Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 192 of 204
Found at i:56654368 original size:14 final size:13
Alignment explanation
Indices: 56654330--56654369 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 13
56654320 CCGAAGCTAT
56654330 CACTTATCACTTTC
1 CACTT-TCACTTTC
56654344 CACTTTCCACTTTC
1 CACTTT-CACTTTC
56654358 CACTTGTCACTT
1 CACTT-TCACTT
56654370 GATCAGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.04
14 22 0.92
15 1 0.04
ACGTcount: A:0.17, C:0.38, G:0.03, T:0.42
Consensus pattern (13 bp):
CACTTTCACTTTC
Found at i:56654370 original size:7 final size:7
Alignment explanation
Indices: 56654337--56654362 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
56654327 TATCACTTAT
56654337 CACTTTC
1 CACTTTC
56654344 CACTTTC
1 CACTTTC
56654351 CACTTTC
1 CACTTTC
56654358 CACTT
1 CACTT
56654363 GTCACTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.42, G:0.00, T:0.42
Consensus pattern (7 bp):
CACTTTC
Found at i:56654384 original size:66 final size:66
Alignment explanation
Indices: 56654285--56654408 Score: 230
Period size: 66 Copynumber: 1.9 Consensus size: 66
56654275 TATCACTTAT
*
56654285 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTTT
1 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTTT
56654350 C
66 C
*
56654351 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTT
1 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
56654409 GTCACTTGAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.36
Consensus pattern (66 bp):
CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTTT
C
Found at i:56656209 original size:29 final size:29
Alignment explanation
Indices: 56656150--56656208 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
56656140 TTTGGTTCGA
*
56656150 TGTGCAATATTATACATGAACTTTAATTT
1 TGTGCAATATTATACATGAAATTTAATTT
* * *
56656179 TGTGTAATTTTATACATTAAATCTTAATTT
1 TGTGCAATATTATACATGAAAT-TTAATTT
56656209 GATTCAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.49
Consensus pattern (29 bp):
TGTGCAATATTATACATGAAATTTAATTT
Found at i:56660001 original size:16 final size:16
Alignment explanation
Indices: 56659980--56660049 Score: 113
Period size: 16 Copynumber: 4.4 Consensus size: 16
56659970 TTTGGTTCGC
*
56659980 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
56659996 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
56660012 TGTAATGGATTAGAGG
1 TGTAATGGATTAGAGG
*
56660028 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
56660044 TGTAAT
1 TGTAAT
56660050 AGCAAATCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.30, C:0.00, G:0.36, T:0.34
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:56660133 original size:39 final size:43
Alignment explanation
Indices: 56660028--56660137 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
56660018 GGATTAGAGG
56660028 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
56660073 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
56660113 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
