10
29 18 0.44
30 4 0.10
ACGTcount: A:0.21, C:0.01, G:0.18, T:0.60
Consensus pattern (26 bp):
TATTTTATGTATGTTATGTACTGTTT
Found at i:57457755 original size:29 final size:30
Alignment explanation
Indices: 57457689--57457939 Score: 143
Period size: 28 Copynumber: 8.9 Consensus size: 30
57457679 GTTTATGTAT
* * *
57457689 TTTATGTATGTTATGCA-G-TATATTACTG
1 TTTATGTATTTTATGTATGTTATGTTACTG
*
57457717 TTTATGTATTTTATGTATGTTATG-TAGTG
1 TTTATGTATTTTATGTATGTTATGTTACTG
*
57457746 TTTATTTATTTTATGTATGTTATGTTACTG
1 TTTATGTATTTTATGTATGTTATGTTACTG
* *
57457776 TTTATGTA-TGTATGTTATGTT-TATTACTG
1 TTTATGTATTTTATG-TATGTTATGTTACTG
* *
57457805 TTTTTGTA-TGTATGTATG-TATG-TA-TG
1 TTTATGTATTTTATGTATGTTATGTTACTG
*
57457831 --TATGTA-TGTATGTATG-TATG-TA-TG
1 TTTATGTATTTTATGTATGTTATGTTACTG
*
57457855 TATGTATGTA-TGTATGTATG-TATG-TA-TG
1 T-T-TATGTATTTTATGTATGTTATGTTACTG
* *
57457883 TATGTATGTA-TGTATGTATGTT-TATTAC-G
1 T-T-TATGTATTTTATGTATGTTATGTTACTG
*
57457912 ATTTTATG-ATGTTATGTTATGTTATGTT
1 --TTTATGTATTTTATG-TATGTTATGTT
57457940 TATTACTATT
Statistics
Matches: 190, Mismatches: 16, Indels: 31
0.80 0.07 0.13
Matches are distributed among these distances:
24 23 0.12
26 2 0.01
27 3 0.02
28 66 0.35
29 65 0.34
30 27 0.14
31 4 0.02
ACGTcount: A:0.22, C:0.02, G:0.20, T:0.56
Consensus pattern (30 bp):
TTTATGTATTTTATGTATGTTATGTTACTG
Found at i:57457764 original size:4 final size:4
Alignment explanation
Indices: 57457757--57457903 Score: 191
Period size: 4 Copynumber: 37.2 Consensus size: 4
57457747 TTATTTATTT
57457757 TATG TATG TTATG TTACTG T-T- TATG TATG TATG TTATG T-T- TAT-
1 TATG TATG -TATG -TA-TG TATG TATG TATG TATG -TATG TATG TATG
*
57457800 TACTG T-T- TTTG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TA-TG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
57457847 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
57457895 TATG TATG T
1 TATG TATG T
57457904 TTATTACGAT
Statistics
Matches: 132, Mismatches: 1, Indels: 20
0.86 0.01 0.13
Matches are distributed among these distances:
2 3 0.02
3 8 0.06
4 106 0.80
5 13 0.10
6 2 0.02
ACGTcount: A:0.22, C:0.01, G:0.22, T:0.54
Consensus pattern (4 bp):
TATG
Found at i:57457791 original size:20 final size:18
Alignment explanation
Indices: 57457678--57457907 Score: 167
Period size: 20 Copynumber: 12.4 Consensus size: 18
57457668 AATATATTAT
*
57457678 TGTTTATGTATTTTATGTA
1 TGTTTATGTA-TGTATGTA
* *
57457697 TG-TTATGCA-GTATATTA
1 TGTTTATGTATGTAT-GTA
*
57457714 CTGTTTATGTATTTTATGTA
1 -TGTTTATGTA-TGTATGTA
*
57457734 TG-TTATGTAGTGTTTATTTA
1 TGTTTATGTA-TG--TATGTA
57457754 T-TTTATGTATGTTATGTTA
1 TGTTTATGTATG-TATG-TA
57457773 CTGTTTATGTATGTATGTTA
1 -TGTTTATGTATGTATG-TA
57457793 TGTTTAT-TACTGT-T-T-
1 TGTTTATGTA-TGTATGTA
*
57457808 T-TGTATGTATGTATGTA
1 TGTTTATGTATGTATGTA
57457825 TG--TATGTATGTATGTA
1 TGTTTATGTATGTATGTA
57457841 TGTATGTATGTATGTATGTA
1 TGT-T-TATGTATGTATGTA
57457861 TGTATGTATGTATGTATGTA
1 TGT-T-TATGTATGTATGTA
57457881 TGTATGTATGTATGTATGTA
1 TGT-T-TATGTATGTATGTA
57457901 TGTTTAT
1 TGTTTAT
57457908 TACGATTTTA
Statistics
Matches: 179, Mismatches: 11, Indels: 43
0.77 0.05 0.18
Matches are distributed among these distances:
14 7 0.04
15 4 0.02
16 21 0.12
17 3 0.02
18 26 0.15
19 25 0.14
20 80 0.45
21 13 0.07
ACGTcount: A:0.22, C:0.02, G:0.20, T:0.56
Consensus pattern (18 bp):
TGTTTATGTATGTATGTA
Found at i:57457939 original size:35 final size:33
Alignment explanation
Indices: 57457815--57457963 Score: 112
Period size: 36 Copynumber: 4.4 Consensus size: 33
57457805 TTTTTGTATG
* *
57457815 TATGTATGTATGTATGTATG--TATGTATG-TATG
1 TATGTATGTATGTATGTATGTTTAT-TACGAT-TT
* *
57457847 TATGTATGTATGTATGTATGTATGTATGTATG-TATG
1 TATGTATGTATGTATGTATGT-T-TAT-TACGAT-TT
57457883 TATGTATGTATGTATGTATGTTTATTACGATTT
1 TATGTATGTATGTATGTATGTTTATTACGATTT
*
57457916 TATG-ATGTTATGTTATGTTATGTTTATTACTA-TT
1 TATGTATG-TATG-TATG-TATGTTTATTACGATTT
*
57457950 TATAATATGTATGT
1 TAT-GTATGTATGT
57457964 TTATCATGTA
Statistics
Matches: 103, Mismatches: 4, Indels: 18
0.82 0.03 0.14
Matches are distributed among these distances:
32 23 0.22
33 12 0.12
34 14 0.14
35 18 0.17
36 36 0.35
ACGTcount: A:0.26, C:0.01, G:0.20, T:0.53
Consensus pattern (33 bp):
TATGTATGTATGTATGTATGTTTATTACGATTT
Found at i:57462896 original size:20 final size:20
Alignment explanation
Indices: 57462871--57462912 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
57462861 AAAAAAGAGG
57462871 ATAAGAGGAGTAGGAGTTAA
1 ATAAGAGGAGTAGGAGTTAA
57462891 ATAAGAGGAGTAGGAGTTAA
1 ATAAGAGGAGTAGGAGTTAA
57462911 AT
1 AT
57462913 GTCTAGAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.33, T:0.21
Consensus pattern (20 bp):
ATAAGAGGAGTAGGAGTTAA
Found at i:57463106 original size:15 final size:15
Alignment explanation
Indices: 57463086--57463115 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
57463076 ACCTCTACTA
57463086 GCTCCAACAGCTCCT
1 GCTCCAACAGCTCCT
*
57463101 GCTCCATCAGCTCCT
1 GCTCCAACAGCTCCT
57463116 TCTGATTCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.47, G:0.13, T:0.23
Consensus pattern (15 bp):
GCTCCAACAGCTCCT
Found at i:57468591 original size:3 final size:3
Alignment explanation
Indices: 57468585--57468628 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
57468575 TTGTTTTCCC
57468585 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
57468629 GAAAAAAAGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:57469049 original size:25 final size:25
Alignment explanation
Indices: 57469021--57469078 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
57469011 AATATTTATA
57469021 TTATATATTTTAATAT-TTAATAATT
1 TTATATATTTTAATATATTAA-AATT
* *
57469046 TTATATATTTTTATTTATTAAAATT
1 TTATATATTTTAATATATTAAAATT
*
57469071 TTTTATAT
1 TTATATAT
57469079 AGTCACCTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (25 bp):
TTATATATTTTAATATATTAAAATT
Found at i:57469604 original size:19 final size:18
Alignment explanation
Indices: 57469571--57469613 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
57469561 CGACCGATTA
*
57469571 ATTTATATTTCTAATATT
1 ATTTATATTTATAATATT
57469589 ATTTATATATTATAATATT
1 ATTTATAT-TTATAATATT
57469608 ATTTAT
1 ATTTAT
57469614 TAAATTTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTATATTTATAATATT
Found at i:57471689 original size:16 final size:19
Alignment explanation
Indices: 57471641--57471690 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 19
57471631 TTTATTCATA
57471641 TAATAAATTATTAATATAGT
1 TAATAAATTATTAATATA-T
57471661 TAATATAATTTATT-AT-T-T
1 TAATA-AA-TTATTAATATAT
57471679 TAATAAATTATT
1 TAATAAATTATT
57471691 TGATATTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 5 0.18
17 2 0.07
18 6 0.21
20 6 0.21
21 4 0.14
22 5 0.18
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATAAATTATTAATATAT
Found at i:57480514 original size:25 final size:24
Alignment explanation
