Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 7 of 82
Found at i:2267884 original size:17 final size:18
Alignment explanation
Indices: 2267855--2267888 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2267845 GATTGAAATT
2267855 TTTTTAAATAATATTTAA
1 TTTTTAAATAATATTTAA
2267873 TTTTTAAA-AATATTTA
1 TTTTTAAATAATATTTA
2267889 TAGTATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTTAAATAATATTTAA
Found at i:2282483 original size:23 final size:23
Alignment explanation
Indices: 2282443--2282489 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2282433 ATTCATCCCC
*
2282443 TAAAAACAGTAACTACTAACCAT
1 TAAAAACAGTAACTACTAAACAT
*
2282466 TAAAAACAGTAGGC-ACTAAACAT
1 TAAAAACAGTA-ACTACTAAACAT
2282489 T
1 T
2282490 GAAATTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.51, C:0.19, G:0.09, T:0.21
Consensus pattern (23 bp):
TAAAAACAGTAACTACTAAACAT
Found at i:2287488 original size:23 final size:24
Alignment explanation
Indices: 2287458--2287503 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
2287448 ATTTTTATTT
2287458 TATTTTTTATTATCA-TATTTTTC
1 TATTTTTTATTATCATTATTTTTC
* *
2287481 TATTTTTTCTTATTATTATTTTT
1 TATTTTTTATTATCATTATTTTT
2287504 TTGTAAGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.74
Consensus pattern (24 bp):
TATTTTTTATTATCATTATTTTTC
Found at i:2287653 original size:11 final size:10
Alignment explanation
Indices: 2287633--2287675 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
2287623 ATTTTTTGGC
2287633 ATTTATTATT
1 ATTTATTATT
2287643 ATTTAATTATT
1 ATTT-ATTATT
2287654 ATTT-TTATTT
1 ATTTATTA-TT
*
2287664 ATTTTTTATT
1 ATTTATTATT
2287674 AT
1 AT
2287676 CATATTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 3 0.10
10 14 0.47
11 13 0.43
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
ATTTATTATT
Found at i:2287655 original size:17 final size:17
Alignment explanation
Indices: 2287635--2287675 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2287625 TTTTTGGCAT
2287635 TTATTATTATTTAATTA
1 TTATTATTATTTAATTA
* * *
2287652 TTATTTTTATTTATTTT
1 TTATTATTATTTAATTA
2287669 TTATTAT
1 TTATTAT
2287676 CATATTTTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATTATTATTTAATTA
Found at i:2287674 original size:23 final size:23
Alignment explanation
Indices: 2287634--2287708 Score: 73
Period size: 23 Copynumber: 3.1 Consensus size: 23
2287624 TTTTTTGGCA
*
2287634 TTTA-TTATTATTTAATTATTATT
1 TTTATTTATT-TTTTATTATTATT
2287657 TTTATTTATTTTTTATTATCATATTT
1 TTTATTTATTTTTTATTAT--TA-TT
*
2287683 TTCTATTT-TTTCTTATTATTATT
1 TT-TATTTATTTTTTATTATTATT
2287706 TTT
1 TTT
2287709 TTGTAAGCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
22 1 0.02
23 16 0.36
24 7 0.16
25 2 0.04
26 14 0.31
27 5 0.11
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTATTTATTTTTTATTATTATT
Found at i:2287698 original size:26 final size:26
Alignment explanation
Indices: 2287655--2287710 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
2287645 TTAATTATTA
*
2287655 TTTTTATTTATTTTTTATTATCATAT
1 TTTTTATTTATTTCTTATTATCATAT
*
2287681 TTTTCTATTT-TTTCTTATTATTAT-T
1 TTTT-TATTTATTTCTTATTATCATAT
2287706 TTTTT
1 TTTTT
2287711 GTAAGCAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 1 0.04
25 5 0.19
26 16 0.59
27 5 0.19
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (26 bp):
TTTTTATTTATTTCTTATTATCATAT
Found at i:2287724 original size:205 final size:206
Alignment explanation
Indices: 2287355--2287762 Score: 766
Period size: 205 Copynumber: 2.0 Consensus size: 206
2287345 TCGAAAACAT
* *
2287355 AAATATTTATATGCAATGATATGCATGATGCAATATATATGCTATGCTAATACAATTATCTATTT
1 AAATATTTATATGCAATGATATGCATGATGCAATATATATGCTATGATAACACAATTATCTATTT
2287420 TTTGGTCATTTATTATTATTTAATTATTATTTTTATTTTATTTTTTATTATCATATTTTTCTATT
66 TTTGGTCATTTATTATTATTTAATTATTATTTTTATTTTATTTTTTATTATCATATTTTTCTATT
2287485 TTTTCTTATTATTATTTTTTTGTAAGCAATCTTTTATCCAAACCTAATGCCTAAAATTTTATATC
131 TTTTCTTATTATTATTTTTTTGTAAGCAATCTTTTATCCAAACCTAATGCCTAAAATTTTATATC
2287550 TATGTTTNATAG
196 TATGTTT-ATAG
*
2287562 AAATATTTATATGCAATGGTATGCATGATGCAATATATATGCTATGATAACACAATTATCTATTT
1 AAATATTTATATGCAATGATATGCATGATGCAATATATATGCTATGATAACACAATTATCTATTT
2287627 TTTGG-CATTTATTATTATTTAATTATTATTTTTA-TTTATTTTTTATTATCATATTTTTCTATT
66 TTTGGTCATTTATTATTATTTAATTATTATTTTTATTTTATTTTTTATTATCATATTTTTCTATT
2287690 TTTTCTTATTATTATTTTTTTGTAAGCAATCTTTTATCCAAACCTAATGCCTAAAATTTTATATC
131 TTTTCTTATTATTATTTTTTTGTAAGCAATCTTTTATCCAAACCTAATGCCTAAAATTTTATATC
2287755 TATGTTTA
196 TATGTTTA
2287763 ATTCTATTTT
Statistics
Matches: 198, Mismatches: 3, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
204 1 0.01
205 101 0.51
206 29 0.15
207 67 0.34
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (206 bp):
AAATATTTATATGCAATGATATGCATGATGCAATATATATGCTATGATAACACAATTATCTATTT
TTTGGTCATTTATTATTATTTAATTATTATTTTTATTTTATTTTTTATTATCATATTTTTCTATT
TTTTCTTATTATTATTTTTTTGTAAGCAATCTTTTATCCAAACCTAATGCCTAAAATTTTATATC
TATGTTTATAG
Found at i:2288015 original size:28 final size:29
Alignment explanation
Indices: 2287958--2288015 Score: 66
Period size: 28 Copynumber: 2.0 Consensus size: 29
2287948 TACATTTGAA
**
2287958 TTATTATTATTATCATTTTTATTATTTAT
1 TTATTATTATTATCATTTTTATTACCTAT
*
2287987 TTATTA-TATATAT-ATTTTTTTTACCTAT
1 TTATTATTAT-TATCATTTTTATTACCTAT
2288015 T
1 T
2288016 ATTTGTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (29 bp):
TTATTATTATTATCATTTTTATTACCTAT
Found at i:2288030 original size:15 final size:16
Alignment explanation
Indices: 2288012--2288050 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
2288002 TTTTTTTACC
2288012 TATTATTTGT-TTATT
1 TATTATTTGTATTATT
2288027 TATTATTT-TATTATT
1 TATTATTTGTATTATT
*
2288042 TATTTTTTG
1 TATTATTTG
2288051 AATGATTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (16 bp):
TATTATTTGTATTATT
Found at i:2288414 original size:17 final size:18
Alignment explanation
Indices: 2288387--2288420 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2288377 TATTTCATTC
2288387 TTTTATGTATTATTATTG
1 TTTTATGTATTATTATTG
*
2288405 TTTTAT-TATTTTTATT
1 TTTTATGTATTATTATT
2288421 CTTGTTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (18 bp):
TTTTATGTATTATTATTG
Found at i:2297631 original size:15 final size:14
Alignment explanation
Indices: 2297611--2297652 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
2297601 CCTCTCTCCT
2297611 TTTTTCATTCTTTCA
1 TTTTTCATT-TTTCA
2297626 TTTTTCATTTTTCA
1 TTTTTCATTTTTCA
*
2297640 TTTATACATTTTT
1 TTT-TTCATTTTT
2297653 TACTCTGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTTCATTTTTCA
Found at i:2297633 original size:7 final size:7
Alignment explanation
Indices: 2297611--2297652 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
2297601 CCTCTCTCCT
2297611 TTTTTCA
1 TTTTTCA
2297618 TTCTTTCA
1 TT-TTTCA
2297626 TTTTTCA
1 TTTTTCA
2297633 TTTTTCA
1 TTTTTCA
*
2297640 TTTATACA
1 TTT-TTCA
2297648 TTTTT
1 TTTTT
2297653 TACTCTGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 18 0.58
8 13 0.42
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTTTCA
Found at i:2297649 original size:22 final size:22
Alignment explanation
Indices: 2297611--2297652 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2297601 CCTCTCTCCT
*
2297611 TTTTTCATTCTTTCATTTTTCA
1 TTTTTCATTCTTACATTTTTCA
2297633 TTTTTCATT-TATACATTTTT
1 TTTTTCATTCT-TACATTTTT
2297653 TACTCTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTTCATTCTTACATTTTTCA
Found at i:2306310 original size:21 final size:22
Alignment explanation
Indices: 2306279--2306321 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
2306269 AGTGTATGTA
2306279 TTATTTATAATTGATAAATTAT
1 TTATTTATAATTGATAAATTAT
*
2306301 TTATTT-TAATTTATAAATTAT
1 TTATTTATAATTGATAAATTAT
2306322 CTAAATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TTATTTATAATTGATAAATTAT
Found at i:2319038 original size:18 final size:18
Alignment explanation
Indices: 2319015--2319051 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2319005 GGAGAAGAAG
2319015 CTATCAAGGAGGAACAAA
1 CTATCAAGGAGGAACAAA
2319033 CTATCAAGGAGGAACAAA
1 CTATCAAGGAGGAACAAA
2319051 C
1 C
2319052 AGAGGAAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.19, G:0.22, T:0.11
Consensus pattern (18 bp):
CTATCAAGGAGGAACAAA
Found at i:2339303 original size:24 final size:24
Alignment explanation
Indices: 2339276--2339321 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
2339266 AAAATATTTT
2339276 TGTTACACGCCAT-GTATAAAAATA
1 TGTTACACGCCATAGT-TAAAAATA
2339300 TGTTACACGCCATAGTTAAAAA
1 TGTTACACGCCATAGTTAAAAA
2339322 AGGTTGTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.28
Consensus pattern (24 bp):
TGTTACACGCCATAGTTAAAAATA
Found at i:2340062 original size:47 final size:47
Alignment explanation
Indices: 2339966--2340098 Score: 153
Period size: 47 Copynumber: 2.8 Consensus size: 47
2339956 TTTTATAAGA
* * * * *
2339966 CATTACGTGAC-AGTTTCTGATAAGACATTACGTGACT-AGTTAATAGG
1 CATTGCGTGACTAGTTTTTGATAAGATATTGCGTGACTAACTT--TAGG
* * *
2340013 CATTGCGTGACTAGTTTTTTATAAGGTATTGTGTGACTAACTTTAGG
1 CATTGCGTGACTAGTTTTTGATAAGATATTGCGTGACTAACTTTAGG
*
2340060 CATTGCGTGATTAGTTTTTGATAAGATATTGCGTGACTA
1 CATTGCGTGACTAGTTTTTGATAAGATATTGCGTGACTA
2340099 GTTTTTGATA