56660138 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:56660304 original size:18 final size:17
Alignment explanation
Indices: 56660283--56660317 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56660273 TTATTATTAA
*
56660283 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
56660301 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
56660318 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:56660383 original size:157 final size:157
Alignment explanation
Indices: 56660170--56660486 Score: 616
Period size: 157 Copynumber: 2.0 Consensus size: 157
56660160 TAGAACACCC
56660170 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
*
56660235 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
56660300 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
*
56660327 TTAGCATAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
56660392 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
56660457 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
56660484 TTA
1 TTA
56660487 ATATTCTTAT
Statistics
Matches: 158, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 158 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:56660461 original size:18 final size:17
Alignment explanation
Indices: 56660440--56660474 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56660430 TTATTATTAA
*
56660440 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
56660458 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
56660475 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:56660578 original size:157 final size:153
Alignment explanation
Indices: 56660244--56660552 Score: 361
Period size: 157 Copynumber: 2.0 Consensus size: 153
56660234 ATTATCAATA
56660244 ATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATT
1 ATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATT
* * * ** * * *
56660309 TAATAAAATTCTTAATAATTAGCATAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAA
66 TAATAAAATTCTTAATAATTAACATAAATATGATTTACTAAATTAATATTGATACTGTTA--TAA
* * * *
56660374 ATTTTAATAAGATTATTAATATCAAT
129 ATATAAATAACATAATTAATAT-AAT
56660400 AATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAAT
1 -ATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAAT
* **
56660465 TTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTG
65 TTAATAAAATTCTTAATAATTAACA-T-AAATATG-ATTTACT-AAAT--TAATAT-TGATACTG
56660530 -TA-AAATATAAATTAACATAATTA
123 TTATAAATATAAA-TAACATAATTA
56660553 TTATTAAATA
Statistics
Matches: 129, Mismatches: 15, Indels: 12
0.83 0.10 0.08
Matches are distributed among these distances:
157 87 0.67
158 1 0.01
159 4 0.03
160 11 0.09
161 13 0.10
163 7 0.05
164 6 0.05
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (153 bp):
ATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATT
TAATAAAATTCTTAATAATTAACATAAATATGATTTACTAAATTAATATTGATACTGTTATAAAT
ATAAATAACATAATTAATATAAT
Found at i:56667131 original size:24 final size:23
Alignment explanation
Indices: 56667081--56667131 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 23