Indices: 57480480--57480528 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
57480470 TTATTTGAAT
*
57480480 TTATATTTATCTTAA-TTATAAATA
1 TTATATTTATC-AAATTTATAAATA
57480504 TTATATGTTATCAAATTTATAAATA
1 TTATAT-TTATCAAATTTATAAATA
57480529 ATTAGTTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (24 bp):
TTATATTTATCAAATTTATAAATA
Found at i:57487335 original size:25 final size:25
Alignment explanation
Indices: 57487307--57487358 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
57487297 CTCGCTTGAA
57487307 CTTCCCAA-TATATGGCTATCCGGAG
1 CTTCCCAATTA-ATGGCTATCCGGAG
* * *
57487332 CTTCCTAATTAATGGCTCTTCGGAG
1 CTTCCCAATTAATGGCTATCCGGAG
57487357 CT
1 CT
57487359 ACCTGTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 21 0.91
26 2 0.09
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (25 bp):
CTTCCCAATTAATGGCTATCCGGAG
Found at i:57487385 original size:74 final size:74
Alignment explanation
Indices: 57487230--57487385 Score: 161
Period size: 74 Copynumber: 2.1 Consensus size: 74
57487220 CAGCTCTTAT
* * * * * * *
57487230 GAGCGTCCCATTATATGGCTCTTCGTGAGCTTCCCGATTAAAGGCTCTTCGGAGTTTCCCGATAT
1 GAGCTTCCCAATATATGGCTATCCGTGAGCTTCCCAATTAAAGGCTCTTCGGAGCTACCCGATAT
**
57487295 GGCTCGCTT
66 GGCTCGCAC
* * * * *
57487304 GAACTTCCCAATATATGGCTATCCG-GAGCTTCCTAATTAATGGCTCTTCGGAGCTACCTGTTAT
1 GAGCTTCCCAATATATGGCTATCCGTGAGCTTCCCAATTAAAGGCTCTTCGGAGCTACCCGATA-
*
57487368 TTGCTCGCAC
65 TGGCTCGCAC
57487378 GAGCTTCC
1 GAGCTTCC
57487386 TGACTATGGC
Statistics
Matches: 65, Mismatches: 16, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
73 31 0.48
74 34 0.52
ACGTcount: A:0.19, C:0.28, G:0.22, T:0.32
Consensus pattern (74 bp):
GAGCTTCCCAATATATGGCTATCCGTGAGCTTCCCAATTAAAGGCTCTTCGGAGCTACCCGATAT
GGCTCGCAC
Found at i:57487456 original size:25 final size:25
Alignment explanation
Indices: 57487354--57487472 Score: 93
Period size: 25 Copynumber: 4.8 Consensus size: 25
57487344 TGGCTCTTCG
* * * *
57487354 GAGCTACCTGTTAT-TTGCTCGCAC
1 GAGCTTCCTGTTATATGGCTCACAT
57487378 GAGCTTCCTG--ACTATGGCTCACAT
1 GAGCTTCCTGTTA-TATGGCTCACAT
* * **
57487402 GAGCTTCCTGTTATTTAGC-CTGGAT
1 GAGCTTCCTGTTATATGGCTC-ACAT
* *
57487427 AAGCTTCTTGTTATATGGCTCACAT
1 GAGCTTCCTGTTATATGGCTCACAT
*
57487452 GAGCTTCCCGTTATATGGCTC
1 GAGCTTCCTGTTATATGGCTC
57487473 GAGAGTGTGT
Statistics
Matches: 72, Mismatches: 17, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
22 1 0.01
23 1 0.01
24 27 0.38
25 41 0.57
26 2 0.03
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.35
Consensus pattern (25 bp):
GAGCTTCCTGTTATATGGCTCACAT
Found at i:57489950 original size:22 final size:20
Alignment explanation
Indices: 57489908--57489953 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
57489898 AAGCTAAGAA
* *
57489908 AATGCCACAAGGGCTAACAG
1 AATGCCACAAGGCCAAACAG
57489928 AATGCCACAAAGGCCAAATCAG
1 AATGCCAC-AAGGCCAAA-CAG
57489950 AATG
1 AATG
57489954 TAATAAAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.36
21 7 0.32
22 7 0.32
ACGTcount: A:0.43, C:0.24, G:0.22, T:0.11
Consensus pattern (20 bp):
AATGCCACAAGGCCAAACAG
Found at i:57494028 original size:17 final size:18
Alignment explanation
Indices: 57494006--57494041 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
57493996 AAAAGAACAA
*
57494006 AATATATATATAAA-TAT
1 AATATATAAATAAACTAT
57494023 AATATATAAATAAACTAT
1 AATATATAAATAAACTAT
57494041 A
1 A
57494042 TAAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
AATATATAAATAAACTAT
Found at i:57494029 original size:13 final size:13
Alignment explanation
Indices: 57494005--57494054 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
57493995 GAAAAGAACA
57494005 AAATAT-ATATAT
1 AAATATAATATAT
57494017 AAATATAATATAT
1 AAATATAATATAT
57494030 AAATA-AACTATAT
1 AAATATAA-TATAT
*
57494043 AAA-AAAATATAT
1 AAATATAATATAT
57494055 GCGTGTGAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 14 0.40
13 21 0.60
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (13 bp):
AAATATAATATAT
Found at i:57494103 original size:12 final size:12
Alignment explanation
Indices: 57494088--57494112 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57494078 TAAAGGTATA
57494088 TATAAAATGAAG
1 TATAAAATGAAG
57494100 TATAAAATGAAG
1 TATAAAATGAAG
57494112 T
1 T
57494113 GTATATAAAC
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:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (12 bp):
TATAAAATGAAG
Found at i:57494908 original size:5 final size:5
Alignment explanation
Indices: 57494890--57494923 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
57494880 ATTTAAAACG
*
57494890 AAATA AAAGAA AAATA AAATA AAATA AAATA AAA
1 AAATA AAA-TA AAATA AAATA AAATA AAATA AAA
57494924 AAGAAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (5 bp):
AAATA
Found at i:57494930 original size:21 final size:21
Alignment explanation
Indices: 57494890--57494931 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
57494880 ATTTAAAACG
*
57494890 AAATAAAAGAAAAATAAAATA
1 AAATAAAAGAAAAAAAAAATA
* *
57494911 AAATAAAATAAAAAAGAAATA
1 AAATAAAAGAAAAAAAAAATA
57494932 TATGTAAATA
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:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (21 bp):
AAATAAAAGAAAAAAAAAATA
Found at i:57504292 original size:18 final size:18
Alignment explanation
Indices: 57504259--57504293 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
57504249 ACCAATCTAA
*
57504259 CAATAAACTTCAGTCAAT
1 CAATAAACTACAGTCAAT
*
57504277 CAATAAACTACTGTCAA
1 CAATAAACTACAGTCAA
57504294 AAGTCCTAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.23, G:0.06, T:0.26
Consensus pattern (18 bp):
CAATAAACTACAGTCAAT
Found at i:57513736 original size:16 final size:17
Alignment explanation
Indices: 57513715--57513769 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
57513705 ATCAAAAGAA
*
57513715 AATAAA-TATGTTTTAT
1 AATAAATTATATTTTAT
57513731 AATAAATTTTATATTTTAT
1 AATAAA--TTATATTTTAT
*
57513750 AATTAAATTATTTTTTAT
1 AA-TAAATTATATTTTAT
57513768 AA
1 AA
57513770 ATACTAATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 6 0.18
18 12 0.36
19 11 0.33
20 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
AATAAATTATATTTTAT
Found at i:57520314 original size:25 final size:28
Alignment explanation
Indices: 57520270--57520323 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 28
57520260 TGTATATATT
*
57520270 TTTTAAATATTTAAATAAATCAAA-ATC
1 TTTTAAATATTTAAAAAAATCAAAGATC
57520297 TTTTAAA-A-TTAAAAAAATCAAAGATC
1 TTTTAAATATTTAAAAAAATCAAAGATC
57520323 T
1 T
57520324 AAACTGATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 13 0.52
26 5 0.20
27 7 0.28
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (28 bp):
TTTTAAATATTTAAAAAAATCAAAGATC
Found at i:57522471 original size:3 final size:3
Alignment explanation
Indices: 57522465--57522510 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