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
47 49 0.68
48 20 0.28
49 3 0.04
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (47 bp):
CATTGCGTGACTAGTTTTTGATAAGATATTGCGTGACTAACTTTAGG
Found at i:2340111 original size:26 final size:26
Alignment explanation
Indices: 2339954--2340127 Score: 125
Period size: 26 Copynumber: 7.1 Consensus size: 26
2339944 ACGTGATTGA
* *
2339954 TTTTTTATAAGACATTACGTGAC-AG
1 TTTTTGATAAGACATTGCGTGACTAG
* *
2339979 TTTCTGATAAGACATTACGTGACTAG
1 TTTTTGATAAGACATTGCGTGACTAG
* *
2340005 ---TTAAT-AGGCATTGCGTGACTAG
1 TTTTTGATAAGACATTGCGTGACTAG
* ** *
2340027 TTTTTTATAAGGTATTGTGTGACTA-
1 TTTTTGATAAGACATTGCGTGACTAG
** * *
2340052 -ACTT--T-AGGCATTGCGTGATTAG
1 TTTTTGATAAGACATTGCGTGACTAG
*
2340074 TTTTTGATAAGATATTGCGTGACTAG
1 TTTTTGATAAGACATTGCGTGACTAG
* *
2340100 TTTTTGATAAGACATTGCATGACCAG
1 TTTTTGATAAGACATTGCGTGACTAG
2340126 TT
1 TT
2340128 GATAGGCATT
Statistics
Matches: 117, Mismatches: 22, Indels: 19
0.74 0.14 0.12
Matches are distributed among these distances:
21 13 0.11
22 16 0.14
23 5 0.04
24 2 0.02
25 26 0.22
26 55 0.47
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (26 bp):
TTTTTGATAAGACATTGCGTGACTAG
Found at i:2340161 original size:23 final size:23
Alignment explanation
Indices: 2340131--2340229 Score: 126
Period size: 23 Copynumber: 4.3 Consensus size: 23
2340121 ACCAGTTGAT
2340131 AGGCATTGCGTGACTTGTTAGTA
1 AGGCATTGCGTGACTTGTTAGTA
* *
2340154 AGGCATTGCATGACTTGTTAGTT
1 AGGCATTGCGTGACTTGTTAGTA
*
2340177 AGGCATTGCGTGATTTGTTAGTA
1 AGGCATTGCGTGACTTGTTAGTA
* * ** *
2340200 AGGTATTGTGTGACTAATTCGTA
1 AGGCATTGCGTGACTTGTTAGTA
2340223 AGGCATT
1 AGGCATT
2340230 ACTTAAAAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.23, C:0.11, G:0.28, T:0.37
Consensus pattern (23 bp):
AGGCATTGCGTGACTTGTTAGTA
Found at i:2340167 original size:45 final size:46
Alignment explanation
Indices: 2340107--2340207 Score: 141
Period size: 46 Copynumber: 2.2 Consensus size: 46
2340097 TAGTTTTTGA
*
2340107 TAAGACATTGCATGACCAGTT-GATAGGCATTGCGTGACTTGTTAG
1 TAAGGCATTGCATGACCAGTTAGATAGGCATTGCGTGACTTGTTAG
** * *
2340152 TAAGGCATTGCATGACTTGTTAGTTAGGCATTGCGTGATTTGTTAG
1 TAAGGCATTGCATGACCAGTTAGATAGGCATTGCGTGACTTGTTAG
*
2340198 TAAGGTATTG
1 TAAGGCATTG
2340208 TGTGACTAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
45 18 0.37
46 31 0.63
ACGTcount: A:0.25, C:0.12, G:0.28, T:0.36
Consensus pattern (46 bp):
TAAGGCATTGCATGACCAGTTAGATAGGCATTGCGTGACTTGTTAG
Found at i:2340179 original size:120 final size:117
Alignment explanation
Indices: 2339932--2340191 Score: 281
Period size: 120 Copynumber: 2.2 Consensus size: 117
2339922 TGCGTGATTG
* * *
2339932 ACTTTGGGCATTACGTGATTGATTTTTTATAAGACATTACGTGACAGTTTCTGATAAGACATTAC
1 ACTTTAGGCATTGCGTGATTGATTTTTGATAAGACATTACGTGACAGTTTCTGATAAGACATTAC
* * * * **
2339997 GTGACTAGTTAATAGGCATTGCGTGACTAGTTTTTTATAAGGTATTGTGTGACTA
66 ATGACCAGTTAATAGGCATTGCGTGAC---TTTGTTATAAGGCATTGCATGACTA
* * *
2340052 ACTTTAGGCATTGCGTGATT-AGTTTTTGATAAGATATTGCGTGACTAGTTTTTGATAAGACATT
1 ACTTTAGGCATTGCGTGATTGA-TTTTTGATAAGACATTACGTGAC-AGTTTCTGATAAGACATT
* * *
2340116 GCATGACCAGTTGATAGGCATTGCGTGAC-TTGTTAGTAAGGCATTGCATGACTT
64 ACATGACCAGTTAATAGGCATTGCGTGACTTTGTTA-TAAGGCATTGCATGACTA
**
2340170 GTTAGTTAGGCATTGCGTGATT
1 ACT--TTAGGCATTGCGTGATT
2340192 TGTTAGTAAG
Statistics
Matches: 118, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
117 5 0.04
118 15 0.13
119 1 0.01
120 55 0.47
121 42 0.36
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (117 bp):
ACTTTAGGCATTGCGTGATTGATTTTTGATAAGACATTACGTGACAGTTTCTGATAAGACATTAC
ATGACCAGTTAATAGGCATTGCGTGACTTTGTTATAAGGCATTGCATGACTA
Found at i:2340274 original size:22 final size:21
Alignment explanation
Indices: 2340249--2340308 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
2340239 TCAATCATGC
*
2340249 AATGTATAAAAACTAGTCACGT
1 AATG-ATAAAAACTAATCACGT
* *
2340271 AATGCCT-AAAACCAATCACGT
1 AATG-ATAAAAACTAATCACGT
2340292 AATGACTAAAAACTAAT
1 AATGA-TAAAAACTAAT
2340309 TGTACGGTGA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.48, C:0.18, G:0.10, T:0.23
Consensus pattern (21 bp):
AATGATAAAAACTAATCACGT
Found at i:2341074 original size:29 final size:27
Alignment explanation
Indices: 2341042--2341107 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
2341032 AAAAACTGTA
2341042 GTTGTTACACGCCATGTTGAAAAAATATT
1 GTTGTTACACGCCATGTT--AAAAATATT
*
2341071 GTTGTTACACGCTATGTTAAAAATATT
1 GTTGTTACACGCCATGTTAAAAATATT
* *
2341098 TTTATTACAC
1 GTTGTTACAC
2341108 TTTAATACCT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 17 0.50
29 17 0.50
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (27 bp):
GTTGTTACACGCCATGTTAAAAATATT
Found at i:2342831 original size:22 final size:22
Alignment explanation
Indices: 2342803--2342884 Score: 85
Period size: 22 Copynumber: 3.7 Consensus size: 22
2342793 GTAGTTTTGG
* *
2342803 TGATTTTTAGGCATTGTGTAAC
1 TGATTTTTAGGTATTGCGTAAC
* *
2342825 TGATTTTTAGGTATTACGTGAC
1 TGATTTTTAGGTATTGCGTAAC
*
2342847 T-AGTTTTTAGGTATTGCGTTAC
1 TGA-TTTTTAGGTATTGCGTAAC
* *
2342869 TAATTTTTAAGTATTG
1 TGATTTTTAGGTATTG
2342885 TGTAGCAGGT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
21 1 0.02
22 49 0.96
23 1 0.02
ACGTcount: A:0.23, C:0.07, G:0.21, T:0.49
Consensus pattern (22 bp):
TGATTTTTAGGTATTGCGTAAC
Found at i:2343057 original size:83 final size:83
Alignment explanation
Indices: 2342914--2343072 Score: 198
Period size: 83 Copynumber: 1.9 Consensus size: 83
2342904 ATTACGTGAC
* * *
2342914 TGATTTTTAGATATCGCGTTACTGGTTGATAGGGCATCGTGTCATTGGTTATTAGACATTACGTG
1 TGATTTTTAGATATCGCGTGACTGGTTGATAGGGCATCGTGTCACTGATTATTAGACATTACGTG
2342979 ACTTAGGCATTCTGTAAT
66 ACTTAGGCATTCTGTAAT
* * * * *
2342997 TGATTTTTAG-TCATTGCGTGACTGGTT-AGTAGGGCATTGTGTGACTGATTTTTA-AGCATTAT
1 TGATTTTTAGAT-ATCGCGTGACTGGTTGA-TAGGGCATCGTGTCACTGATTATTAGA-CATTAC
2343059 GTGACTTAGGCATT
63 GTGACTTAGGCATT
2343073 GCCTAAAAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
82 3 0.05
83 62 0.95
ACGTcount: A:0.22, C:0.12, G:0.25, T:0.41
Consensus pattern (83 bp):
TGATTTTTAGATATCGCGTGACTGGTTGATAGGGCATCGTGTCACTGATTATTAGACATTACGTG
ACTTAGGCATTCTGTAAT
Found at i:2343111 original size:22 final size:21
Alignment explanation
Indices: 2343072--2343159 Score: 86
Period size: 21 Copynumber: 4.1 Consensus size: 21
2343062 ACTTAGGCAT
* *
2343072 TGCCTAAAAATCAATCACGCAA
1 TGCCT-AAAACCAGTCACGCAA
* *
2343094 TGCCTACAACTCAGTCACGTAA
1 TGCCTAAAAC-CAGTCACGCAA
**
2343116 TGTTTAAAACCAGTCACGCAA
1 TGCCTAAAACCAGTCACGCAA
**
2343137 TGTTTAAAACCAGTCACGCAA
1 TGCCTAAAACCAGTCACGCAA
2343158 TG
1 TG
2343160 TTTAAGTCAC
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
21 36 0.63
22 21 0.37
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.23
Consensus pattern (21 bp):
TGCCTAAAACCAGTCACGCAA
Found at i:2343131 original size:21 final size:21
Alignment explanation
Indices: 2343086--2343164 Score: 113
Period size: 21 Copynumber: 3.7 Consensus size: 21
2343076 TAAAAATCAA
** *
2343086 TCACGCAATGCCTACAACTCAG
1 TCACGCAATGTTTAAAAC-CAG
*
2343108 TCACGTAATGTTTAAAACCAG
1 TCACGCAATGTTTAAAACCAG
2343129 TCACGCAATGTTTAAAACCAG
1 TCACGCAATGTTTAAAACCAG
2343150 TCACGCAATGTTTAA
1 TCACGCAATGTTTAA
2343165 GTCACGTAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
21 38 0.73
22 14 0.27
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.25
Consensus pattern (21 bp):
TCACGCAATGTTTAAAACCAG
Found at i:2346493 original size:34 final size:34
Alignment explanation
Indices: 2346450--2346519 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
2346440 GTACCAATTG
* *
2346450 ATTAAAATTATATCTTGGATTGGAAATGCTAATA
1 ATTAAAATTATATCTTGGATTAGAAAGGCTAATA
*
2346484 ATTAAAATTATATCTTGGATTAGAACGGCTAATA
1 ATTAAAATTATATCTTGGATTAGAAAGGCTAATA
2346518 AT
1 AT
2346520 CAAGAAACCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.37
Consensus pattern (34 bp):
ATTAAAATTATATCTTGGATTAGAAAGGCTAATA
Found at i:2353516 original size:27 final size:27
Alignment explanation
Indices: 2353478--2353531 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
2353468 TCAGCAAGTT
*
2353478 TTTGACCTATTTCACAGAATTTTTCGA
1 TTTGACCCATTTCACAGAATTTTTCGA
*
2353505 TTTGACCCATTTCATAGAATTTTTCGA
1 TTTGACCCATTTCACAGAATTTTTCGA
2353532 ATCGGATTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.44
Consensus pattern (27 bp):
TTTGACCCATTTCACAGAATTTTTCGA
Found at i:2361576 original size:22 final size:22
Alignment explanation
Indices: 2361551--2361592 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2361541 TACGTGATTG
*
2361551 GTTTTAGGCATTACGTGACTAA
1 GTTTTAGACATTACGTGACTAA
* *
2361573 GTTTTATACATTGCGTGACT
1 GTTTTAGACATTACGTGACT
2361593 GATTTTTAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.40
Consensus pattern (22 bp):
GTTTTAGACATTACGTGACTAA
Found at i:2361668 original size:23 final size:24
Alignment explanation
Indices: 2361610--2361696 Score: 85
Period size: 23 Copynumber: 3.8 Consensus size: 24
2361600 AAGCAATGCT
*
2361610 TAAGTCACGCAATGCCTTACTAAC
1 TAAGTCACGCAATACCTTACTAAC
* *
2361634 T-AGTGACACAATACCTTACTAA-
1 TAAGTCACGCAATACCTTACTAAC
*
2361656 TAAGTCACGCAATGCC-TA-TCAAC
1 TAAGTCACGCAATACCTTACT-AAC
*
2361679 T-AGTCATGCAATACCTTA
1 TAAGTCACGCAATACCTTA
2361697 TCAGAAACTA
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