56667071 TTTTTTTGCT
56667081 AATTTAGGTTTTATTTTTTAATTA
1 AATTTAGGTTTTATTTTTTAA-TA
*
56667105 AATTTAGTTTTTAAATTTTTTAA-A
1 AATTTAGGTTTT--ATTTTTTAATA
56667129 AAT
1 AAT
56667132 AATCAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 15 0.62
26 9 0.38
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (23 bp):
AATTTAGGTTTTATTTTTTAATA
Found at i:56667176 original size:27 final size:28
Alignment explanation
Indices: 56667124--56667177 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
56667114 TTTAAATTTT
**
56667124 TTAAAAATAATCAAATTTTAGTATTAAC
1 TTAAAAATAATCAAATTTTACCATTAAC
*
56667152 TTAAAAATAAT-AATTTTTACCATTAA
1 TTAAAAATAATCAAATTTTACCATTAA
56667178 TCTTTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (28 bp):
TTAAAAATAATCAAATTTTACCATTAAC
Found at i:56669258 original size:73 final size:73
Alignment explanation
Indices: 56669147--56669295 Score: 280
Period size: 73 Copynumber: 2.0 Consensus size: 73
56669137 TGTAGTTAAG
56669147 TATATATTAATGATAGTTCATTTTACCGATGATGACTCGATCTTAAATAAAATTTATTTGAATGT
1 TATATATTAATGATAGTTCATTTTACCGATGATGACTCGATCTTAAATAAAATTTATTTGAATGT
56669212 TTGTAATT
66 TTGTAATT
* *
56669220 TATATATTAATGATAGTTTATTTTACTGATGATGACTCGATCTTAAATAAAATTTATTTGAATGT
1 TATATATTAATGATAGTTCATTTTACCGATGATGACTCGATCTTAAATAAAATTTATTTGAATGT
56669285 TTGTAATT
66 TTGTAATT
56669293 TAT
1 TAT
56669296 TAAAATATAA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (73 bp):
TATATATTAATGATAGTTCATTTTACCGATGATGACTCGATCTTAAATAAAATTTATTTGAATGT
TTGTAATT
Found at i:56669278 original size:36 final size:36
Alignment explanation
Indices: 56669166--56669278 Score: 86
Period size: 36 Copynumber: 3.1 Consensus size: 36
56669156 ATGATAGTTC
*
56669166 ATTTTACCGATGATGACTCGATCTTAAATAAAATTT
1 ATTTTACTGATGATGACTCGATCTTAAATAAAATTT
* * * * ** * * * *
56669202 ATTTGAATG-T-TTGTAATTTATATATTAATGATAGTTT
1 ATTTTACTGATGATG-ACTCGATCT-TAAAT-AAAATTT
56669239 ATTTTACTGATGATGACTCGATCTTAAATAAAATTT
1 ATTTTACTGATGATGACTCGATCTTAAATAAAATTT
56669275 ATTT
1 ATTT
56669279 GAATGTTTGT
Statistics
Matches: 51, Mismatches: 21, Indels: 10
0.62 0.26 0.12
Matches are distributed among these distances:
34 2 0.04
35 6 0.12
36 19 0.37
37 16 0.31
38 6 0.12
39 2 0.04
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.46
Consensus pattern (36 bp):
ATTTTACTGATGATGACTCGATCTTAAATAAAATTT
Found at i:56670261 original size:15 final size:16
Alignment explanation
Indices: 56670232--56670262 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
56670222 ATGAAAAAGG
56670232 GAAGAAAATAGAGAGA
1 GAAGAAAATAGAGAGA
56670248 GAAGAAAA-AGAGAGA
1 GAAGAAAATAGAGAGA
56670263 AAAAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (16 bp):
GAAGAAAATAGAGAGA
Found at i:56674464 original size:224 final size:225
Alignment explanation
Indices: 56674073--56674521 Score: 873
Period size: 224 Copynumber: 2.0 Consensus size: 225
56674063 GGAAAATGAT
56674073 AGAAATGAAGCATCTTAAAATACAATGATTGATACACATTGCCGCTAAAGCAGACAGCAAATACA
1 AGAAATGAAGCATCTTAAAATACAATGATTGATACACATTGCCGCTAAAGCAGACAGCAAATACA
*