57522455 ATTATTATTA
*
57522465 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTC TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
57522511 CATTATTGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.02, G:0.30, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:57526986 original size:45 final size:45
Alignment explanation
Indices: 57526881--57527347 Score: 227
Period size: 45 Copynumber: 10.4 Consensus size: 45
57526871 AAACCACAGG
* *
57526881 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGATAGCAAA
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGATACCAAA
* * * * * * *
57526926 TATCATTTCCCTGAAGTTGTAGTGGAACAGGTTGAAGTTACCAAT
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGATACCAAA
* * * * *
57526971 TCTTATCTCCTTGAAGTTCTAGTGGAGTAGATCGAAGCTA-CAAA
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGATACCAAA
* * * * ** * *
57527015 TCTTTTATCCTTGAAATTACATTGGAGCAGATCGAAG---CCACAA
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGATACCA-AA
* * * *
57527058 TCCTTATCTCCCTAAAGTTGTAGTAGAGCAGGA-TAAAAATACACAAA
1 T-CTTATCTCCCTGAAGTTGTAGTGGAGCA-GATTGAAGATAC-CAAA
* * * * *
57527105 CCTTATCTCCCTAAAGTTGCAGTGGAGCA-AGTTGAAGTTACCAAT
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGA-TTGAAGATACCAAA
* * * ** * * * *
57527150 TCATATCTCCTTGAAATTCCAGCGGAGTAGATCGAAGCTA-CAAA
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGATACCAAA
* * ** * * * * ** *
57527194 TCTCT-TCTCCCTAAAATTACATTGAAGCAGATCGATGCCA-CAAT
1 TCT-TATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGATACCAAA
* * * * *
57527238 TCTTATCCCCCTGAAGTTGCAGTGGAGCAGGA-TAAAAATATACAAA
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCA-GATTGAAGATA-CCAAA
* * *
57527284 CCTTATCTCCCTGAAGTTATAGTGGAGCAGATTGAA-ATTACCAAT
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGA-TACCAAA
**
57527329 TCTTATCTCTTTGAAGTTG
1 TCTTATCTCCCTGAAGTTG
57527348 CAACGGAGTA
Statistics
Matches: 312, Mismatches: 92, Indels: 36
0.71 0.21 0.08
Matches are distributed among these distances:
42 2 0.01
43 4 0.01
44 112 0.36
45 123 0.39
46 66 0.21
47 3 0.01
48 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGATACCAAA
Found at i:57527181 original size:179 final size:179
Alignment explanation
Indices: 57526933--57527408 Score: 659
Period size: 179 Copynumber: 2.7 Consensus size: 179
57526923 AAATATCATT
* * * *
57526933 TCCCTGAAGTTGTAGTGGAACAGGTTGAAGTTACCAATTCTTATCTCCTTGAAGTTCTAGTGGAG
1 TCCCTGAAGTTGTAGTGGAGCAAGTTGAAGTTACCAATTCTTATCTCCTTGAAGTTCCAGCGGAG
* *
57526998 TAGATCGAAGCTACAAATCTTTTATCCTTGAAATTACATTGGAGCAGATCGAAGCCACAATCCTT
66 TAGATCGAAGCTACAAATCTTTTCTCCCTGAAATTACATTGGAGCAGATCGAAGCCACAATCCTT
* *
57527063 ATCTCCCTAAAGTTGTAGTAGAGCAGGATAAAAATACACAAACCTTATC
131 ATCCCCCTAAAGTTGCAGTAGAGCAGGATAAAAATACACAAACCTTATC
* * * *
57527112 TCCCTAAAGTTGCAGTGGAGCAAGTTGAAGTTACCAATTCATATCTCCTTGAAATTCCAGCGGAG
1 TCCCTGAAGTTGTAGTGGAGCAAGTTGAAGTTACCAATTCTTATCTCCTTGAAGTTCCAGCGGAG
* * * * *
57527177 TAGATCGAAGCTACAAATCTCTTCTCCCTAAAATTACATTGAAGCAGATCGATGCCACAATTCTT
66 TAGATCGAAGCTACAAATCTTTTCTCCCTGAAATTACATTGGAGCAGATCGAAGCCACAATCCTT
* * *
57527242 ATCCCCCTGAAGTTGCAGTGGAGCAGGATAAAAATATACAAACCTTATC
131 ATCCCCCTAAAGTTGCAGTAGAGCAGGATAAAAATACACAAACCTTATC
* * * * *
57527291 TCCCTGAAGTTATAGTGGAGC-AGATTGAAATTACCAATTCTTATCTCTTTGAAGTTGCAACGGA
1 TCCCTGAAGTTGTAGTGGAGCAAG-TTGAAGTTACCAATTCTTATCTCCTTGAAGTTCCAGCGGA
* * * *
57527355 GTAGATCAAAACTACAAGT-TTCTTCTCCCTGAAATTACATTGGAGCGGATCGAA
65 GTAGATCGAAGCTACAAATCTT-TTCTCCCTGAAATTACATTGGAGCAGATCGAA
57527409 ACACCAGTTC
Statistics
Matches: 258, Mismatches: 37, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
178 3 0.01
179 255 0.99
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (179 bp):
TCCCTGAAGTTGTAGTGGAGCAAGTTGAAGTTACCAATTCTTATCTCCTTGAAGTTCCAGCGGAG
TAGATCGAAGCTACAAATCTTTTCTCCCTGAAATTACATTGGAGCAGATCGAAGCCACAATCCTT
ATCCCCCTAAAGTTGCAGTAGAGCAGGATAAAAATACACAAACCTTATC
Found at i:57529050 original size:6 final size:6
Alignment explanation
Indices: 57529039--57529095 Score: 69
Period size: 6 Copynumber: 9.5 Consensus size: 6
57529029 CTTAACTTCC
* * * * *
57529039 ATTGTT ATTGTT ATTGTT ATTATT GTTGTT GTTGTT GTTGTT GTTGTT
1 ATTGTT ATTGTT ATTGTT ATTGTT ATTGTT ATTGTT ATTGTT ATTGTT
57529087 ATTGTT ATT
1 ATTGTT ATT
57529096 TTTTATGGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.12, C:0.00, G:0.21, T:0.67
Consensus pattern (6 bp):
ATTGTT
Found at i:57529067 original size:3 final size:3
Alignment explanation
Indices: 57529040--57529092 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
57529030 TTAACTTCCA
* * * * *
57529040 TTG TTA TTG TTA TTG TTA TTA TTG TTG TTG TTG TTG TTG TTG TTG TTA
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
57529088 TTG TT
1 TTG TT
57529093 ATTTTTTATG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.09, C:0.00, G:0.23, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:57530182 original size:27 final size:26
Alignment explanation
Indices: 57530142--57530200 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
57530132 ATTATTATAT
* *
57530142 TTAATTTTTAAAATATTTTATATAACA
1 TTAATTTTTAAAATAATGTATATAA-A
*
57530169 TTAA-TTTTATAAATAATGTATATCAA
1 TTAATTTTTA-AAATAATGTATATAAA
57530195 TTAATT
1 TTAATT
57530201 AAAACATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 10 0.37
27 17 0.63
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (26 bp):
TTAATTTTTAAAATAATGTATATAAA
Found at i:57534514 original size:9 final size:9
Alignment explanation
Indices: 57534502--57534532 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
57534492 AATGGGGTAG
57534502 ATGGGGCCA
1 ATGGGGCCA
*
57534511 ATGGGGCTA
1 ATGGGGCCA
57534520 ATGGGGCCA
1 ATGGGGCCA
57534529 ATGG
1 ATGG
57534533 TGCAGCCCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.23, C:0.16, G:0.45, T:0.16
Consensus pattern (9 bp):
ATGGGGCCA
Found at i:57534514 original size:18 final size:18
Alignment explanation
Indices: 57534491--57534532 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
57534481 GAGCTAGGGT
57534491 CAATGGGG-TAGATGGGGC
1 CAATGGGGCTA-ATGGGGC
57534509 CAATGGGGCTAATGGGGC
1 CAATGGGGCTAATGGGGC
57534527 CAATGG
1 CAATGG
57534533 TGCAGCCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.24, C:0.14, G:0.45, T:0.17
Consensus pattern (18 bp):
CAATGGGGCTAATGGGGC
Found at i:57535368 original size:27 final size:27
Alignment explanation
Indices: 57535338--57535389 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
57535328 CCGCCATGAG
57535338 TTGCCGGTTAGCAGTACCGATGAACAA
1 TTGCCGGTTAGCAGTACCGATGAACAA
57535365 TTGCCGGTTAGCAGTACCGATGAAC
1 TTGCCGGTTAGCAGTACCGATGAAC
57535390 TATCTAGCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (27 bp):
TTGCCGGTTAGCAGTACCGATGAACAA
Found at i:57536885 original size:22 final size:24
Alignment explanation
Indices: 57536843--57536887 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