21 1 0.02
22 17 0.33
23 32 0.63
24 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.26
Consensus pattern (24 bp):
TAAGTCACGCAATACCTTACTAAC
Found at i:2361695 original size:45 final size:46
Alignment explanation
Indices: 2361610--2361696 Score: 124
Period size: 45 Copynumber: 1.9 Consensus size: 46
2361600 AAGCAATGCT
*
2361610 TAAGTCACGCAATGCCTTACTAACTAGTGACACAATACCTTACTAA
1 TAAGTCACGCAATGCCTTACTAACTAGTCACACAATACCTTACTAA
**
2361656 TAAGTCACGCAATGCC-TA-TCAACTAGTCATGCAATACCTTA
1 TAAGTCACGCAATGCCTTACT-AACTAGTCACACAATACCTTA
2361697 TCAGAAACTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
44 1 0.03
45 20 0.54
46 16 0.43
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.26
Consensus pattern (46 bp):
TAAGTCACGCAATGCCTTACTAACTAGTCACACAATACCTTACTAA
Found at i:2361705 original size:26 final size:25
Alignment explanation
Indices: 2361612--2361957 Score: 231
Period size: 26 Copynumber: 14.6 Consensus size: 25
2361602 GCAATGCTTA
*
2361612 AGTCACGCAATGCCTTA-C-TAACT
1 AGTCACGCAATGCCTTATCAAAACT
* * * *
2361635 AGTGACACAATACCTTA-C-TAA-T
1 AGTCACGCAATGCCTTATCAAAACT
2361657 AAGTCACGCAATGCC-TATC--AACT
1 -AGTCACGCAATGCCTTATCAAAACT
* *
2361680 AGTCATGCAATACCTTATCAGAAACT
1 AGTCACGCAATGCCTTATCA-AAACT
**
2361706 AGTCACGCAATGCC----CAAAGTT
1 AGTCACGCAATGCCTTATCAAAACT
*
2361727 AGTCACGCAATGCC-TATC--ACCT
1 AGTCACGCAATGCCTTATCAAAACT
*
2361749 AGTCACGCAATGCC-TATC--ACCT
1 AGTCACGCAATGCCTTATCAAAACT
* *
2361771 AGTCACGCAATGTCTTATTAGAAACT
1 AGTCACGCAATGCCTTATCA-AAACT
2361797 AGTCACGCAATGCCTTATCAAAAACT
1 AGTCACGCAATGCCTTATC-AAAACT
2361823 AGTCACGCAATGCCTTATCAAAAACT
1 AGTCACGCAATGCCTTATC-AAAACT
* *
2361849 AGTCACGTAATGCC----C-AAAGT
1 AGTCACGCAATGCCTTATCAAAACT
* * *
2361869 CAGTCACGTAATGTC-TAT--TAACT
1 -AGTCACGCAATGCCTTATCAAAACT
*
2361892 AGTCACGCAATGTCTTATCAAAAACT
1 AGTCACGCAATGCCTTATC-AAAACT
* * *
2361918 AGACACGTAATGCCTTATCAAAAAT
1 AGTCACGCAATGCCTTATCAAAACT
*
2361943 CAGTCACGTAATGCC
1 -AGTCACGCAATGCC
2361958 CAAAGTCAGT
Statistics
Matches: 268, Mismatches: 31, Indels: 45
0.78 0.09 0.13
Matches are distributed among these distances:
20 4 0.01
21 30 0.11
22 70 0.26
23 44 0.16
24 1 0.00
25 5 0.02
26 113 0.42
27 1 0.00
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.25
Consensus pattern (25 bp):
AGTCACGCAATGCCTTATCAAAACT
Found at i:2361741 original size:69 final size:69
Alignment explanation
Indices: 2361658--2361931 Score: 286
Period size: 69 Copynumber: 3.9 Consensus size: 69
2361648 CTTACTAATA
* * *
2361658 AGTCACGCAATGCCTATCAACTAGTCATGCAATACCTTATCAGAAACTAGTCACGCAATGCCCAA
1 AGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATGCCCAA
2361723 AGTT
66 AGTT
* *
2361727 AGTCACGCAATGCCTATCACCTAGTCACGCAATGCC-TATC---ACCTAGTCACGCAATGTCTTA
1 AGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATG-C---
** **
2361788 TTAGAAACT
62 CCA-AAGTT
*
2361797 AGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGTAATGC
1 AGTCACGCAATGCC-TATC---AACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATGC
*
2361862 CCAAAGTC
62 CCAAAGTT
* * * * * *
2361870 AGTCACGTAATGTCTATTAACTAGTCACGCAATGTCTTATCAAAAACTAGACACGTAATGCC
1 AGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATGCC
2361932 TTATCAAAAA
Statistics
Matches: 171, Mismatches: 21, Indels: 26
0.78 0.10 0.12
Matches are distributed among these distances:
65 15 0.09
66 1 0.01
68 4 0.02
69 76 0.44
70 17 0.10
71 4 0.02
72 3 0.02
73 14 0.08
74 18 0.11
75 4 0.02
77 1 0.01
78 14 0.08
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.24
Consensus pattern (69 bp):
AGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATGCCCAA
AGTT
Found at i:2361901 original size:95 final size:95
Alignment explanation
Indices: 2361793--2361971 Score: 315
Period size: 95 Copynumber: 1.9 Consensus size: 95
2361783 TCTTATTAGA
*
2361793 AACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATGCCTTATCAAAAA-CTAGTCACGT
1 AACTAGTCACGCAATGCCTTATCAAAAACTAGACACGCAATGCCTTATCAAAAATC-AGTCACGT
2361857 AATGCCCAAAGTCAGTCACGTAATGTCTATT
65 AATGCCCAAAGTCAGTCACGTAATGTCTATT
* *
2361888 AACTAGTCACGCAATGTCTTATCAAAAACTAGACACGTAATGCCTTATCAAAAATCAGTCACGTA
1 AACTAGTCACGCAATGCCTTATCAAAAACTAGACACGCAATGCCTTATCAAAAATCAGTCACGTA
2361953 ATGCCCAAAGTCAGTCACG
66 ATGCCCAAAGTCAGTCACG
2361972 CAATATCCAA
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
95 79 0.99
96 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (95 bp):
AACTAGTCACGCAATGCCTTATCAAAAACTAGACACGCAATGCCTTATCAAAAATCAGTCACGTA
ATGCCCAAAGTCAGTCACGTAATGTCTATT
Found at i:2361965 original size:69 final size:67
Alignment explanation
Indices: 2361823--2361955 Score: 158
Period size: 69 Copynumber: 1.9 Consensus size: 67
2361813 ATCAAAAACT
* * **
2361823 AGTCACGCAATGCCTTATCAAAAACTAGTCACGTAATGCCCAAAGTCAGTCACGTAATGTCTATT
1 AGTCACGCAATGCCTTATCAAAAACTAGACACGTAATGCCCAAAATCAGTCACGTAATGTC-ACC
2361888 AAC
65 AAC
*
2361891 TAGTCACGCAATGTCTTATCAAAAACTAGACACGTAATGCCTTATCAAAAATCAGTCACGTAATG
1 -AGTCACGCAATGCCTTATCAAAAACTAGACACGTAATGCC----C-AAAATCAGTCACGTAATG
2361956 CCCAAAGTCA
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
69 38 0.68
73 1 0.02
74 17 0.30
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (67 bp):
AGTCACGCAATGCCTTATCAAAAACTAGACACGTAATGCCCAAAATCAGTCACGTAATGTCACCA
AC
Found at i:2361966 original size:21 final size:21
Alignment explanation
Indices: 2361942--2361999 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
2361932 TTATCAAAAA
* *
2361942 TCAGTCACGTAATGCCCAAAG
1 TCAGTCACGCAATACCCAAAG
*
2361963 TCAGTCACGCAATATCCAAAG
1 TCAGTCACGCAATACCCAAAG
2361984 TCAGTCACGCAATACC
1 TCAGTCACGCAATACC
2362000 TAAAAACTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.34, C:0.31, G:0.16, T:0.19
Consensus pattern (21 bp):
TCAGTCACGCAATACCCAAAG
Found at i:2376811 original size:16 final size:16
Alignment explanation
Indices: 2376782--2376824 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
2376772 TTTTATTAAT
*
2376782 TATTTTTT-ACTTTTA
1 TATTTTTTAATTTTTA
2376797 TATTTTTTAATTTTTA
1 TATTTTTTAATTTTTA
*
2376813 TACATTTTTAAT
1 TA-TTTTTTAAT
2376825 ATAATTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 8 0.33
16 8 0.33
17 8 0.33
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTTTTAATTTTTA
Found at i:2405527 original size:16 final size:16
Alignment explanation
Indices: 2405503--2405534 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2405493 GATATAAAGA
2405503 GAGTCAATGAACGAGG
1 GAGTCAATGAACGAGG
*
2405519 GAGTTAATGAACGAGG
1 GAGTCAATGAACGAGG
2405535 ACGACATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.09, G:0.38, T:0.16
Consensus pattern (16 bp):
GAGTCAATGAACGAGG
Found at i:2408453 original size:29 final size:29
Alignment explanation
Indices: 2408403--2408458 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
2408393 ATCTTGTGAT
* **
2408403 TTTTTTTTAATTAGCATTTTGTAAATATC
1 TTTTTTCTAATTAGCAACTTGTAAATATC
*
2408432 TTTTTTCTAATTAGTAACTTGTAAATA
1 TTTTTTCTAATTAGCAACTTGTAAATA
2408459 ATTTTTATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (29 bp):
TTTTTTCTAATTAGCAACTTGTAAATATC
Found at i:2408464 original size:29 final size:28
Alignment explanation
Indices: 2408401--2408469 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
2408391 ATATCTTGTG
* **
2408401 ATTTTTTTTTAATTAGCATTTTGTAAAT
1 ATTTTTTTCTAATTAGCAACTTGTAAAT
*
2408429 ATCTTTTTTCTAATTAGTAACTTGTAAAT
1 AT-TTTTTTCTAATTAGCAACTTGTAAAT
2408458 AATTTTTATTCT
1 -ATTTTT-TTCT
2408470 CATAAGAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 2 0.06
29 26 0.76
30 6 0.18
ACGTcount: A:0.29, C:0.07, G:0.06, T:0.58
Consensus pattern (28 bp):
ATTTTTTTCTAATTAGCAACTTGTAAAT
Found at i:2410043 original size:19 final size:19
Alignment explanation
Indices: 2410009--2410045 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2409999 TCTAGTCACG
2410009 CAAAAAATATATGTTAAAC
1 CAAAAAATATATGTTAAAC
2410028 CAAATAAATATA-GTTAAA
1 CAAA-AAATATATGTTAAA
2410046 GCCCAAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.27
Consensus pattern (19 bp):
CAAAAAATATATGTTAAAC
Found at i:2412797 original size:81 final size:81
Alignment explanation
Indices: 2412662--2412826 Score: 330
Period size: 81 Copynumber: 2.0 Consensus size: 81
2412652 CTTTCTTGCT
2412662 CATGGTTACCTGATTCCTTTTAGCTTTATCTTATTCTATGGCTACTAAACTAATCTACAGCTAAC
1 CATGGTTACCTGATTCCTTTTAGCTTTATCTTATTCTATGGCTACTAAACTAATCTACAGCTAAC
2412727 TTAGTAACCAGATGAC
66 TTAGTAACCAGATGAC
2412743 CATGGTTACCTGATTCCTTTTAGCTTTATCTTATTCTATGGCTACTAAACTAATCTACAGCTAAC
1 CATGGTTACCTGATTCCTTTTAGCTTTATCTTATTCTATGGCTACTAAACTAATCTACAGCTAAC
2412808 TTAGTAACCAGATGAC
66 TTAGTAACCAGATGAC
2412824 CAT
1 CAT
2412827 TCAACAATCA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 84 1.00
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.37
Consensus pattern (81 bp):
CATGGTTACCTGATTCCTTTTAGCTTTATCTTATTCTATGGCTACTAAACTAATCTACAGCTAAC
TTAGTAACCAGATGAC
Found at i:2415377 original size:7 final size:7
Alignment explanation
Indices: 2415365--2415400 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
2415355 AGATTCACAC
2415365 GGAGCAA
1 GGAGCAA
2415372 GGAGCAA
1 GGAGCAA
2415379 GGAGCAA
1 GGAGCAA
2415386 GGAGCAA
1 GGAGCAA
2415393 GGAGCAA
1 GGAGCAA
2415400 G
1 G