56674138 CTCTTAAATGGCATATAAATCTTGAAAGCTAGCCTTATGACACTTACCAAGACAAGCTCACAAAT
66 CTCTTAAACGGCATATAAATCTTGAAAGCTAGCCTTATGACACTTACCAAGACAAGCTCACAAAT
56674203 AATCCAACTAAAACTACACTACCAGGGACTCCGGCTCTTCACATTTTTCTTGAAATATTCATATC
131 AATCCAACTAAAACTACACTACCAGGGACTCCGGCTCTTCACATTTTTCTTGAAATATTCATATC
56674268 GTATTCATATCCTTAAAGCATATGAAAATC
196 GTATTCATATCCTTAAAGCATATGAAAATC
*
56674298 AGAAATGAAGCATCTTAAAATACAATGA-TGATACACATTGCCGCTAAAGCAGACAGCAACTACA
1 AGAAATGAAGCATCTTAAAATACAATGATTGATACACATTGCCGCTAAAGCAGACAGCAAATACA
56674362 CTCTTAAACGGCATATAAATCTTGAAAGCTAGCCTTATGACACTTACCAAGACAAGCTCACAAAT
66 CTCTTAAACGGCATATAAATCTTGAAAGCTAGCCTTATGACACTTACCAAGACAAGCTCACAAAT
56674427 AATCCAACTAAAACTACACTACCAGGGACTCCGGCTCTTCACATTTTTCTTGAAATATTCATATC
131 AATCCAACTAAAACTACACTACCAGGGACTCCGGCTCTTCACATTTTTCTTGAAATATTCATATC
56674492 GTATTCATATCCTTAAAGCATATGAAAATC
196 GTATTCATATCCTTAAAGCATATGAAAATC
56674522 TTGGAAAAAT
Statistics
Matches: 222, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
224 194 0.87
225 28 0.13
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (225 bp):
AGAAATGAAGCATCTTAAAATACAATGATTGATACACATTGCCGCTAAAGCAGACAGCAAATACA
CTCTTAAACGGCATATAAATCTTGAAAGCTAGCCTTATGACACTTACCAAGACAAGCTCACAAAT
AATCCAACTAAAACTACACTACCAGGGACTCCGGCTCTTCACATTTTTCTTGAAATATTCATATC
GTATTCATATCCTTAAAGCATATGAAAATC
Found at i:56675507 original size:29 final size:28
Alignment explanation
Indices: 56675465--56675526 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 28
56675455 AACTCTTCAA
*
56675465 ATTTTCGAAATTTAGTCCATTTACTTTT
1 ATTTTCGAAATTTAGTCCATCTACTTTT
* *
56675493 ATTTTCAGGAATTTAGTCCCTCTACTTTT
1 ATTTTC-GAAATTTAGTCCATCTACTTTT
*
56675522 CTTTT
1 ATTTT
56675527 TTAAGGAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.21, C:0.18, G:0.08, T:0.53
Consensus pattern (28 bp):
ATTTTCGAAATTTAGTCCATCTACTTTT
Found at i:56680275 original size:10 final size:10
Alignment explanation
Indices: 56680253--56680283 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
56680243 ACTCCGAATC
56680253 ATGAAACTATA
1 ATGAAA-TATA
56680264 ATGAAATATA
1 ATGAAATATA
56680274 ATGAAATATA
1 ATGAAATATA
56680284 GGATCAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.70
11 6 0.30
ACGTcount: A:0.58, C:0.03, G:0.10, T:0.29
Consensus pattern (10 bp):
ATGAAATATA
Found at i:56681828 original size:6 final size:6
Alignment explanation
Indices: 56681812--56681855 Score: 79
Period size: 6 Copynumber: 7.3 Consensus size: 6
56681802 TCCATTACTA
*
56681812 GGATTT AGATTT GGATTT GGATTT GGATTT GGATTT GGATTT GG
1 GGATTT GGATTT GGATTT GGATTT GGATTT GGATTT GGATTT GG
56681856 GTTGGGGGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.48
Consensus pattern (6 bp):
GGATTT
Found at i:56684132 original size:18 final size:18
Alignment explanation
Indices: 56684111--56684215 Score: 93
Period size: 18 Copynumber: 5.8 Consensus size: 18
56684101 GATCATCAAT
*
56684111 CTTACTCAAATCACCGAG
1 CTTACTCAAATCACCAAG
* *
56684129 CTTACTCAAACCTCCAAG
1 CTTACTCAAATCACCAAG
* * *
56684147 CGTACTGAAATCGCCAAG
1 CTTACTCAAATCACCAAG
* * * * *