57536833 CAAAATTGAT
*
57536843 TTATTTTATTAAAAATTAAATAAA
1 TTATTTTATTAAAAATGAAATAAA
57536867 TTATTTT-TT-AAAATGAAATAA
1 TTATTTTATTAAAAATGAAATAA
57536888 TTAAATTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 2 0.10
24 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TTATTTTATTAAAAATGAAATAAA
Found at i:57537318 original size:18 final size:19
Alignment explanation
Indices: 57537278--57537334 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 19
57537268 TTAAAAGAGC
* * *
57537278 ATAAAAAAATATAGAAAGTT
1 ATAAAAAATTACAGAAA-AT
57537298 ATAAAAAATTACA-AAAAT
1 ATAAAAAATTACAGAAAAT
*
57537316 ATAAGAAATTACAGAAAAT
1 ATAAAAAATTACAGAAAAT
57537335 TATTTAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 13 0.41
19 8 0.25
20 11 0.34
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.23
Consensus pattern (19 bp):
ATAAAAAATTACAGAAAAT
Found at i:57537333 original size:28 final size:28
Alignment explanation
Indices: 57537282--57537363 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 28
57537272 AAGAGCATAA
*
57537282 AAAAATATAGAAAGTTATAAAAAATTAC
1 AAAAATATAGAAAGTTACAAAAAATTAC
* *
57537310 AAAAATATAAGAAA-TTACAGAAAATTATTT
1 AAAAATAT-AGAAAGTTACAAAAAATTA--C
* * *
57537340 AAAAAAATAGGAATTTACAAAAAA
1 AAAAATATAGAAAGTTACAAAAAA
57537364 AATTATATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
28 19 0.43
29 9 0.20
30 16 0.36
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.24
Consensus pattern (28 bp):
AAAAATATAGAAAGTTACAAAAAATTAC
Found at i:57546628 original size:28 final size:28
Alignment explanation
Indices: 57546588--57546642 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
57546578 TTCAATAAGA
57546588 AAAGAAAGATGTAATGAGTGATGACAGC
1 AAAGAAAGATGTAATGAGTGATGACAGC
57546616 AAAGAAAGATGTAATGAGTGATGACAG
1 AAAGAAAGATGTAATGAGTGATGACAG
57546643 AGCCAGTGCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.47, C:0.05, G:0.29, T:0.18
Consensus pattern (28 bp):
AAAGAAAGATGTAATGAGTGATGACAGC
Found at i:57551660 original size:54 final size:53
Alignment explanation
Indices: 57551585--57551781 Score: 227
Period size: 54 Copynumber: 3.7 Consensus size: 53
57551575 ATCAGATTAA
* * *
57551585 AAAAAATTTAGATTTTAGACACCCTATAGG-TAACACCCCTTTTATCAATTTTTTT
1 AAAAAA-TTAGGTTTTGGACACCCTAT-GGCCAACACCCCTTTTATCAA-TTTTTT
* ** ***
57551640 AAAAAATTAGGTTTTGGACACCCCATGGCCGGCACCCCTTTTATCAATTTAAA
1 AAAAAATTAGGTTTTGGACACCCTATGGCCAACACCCCTTTTATCAATTTTTT
*
57551693 AAGAAAATTGGGTTTTGGACACCCTATGGCCAACACCCCTTTTATCAA-TTTTT
1 AA-AAAATTAGGTTTTGGACACCCTATGGCCAACACCCCTTTTATCAATTTTTT
* * *
57551746 AAAAAAATAGGTTTTGGACACCCCATGGCCGACACC
1 AAAAAATTAGGTTTTGGACACCCTATGGCCAACACC
57551782 TCCATTAAAA
Statistics
Matches: 120, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
52 30 0.25
53 11 0.09
54 73 0.61
55 6 0.05
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (53 bp):
AAAAAATTAGGTTTTGGACACCCTATGGCCAACACCCCTTTTATCAATTTTTT
Found at i:57551776 original size:106 final size:105
Alignment explanation
Indices: 57551543--57551781 Score: 313
Period size: 106 Copynumber: 2.3 Consensus size: 105
57551533 ATTTTTTTTG
** * * *
57551543 GGTTTTGGACATTCCATGGCCAGTACCCCTTTATCAGATTAAAAAAAATTTAGATTTTAGACACC
1 GGTTTTGGACACCCCATGGCCGGCACCCCTTTATCAGATTAAAAAAAAATTAGATTTTAGACACC
* *
57551608 CTATAGGTAACACCCCTTTTATCAATTTTTTTAAAAAATTA
66 CTATAGGCAACACCCCTTTTATCAA-TTTTTTAAAAAAATA
* * *
57551649 GGTTTTGGACACCCCATGGCCGGCACCCCTTTTATCA-ATTTAAAAAGAAAATTGGGTTTTGGAC
1 GGTTTTGGACACCCCATGGCCGGCACCCC-TTTATCAGA-TTAAAAA-AAAATTAGATTTTAGAC
57551713 ACCCTAT-GGCCAACACCCCTTTTATCAA-TTTTTAAAAAAATA
63 ACCCTATAGG-CAACACCCCTTTTATCAATTTTTTAAAAAAATA
*
57551755 GGTTTTGGACACCCCATGGCCGACACC
1 GGTTTTGGACACCCCATGGCCGGCACC
57551782 TCCATTAAAA
Statistics
Matches: 118, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
106 65 0.55
107 16 0.14
108 37 0.31
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (105 bp):
GGTTTTGGACACCCCATGGCCGGCACCCCTTTATCAGATTAAAAAAAAATTAGATTTTAGACACC
CTATAGGCAACACCCCTTTTATCAATTTTTTAAAAAAATA
Found at i:57555416 original size:22 final size:22
Alignment explanation
Indices: 57555388--57555432 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
57555378 ACAGATAAAT
* *
57555388 AATTGATTTATAGAGACAAAAA
1 AATTGATATATAAAGACAAAAA
*
57555410 AATTGATATATAAATACAAAAA
1 AATTGATATATAAAGACAAAAA
57555432 A
1 A
57555433 TAACATGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.27
Consensus pattern (22 bp):
AATTGATATATAAAGACAAAAA
Found at i:57556567 original size:22 final size:23
Alignment explanation
Indices: 57556514--57556569 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
57556504 CCCGTTTTTA
* * *
57556514 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
57556537 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
57556559 ATTAAAATTAA
1 ATTAAAATTAA
57556570 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:57556582 original size:16 final size:16
Alignment explanation
Indices: 57556545--57556584 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
57556535 TTAATAAAAT
* *
57556545 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
57556561 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
57556577 TAAAATTA
1 TAAAATTA
57556585 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:57556690 original size:9 final size:9
Alignment explanation
Indices: 57556657--57556684 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
57556647 TTTATCAAAT
57556657 TATTAATTG
1 TATTAATTG
57556666 TATTAATTG
1 TATTAATTG
57556675 TATTAATTG
1 TATTAATTG
57556684 T
1 T
57556685 TGTAATAAAA
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:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:57556694 original size:68 final size:68
Alignment explanation
Indices: 57556573--57556782 Score: 388
Period size: 68 Copynumber: 3.1 Consensus size: 68
57556563 AAATTAATTG
*
57556573 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
57556636 TGA
66 TGA
57556639 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
57556704 TGA
66 TGA
*
57556707 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
57556772 TGA
66 TGA
57556775 TTAGTAAA
1 TTAGTAAA
57556783 ACAAACTTGA
Statistics
Matches: 140, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
66 26 0.19
68 114 0.81
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:57556737 original size:9 final size:9
Alignment explanation
Indices: 57556725--57556752 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
57556715 TTTATCAAAT
57556725 TATTAATTG
1 TATTAATTG
57556734 TATTAATTG
1 TATTAATTG
57556743 TATTAATTG
1 TATTAATTG
57556752 T
1 T
57556753 TGTAACAAAA
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:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:57556878 original size:24 final size:23
Alignment explanation