2415401 CACTTATCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.42, C:0.14, G:0.44, T:0.00
Consensus pattern (7 bp):
GGAGCAA
Found at i:2418817 original size:35 final size:35
Alignment explanation
Indices: 2418771--2418896 Score: 126
Period size: 35 Copynumber: 3.6 Consensus size: 35
2418761 GAATAAGTAA
* *
2418771 AACAAGTGAAGTATTACTTCACGCAAAACAACTAG
1 AACAAGTGAAGTACTACTTCACGCAGAACAACTAG
** * * * *
2418806 AACAAGTGAAGTGTTACTTTACGCAGAATAATTAA
1 AACAAGTGAAGTACTACTTCACGCAGAACAACTAG
* **
2418841 AACAAGTGAAGTACTACTTAAAACAGAACAACTAG
1 AACAAGTGAAGTACTACTTCACGCAGAACAACTAG
* * *
2418876 AATAAGTAAAGCACTACTTCA
1 AACAAGTGAAGTACTACTTCA
2418897 TATAGAACAA
Statistics
Matches: 73, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 73 1.00
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (35 bp):
AACAAGTGAAGTACTACTTCACGCAGAACAACTAG
Found at i:2418894 original size:70 final size:70
Alignment explanation
Indices: 2418760--2418894 Score: 171
Period size: 70 Copynumber: 1.9 Consensus size: 70
2418750 TATTGTATAA
* * ** * ***
2418760 AGAATAAGTAAAACAAGTGAAGTATTACTTCACGCAAAACAACTAGAACAAGTGAAGTGTTACTT
1 AGAATAAGTAAAACAAGTGAAGTACTACTTAAAACAAAACAACTAGAACAAGTAAAGCACTACTT
2418825 TACGC
66 TACGC
* * *
2418830 AGAATAATTAAAACAAGTGAAGTACTACTTAAAACAGAACAACTAGAATAAGTAAAGCACTACTT
1 AGAATAAGTAAAACAAGTGAAGTACTACTTAAAACAAAACAACTAGAACAAGTAAAGCACTACTT
2418895 CATATAGAAC
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
70 54 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (70 bp):
AGAATAAGTAAAACAAGTGAAGTACTACTTAAAACAAAACAACTAGAACAAGTAAAGCACTACTT
TACGC
Found at i:2420387 original size:12 final size:12
Alignment explanation
Indices: 2420370--2420395 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2420360 GAGTTAACTT
2420370 ATACTAAAAAGC
1 ATACTAAAAAGC
2420382 ATACTAAAAAGC
1 ATACTAAAAAGC
2420394 AT
1 AT
2420396 GAAAATTTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.15, G:0.08, T:0.19
Consensus pattern (12 bp):
ATACTAAAAAGC
Found at i:2423626 original size:22 final size:22
Alignment explanation
Indices: 2423580--2423631 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
2423570 CAAATCTCTA
*
2423580 TGCAGCGAGCTTGAGTTCTAGC
1 TGCAGCGAGCTAGAGTTCTAGC
2423602 TGCAGCGAGCTAGAAG-TCTCA-C
1 TGCAGCGAGCTAG-AGTTCT-AGC
2423624 TGCAGCGA
1 TGCAGCGA
2423632 AAAACTTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 24 0.89
23 3 0.11
ACGTcount: A:0.23, C:0.25, G:0.31, T:0.21
Consensus pattern (22 bp):
TGCAGCGAGCTAGAGTTCTAGC
Found at i:2431659 original size:10 final size:12
Alignment explanation
Indices: 2431632--2431670 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
2431622 CAAAGCTTCC
2431632 CTCTCTAAATTCT
1 CTCTCT-AATTCT
2431645 CTCTCTAATTCT
1 CTCTCTAATTCT
2431657 CTCTCTAATTCT
1 CTCTCTAATTCT
2431669 CT
1 CT
2431671 TCTTATTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 20 0.77
13 6 0.23
ACGTcount: A:0.18, C:0.33, G:0.00, T:0.49
Consensus pattern (12 bp):
CTCTCTAATTCT
Found at i:2433325 original size:102 final size:101
Alignment explanation
Indices: 2433023--2433325 Score: 284
Period size: 102 Copynumber: 3.0 Consensus size: 101
2433013 TTAAAAAAAA
* * *
2433023 TCATATTTAGCCACTAGCTTTATCGCTTATATTTTGGCTGTAATTATATTATACTATTAGTCACA
1 TCATATTTAGCCGCTAGCTTTATCGCTCATATTTTGGCTGTAATGATATTATACTATTAGTCACA
* * *
2433088 AGCTTTATTGCTCATTCTTTGACCATAGTTCATCAC
66 AGCTTTATCGCTCATTCTTTGACCATAGTTTATTAC
* * ** * * * ** * * * *
2433124 TCTTACTTCAATCGCAAGGTTTACCGCTCATATTTTGGCTACAATGATATTTTTCTATTGGTCTC
1 TCATA-TTTAGCCGCTAGCTTTATCGCTCATATTTTGGCTGTAATGATATTATACTATTAGTCAC
** * * * *
2433189 AAATTTTATCGCTTATTCTTTGATCATAATTTATTAT
65 AAGCTTTATCGCTCATTCTTTGACCATAGTTTATTAC
* * * * *
2433226 TCATATTTTAGCCGCTAGCTTTATTGCTCATAATTTGGCTGTAATGATGTTATGCTATTAGCCAC
1 TCATA-TTTAGCCGCTAGCTTTATCGCTCATATTTTGGCTGTAATGATATTATACTATTAGTCAC
* *
2433291 AAGCTTTATCGCTCATT-TCTTGGCCCTAGTTTATT
65 AAGCTTTATCGCTCATTCT-TTGACCATAGTTTATT
2433326 GCTTACAAAT
Statistics
Matches: 150, Mismatches: 50, Indels: 3
0.74 0.25 0.01
Matches are distributed among these distances:
101 5 0.03
102 145 0.97
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.45
Consensus pattern (101 bp):
TCATATTTAGCCGCTAGCTTTATCGCTCATATTTTGGCTGTAATGATATTATACTATTAGTCACA
AGCTTTATCGCTCATTCTTTGACCATAGTTTATTAC
Found at i:2434288 original size:18 final size:18
Alignment explanation
Indices: 2434265--2434314 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
2434255 ACCTCGACAG
*
2434265 TAGGAATAACCTCAGTGT
1 TAGGAATAACCTCAGTAT
* *
2434283 TGGGAACAACCTCAGTAT
1 TAGGAATAACCTCAGTAT
*
2434301 TAGGAATACCCTCA
1 TAGGAATAACCTCA
2434315 TCTTGAATAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (18 bp):
TAGGAATAACCTCAGTAT
Found at i:2438060 original size:35 final size:35
Alignment explanation
Indices: 2438014--2438140 Score: 146
Period size: 35 Copynumber: 3.6 Consensus size: 35
2438004 TATTATACAA
* * *
2438014 AGAACAACTAAAACAAGTAAAGTGCTACATCACGC
1 AGAACAACTAAAACAAGTAAAGTGTTACTTCAAGC
* * *
2438049 AGAACAACTAAAACAAATGAAGTGTTACTTCATGC
1 AGAACAACTAAAACAAGTAAAGTGTTACTTCAAGC
* * * *
2438084 AGAACAACTAAAATAAGTGAAGTATTACTTAAAGC
1 AGAACAACTAAAACAAGTAAAGTGTTACTTCAAGC
* *
2438119 AGAACAACTAGAATAAGTAAAG
1 AGAACAACTAAAACAAGTAAAG
2438141 CACTACTCAA
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 80 1.00
ACGTcount: A:0.50, C:0.16, G:0.15, T:0.19
Consensus pattern (35 bp):
AGAACAACTAAAACAAGTAAAGTGTTACTTCAAGC
Found at i:2438899 original size:47 final size:47
Alignment explanation
Indices: 2438837--2438931 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
2438827 CCATTTACAT
*
2438837 AGTTCAATTCAAATGTACAAGGGATTTGTATCATCTCCCGTACATTC
1 AGTTCAATTCAAATGTACAAGGGATTTGGATCATCTCCCGTACATTC
*
2438884 AGTTCAATTCAAATGTACAAGGGATTTGGCTCATCTCCCGTACATTC
1 AGTTCAATTCAAATGTACAAGGGATTTGGATCATCTCCCGTACATTC
2438931 A
1 A
2438932 ACATTCCCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (47 bp):
AGTTCAATTCAAATGTACAAGGGATTTGGATCATCTCCCGTACATTC
Found at i:2446646 original size:156 final size:156
Alignment explanation
Indices: 2446358--2446671 Score: 436
Period size: 156 Copynumber: 2.0 Consensus size: 156
2446348 CTACGTTCAC
* * * *
2446358 GGACAATAAATTGATCTTTACGGTTTCTTAAACTAACCTAAAATCCCTTGCATACCCTCTCTTAT
1 GGACAATAAATTGATCTTTACGGTTTCTCAAACTAACCTAAAATCCCTTACATACCCTCTCTCAA
* * * * * * *
2446423 TAGCCCTCCAACAACAATCACTAAATTAGTCTAAACTCTATCTAAAGTGAACTCTTATATGCTCA
66 TAACCCTCCAACAACAATCACCAAATTACTCTAAACTCCACCTAAAGTGAACCCTTATATGCGCA
2446488 GTATCAT-TCTAATATATAGTCAATGT
131 GTATC-TCTCTAATATATAGTCAATGT
* * **
2446514 GGACAATAAATTGA-CTTTTATGGTTTCTCAAACTAACCTAAGATCTTTTACATACCCTCTCTCA
1 GGACAATAAATTGATC-TTTACGGTTTCTCAAACTAACCTAAAATCCCTTACATACCCTCTCTCA
2446578 ATAACCCTCCAACAACAATCACCAAATTACTCTAAACTCCACCTACAA-TGAACCCTTATATGCG
65 ATAACCCTCCAACAACAATCACCAAATTACTCTAAACTCCACCTA-AAGTGAACCCTTATATGCG
*
2446642 CAGTATCTCTCTAATATATAGTCGATGT
129 CAGTATCTCTCTAATATATAGTCAATGT
2446670 GG
1 GG
2446672 GATTCATGAC
Statistics
Matches: 139, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
155 2 0.01
156 135 0.97
157 2 0.01
ACGTcount: A:0.34, C:0.25, G:0.09, T:0.32
Consensus pattern (156 bp):
GGACAATAAATTGATCTTTACGGTTTCTCAAACTAACCTAAAATCCCTTACATACCCTCTCTCAA
TAACCCTCCAACAACAATCACCAAATTACTCTAAACTCCACCTAAAGTGAACCCTTATATGCGCA
GTATCTCTCTAATATATAGTCAATGT
Found at i:2447454 original size:26 final size:26
Alignment explanation
Indices: 2447423--2447476 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
2447413 TATGATAGTA
2447423 TTTCAACCACAATTTACCAAAAGCTT
1 TTTCAACCACAATTTACCAAAAGCTT
2447449 TTTCAACCACAATTTACCAAAAGCTT
1 TTTCAACCACAATTTACCAAAAGCTT
2447475 TT
1 TT
2447477 GAGTACTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (26 bp):
TTTCAACCACAATTTACCAAAAGCTT
Found at i:2450464 original size:20 final size:20
Alignment explanation
Indices: 2450436--2450473 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2450426 AGTTTATCAA
2450436 AATTCATTTTCATAAAATTC
1 AATTCATTTTCATAAAATTC
*
2450456 AATTTATTTTCATAAAAT
1 AATTCATTTTCATAAAAT
2450474 GATTTTCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTCATTTTCATAAAATTC
Found at i:2455864 original size:15 final size:17
Alignment explanation
Indices: 2455836--2455871 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
2455826 CCTTTATAGA
2455836 TTTTATTGTAG-TTTTG
1 TTTTATTGTAGTTTTTG
2455852 TTTTATT-TAGTTTTTG
1 TTTTATTGTAGTTTTTG
2455868 TTTT
1 TTTT
2455872 TCTATTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.11, C:0.00, G:0.14, T:0.75
Consensus pattern (17 bp):
TTTTATTGTAGTTTTTG
Found at i:2462617 original size:24 final size:23
Alignment explanation
Indices: 2462569--2462627 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
2462559 AATATGTAAT
*
2462569 TATAGGTTATATATTTTAAATGA
1 TATAAGTTATATATTTTAAATGA
* *
2462592 TATAAGTTATATTTTTTTAATAGA
1 TATAAGTTATATATTTTAAAT-GA
2462616 TATAAGTTATAT
1 TATAAGTTATAT
2462628 GTTAATATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 18 0.56
24 14 0.44
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (23 bp):
TATAAGTTATATATTTTAAATGA
Found at i:2462850 original size:15 final size:16
Alignment explanation
Indices: 2462814--2462853 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