56684165 CGTGCACAAATCTCCGAG
1 CTTACTCAAATCACCAAG
* *
56684183 ATTACTCAAATCGCCAAG
1 CTTACTCAAATCACCAAG
56684201 CTTACTCAAATCACC
1 CTTACTCAAATCACC
56684216 TCCAACCTGC
Statistics
Matches: 67, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.33, C:0.33, G:0.12, T:0.21
Consensus pattern (18 bp):
CTTACTCAAATCACCAAG
Found at i:56684211 original size:36 final size:36
Alignment explanation
Indices: 56684112--56684212 Score: 112
Period size: 36 Copynumber: 2.8 Consensus size: 36
56684102 ATCATCAATC
* * * *
56684112 TTACTCAAATCACCGAGCTTACTCAAACCTCCAAGC
1 TTACTCAAATCGCCAAGCTTACTCAAATCTCCAAGA
* * * * * *
56684148 GTACTGAAATCGCCAAGCGTGCACAAATCTCCGAGA
1 TTACTCAAATCGCCAAGCTTACTCAAATCTCCAAGA
56684184 TTACTCAAATCGCCAAGCTTACTCAAATC
1 TTACTCAAATCGCCAAGCTTACTCAAATC
56684213 ACCTCCAACC
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.34, C:0.32, G:0.13, T:0.22
Consensus pattern (36 bp):
TTACTCAAATCGCCAAGCTTACTCAAATCTCCAAGA
Found at i:56687664 original size:114 final size:112
Alignment explanation
Indices: 56687459--56687842 Score: 486
Period size: 114 Copynumber: 3.4 Consensus size: 112
56687449 CCTTAGTAGC
* *
56687459 CACTCCTGGAGAACTTTGGGCAGTCGAGATGGCATCGGATGAGACCTGCTTGATGAACCCAGAGG
1 CACTCCTGGAGAA-TTTGGGCAGCCGAGATGGCATCGGATGAGACCTGCTTGATGAATCCAGAGG
*
56687524 CAGTGCCCAACAGTCCAGAATTCTGAGCCTGAGGAGACCTTTCCCCAGA
65 CAGTGCCCAACAGTCCAGAATGCTGAGCCTGAGGAGACC-TTCCCCAGA
* *
56687573 CCCTCCTGGAGACATTTGGGCAACCGAGATGGCATCGGATGAGACCTGCTTGATGAATCCAGAGG
1 CACTCCTGGAGA-ATTTGGGCAGCCGAGATGGCATCGGATGAGACCTGCTTGATGAATCCAGAGG
* * * * *
56687638 CAGTACCCAACAGTTCAGAAGGCTGAGCCTGAGGAGACCCTCCCTCAAA
65 CAGTGCCCAACAGTCCAGAATGCTGAGCCTGAGGAGACCTTCCC-CAGA
* * *
56687687 CACTCCTGGAG--TTTGGGCAGCCGAGATGGCATCGGAAGAGATCTGCTTGATGAGTCCAGAGGC
1 CACTCCTGGAGAATTTGGGCAGCCGAGATGGCATCGGATGAGACCTGCTTGATGAATCCAGAGGC
* * * *
56687750 AGTGCCCGACAGTCCAGAATGCTGAACCTGAGGAGGCCCTCCCCCAG-
66 AGTGCCCAACAGTCCAGAATGCTGAGCCTGAGGA-GACCTTCCCCAGA
* * * * *
56687797 CTGCTCCTGGAGACATTTGTGCAGCCGAGATAGCTTCAGATGAGAC
1 C-ACTCCTGGAGA-ATTTGGGCAGCCGAGATGGCATCGGATGAGAC
56687843 ATCCTAGACA
Statistics
Matches: 232, Mismatches: 31, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
110 1 0.00
111 88 0.38
112 6 0.03
113 4 0.02
114 132 0.57
115 1 0.00
ACGTcount: A:0.25, C:0.27, G:0.29, T:0.19
Consensus pattern (112 bp):
CACTCCTGGAGAATTTGGGCAGCCGAGATGGCATCGGATGAGACCTGCTTGATGAATCCAGAGGC
AGTGCCCAACAGTCCAGAATGCTGAGCCTGAGGAGACCTTCCCCAGA
Found at i:56689894 original size:15 final size:15
Alignment explanation
Indices: 56689874--56689927 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
56689864 TGATAAACTA
56689874 AAAAATTAAGTGTTG
1 AAAAATTAAGTGTTG
*
56689889 AAAAA-TATGTGTTG
1 AAAAATTAAGTGTTG
* * *
56689903 AAAAAATAAATATTG
1 AAAAATTAAGTGTTG
*
56689918 AAGAATTAAG
1 AAAAATTAAG
56689928 GGTTATATTA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
14 13 0.42
15 18 0.58
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.30
Consensus pattern (15 bp):
AAAAATTAAGTGTTG
Found at i:56690250 original size:41 final size:40