Indices: 57556849--57556893 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
57556839 AAATAAACTT
*
57556849 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAAATA-TATATTTTA
57556873 AAAATAAAAAAATATATATTT
1 AAAATAAAAAAATATATATTT
57556894 AATATTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAATAAAAAAATATATATTTTA
Found at i:57557219 original size:38 final size:36
Alignment explanation
Indices: 57557077--57557302 Score: 123
Period size: 38 Copynumber: 5.9 Consensus size: 36
57557067 ATTTTGAAAT
* *
57557077 AAAATATTAAAAATCAAATAAGAACAGATAAATTTTGAA
1 AAAATATTATAAA--AAATAAGAACTGATAAATTTT-AA
* * * * * * *
57557116 GAAAGAGTTTTAAAAAATAAAAACTAAAAAATTCTAA
1 AAAATA-TTATAAAAAATAAGAACTGATAAATTTTAA
* * *
57557153 AAAATATTTTAAAAATTTACA-AATTGATAAATTTTATA
1 AAAATATTATAAAAA-ATA-AGAACTGATAAATTTTA-A
*
57557191 AAAATATTAATAAAAAATAAGAACTGATAATTTTTGAA
1 AAAATATT-ATAAAAAATAAGAACTGATAAATTTT-AA
* * * * *
57557229 AACATATTTTAAAAAAATATGATCTGATAAAATTTTCA
1 AAAATATTAT-AAAAAATAAGAACTGAT-AAATTTTAA
* * *
57557267 AAAAGATTAAAAATAAAATATGAA-TGTATAAATTTT
1 AAAATATT-ATAA-AAAATAAGAACTG-ATAAATTTT
57557303 CGAACAAAAT
Statistics
Matches: 144, Mismatches: 31, Indels: 25
0.72 0.16 0.12
Matches are distributed among these distances:
36 9 0.06
37 21 0.15
38 81 0.56
39 28 0.19
40 5 0.03
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.32
Consensus pattern (36 bp):
AAAATATTATAAAAAATAAGAACTGATAAATTTTAA
Found at i:57561862 original size:29 final size:30
Alignment explanation
Indices: 57561809--57561872 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 30
57561799 CAACTTAACA
57561809 AACAAATGCCTCTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
*
57561839 AACAAATGCCT-TTAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
57561868 AACAA
1 AACAA
57561873 TAAAATAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 22 0.67
30 11 0.33
ACGTcount: A:0.58, C:0.16, G:0.03, T:0.23
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAACAAAATT
Found at i:57561978 original size:21 final size:21
Alignment explanation
Indices: 57561954--57561995 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
57561944 AAATAGGGGA
* *
57561954 AAAAAACAAGAAAATAACATT
1 AAAAAACAAAAAAAGAACATT
57561975 AAAAAACAAAAAAAGAACATT
1 AAAAAACAAAAAAAGAACATT
57561996 TTTTTGTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.74, C:0.10, G:0.05, T:0.12
Consensus pattern (21 bp):
AAAAAACAAAAAAAGAACATT
Found at i:57564545 original size:23 final size:23
Alignment explanation
Indices: 57564499--57564548 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
57564489 GTTTTAAGTT
*
57564499 TTTATATGTATTATTATTTGAAA
1 TTTATATGTATCATTATTTGAAA
57564522 TTTACTATGTATCATTATTT-AAA
1 TTTA-TATGTATCATTATTTGAAA
57564545 TTTA
1 TTTA
57564549 ACATATTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (23 bp):
TTTATATGTATCATTATTTGAAA
Found at i:57570016 original size:21 final size:21
Alignment explanation
Indices: 57569967--57570016 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
57569957 ATAATTTTTG
* *
57569967 AATTTTTGAAAATTTATTTTA
1 AATTTTTTAAAATTTACTTTA
57569988 AATTTTTTAAAA-TTACTTTA
1 AATTTTTTAAAATTTACTTTA
57570008 AACTTTTTT
1 AA-TTTTTT
57570017 TTTGTAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (21 bp):
AATTTTTTAAAATTTACTTTA
Found at i:57575403 original size:61 final size:61
Alignment explanation
Indices: 57575326--57575449 Score: 169
Period size: 61 Copynumber: 2.0 Consensus size: 61
57575316 TTCAAGAACC
* * ** * *
57575326 TTGCGATCGGACCACTTCACT-TTATATTAAAGCTAGGTACCCAATTTTGGTAAAAGAAAAT
1 TTGCGACCGGAACACTTCA-TATTATATTAAAGCTAGCCAACCAAATTTGGTAAAAGAAAAT
*
57575387 TTGCGACCGGAACACTTCATATTGTATTAAAGCTAGCCAACCAAATTTGGTAAAAGAAAAT
1 TTGCGACCGGAACACTTCATATTATATTAAAGCTAGCCAACCAAATTTGGTAAAAGAAAAT
57575448 TT
1 TT
57575450 TAAGGTGGAG
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 1 0.02
61 54 0.98
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (61 bp):
TTGCGACCGGAACACTTCATATTATATTAAAGCTAGCCAACCAAATTTGGTAAAAGAAAAT
Found at i:57576225 original size:21 final size:23
Alignment explanation
Indices: 57576199--57576249 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
57576189 TATTTTTAAA
57576199 AAAAAATTATAAA-AAT-TA-AT
1 AAAAAATTATAAATAATATATAT
*
57576219 AACAAAATTCTAAATAATATATAT
1 AA-AAAATTATAAATAATATATAT
57576243 AAAAAAT
1 AAAAAAT
57576250 AGAAACTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 2 0.08
21 10 0.38
22 3 0.12
23 7 0.27
24 4 0.15
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (23 bp):
AAAAAATTATAAATAATATATAT
Found at i:57579080 original size:19 final size:19
Alignment explanation
Indices: 57579052--57579101 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
57579042 AACTTGAGTT
57579052 AAATTAAAAATTATCA-ATTA
1 AAATT-AAAATTAT-ATATTA
*
57579072 AAGA-TAAAAATATATATTA
1 AA-ATTAAAATTATATATTA
57579091 AAATTAAAATT
1 AAATTAAAATT
57579102 CAAATAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
18 2 0.08
19 19 0.76
20 3 0.12
21 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
AAATTAAAATTATATATTA
Found at i:57579635 original size:7 final size:7
Alignment explanation
Indices: 57579625--57579649 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
57579615 TTTAAATAAA
57579625 AAATTAC
1 AAATTAC
57579632 AAATTAC
1 AAATTAC
57579639 AAATTAC
1 AAATTAC
57579646 AAAT
1 AAAT
57579650 CCAATAATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATTAC
Found at i:57596386 original size:5 final size:5
Alignment explanation
Indices: 57596376--57596400 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
57596366 TTAATTTAGC
57596376 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
57596401 TAGTTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:57596407 original size:11 final size:11
Alignment explanation
Indices: 57596377--57596414 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
57596367 TAATTTAGCA
57596377 TTTTATTTTA-
1 TTTTATTTTAT
57596387 TTTTATTTTAT
1 TTTTATTTTAT
*
57596398 TTTTAGTTTAAT
1 TTTTA-TTTTAT
57596410 TTTTA
1 TTTTA
57596415 CATTCTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.40
11 5 0.20
12 10 0.40
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:57596914 original size:102 final size:102
Alignment explanation
Indices: 57596787--57596989 Score: 361
Period size: 102 Copynumber: 2.0 Consensus size: 102
57596777 CATTTTGTTC
*
57596787 AGTTCGATGGTTTGCAAGAAGAAGATCCAAATACTCATTTGGCTATTTTTTTAGAAATCTACGAT
1 AGTTCGATGGTTTGCAAGAAGAAGATCCAAATACTCATTTGGCTAATTTTTTAGAAATCTACGAT
*
57596852 ACTTTCAAAATTAATGGCGTCACTAATGACACCATTT
66 ACTTTCAAAATTAATGGCGTCACTAACGACACCATTT
* *
57596889 AGTTCGATGGTTTGCAAGACGAAGATCCAAATACTCATTTGGCTAATTTTTTAGAAATCTATGAT
1 AGTTCGATGGTTTGCAAGAAGAAGATCCAAATACTCATTTGGCTAATTTTTTAGAAATCTACGAT
*
57596954 ACTTTCAAAATTAATGGCGTCACTGACGACACCATT
66 ACTTTCAAAATTAATGGCGTCACTAACGACACCATT