2462804 CTATATAAAC
*
2462814 AAAACTTATAATTTATT
1 AAAA-TTATAACTTATT
2462831 AAAATTATAACTTA-T
1 AAAATTATAACTTATT
2462846 AAAATTAT
1 AAAATTAT
2462854 TAGTGTTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 9 0.41
17 4 0.18
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAATTATAACTTATT
Found at i:2472175 original size:28 final size:29
Alignment explanation
Indices: 2472129--2472190 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
2472119 GATGGATATT
* * * *
2472129 TTTTAACTCATTAGCAGTGGACGAATAC-
1 TTTTAACCCATCAGAAGTGGAAGAATACA
2472157 TTTTAACCCATCAGAAGTGGAAGAATACA
1 TTTTAACCCATCAGAAGTGGAAGAATACA
2472186 TTTTA
1 TTTTA
2472191 GGTTTTAGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 24 0.83
29 5 0.17
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (29 bp):
TTTTAACCCATCAGAAGTGGAAGAATACA
Found at i:2472626 original size:17 final size:17
Alignment explanation
Indices: 2472580--2472628 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
2472570 TATATTAAGG
2472580 AATGAAAATAAAATAT-
1 AATGAAAATAAAATATA
* *
2472596 -AT-AAGATTATAATATA
1 AATGAA-AATAAAATATA
2472612 AATGAAAATAAAATATA
1 AATGAAAATAAAATATA
2472629 TGACATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 7
0.69 0.11 0.19
Matches are distributed among these distances:
14 2 0.08
15 10 0.40
17 11 0.44
18 2 0.08
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
AATGAAAATAAAATATA
Found at i:2472631 original size:15 final size:15
Alignment explanation
Indices: 2472581--2472645 Score: 51
Period size: 15 Copynumber: 4.1 Consensus size: 15
2472571 ATATTAAGGA
2472581 ATGAAAATAAAATAT
1 ATGAAAATAAAATAT
* *
2472596 AT-AAGATTATAATATAA
1 ATGAA-A--ATAAAATAT
2472613 ATGAAAATAAAATAT
1 ATGAAAATAAAATAT
* *
2472628 ATGACATTAAAAATAT
1 ATGAAAAT-AAAATAT
2472644 AT
1 AT
2472646 TTAAGATATG
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
14 2 0.05
15 16 0.41
16 9 0.23
17 10 0.26
18 2 0.05
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.31
Consensus pattern (15 bp):
ATGAAAATAAAATAT
Found at i:2473537 original size:33 final size:33
Alignment explanation
Indices: 2473461--2473602 Score: 167
Period size: 34 Copynumber: 4.1 Consensus size: 33
2473451 GACCATCAAT
*
2473461 TGTGATAAAAAATACATACTTAAGTTATGACTG
1 TGTGATAAAAAATACATACTTAAGTTGTGACTG
* *
2473494 TGGGATTAAAAAATACATACTCAAGTTGTGACTG
1 TGTGA-TAAAAAATACATACTTAAGTTGTGACTG
* *
2473528 TGTGATAAAAAATACATACTTAAGTTGTAACCATCAAT
1 TGTGATAAAAAATACATACTTAAGTTGTGA-C-T---G
2473566 TGTGATAAAAAAAATACATACTTAAGTTGTGACTG
1 TGTGAT--AAAAAATACATACTTAAGTTGTGACTG
2473601 TG
1 TG
2473603 GGATTGCATT
Statistics
Matches: 92, Mismatches: 9, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
33 27 0.29
34 31 0.34
35 3 0.03
38 7 0.08
39 1 0.01
40 23 0.25
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (33 bp):
TGTGATAAAAAATACATACTTAAGTTGTGACTG
Found at i:2475357 original size:355 final size:355
Alignment explanation
Indices: 2474689--2475404 Score: 1038
Period size: 355 Copynumber: 2.0 Consensus size: 355
2474679 TTAGTAATTT
* *
2474689 ATATATTTAATGTTCTCTTATGTCAACTTGTCCGTTTCTTATTTTGTATCTTAGCTTATTGAAGA
1 ATAT-TTTAATATTCTCTTATGTCAACTTGTCCGTTTCTTATTATGTATCTTAGCTTATTGAAGA
* * *
2474754 AAAATATTGATATTTATCTTGCTAGATCCAAAATCAATAATGAAAATATATGTCTAGCAGATATT
65 AAAATATTGATATTTATATTGCTAGATCCAAAATCAATAATGAAAATATATGTCTAACAGACATT
* * *
2474819 GCTACAATATACACTATATTTAAAGATAAAAAATATTTTTCTCACTTGACAATGGAAGAAACTAA
130 GCTACAATATACACTATATTTAAAGATAAAAAATATTTTTCTCACTTGACAATGAAAAAAACCAA
* * * * * * **
2474884 TGTTAATATAATATCTGGTAGTACAAGATTAATTGAAGGCTCCGAAAGAGTTAATATTTTGTTAC
195 TGTTAATACAAAATCTAGTAGTACAAGATTAATTGAAGACTCCGAAAGAATCAATATTTTACTAC
* * * * * * *
2474949 CTAGAGGAACAAAGTTCTTAATAGAGGATGCATTATTTTCTACTAAATCTCAAAGAAATTTATTA
260 CCAAAGGAACAAAGTTCATAATAGAAGATACATTATTTTCTACTAAATCTCAAAAAAATTCATTA
2475014 AGTTTTAAAGATATTCGTTTAAATAGATATC
325 AGTTTTAAAGATATTCGTTTAAATAGATATC
* **
2475045 ATATTTTAATATTCTCTTATGTCAACTTGTCTGTTTCTTATTATGTATCTTTTCTTATTGAAGAA
1 ATATTTTAATATTCTCTTATGTCAACTTGTCCGTTTCTTATTATGTATCTTAGCTTATTGAAGAA
* * * * *
2475110 AAATATTGATATTTATATTGTTGGATCCAAGATCAATGATGCAAATATATGTCTAACAGACATTG
66 AAATATTGATATTTATATTGCTAGATCCAAAATCAATAATGAAAATATATGTCTAACAGACATTG
* * * *
2475175 TTACAA-ATCACATTATATTTAAAGATAAGAAATATTTTTTTCACTTGACAATGAAAAAAACCAA
131 CTACAATAT-ACACTATATTTAAAGATAAAAAATATTTTTCTCACTTGACAATGAAAAAAACCAA
*
2475239 TGTTAATACAAAATCTAGTAGTACAAGATTGATTGAAGACTCCGAAAGAATCAATATTTTACTAC
195 TGTTAATACAAAATCTAGTAGTACAAGATTAATTGAAGACTCCGAAAGAATCAATATTTTACTAC
* *
2475304 CCAAAGGAGCAAAGTTCATAATAGAAGATACATTATTTTCTACTAAGTCTCAAAAAAATTCATTA
260 CCAAAGGAACAAAGTTCATAATAGAAGATACATTATTTTCTACTAAATCTCAAAAAAATTCATTA
* * *
2475369 AGTTTTAAATATATTTGTTTAAATGGATATC
325 AGTTTTAAAGATATTCGTTTAAATAGATATC
2475400 ATATT
1 ATATT
2475405 GAGACAACAA
Statistics
Matches: 318, Mismatches: 41, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
354 2 0.01
355 312 0.98
356 4 0.01
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (355 bp):
ATATTTTAATATTCTCTTATGTCAACTTGTCCGTTTCTTATTATGTATCTTAGCTTATTGAAGAA
AAATATTGATATTTATATTGCTAGATCCAAAATCAATAATGAAAATATATGTCTAACAGACATTG
CTACAATATACACTATATTTAAAGATAAAAAATATTTTTCTCACTTGACAATGAAAAAAACCAAT
GTTAATACAAAATCTAGTAGTACAAGATTAATTGAAGACTCCGAAAGAATCAATATTTTACTACC
CAAAGGAACAAAGTTCATAATAGAAGATACATTATTTTCTACTAAATCTCAAAAAAATTCATTAA
GTTTTAAAGATATTCGTTTAAATAGATATC
Found at i:2479695 original size:27 final size:27
Alignment explanation
Indices: 2479644--2479695 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
2479634 ATGTCCTGGT
*
2479644 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTGACCCTGA
*
2479671 GGTGGTAAAATTACCATTTT-ACCCT
1 GGTGG-AAAATTACAATTTTGACCCT
2479696 TTTACTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTGACCCTGA
Found at i:2479766 original size:20 final size:20
Alignment explanation
Indices: 2479749--2479786 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2479739 CCTCAAATCT
2479749 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
2479769 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
2479787 GGGGCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:2481411 original size:26 final size:26
Alignment explanation
Indices: 2481382--2481440 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
2481372 ATTTTCTAGT
* *
2481382 TTTCCTTTGT-TTTTCTCTTTTCTTCC
1 TTTCCTTTCTATTTTCTCTCTTCTT-C
* *
2481408 TTTCCTCTCTATTTTCTCTCTTGTTC
1 TTTCCTTTCTATTTTCTCTCTTCTTC
2481434 TTTCCTT
1 TTTCCTT
2481441 ATGGCCGGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.02, C:0.29, G:0.03, T:0.66
Consensus pattern (26 bp):
TTTCCTTTCTATTTTCTCTCTTCTTC
Found at i:2482988 original size:12 final size:11
Alignment explanation
Indices: 2482971--2483004 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
2482961 GCCAGTCAAC
2482971 AAAGAAGAAAGA
1 AAAGAAGAAA-A
2482983 AAAGAAGAAAA
1 AAAGAAGAAAA
2482994 AAAGAA-AAAA
1 AAAGAAGAAAA
2483004 A
1 A
2483005 TTAAAATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 5 0.23
11 7 0.32
12 10 0.45
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAGAAGAAAA
Found at i:2483110 original size:22 final size:20
Alignment explanation
Indices: 2483084--2483130 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
2483074 AAAAAATTAA
*
2483084 ATTAAAATTTTAATTATAAGTT
1 ATTAAAATTTTAA--ATAAATT
*
2483106 ATTAATATTTTAAATAAATT
1 ATTAAAATTTTAAATAAATT
2483126 ATTAA
1 ATTAA
2483131 TTATAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
22 12 0.52
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
ATTAAAATTTTAAATAAATT
Found at i:2483127 original size:20 final size:21
Alignment explanation
Indices: 2483084--2483131 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
2483074 AAAAAATTAA
* *
2483084 ATTAAAATTTTAATTATAAGTT
1 ATTAATATTTTAA-TATAAATT
2483106 ATTAATATTTTAA-ATAAATT
1 ATTAATATTTTAATATAAATT
2483126 ATTAAT
1 ATTAAT
2483132 TATAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.50
22 12 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
ATTAATATTTTAATATAAATT
Found at i:2484182 original size:27 final size:25
Alignment explanation
Indices: 2484143--2484197 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 25
2484133 GTCTTAGACA
* *
2484143 AAAGATAGAAAAAGAAAAGAGACAAAG
1 AAAGAAAGAAAAA-AAAA-AGAAAAAG
*
2484170 AAAGAAAGCAAAAAAAAAGAAAAAG
1 AAAGAAAGAAAAAAAAAAGAAAAAG
2484195 AAA
1 AAA
2484198 TGAGAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 10 0.40
26 4 0.16
27 11 0.44
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (25 bp):
AAAGAAAGAAAAAAAAAAGAAAAAG
Found at i:2488441 original size:35 final size:35
Alignment explanation
Indices: 2488392--2488460 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
2488382 TTAAACAGAC
* *
2488392 CTCATGAACCCAATAAATATTGAATGAGACCAACT
1 CTCATGAACCCAATAAATAGTGAATCAGACCAACT
*
2488427 CTCATGAACTCAATAAATAGTGAATCAGACCAAC
1 CTCATGAACCCAATAAATAGTGAATCAGACCAAC
2488461 ATAACCCTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.43, C:0.23, G:0.12, T:0.22
Consensus pattern (35 bp):
CTCATGAACCCAATAAATAGTGAATCAGACCAACT
Found at i:2492966 original size:2 final size:2
Alignment explanation
Indices: 2492959--2492986 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2492949 TACTTTACTG