Alignment explanation
Indices: 56690193--56690388 Score: 275
Period size: 41 Copynumber: 4.8 Consensus size: 40
56690183 TTTCGGGGGC
56690193 TTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGA
1 TTTAGCGGCGTTTTTAT-TAAGCGCCGCTAATGTTCTGGGA
*
56690234 TTTAGCGACGTTTTTATGTAAGCGCCGCTAATGTTCTGGGA
1 TTTAGCGGCGTTTTTAT-TAAGCGCCGCTAATGTTCTGGGA
*
56690275 TTTAGCGGCATTTTTATTTAAGCGCCGCTAATGTTCTGGGA
1 TTTAGCGGCGTTTTTA-TTAAGCGCCGCTAATGTTCTGGGA
* * * * *
56690316 TTTTGTGGCATTTTTAATTAAGCGTCGCTAATGTTCTGGGC
1 TTTAGCGGCGTTTTT-ATTAAGCGCCGCTAATGTTCTGGGA
*
56690357 TTTAGCGGCGTTTTTATTGATGCGCCGCTAAT
1 TTTAGCGGCGTTTTTATT-AAGCGCCGCTAAT
56690389 TCGCAGGCCT
Statistics
Matches: 140, Mismatches: 12, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
40 3 0.02
41 135 0.96
42 2 0.01
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.39
Consensus pattern (40 bp):
TTTAGCGGCGTTTTTATTAAGCGCCGCTAATGTTCTGGGA
Found at i:56690447 original size:123 final size:123
Alignment explanation
Indices: 56690193--56690453 Score: 280
Period size: 123 Copynumber: 2.1 Consensus size: 123
56690183 TTTCGGGGGC
* *
56690193 TTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGATTTAGCGACGTTTTTATGTAAGCG
1 TTTAGTGGCATTTTTATGTAAGCGCCGCTAATGTTCTGGGATTTAGCGACGTTTTTATGTAAGCG
* * * ** * * *
56690258 CCGCTAATGTTCTGGGATTTAGCGGCATTTTTATTTAAGCGCCGCTAATGTTCTGGGA
66 CCGCTAATGTGCAGGCATTTAGCGGCATTTTTATAAAAACGCCGCTAATGCTCTGGCA
* * * * *
56690316 TTTTGTGGCATTTTTAAT-TAAGCGTCGCTAATGTTCTGGGCTTTAGCGGCGTTTTTAT-TGATG
1 TTTAGTGGCATTTTT-ATGTAAGCGCCGCTAATGTTCTGGGATTTAGCGACGTTTTTATGT-AAG
* * *
56690379 CGCCGCTAAT-TCGCAGGCCTTTAGCGGCGCTTTTT-TAAAAAACGCCGCTAATGCTCT-TCA
64 CGCCGCTAATGT-GCAGGCATTTAGCGGC-ATTTTTAT-AAAAACGCCGCTAATGCTCTGGCA
56690439 TTTAGTGGCATTTTT
1 TTTAGTGGCATTTTT
56690454 GGAAAGCGCC
Statistics
Matches: 114, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
122 2 0.02
123 89 0.78
124 23 0.20
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (123 bp):
TTTAGTGGCATTTTTATGTAAGCGCCGCTAATGTTCTGGGATTTAGCGACGTTTTTATGTAAGCG
CCGCTAATGTGCAGGCATTTAGCGGCATTTTTATAAAAACGCCGCTAATGCTCTGGCA
Found at i:56690844 original size:16 final size:16
Alignment explanation
Indices: 56690823--56690892 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
56690813 CTATAGTATG
56690823 TAGTTTAAGGGTTTTA
1 TAGTTTAAGGGTTTTA
*
56690839 TAGTTTAA-GGTTTAA
1 TAGTTTAAGGGTTTTA
** * *
56690854 T-GTTTACTATAG-TATG
1 TAGTTTA--AGGGTTTTA
56690870 TAGTTTAAGGGTTTTA
1 TAGTTTAAGGGTTTTA
56690886 TAGTTTA
1 TAGTTTA
56690893 TGGTTTAGGG
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
14 5 0.12
15 9 0.22
16 20 0.50
17 6 0.15
ACGTcount: A:0.27, C:0.01, G:0.21, T:0.50
Consensus pattern (16 bp):
TAGTTTAAGGGTTTTA
Found at i:56690851 original size:23 final size:23
Alignment explanation
Indices: 56690825--56690905 Score: 80
Period size: 23 Copynumber: 3.5 Consensus size: 23
56690815 ATAGTATGTA
56690825 GTTTAAGGGTTTTATAGTTTAAG
1 GTTTAAGGGTTTTATAGTTTAAG
*
56690848 GTTTAA-TGTTTACTATAGTATGT-A-
1 GTTTAAGGGTTT--TATAGT-T-TAAG
*
56690872 GTTTAAGGGTTTTATAGTTTATG