57596990 CGCCTACGGT
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 96 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (102 bp):
AGTTCGATGGTTTGCAAGAAGAAGATCCAAATACTCATTTGGCTAATTTTTTAGAAATCTACGAT
ACTTTCAAAATTAATGGCGTCACTAACGACACCATTT
Found at i:57599962 original size:19 final size:18
Alignment explanation
Indices: 57599938--57599973 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
57599928 CCCGCCCCCA
57599938 CCCACACACGACACCTCCT
1 CCCACACACGAC-CCTCCT
*
57599957 CCCACATACGACCCTCC
1 CCCACACACGACCCTCC
57599974 GTCGTAACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.25, C:0.58, G:0.06, T:0.11
Consensus pattern (18 bp):
CCCACACACGACCCTCCT
Found at i:57600041 original size:7 final size:7
Alignment explanation
Indices: 57600029--57600085 Score: 60
Period size: 7 Copynumber: 7.7 Consensus size: 7
57600019 CTTTTCTTTA
57600029 TTTTATT
1 TTTTATT
57600036 TTTTATT
1 TTTTATT
57600043 TATTTATT
1 T-TTTATT
57600051 TTTTATT
1 TTTTATT
*
57600058 ATTTATT
1 TTTTATT
*
57600065 ATATTATT
1 -TTTTATT
*
57600073 TATTATT
1 TTTTATT
57600080 ATTTTA
1 -TTTTA
57600086 CTGATTTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
7 27 0.63
8 16 0.37
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTATT
Found at i:57600046 original size:4 final size:4
Alignment explanation
Indices: 57600025--57600116 Score: 63
Period size: 4 Copynumber: 23.8 Consensus size: 4
57600015 TACCCTTTTC
57600025 TTTA TTTTA TTT- TTTA TTTA TTTA TTT- TTTA -TTA TTTA -TTA TATTA
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA
* * * *
57600071 TTTA -TTA -TTA TTTTA CTGA TTTT TTTGA -TGA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA -TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTT
57600117 TGTTTTATTA
Statistics
Matches: 70, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
3 19 0.27
4 40 0.57
5 11 0.16
ACGTcount: A:0.23, C:0.01, G:0.03, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:57600054 original size:22 final size:22
Alignment explanation
Indices: 57600029--57600125 Score: 85
Period size: 22 Copynumber: 4.5 Consensus size: 22
57600019 CTTTTCTTTA
*
57600029 TTTTATTTTTTATTTATTTATT
1 TTTTATTATTTATTTATTTATT
57600051 TTTTATTATTTA-TTATATTATT
1 TTTTATTATTTATTTAT-TTATT
* * *
57600073 TATTATTATTTTACTGA-TT-TT
1 TTTTATTA-TTTATTTATTTATT
* *
57600094 TTTGATGATTTATTTATTTATT
1 TTTTATTATTTATTTATTTATT
57600116 TTGTT-TTATT
1 TT-TTATTATT
57600126 ATTCTTATGC
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
20 6 0.10
21 13 0.22
22 33 0.56
23 5 0.08
24 2 0.03
ACGTcount: A:0.22, C:0.01, G:0.04, T:0.73
Consensus pattern (22 bp):
TTTTATTATTTATTTATTTATT
Found at i:57600173 original size:19 final size:20
Alignment explanation
Indices: 57600151--57600193 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
57600141 TATTAATTTT
57600151 ATTTTAATT-TATTTCTTTC
1 ATTTTAATTATATTTCTTTC
* *
57600170 A-TTTAGTTATATTTCTTTT
1 ATTTTAATTATATTTCTTTC
57600189 ATTTT
1 ATTTT
57600194 TAGTATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 6 0.30
19 11 0.55
20 3 0.15
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.70
Consensus pattern (20 bp):
ATTTTAATTATATTTCTTTC
Found at i:57600320 original size:6 final size:6
Alignment explanation
Indices: 57600259--57600324 Score: 51
Period size: 6 Copynumber: 10.5 Consensus size: 6
57600249 AGTTTATTTC
* * * * * *
57600259 TTTTCT TTTTCT TTTTAT CTTTAT TTTTGT TTTTGT TTTTGT TTTTAGT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTA-T
57600308 TGCTTTAT TTTTAT TTT
1 T--TTTAT TTTTAT TTT
57600325 CTTAGACTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
6 44 0.85
7 2 0.04
8 2 0.04
9 4 0.08
ACGTcount: A:0.08, C:0.06, G:0.08, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:57603733 original size:26 final size:25
Alignment explanation
Indices: 57603688--57603739 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
57603678 AAGTTTTAAA
57603688 TAAAAAATTATCTCTAAAAATCTTC
1 TAAAAAATTATCTCTAAAAATCTTC
* *
57603713 TAAAATAATT-TCTTTAGAAAATTTTC
1 TAAAA-AATTATCTCTA-AAAATCTTC
57603739 T
1 T
57603740 CTCTACAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (25 bp):
TAAAAAATTATCTCTAAAAATCTTC
Found at i:57603955 original size:61 final size:58
Alignment explanation
Indices: 57603848--57603963 Score: 169
Period size: 61 Copynumber: 1.9 Consensus size: 58
57603838 ATCACTTCAA
* * *
57603848 TATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAATC
1 TATTAAATTAATAGAATACTTATCAAGATAAATATTAAATTAAATTTAAAATTAAATC
*
57603906 TATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAATTTAAAATTAA
1 TATTAAATTAATAGAATACTTA--T-CAAGATAAATATTAAATTAAATTTAAAATTAA
57603964 GATAATCACT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 20 0.39
60 1 0.02
61 30 0.59
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (58 bp):
TATTAAATTAATAGAATACTTATCAAGATAAATATTAAATTAAATTTAAAATTAAATC
Found at i:57603989 original size:20 final size:18
Alignment explanation
Indices: 57603939--57603990 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
57603929 CTACAAGATA
57603939 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
*
57603956 AAAATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
57603976 AATATTAAATTAATA
1 AATATTAAATTAATA
57603991 AAATATTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 10 0.36
18 1 0.04
19 3 0.11
20 14 0.50
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:57606245 original size:25 final size:24
Alignment explanation
Indices: 57606200--57606248 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
57606190 ATATAGTTTT
57606200 TATATTATTTATAAAGGTTATAATA
1 TATATTATTTATAAA-GTTATAATA
57606225 TATATTATATTATAATA-TTATAAT
1 TATATTAT-TTATAA-AGTTATAAT
57606249 TAAACAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 15 0.68
26 6 0.27
27 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
TATATTATTTATAAAGTTATAATA
Found at i:57606313 original size:5 final size:5
Alignment explanation
Indices: 57606303--57606327 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
57606293 AACCGAAACT
57606303 AAGAA AAGAA AAGAA AAGAA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA
57606328 GAACAACCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:57607167 original size:40 final size:41
Alignment explanation
Indices: 57607119--57607213 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
57607109 CTATATGATT
* *
57607119 AGCACTAAGTGTGC-AAATTAAATGATGAGGTTGAATAACG
1 AGCACTAAGTGTGCAAAATTAAATAATGAGGTTAAATAACG
* *
57607159 AGCACTAAGTATGCAAAATTAAATAATGATGTTAAATAACG
1 AGCACTAAGTGTGCAAAATTAAATAATGAGGTTAAATAACG
*
57607200 GGCACTAAGTGTGC
1 AGCACTAAGTGTGC
57607214 GAAACCGAGA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 13 0.27
41 35 0.73
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.25
Consensus pattern (41 bp):
AGCACTAAGTGTGCAAAATTAAATAATGAGGTTAAATAACG