2492959 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2492987 CTACCGCTTC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2497965 original size:19 final size:19
Alignment explanation
Indices: 2497941--2497980 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
2497931 GCAAGGTTTA
2497941 TTGACAAATCCATCTCACT
1 TTGACAAATCCATCTCACT
2497960 TTGACAAATCCATCTCACT
1 TTGACAAATCCATCTCACT
2497979 TT
1 TT
2497981 AAGAATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.35
Consensus pattern (19 bp):
TTGACAAATCCATCTCACT
Found at i:2498432 original size:16 final size:16
Alignment explanation
Indices: 2498395--2498433 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2498385 GGACAAATGT
*
2498395 TGACATGGCACAATGC
1 TGACATGGCACAATAC
* *
2498411 TAACATGGCATAATAC
1 TGACATGGCACAATAC
2498427 TGACATG
1 TGACATG
2498434 TCCACATGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (16 bp):
TGACATGGCACAATAC
Found at i:2504055 original size:3 final size:3
Alignment explanation
Indices: 2504047--2504082 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2504037 AGTGCTTATA
2504047 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
2504083 GATGAGAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2504365 original size:2 final size:2
Alignment explanation
Indices: 2504358--2504422 Score: 76
Period size: 2 Copynumber: 32.0 Consensus size: 2
2504348 AAATAAAAGA
** ** *
2504358 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT NN NN NT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2504400 AT AT AT AT GAT AT AT AT AT AT AT
1 AT AT AT AT -AT AT AT AT AT AT AT
2504423 TTCTTTGCCA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
2 56 0.97
3 2 0.03
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2505259 original size:16 final size:16
Alignment explanation
Indices: 2505224--2505265 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
2505214 ATGAAAATTT
*
2505224 ATTAATTAATTGAGAT
1 ATTAATTAATTGAGAA
* *
2505240 ATTATTTAATTGATAA
1 ATTAATTAATTGAGAA
2505256 ATTAA-TAATT
1 ATTAATTAATT
2505266 TATTAATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (16 bp):
ATTAATTAATTGAGAA
Found at i:2507467 original size:16 final size:16
Alignment explanation
Indices: 2507428--2507458 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2507418 ACAAACCTTG
2507428 AAGGAGAGAAAGTCGA
1 AAGGAGAGAAAGTCGA
2507444 AAGGAGAGAAAGTCG
1 AAGGAGAGAAAGTCG
2507459 GAATGAGAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.06, G:0.39, T:0.06
Consensus pattern (16 bp):
AAGGAGAGAAAGTCGA
Found at i:2514102 original size:21 final size:22
Alignment explanation
Indices: 2514060--2514115 Score: 96
Period size: 21 Copynumber: 2.6 Consensus size: 22
2514050 TTCAATGATC
2514060 TTTAAACTTGTTTGAATAAGCT
1 TTTAAACTTGTTTGAATAAGCT
*
2514082 TTTGAACTTGTTTGAAT-AGCT
1 TTTAAACTTGTTTGAATAAGCT
2514103 TTTAAACTTGTTT
1 TTTAAACTTGTTT
2514116 AAATTAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 16 0.50
22 16 0.50
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (22 bp):
TTTAAACTTGTTTGAATAAGCT
Found at i:2514126 original size:21 final size:20
Alignment explanation
Indices: 2514060--2514129 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 20
2514050 TTCAATGATC
2514060 TTTAAACTTGTTTGAATAAGCT
1 TTTAAACTTGTTTGAATAA--T
* *
2514082 TTTGAACTTGTTTGAATAGCT
1 TTTAAACTTGTTTGAATA-AT
*
2514103 TTTAAACTTGTTTAAATTAAT
1 TTTAAACTTGTTTGAA-TAAT
2514124 TTTAAA
1 TTTAAA
2514130 TCTCTTTTAC
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 22 0.54
22 19 0.46
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.49
Consensus pattern (20 bp):
TTTAAACTTGTTTGAATAAT
Found at i:2514845 original size:28 final size:28
Alignment explanation
Indices: 2514799--2514868 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
2514789 AGTATTTAAA
*
2514799 AGTTGTGCTTGAACATTGAAAAAACAAT
1 AGTTATGCTTGAACATTGAAAAAACAAT
* * * *
2514827 GGTTATGCTTGATCTTTGAAAAGACAAT
1 AGTTATGCTTGAACATTGAAAAAACAAT
2514855 AGTTATGCTTGAAC
1 AGTTATGCTTGAAC
2514869 CTTTAAAAGG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (28 bp):
AGTTATGCTTGAACATTGAAAAAACAAT
Found at i:2514876 original size:28 final size:28
Alignment explanation
Indices: 2514799--2514877 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
2514789 AGTATTTAAA
* * * *
2514799 AGTTGTGCTTGAACATTGAAAAAACAAT
1 AGTTATGCTTGAACCTTTAAAAGACAAT
* *
2514827 GGTTATGCTTG-ATCTTTGAAAAGACAAT
1 AGTTATGCTTGAACCTTT-AAAAGACAAT
2514855 AGTTATGCTTGAACCTTTAAAAG
1 AGTTATGCTTGAACCTTTAAAAG
2514878 GTATTGTATT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
27 3 0.07
28 33 0.80
29 5 0.12
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (28 bp):
AGTTATGCTTGAACCTTTAAAAGACAAT
Found at i:2521652 original size:25 final size:25
Alignment explanation
Indices: 2521618--2521667 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
2521608 GGGGTACTTG
2521618 AAACAATCTTATGTTAGGCAACTAT
1 AAACAATCTTATGTTAGGCAACTAT
*
2521643 AAACAATCTTATGTTGGGCAACTAT
1 AAACAATCTTATGTTAGGCAACTAT
2521668 CATATGATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (25 bp):
AAACAATCTTATGTTAGGCAACTAT
Found at i:2526612 original size:16 final size:15
Alignment explanation
Indices: 2526569--2526608 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2526559 TTTTTATTTT
*
2526569 TTATTAATTTTAAAAA
1 TTATT-ATTTTATAAA
2526585 TTATTATTTTATAAA
1 TTATTATTTTATAAA
2526600 TTA-TATTTT
1 TTATTATTTT
2526609 TTATTTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.26
15 12 0.52
16 5 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATTATTTTATAAA
Found at i:2527458 original size:2 final size:2
Alignment explanation
Indices: 2527451--2527483 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2527441 ACATACATAC
2527451 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2527484 AANNNNNNNN
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2528713 original size:433 final size:432
Alignment explanation
Indices: 2527907--2529033 Score: 1943
Period size: 433 Copynumber: 2.6 Consensus size: 432
2527897 GACCATCTCG
*
2527907 GATTCGTGTCATTTTTAAATTCAAGTTGTTGAATTTCTCAAAATCAAATCAGATTGAATTTTAAT
1 GATTCGTGTCATTTTTAAATTCAAGTTGTTGAATTTCTCAAAATCAAATCAGATTGAATTTTAAC
2527972 AAATTATTCGGATTTGTTTCATTTCATGTTAATTTTTTAGATCGTTCAGATTCAAGTCATTTTGA
66 AAATTATTCGGATTTGTTTCATTTCATGTTAATTTTTTAGATCGTTCAGATTCAAGTCATTTTGA
* *
2528037 GTTTGAATCATTTCAAGTTCAATTCGTTTTAGAATTCAAATCAATTTGAATTTGAGTTGAGTGGA
131 GTTTGAATCATTTCAAGTTCAATTCGTTTTAGAAATCAAATCAATTTGAATTTGAGTTGAG-CGA
* *
2528102 GATTGATTTTTAACTTTTTTTAATTAAATTGGATTGAGTTGACTTCAAATTCAAATAGATTGAAT
195 GATTGATTTTTAATTTTTTTTAATTAAATTGGATTGAGTCGACTTCAAATTCAAATAGATTGAAT
* *
2528167 TTATTTTTCATTTTGGATTAATTTTGTCTTAAATTTATATTTGTGAGATGAATTTTATGAATAAG
260 TTATTTTTCATTTTGGATCAATTTTGTCTTAAATTTATATTTGTGAGATGAATTTTATGAATAAA
* *
2528232 ATGATACAATATCAACATCACCAGGTGCAAAATGAGGAAAGTATCCCTTCCTATGCCTACCTTTG
325 ATGATACAATATCAACATCACAAAGTGCAAAATGAGGAAAGTATCCCTTCCTATGCCTACCTTTG
* *
2528297 TTCTCGACTTCTATGGAAAAAGAAATTGACAATTCAATCAAGT
390 TTCTCGACTTATATGGAAAAAGAAACTGACAATTCAATCAAGT
*
2528340 GATTCGTGTCATTTTTAAATTCAAGTTGTTAAATTTCTCAAAATCAAATCAGATTGAATTTTAAC
1 GATTCGTGTCATTTTTAAATTCAAGTTGTTGAATTTCTCAAAATCAAATCAGATTGAATTTTAAC
* *
2528405 AAATTATTCGGATGTGTTTCATTTCATGTTAATTTTTTAGATCGTTCAGATTCAAGTCATTTTAA
66 AAATTATTCGGATTTGTTTCATTTCATGTTAATTTTTTAGATCGTTCAGATTCAAGTCATTTTGA
* * *
2528470 GTTTGAATCATTTCAAGTTCAATTCATTTTAGAAATCAAATCAATTTAAATTTGAGTTGAACAGA
131 GTTTGAATCATTTCAAGTTCAATTCGTTTTAGAAATCAAATCAATTTGAATTTGAGTTGAGC-GA
*
2528535 GATT-ATTTTTAAATTTTTTTTAATTAAATTGGATTGAGTCGACTTCAAATTCATATAGATTGAA
195 GATTGATTTTT-AATTTTTTTTAATTAAATTGGATTGAGTCGACTTCAAATTCAAATAGATTGAA
*
2528599 TTTATTTTTTATTTTGGATCAATTTTGTCTTAAATTTATATTTGTGAGATGAATTTTATGAATAA
259 TTTATTTTTCATTTTGGATCAATTTTGTCTTAAATTTATATTTGTGAGATGAATTTTATGAATAA
*
2528664 AATGGTACAATATCAACATCACAAAGTGCAAAATGAGGAAAGTATCCCTTCCTATGCCTACCTTT
324 AATGATACAATATCAACATCACAAAGTGCAAAATGAGGAAAGTATCCCTTCCTATGCCTACCTTT
*
2528729 GTTCTCGACTTATATGGAAAAAGATACTGACAATTCAATCAAGT
389 GTTCTCGACTTATATGGAAAAAGAAACTGACAATTCAATCAAGT
*
2528773 GATTCGTGTCATTTTTAAATTCAAGTTGTTGAATTTCTCAAAATCAAATTAGATTGAATTTTAAC
1 GATTCGTGTCATTTTTAAATTCAAGTTGTTGAATTTCTCAAAATCAAATCAGATTGAATTTTAAC
* * *
2528838 AAATTATTCGAATTTGTTTCATTTCATGTTAATTTTTTAAATCGTTCAGATTCAAGTTATTTTGA
66 AAATTATTCGGATTTGTTTCATTTCATGTTAATTTTTTAGATCGTTCAGATTCAAGTCATTTTGA
* * *
2528903 GTTTGAATCATTTCAAGTTTAATTTGTTTTA-AAATTCAAATCAATTTGAATTTCAGTTGAGCGA
131 GTTTGAATCATTTCAAGTTCAATTCGTTTTAGAAA-TCAAATCAATTTGAATTTGAGTTGAGCG-
2528967 AGATTGATTTTTAATTTTTTTTAATTAAATTGGATTGAGTCGACTTCAAATTCAAATAGATTGAA
194 AGATTGATTTTTAATTTTTTTTAATTAAATTGGATTGAGTCGACTTCAAATTCAAATAGATTGAA
2529032 TT
259 TT
2529034 AATGACAAAT
Statistics
Matches: 654, Mismatches: 35, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
432 10 0.02
433 638 0.98
434 6 0.01
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (432 bp):
GATTCGTGTCATTTTTAAATTCAAGTTGTTGAATTTCTCAAAATCAAATCAGATTGAATTTTAAC
AAATTATTCGGATTTGTTTCATTTCATGTTAATTTTTTAGATCGTTCAGATTCAAGTCATTTTGA
GTTTGAATCATTTCAAGTTCAATTCGTTTTAGAAATCAAATCAATTTGAATTTGAGTTGAGCGAG