1 GTTTAAGGGTTTTATAGTTTAAG
56690895 GTTT-AGGGTTT
1 GTTTAAGGGTTT
56690906 GTTATATCGG
Statistics
Matches: 48, Mismatches: 3, Indels: 15
0.73 0.05 0.23
Matches are distributed among these distances:
21 1 0.02
22 12 0.25
23 16 0.33
24 12 0.25
25 6 0.12
26 1 0.02
ACGTcount: A:0.23, C:0.01, G:0.25, T:0.51
Consensus pattern (23 bp):
GTTTAAGGGTTTTATAGTTTAAG
Found at i:56690941 original size:22 final size:21
Alignment explanation
Indices: 56690916--56690956 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
56690906 GTTATATCGG
56690916 GTTTGTGA-TTTAGTGTTTTAAA
1 GTTTG-GAGTTTAGT-TTTTAAA
56690938 GTTTGGAGTTTAGTTTTTA
1 GTTTGGAGTTTAGTTTTTA
56690957 TAGTCAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.20, C:0.00, G:0.24, T:0.56
Consensus pattern (21 bp):
GTTTGGAGTTTAGTTTTTAAA
Found at i:56694292 original size:66 final size:66
Alignment explanation
Indices: 56694222--56694352 Score: 217
Period size: 66 Copynumber: 2.0 Consensus size: 66
56694212 CACAGTTGAG
* * *
56694222 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAGAGCAGATGCGGCAGCGAGAGAAGCAGA
1 GTTCAAAAGAAATATGAAGAACTCCAGCGACAACTTAAAGCAGATGCGGCAGCCAGAGAAGCAGA
56694287 A
66 A
* *
56694288 GTTCAAAAGAAATATGAAGAACTCCAGCGACAACTTAAAGCTGATGCGGCATCCAGAGAAGCAGA
1 GTTCAAAAGAAATATGAAGAACTCCAGCGACAACTTAAAGCAGATGCGGCAGCCAGAGAAGCAGA
56694353 GGCTGCAGCG
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.15
Consensus pattern (66 bp):
GTTCAAAAGAAATATGAAGAACTCCAGCGACAACTTAAAGCAGATGCGGCAGCCAGAGAAGCAGA
A
Found at i:56694755 original size:43 final size:44
Alignment explanation
Indices: 56694700--56694799 Score: 177
Period size: 43 Copynumber: 2.3 Consensus size: 44
56694690 CCAAACAAAA
56694700 AGTGGCGTTTGTGTTAG-AAGCGCCGCTAAAGAACATGTTCTTT
1 AGTGGCGTTTGTGTTAGAAAGCGCCGCTAAAGAACATGTTCTTT
56694743 AGTGGCGTTTGTG-TAGAAAGCGCCGCTAAAGAACATGTTCTTT
1 AGTGGCGTTTGTGTTAGAAAGCGCCGCTAAAGAACATGTTCTTT
*
56694786 AGCGGCGTTTGTGT
1 AGTGGCGTTTGTGT
56694800 AAAATGCGCT
Statistics
Matches: 54, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
42 3 0.06
43 51 0.94
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (44 bp):
AGTGGCGTTTGTGTTAGAAAGCGCCGCTAAAGAACATGTTCTTT
Found at i:56695515 original size:26 final size:25
Alignment explanation
Indices: 56695462--56695511 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
56695452 AAAAGAAATT
*
56695462 TAAAAATGTATAAATAATTAATAAAG
1 TAAAAATG-ATAAATAATGAATAAAG
56695488 TAAAAATG-TAAATAATGAACTAAA
1 TAAAAATGATAAATAATGAA-TAAA
56695512 AGTACGTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 10 0.45
25 4 0.18
26 8 0.36
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.28
Consensus pattern (25 bp):
TAAAAATGATAAATAATGAATAAAG
Found at i:56695704 original size:6 final size:6
Alignment explanation
Indices: 56695688--56695723 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
56695678 GATTTTAATG
*
56695688 TAGAT- TAGATA TAGATA TAGATA TAGATA TAAATA T
1 TAGATA TAGATA TAGATA TAGATA TAGATA TAGATA T
56695724 TTCTCCTGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (6 bp):