Found at i:57610140 original size:49 final size:48
Alignment explanation
Indices: 57610050--57610146 Score: 158
Period size: 49 Copynumber: 2.0 Consensus size: 48
57610040 TTTCTTTGCT
* *
57610050 TAAAAACGCCTAAGTCAGCCTAACTCGCAATGATAACGGATTCAACAG
1 TAAAAACACCTAAGTCAGCCTAACTCGCAATGATAAAGGATTCAACAG
*
57610098 TAAAAACACCTAAGTCAGCTTAATCTCGCAATGATAAAGGATTCAACAG
1 TAAAAACACCTAAGTCAGCCTAA-CTCGCAATGATAAAGGATTCAACAG
57610147 AATTCCCTCA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 21 0.47
49 24 0.53
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (48 bp):
TAAAAACACCTAAGTCAGCCTAACTCGCAATGATAAAGGATTCAACAG
Found at i:57610361 original size:17 final size:17
Alignment explanation
Indices: 57610339--57610402 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
57610329 CATTAAGGGC
*
57610339 TACAATTAAAAGTTGTA
1 TACAATTAGAAGTTGTA
*
57610356 TACAATTAGAACTCTAAG-A
1 TACAATTAGAAGT-T--GTA
*
57610375 TACAATTAGAAGCTGTA
1 TACAATTAGAAGTTGTA
57610392 TACAATTAGAA
1 TACAATTAGAA
57610403 CTCTAAGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 1 0.03
17 23 0.59
18 2 0.05
19 12 0.31
20 1 0.03
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (17 bp):
TACAATTAGAAGTTGTA
Found at i:57610379 original size:19 final size:19
Alignment explanation
Indices: 57610355--57610411 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
57610345 TAAAAGTTGT
57610355 ATACAATTAGAACTCTAAG
1 ATACAATTAGAACTCTAAG
*
57610374 ATACAATTAGAA-GCT--G
1 ATACAATTAGAACTCTAAG
57610390 TATACAATTAGAACTCTAAG
1 -ATACAATTAGAACTCTAAG
57610410 AT
1 AT
57610412 TACATAATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
16 1 0.03
17 12 0.38
18 4 0.12
19 14 0.44
20 1 0.03
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (19 bp):
ATACAATTAGAACTCTAAG
Found at i:57610379 original size:36 final size:36
Alignment explanation
Indices: 57610339--57610411 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
57610329 CATTAAGGGC
*
57610339 TACAATTAAAAGTTGTATACAATTAGAACTCTAAGA
1 TACAATTAAAAGCTGTATACAATTAGAACTCTAAGA
*
57610375 TACAATTAGAAGCTGTATACAATTAGAACTCTAAGA
1 TACAATTAAAAGCTGTATACAATTAGAACTCTAAGA
57610411 T
1 T
57610412 TACATAATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (36 bp):
TACAATTAAAAGCTGTATACAATTAGAACTCTAAGA
Found at i:57610672 original size:2 final size:2
Alignment explanation
Indices: 57610665--57610692 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
57610655 TCTTCGAATC
57610665 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57610693 TGAATTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57612596 original size:49 final size:49
Alignment explanation
Indices: 57612524--57612655 Score: 184
Period size: 49 Copynumber: 2.8 Consensus size: 49
57612514 TCGTGAAAAT
57612524 TAAGTTTTGAGTCTCGTACCTAATTTCAAACTCAATTACAAAAGTTTTG
1 TAAGTTTTGAGTCTCGTACCTAATTTCAAACTCAATTACAAAAGTTTTG
*
57612573 TAAGTTTTGAGTCTCGTATCTAATTTCAAACTCAATTACAAAA-----G
1 TAAGTTTTGAGTCTCGTACCTAATTTCAAACTCAATTACAAAAGTTTTG
** * *
57612617 TAAGTTTTGAGTCTCCAACCCAATTTCAAACCCAATTAC
1 TAAGTTTTGAGTCTCGTACCTAATTTCAAACTCAATTAC
57612656 TTATTTACGA
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
44 35 0.45
49 42 0.55
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.36
Consensus pattern (49 bp):
TAAGTTTTGAGTCTCGTACCTAATTTCAAACTCAATTACAAAAGTTTTG
Found at i:57617846 original size:17 final size:17
Alignment explanation
Indices: 57617826--57617862 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
57617816 AACTTTTGAA
57617826 TTAGTGAATTTTGTGAT
1 TTAGTGAATTTTGTGAT
57617843 TTAGTGAATTTTGTGAT
1 TTAGTGAATTTTGTGAT
57617860 TTA
1 TTA
57617863 AAAAGAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (17 bp):
TTAGTGAATTTTGTGAT
Found at i:57618158 original size:12 final size:12
Alignment explanation
Indices: 57618141--57618165 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57618131 GACGGTTTGG
57618141 GCAAGAAAATCA
1 GCAAGAAAATCA
57618153 GCAAGAAAATCA
1 GCAAGAAAATCA
57618165 G
1 G
57618166 GAGAAATAAG
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:0.56, C:0.16, G:0.20, T:0.08
Consensus pattern (12 bp):
GCAAGAAAATCA
Found at i:57618662 original size:46 final size:46
Alignment explanation
Indices: 57618610--57618699 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
57618600 GGTAAATTGT
*
57618610 GAAAAGTAGGTATGGTGCTTCGGTGAAGAAAACCATACTGAGTTGC
1 GAAAAGTAGGTATGGTGCTTCAGTGAAGAAAACCATACTGAGTTGC
* *
57618656 GAAAAGTAGGTATGGTGTTTCAGTGAAGGAAACCATACTGAGTT
1 GAAAAGTAGGTATGGTGCTTCAGTGAAGAAAACCATACTGAGTT
57618700 AAAGCATTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (46 bp):
GAAAAGTAGGTATGGTGCTTCAGTGAAGAAAACCATACTGAGTTGC
Found at i:57623237 original size:23 final size:23
Alignment explanation
Indices: 57623211--57623286 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
57623201 ATAAGTGCCA
57623211 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
57623234 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
57623257 CACTGAAATGTAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
57623280 CACTGAT
1 CACTGAT
57623287 CAATAACACT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:57623386 original size:8 final size:8
Alignment explanation
Indices: 57623373--57623401 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
57623363 ACCCGGGACT
57623373 CACTGTAA
1 CACTGTAA
57623381 CACTGTAA
1 CACTGTAA
57623389 CACTGTAA
1 CACTGTAA
57623397 CACTG
1 CACTG
57623402 GTCTCTAGTG
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:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:57623539 original size:18 final size:17
Alignment explanation
Indices: 57623506--57623544 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
57623496 ATTTTCCTTC
57623506 CACATTCAAAATTAATT
1 CACATTCAAAATTAATT
57623523 CACATATC-AAATATAATT
1 CACAT-TCAAAAT-TAATT
57623541 CACA
1 CACA
57623545 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.31
Consensus pattern (17 bp):
CACATTCAAAATTAATT
Found at i:57637275 original size:52 final size:52
Alignment explanation
Indices: 57637197--57637297 Score: 193
Period size: 52 Copynumber: 1.9 Consensus size: 52
57637187 TTAAGACTTT
*
57637197 GCAAGTTAGTAGTTAAAGTTCTATTTAGAGAGATTAAATCTTGAGACCTGAC
1 GCAAGTTAGTAGTCAAAGTTCTATTTAGAGAGATTAAATCTTGAGACCTGAC
57637249 GCAAGTTAGTAGTCAAAGTTCTATTTAGAGAGATTAAATCTTGAGACCT
1 GCAAGTTAGTAGTCAAAGTTCTATTTAGAGAGATTAAATCTTGAGACCT
57637298 AACAGCCATG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.33
Consensus pattern (52 bp):
GCAAGTTAGTAGTCAAAGTTCTATTTAGAGAGATTAAATCTTGAGACCTGAC
Found at i:57646371 original size:28 final size:28
Alignment explanation
Indices: 57646340--57646401 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
57646330 TTATTTCTAT
57646340 CTTCTTTGCCATATATTATCATTACCGA
1 CTTCTTTGCCATATATTATCATTACCGA
57646368 CTTCTTTGCCATATATTATCATTACCGA