ATTGATTTTTAATTTTTTTTAATTAAATTGGATTGAGTCGACTTCAAATTCAAATAGATTGAATT
TATTTTTCATTTTGGATCAATTTTGTCTTAAATTTATATTTGTGAGATGAATTTTATGAATAAAA
TGATACAATATCAACATCACAAAGTGCAAAATGAGGAAAGTATCCCTTCCTATGCCTACCTTTGT
TCTCGACTTATATGGAAAAAGAAACTGACAATTCAATCAAGT
Found at i:2536952 original size:21 final size:21
Alignment explanation
Indices: 2536928--2536974 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
2536918 TTTTACCTTC
*
2536928 AGGGCCATGTTTTTGTGTCTA
1 AGGGCCATGTTTTTGTATCTA
2536949 AGGGCCATGTTTTTGTATCTA
1 AGGGCCATGTTTTTGTATCTA
2536970 AGGGC
1 AGGGC
2536975 TGTCCATGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.15, G:0.30, T:0.38
Consensus pattern (21 bp):
AGGGCCATGTTTTTGTATCTA
Found at i:2551005 original size:30 final size:30
Alignment explanation
Indices: 2550969--2551028 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
2550959 TTAATCAAAT
* *
2550969 TCTTATATTTTTATTTTTAATCAATTAAGC
1 TCTTATACTTTTATTTTTAATCAAATAAGC
2550999 TCTTATACTTTTATTTTTAATCAAATAAGC
1 TCTTATACTTTTATTTTTAATCAAATAAGC
2551029 CTTTATGACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.12, G:0.03, T:0.53
Consensus pattern (30 bp):
TCTTATACTTTTATTTTTAATCAAATAAGC
Found at i:2552856 original size:7 final size:7
Alignment explanation
Indices: 2552840--2552915 Score: 70
Period size: 7 Copynumber: 11.1 Consensus size: 7
2552830 TGGGAGAGAG
*
2552840 AAGAAGA
1 AAGAAAA
2552847 AAGAAAA
1 AAGAAAA
2552854 AAGAAAA
1 AAGAAAA
2552861 AAG-AAA
1 AAGAAAA
*
2552867 TA-AAAA
1 AAGAAAA
2552873 AAGAAAA
1 AAGAAAA
*
2552880 AA-AGAA
1 AAGAAAA
2552886 AAGAAAA
1 AAGAAAA
2552893 AGAGAAAA
1 A-AGAAAA
2552901 AA-AAGAA
1 AAGAA-AA
*
2552908 ACGAAAA
1 AAGAAAA
2552915 A
1 A
2552916 GGATTTGGGT
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
6 15 0.26
7 33 0.58
8 9 0.16
ACGTcount: A:0.82, C:0.01, G:0.16, T:0.01
Consensus pattern (7 bp):
AAGAAAA
Found at i:2552859 original size:11 final size:10
Alignment explanation
Indices: 2552843--2552908 Score: 66
Period size: 11 Copynumber: 6.6 Consensus size: 10
2552833 GAGAGAGAAG
2552843 AAGAAAGAAAA
1 AAGAAA-AAAA
*
2552854 AAGAAAAAAG
1 AAGAAAAAAA
*
2552864 AA-ATAAAAA
1 AAGAAAAAAA
2552873 AAG--AAAAA
1 AAGAAAAAAA
2552881 AAGAAAAGAAA
1 AAGAAAA-AAA
2552892 AAGAGAAAAAA
1 AAGA-AAAAAA
2552903 AAGAAA
1 AAGAAA
2552909 CGAAAAAGGA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
8 8 0.17
9 7 0.15
10 9 0.19
11 20 0.43
12 3 0.06
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:2552874 original size:12 final size:12
Alignment explanation
Indices: 2552840--2552915 Score: 62
Period size: 13 Copynumber: 5.7 Consensus size: 12
2552830 TGGGAGAGAG
2552840 AAGAAGAAAGAAAA
1 AAGAA-AAA-AAAA
2552854 AAGAAAAAAGAAA
1 AAGAAAAAA-AAA
*
2552867 TAAAAAAAGAAAAA
1 -AAGAAAA-AAAAA
2552881 AAGAAAAGAAAAA
1 AAGAAAA-AAAAA
*
2552894 GAGAAAAAAAAGA
1 AAGAAAAAAAA-A
2552907 AACGAAAAA
1 AA-GAAAAA
2552916 GGATTTGGGT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
12 5 0.09
13 26 0.49
14 20 0.38
15 2 0.04
ACGTcount: A:0.82, C:0.01, G:0.16, T:0.01
Consensus pattern (12 bp):
AAGAAAAAAAAA
Found at i:2552874 original size:19 final size:19
Alignment explanation
Indices: 2552846--2552902 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 19
2552836 AGAGAAGAAG
2552846 AAAGAAAAAAGAAAAAAGA
1 AAAGAAAAAAGAAAAAAGA
2552865 AATA-AAAAAAGAAAAAAAGA
1 AA-AGAAAAAAG-AAAAAAGA
2552885 AAAGAAAAAGAGAAAAAA
1 AAAGAAAAA-AGAAAAAA
2552903 AAGAAACGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
19 10 0.29
20 22 0.65
21 2 0.06
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (19 bp):
AAAGAAAAAAGAAAAAAGA
Found at i:2552879 original size:8 final size:8
Alignment explanation
Indices: 2552846--2552908 Score: 53
Period size: 8 Copynumber: 7.9 Consensus size: 8
2552836 AGAGAAGAAG
2552846 AAAG-AAA
1 AAAGAAAA
2552853 AAAG-AAA
1 AAAGAAAA
2552860 AAAGAAATA
1 AAAGAAA-A
2552869 AAA-AAAGA
1 AAAGAAA-A
2552877 AAA-AAAGA
1 AAAGAAA-A
2552885 AAAGAAAA
1 AAAGAAAA
*
2552893 AGAGAAAAA
1 AAAG-AAAA
2552902 AAAGAAA
1 AAAGAAA
2552909 CGAAAAAGGA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
7 11 0.22
8 24 0.49
9 14 0.29
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (8 bp):
AAAGAAAA
Found at i:2552914 original size:11 final size:10
Alignment explanation
Indices: 2552838--2552916 Score: 56
Period size: 11 Copynumber: 7.8 Consensus size: 10
2552828 GCTGGGAGAG
*
2552838 AGAAGAAGAA
1 AGAAAAAGAA
*
2552848 AGAAAAA-AG
1 AGAAAAAGAA
2552857 A-AAAAAGAA
1 AGAAAAAGAA
*
2552866 ATAAAAA-AA
1 AGAAAAAGAA
*
2552875 GAAAAAAAGAAA
1 -AGAAAAAG-AA
2552887 AGAAAAAGAGA
1 AGAAAAAGA-A
*
2552898 AAAAAAAGAA
1 AGAAAAAGAA
2552908 ACGAAAAAG
1 A-GAAAAAG
2552917 GATTTGGGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
8 5 0.09
9 6 0.11
10 20 0.36
11 22 0.40
12 2 0.04
ACGTcount: A:0.80, C:0.01, G:0.18, T:0.01
Consensus pattern (10 bp):
AGAAAAAGAA
Found at i:2552916 original size:22 final size:20
Alignment explanation
Indices: 2552843--2552916 Score: 89
Period size: 22 Copynumber: 3.6 Consensus size: 20
2552833 GAGAGAGAAG
2552843 AAGAAAGAAAAA-AG-AAAA
1 AAGAAAGAAAAAGAGAAAAA
* *
2552861 AAGAAATAAAAAAAGAAAAA
1 AAGAAAGAAAAAGAGAAAAA
2552881 AAGAAAAGAAAAAGAGAAAAAA
1 AAG-AAAGAAAAAGAG-AAAAA
2552903 AAGAAACGAAAAAG
1 AAGAAA-GAAAAAG
2552917 GATTTGGGTC
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
18 11 0.23
19 2 0.04
20 7 0.15
21 13 0.27
22 15 0.31
ACGTcount: A:0.81, C:0.01, G:0.16, T:0.01
Consensus pattern (20 bp):
AAGAAAGAAAAAGAGAAAAA
Found at i:2553537 original size:7 final size:7
Alignment explanation
Indices: 2553527--2553559 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
2553517 ATATAAAATG
2553527 AAATAAT
1 AAATAAT
2553534 AAATAA-
1 AAATAAT
2553540 AAATAAT
1 AAATAAT
*
2553547 ATATAAT
1 AAATAAT
2553554 AAATAA
1 AAATAA
2553560 CAAAATAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAATAAT
Found at i:2553565 original size:28 final size:27
Alignment explanation
Indices: 2553510--2553591 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 27
2553500 AATAATTATT
*
2553510 TAAAAAAATATAAAATGAAATAATAAA
1 TAAAAAAATATAAAATGAAATAAAAAA
*
2553537 TAAAAATAATATATAAT-AAATAACAAAA
1 TAAAAA-AATATAAAATGAAATAA-AAAA
* **
2553565 TAACAAAATA-ACAAAAAAAATAAAAAA
1 TAAAAAAATATA-AAATGAAATAAAAAA
2553592 GGAAAATATT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
26 1 0.02
27 22 0.48
28 23 0.50
ACGTcount: A:0.76, C:0.04, G:0.01, T:0.20
Consensus pattern (27 bp):
TAAAAAAATATAAAATGAAATAAAAAA
Found at i:2553567 original size:8 final size:8
Alignment explanation
Indices: 2553554--2553580 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
2553544 AATATATAAT
2553554 AAATAACA
1 AAATAACA
2553562 AAATAACA
1 AAATAACA
2553570 AAATAACA
1 AAATAACA
2553578 AAA
1 AAA
2553581 AAAATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.78, C:0.11, G:0.00, T:0.11
Consensus pattern (8 bp):
AAATAACA
Found at i:2555632 original size:28 final size:28
Alignment explanation
Indices: 2555545--2555621 Score: 145
Period size: 28 Copynumber: 2.8 Consensus size: 28
2555535 TTTTAGAGTA
*
2555545 TAGGGGCAAAATGGTAATTTTGCCACCC
1 TAGGGGCAAAATAGTAATTTTGCCACCC
2555573 TAGGGGCAAAATAGTAATTTTGCCACCC
1 TAGGGGCAAAATAGTAATTTTGCCACCC
2555601 TAGGGGCAAAATAGTAATTTT
1 TAGGGGCAAAATAGTAATTTT
2555622 TCACCACTAG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.27
Consensus pattern (28 bp):
TAGGGGCAAAATAGTAATTTTGCCACCC
Found at i:2557769 original size:18 final size:18
Alignment explanation
Indices: 2557723--2557774 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
2557713 GATTTCTCTA
*
2557723 TAAATATT-TT-TTTTAG
1 TAAATATTATTATTTTAT
* *
2557739 AAAATA-TAATATTTTAT
1 TAAATATTATTATTTTAT
2557756 TAAATATTATTATTTTAT
1 TAAATATTATTATTTTAT
2557774 T
1 T
2557775 CAAACAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 1 0.04
16 6 0.21
17 10 0.36
18 11 0.39
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
TAAATATTATTATTTTAT
Found at i:2557805 original size:21 final size:20
Alignment explanation
Indices: 2557755--2557806 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 20
2557745 TAATATTTTA
* *
2557755 TTAAAT-ATTATTATTTTAT
1 TTAAATAATTATAATTTCAT
* *
2557774 TCAAACAATTATAATTTCATT
1 TTAAATAATTATAATTTCA-T
2557795 TTAAATAATTAT
1 TTAAATAATTAT
2557807 TTTAGACATC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 4 0.16
20 10 0.40
21 11 0.44
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (20 bp):
TTAAATAATTATAATTTCAT
Found at i:2563261 original size:59 final size:59
Alignment explanation
Indices: 2563197--2563496 Score: 361
Period size: 59 Copynumber: 5.1 Consensus size: 59
2563187 CAATTAAGTT
* * *
2563197 GAACCTATTTTAAGATAGGTCGAACCTAGATCAAGTCTAGGAATTTCAATATTTGAATT
1 GAACCTGTTTTAAGATAGGTCGAACCTAGATCAAGTCTAGGAATTTCAATTTTTGAATC
* * * *
2563256 GAACCTGTTTTGAA-ATAGGTTGAACCTAGATTACGTATAGGAATTTCAATTTTTGAATC
1 GAACCTGTTTT-AAGATAGGTCGAACCTAGATCAAGTCTAGGAATTTCAATTTTTGAATC
* * * * *
2563315 GAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAATCTAGAAATATCAATTTTTTAAATC
1 GAACCTGTTTTAAGATAGGTCGAACCTAGATCAAGTCTAGGAATTTCAA-TTTTTGAATC
* * * * *
2563375 GAACTTATTTTAAGATAGGTCGAACCTATATTAAGTCTAGGAATTTTAATTTTTGAATC
1 GAACCTGTTTTAAGATAGGTCGAACCTAGATCAAGTCTAGGAATTTCAATTTTTGAATC