1 CTTCTTTGCCATATATTATCATTACCGA
57646396 CGTTCT
1 C-TTCT
57646402 ACTTTCTGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 29 0.88
29 4 0.12
ACGTcount: A:0.23, C:0.26, G:0.08, T:0.44
Consensus pattern (28 bp):
CTTCTTTGCCATATATTATCATTACCGA
Found at i:57648596 original size:61 final size:62
Alignment explanation
Indices: 57648525--57648649 Score: 141
Period size: 61 Copynumber: 2.0 Consensus size: 62
57648515 TAAAGTTATG
* * *
57648525 TGAATTTTTTAGAATTCCAAT-T-AAAATGATA-AATTTTGTAAACATT-GAGGGCTAAATTTGT
1 TGAATGTTTTA-AATT-CAATATCAAAATGATATAA-TGTATAAACATTGGAGGGCTAAATTTGT
* * *
57648586 TGAATGTTTTATATTTAATATCAAATTGATATAATGTATAAACATTGGAGGGCTAAATTTGT
1 TGAATGTTTTAAATTCAATATCAAAATGATATAATGTATAAACATTGGAGGGCTAAATTTGT
57648648 TG
1 TG
57648650 TTAGATAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
59 3 0.06
60 4 0.07
61 28 0.52
62 19 0.35
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.42
Consensus pattern (62 bp):
TGAATGTTTTAAATTCAATATCAAAATGATATAATGTATAAACATTGGAGGGCTAAATTTGT
Found at i:57653189 original size:12 final size:13
Alignment explanation
Indices: 57653163--57653192 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
57653153 TTCTTACTGA
57653163 TCTTTACTGAAAC
1 TCTTTACTGAAAC
57653176 TCTTTACT-AAAC
1 TCTTTACTGAAAC
57653188 TCTTT
1 TCTTT
57653193 TGGCGAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.27, C:0.23, G:0.03, T:0.47
Consensus pattern (13 bp):
TCTTTACTGAAAC
Found at i:57654232 original size:16 final size:17
Alignment explanation
Indices: 57654213--57654247 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
57654203 TGTAATGATA
*
57654213 AATGATAT-TTAAATAT
1 AATGATATATAAAATAT
57654229 AATGATATATAAAATAT
1 AATGATATATAAAATAT
57654246 AA
1 AA
57654248 ATTGATCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (17 bp):
AATGATATATAAAATAT
Found at i:57654926 original size:21 final size:20
Alignment explanation
Indices: 57654900--57654948 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
57654890 ACGGTGATGG
*
57654900 TGAGATTGATTACTGTAACAA
1 TGAGATTGA-TACTATAACAA
* *
57654921 TGAGATAGGATACTATAACAG
1 TGAGAT-TGATACTATAACAA
57654942 TGAGATT
1 TGAGATT
57654949 AAAAACAACG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (20 bp):
TGAGATTGATACTATAACAA
Found at i:57655794 original size:26 final size:26
Alignment explanation
Indices: 57655765--57655818 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
57655755 TTAAAATTTT
* * *
57655765 TTCGAATCGAGTCGAGTGAAATGAAA
1 TTCGAATCAAGTCGAATCAAATGAAA
*
57655791 TTCGAGTCAAGTCGAATCAAATGAAA
1 TTCGAATCAAGTCGAATCAAATGAAA
57655817 TT
1 TT
57655819 GTGAGTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (26 bp):
TTCGAATCAAGTCGAATCAAATGAAA
Found at i:57655812 original size:21 final size:21
Alignment explanation
Indices: 57655771--57655812 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
57655761 TTTTTTCGAA
* *
57655771 TCGAGTCGAGTGAAATGAAAT
1 TCGAGTCAAGTGAAATCAAAT
57655792 TCGAGTCAAGTCG-AATCAAAT
1 TCGAGTCAAGT-GAAATCAAAT
57655813 GAAATTGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (21 bp):
TCGAGTCAAGTGAAATCAAAT
Found at i:57656027 original size:29 final size:29
Alignment explanation
Indices: 57655994--57656053 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
57655984 GGTCCCAAAA
57655994 TTATTAGTCTAGAAAATTTT-TAAATTTTT
1 TTATTAGTCTAGAAAATTTTAT-AATTTTT
** * *
57656023 TTATTTTTTTTGAAAATTTTATAATTTTT
1 TTATTAGTCTAGAAAATTTTATAATTTTT
57656052 TT
1 TT
57656054 GTTGAGAGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (29 bp):
TTATTAGTCTAGAAAATTTTATAATTTTT
Found at i:57658038 original size:30 final size:29
Alignment explanation
Indices: 57658004--57658083 Score: 90
Period size: 28 Copynumber: 2.7 Consensus size: 29
57657994 TTAAATTAAT
* *
57658004 AAATTTACTTTTATGATTCATATAATAAAC
1 AAATTTAATTTTATGA-TCATATAACAAAC
* * *
57658034 AAATTTATTTTTTTGA-CTTATAACAAAC
1 AAATTTAATTTTATGATCATATAACAAAC
57658062 AAATTTAATTTTATGACTCATA
1 AAATTTAATTTTATGA-TCATA
57658084 CTTTTACATA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
28 24 0.59
30 17 0.41
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (29 bp):
AAATTTAATTTTATGATCATATAACAAAC
Found at i:57666210 original size:15 final size:16
Alignment explanation
Indices: 57666178--57666220 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
57666168 ATTTTGAAGA
* *
57666178 ATTTTGAAATGAAGTC
1 ATTTTAAAATGCAGTC
57666194 ATTTTAAAATGCA-TC
1 ATTTTAAAATGCAGTC
*
57666209 ATTTCAAAATGC
1 ATTTTAAAATGC
57666221 TAGCATTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (16 bp):
ATTTTAAAATGCAGTC
Found at i:57670098 original size:16 final size:16
Alignment explanation
Indices: 57670077--57670114 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
57670067 TTGGTTTCAC
57670077 GTAAATTAGTTTTTGA
1 GTAAATTAGTTTTTGA
*
57670093 GTAAATTGGTTTTTGA
1 GTAAATTAGTTTTTGA
57670109 GTAAAT
1 GTAAAT
57670115 CATATTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (16 bp):
GTAAATTAGTTTTTGA
Found at i:57672694 original size:31 final size:32
Alignment explanation
Indices: 57672653--57672712 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
57672643 AATATTACTA
57672653 TAGTGACAGCAATGAAGGCTAAAACAGGACTG
1 TAGTGACAGCAATGAAGGCTAAAACAGGACTG
* *
57672685 TAGTG-CAGCAATGAAGGTTGAAACAGGA
1 TAGTGACAGCAATGAAGGCTAAAACAGGA
57672713 GAGAAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.40, C:0.13, G:0.30, T:0.17
Consensus pattern (32 bp):
TAGTGACAGCAATGAAGGCTAAAACAGGACTG
Found at i:57675570 original size:20 final size:20
Alignment explanation
Indices: 57675545--57675583 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
57675535 TGTGAAGTTT
*
57675545 ATTGATCAGTATTTTATATA
1 ATTGATCAATATTTTATATA
*
57675565 ATTGATGAATATTTTATAT
1 ATTGATCAATATTTTATAT
57675584 TAGAAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (20 bp):
ATTGATCAATATTTTATATA
Found at i:57679274 original size:14 final size:14
Alignment explanation
Indices: 57679255--57679284 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
57679245 GTATTTTGAC
*
57679255 TTGTAATTGTTTTA
1 TTGTAATTATTTTA
57679269 TTGTAATTATTTTA
1 TTGTAATTATTTTA
57679283 TT
1 TT
57679285 AATTTGATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (14 bp):
TTGTAATTATTTTA
Found at i:57681044 original size:53 final size:53
Alignment explanation
Indices: 57680986--57681094 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
57680976 CACGGTATAT
57680986 ACATGCTAATGAAATTGATAACAATTTAGTTATTAACTAATATATTATGTTTG
1 ACATGCTAATGAAATTGATAACAATTTAGTTATTAACTAATATATTATGTTTG
57681039 ACATGCTAATGAAATTGATAACAATTTAGTTATTAACTAATATATTATGTTTG
1 ACATGCTAATGAAATTGATAACAATTTAGTTATTAACTAATATATTATGTTTG
57681092 ACA
1 ACA
57681095 GGTAGTTGTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.40
Consensus pattern (53 bp):
ACATGCTAATGAAATTGATAACAATTTAGTTATTAACTAATATATTATGTTTG
Done.