** * * *
2563434 GAATATGTTTTAAGATAGGTTGAGCCTAGATCAAGTCTAGGAATGTCAA-TTTTGAAATC
1 GAACCTGTTTTAAGATAGGTCGAACCTAGATCAAGTCTAGGAATTTCAATTTTTG-AATC
2563493 GAAC
1 GAAC
2563497 TTGTCTCGAG
Statistics
Matches: 201, Mismatches: 36, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
58 7 0.03
59 143 0.71
60 51 0.25
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (59 bp):
GAACCTGTTTTAAGATAGGTCGAACCTAGATCAAGTCTAGGAATTTCAATTTTTGAATC
Found at i:2563443 original size:119 final size:118
Alignment explanation
Indices: 2563204--2563498 Score: 394
Period size: 119 Copynumber: 2.5 Consensus size: 118
2563194 GTTGAACCTA
* * * * * * *
2563204 TTTTAAGATAGGTCGAACCTAGATCAAGTCTAGGAATTTCAATATTTGAATTGAACCTGTTTTGA
1 TTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATATCAATTTTTAAATCGAACTTATTTTGA
* * *
2563269 AATAGGTTGAACCTAGATTACGTATAGGAATTTCAATTTTTGAATCGAACCTG
66 AATAGGTCGAACCTAGATTAAGTATAGGAATTTCAATTTTTGAATCGAACATG
* *
2563322 TTTTAAGATAGGTCGAGCCTAGATCAAATCTAGAAATATCAATTTTTTAAATCGAACTTATTTT-
1 TTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATATCAA-TTTTTAAATCGAACTTATTTTG
* * * *
2563386 AAGATAGGTCGAACCTATATTAAGTCTAGGAATTTTAATTTTTGAATCGAATATG
65 AA-ATAGGTCGAACCTAGATTAAGTATAGGAATTTCAATTTTTGAATCGAACATG
* * *
2563441 TTTTAAGATAGGTTGAGCCTAGATCAAGTCTAGGAATGTCAATTTTGAAATCGAACTT
1 TTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATATCAATTTTTAAATCGAACTT
2563499 GTCTCGAGAT
Statistics
Matches: 154, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
118 55 0.36
119 99 0.64
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (118 bp):
TTTTAAGATAGGTCGAGCCTAGATCAAGTCTAGGAATATCAATTTTTAAATCGAACTTATTTTGA
AATAGGTCGAACCTAGATTAAGTATAGGAATTTCAATTTTTGAATCGAACATG
Found at i:2563747 original size:17 final size:18
Alignment explanation
Indices: 2563727--2563760 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2563717 ATCCATCAAA
2563727 AATAAA-AATAAAAAAAT
1 AATAAATAATAAAAAAAT
*
2563744 AATAAATCATAAAAAAA
1 AATAAATAATAAAAAAA
2563761 GGAAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (18 bp):
AATAAATAATAAAAAAAT
Found at i:2564078 original size:18 final size:17
Alignment explanation
Indices: 2564021--2564078 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
2564011 AGAGATACAA
* *
2564021 AAAAGACAAAACAAAAAA
1 AAAAGA-AAACCAAAAAT
2564039 AAAAG-AAACCAAAACACT
1 AAAAGAAAACCAAAA-A-T
2564057 AAAAGAAAACCAAAAAT
1 AAAAGAAAACCAAAAAT
2564074 GAAAA
1 -AAAA
2564079 ATAAGTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
16 8 0.24
17 2 0.06
18 15 0.44
19 9 0.26
ACGTcount: A:0.76, C:0.14, G:0.07, T:0.03
Consensus pattern (17 bp):
AAAAGAAAACCAAAAAT
Found at i:2564249 original size:16 final size:16
Alignment explanation
Indices: 2564225--2564263 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
2564215 CTGCGGTTAG
* *
2564225 GAGAGAGAGGAAGAAA
1 GAGAAAGAGAAAGAAA
2564241 GAGAAAGAGAAAGAAA
1 GAGAAAGAGAAAGAAA
2564257 GAGAAAG
1 GAGAAAG
2564264 TGAAGAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
GAGAAAGAGAAAGAAA
Found at i:2564324 original size:13 final size:12
Alignment explanation
Indices: 2564301--2564376 Score: 73
Period size: 13 Copynumber: 5.9 Consensus size: 12
2564291 AGAGACGAAG
2564301 AAAGAAAAAAGAA
1 AAAG-AAAAAGAA
*
2564314 GAAAGAAAAAGCA
1 -AAAGAAAAAGAA
2564327 AAAGAAAGAA-AGA
1 AAAGAAA-AAGA-A
2564340 AAAGAAAAAAGGAA
1 AAAG-AAAAA-GAA
*
2564354 AAAAAAAAAGAA
1 AAAGAAAAAGAA
2564366 AAAGAAAAAGA
1 AAAGAAAAAGA
2564377 TTTGGGTCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
12 20 0.38
13 21 0.40
14 11 0.21
15 1 0.02
ACGTcount: A:0.80, C:0.01, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAGAA
Found at i:2564329 original size:6 final size:6
Alignment explanation
Indices: 2564301--2564376 Score: 73
Period size: 6 Copynumber: 11.8 Consensus size: 6
2564291 AGAGACGAAG
*
2564301 AAAGAAA AAAGAA GAAAGAA AAAGCA AAAGAA AGAA-AGA AAAGAAA AAAGGAA
1 AAAG-AA AAAGAA -AAAGAA AAAGAA AAAGAA A-AAGA-A AAAG-AA AAA-GAA
*
2564354 AAAAAA AAAGAA AAAGAA AAAGA
1 AAAGAA AAAGAA AAAGAA AAAGA
2564377 TTTGGGTCAA
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
6 34 0.58
7 23 0.39
8 2 0.03
ACGTcount: A:0.80, C:0.01, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:2564329 original size:20 final size:19
Alignment explanation
Indices: 2564301--2564374 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 19
2564291 AGAGACGAAG
*
2564301 AAAGAAAAAAGAAGAAAGAA
1 AAAG-AAAAAGAAAAAAGAA
*
2564321 AAAGCAAAAGAAAGAAAG-A
1 AAAGAAAAAGAAA-AAAGAA
2564340 AAAGAAAAAAGGAAAAAA-AA
1 AAAG-AAAAA-GAAAAAAGAA
2564360 AAAGAAAAAGAAAAA
1 AAAGAAAAAGAAAAA
2564375 GATTTGGGTC
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
18 6 0.13
19 17 0.36
20 20 0.43
21 4 0.09
ACGTcount: A:0.81, C:0.01, G:0.18, T:0.00
Consensus pattern (19 bp):
AAAGAAAAAGAAAAAAGAA
Found at i:2564667 original size:14 final size:15
Alignment explanation
Indices: 2564650--2564696 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
2564640 TGGAAAGTAA
2564650 AAATAAAAAAAT-AT
1 AAATAAAAAAATCAT
* *
2564664 AAATAAATAAATGAT
1 AAATAAAAAAATCAT
*
2564679 AATATTAAAAAATCAT
1 AA-ATAAAAAAATCAT
2564695 AA
1 AA
2564697 TACAAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 11 0.41
15 4 0.15
16 12 0.44
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (15 bp):
AAATAAAAAAATCAT
Found at i:2564670 original size:20 final size:21
Alignment explanation
Indices: 2564628--2564670 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2564618 TTAGTGTTAG
*
2564628 AAAATAAAAAAATGGAAAGTA
1 AAAATAAAAAAATAGAAAGTA
*
2564649 AAAATAAAAAAATATAAA-TA
1 AAAATAAAAAAATAGAAAGTA
2564669 AA
1 AA
2564671 TAAATGATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (21 bp):
AAAATAAAAAAATAGAAAGTA
Found at i:2564726 original size:15 final size:16
Alignment explanation
Indices: 2564706--2564735 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2564696 ATACAAATAT
2564706 AAAAATTAT-AAAAAA
1 AAAAATTATGAAAAAA
2564721 AAAAATTATGAAAAA
1 AAAAATTATGAAAAA
2564736 GAATAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (16 bp):
AAAAATTATGAAAAAA
Found at i:2564768 original size:27 final size:25
Alignment explanation
Indices: 2564706--2564768 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 25
2564696 ATACAAATAT
* * *
2564706 AAAAATTATAAAAAAAAAAATTATG
1 AAAAAATATAAAAAAAAAAAATAAG
2564731 AAAAAGA-ATAAAGAAATAAAAAATAAG
1 AAAAA-ATATAAA-AAA-AAAAAATAAG
2564758 AAAAAATATAA
1 AAAAAATATAA
2564769 TAATAAAGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 10 0.32
26 4 0.13
27 17 0.55
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.17
Consensus pattern (25 bp):
AAAAAATATAAAAAAAAAAAATAAG
Found at i:2564950 original size:13 final size:13
Alignment explanation
Indices: 2564934--2564975 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2564924 ATATAAAATG
2564934 AAATAATAAATAA
1 AAATAATAAATAA
*
2564947 AAATAATATATAA
1 AAATAATAAATAA
*
2564960 TAAT-ATATAATAA
1 AAATAATA-AATAA
2564973 AAA
1 AAA
2564976 ATAACAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 3 0.12
13 21 0.88
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAATAAATAA
Found at i:2577418 original size:14 final size:15
Alignment explanation
Indices: 2577391--2577424 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2577381 ACGCCTCGTT
2577391 AAAACCTTACAAGGAA
1 AAAACCTTA-AAGGAA
2577407 AAAACCTT-AAGGAA
1 AAAACCTTAAAGGAA
2577421 AAAA
1 AAAA
2577425 TTTGAGTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
16 8 0.44
ACGTcount: A:0.62, C:0.15, G:0.12, T:0.12
Consensus pattern (15 bp):
AAAACCTTAAAGGAA
Found at i:2581497 original size:26 final size:26
Alignment explanation
Indices: 2581476--2581565 Score: 96
Period size: 26 Copynumber: 3.5 Consensus size: 26
2581466 CCACTTCTGG
* **
2581476 TGGTAAATTTATCTATCTACTTCTTG
1 TGGTAAAATTATCTATCTACTTCTAA
*
2581502 TAGTAAAATTAT-TCATAC-ACTTCTAA
1 TGGTAAAATTATCT-AT-CTACTTCTAA
2581528 TGGTAAAATTATCTAT-TCACTTCTAA
1 TGGTAAAATTATCTATCT-ACTTCTAA
2581554 TGGTAAAATTAT
1 TGGTAAAATTAT
2581566 TTTGAATTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
25 1 0.02
26 51 0.94
27 2 0.04
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.43
Consensus pattern (26 bp):
TGGTAAAATTATCTATCTACTTCTAA
Found at i:2581532 original size:52 final size:52
Alignment explanation
Indices: 2581467--2581566 Score: 130
Period size: 52 Copynumber: 1.9 Consensus size: 52
2581457 AGTATCCATC
** * **
2581467 CACTTCTGGTGGTAAATTTATCTA-TCTACTTCTTGTAGTAAAATTATTCATA
1 CACTTCTAATGGTAAAATTATCTATTC-ACTTCTAATAGTAAAATTATTCATA
*
2581519 CACTTCTAATGGTAAAATTATCTATTCACTTCTAATGGTAAAATTATT
1 CACTTCTAATGGTAAAATTATCTATTCACTTCTAATAGTAAAATTATT
2581567 TTGAATTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 39 0.95
53 2 0.05
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (52 bp):
CACTTCTAATGGTAAAATTATCTATTCACTTCTAATAGTAAAATTATTCATA
Found at i:2589205 original size:14 final size:15
Alignment explanation
Indices: 2589186--2589216 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2589176 ATAATTTGAT
2589186 ATTAAAATTT-TAAA
1 ATTAAAATTTATAAA
2589200 ATTAAAATTTATAAA
1 ATTAAAATTTATAAA
2589215 AT
1 AT
2589217 GAGAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTAAAATTTATAAA
Done.