TAGATA
Found at i:56698374 original size:3 final size:3
Alignment explanation
Indices: 56698366--56698434 Score: 122
Period size: 3 Copynumber: 23.0 Consensus size: 3
56698356 TTTCCGTTTA
56698366 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
56698414 TAT TAT TA- TATT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT
56698435 ATGTTTANNN
Statistics
Matches: 64, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
3 60 0.94
4 2 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:56700638 original size:18 final size:18
Alignment explanation
Indices: 56700612--56700648 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
56700602 AAATTTAAAT
* *
56700612 TTTATATTTATATTTACA
1 TTTACATTTATATTAACA
56700630 TTTACATTTATATTAACA
1 TTTACATTTATATTAACA
56700648 T
1 T
56700649 CAAATAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTACATTTATATTAACA
Found at i:56701229 original size:12 final size:12
Alignment explanation
Indices: 56701212--56701238 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
56701202 TATAAGACTC
56701212 TAACCTAAATTT
1 TAACCTAAATTT
56701224 TAACCTAAATTT
1 TAACCTAAATTT
56701236 TAA
1 TAA
56701239 GACTCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (12 bp):
TAACCTAAATTT
Found at i:56705812 original size:19 final size:19
Alignment explanation
Indices: 56705778--56705814 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
56705768 GTGTGTGTGT
* *
56705778 GTATAAAAGTAGTTTAAAC
1 GTATAAAAGAACTTTAAAC
56705797 GTATAAAAGAACTTTAAA
1 GTATAAAAGAACTTTAAA
56705815 ATATATTAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.05, G:0.14, T:0.30
Consensus pattern (19 bp):
GTATAAAAGAACTTTAAAC
Found at i:56709806 original size:32 final size:33
Alignment explanation
Indices: 56709770--56709831 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
56709760 AAATACATCA
*
56709770 AATAAACT-AAAA-ATATTAAATAAATATTTTCT
1 AATAAACTCAAAATAAATTAAA-AAATATTTTCT
*
56709802 AATAAATTCAAAATAAATTAAAAAATATTT
1 AATAAACTCAAAATAAATTAAAAAATATTT
56709832 ATATTTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 7 0.27
33 12 0.46
34 7 0.27
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (33 bp):
AATAAACTCAAAATAAATTAAAAAATATTTTCT
Found at i:56709911 original size:17 final size:19
Alignment explanation
Indices: 56709889--56709923 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
56709879 TTATAATAGT
56709889 AACAAAA-TTA-ACAATAA
1 AACAAAAGTTATACAATAA
56709906 AACAAAAGTTATACAATA
1 AACAAAAGTTATACAATA
56709924 TAATAGTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (19 bp):
AACAAAAGTTATACAATAA
Found at i:56720058 original size:14 final size:15
Alignment explanation
Indices: 56720041--56720074 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
56720031 TAAATAATCA
*
56720041 TTTTAAT-ATAATAT
1 TTTTAATGATAACAT
56720055 TTTTAATGATAACAT
1 TTTTAATGATAACAT
56720070 TTTTA
1 TTTTA
56720075 TTTTTATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (15 bp):
TTTTAATGATAACAT
Found at i:56720817 original size:33 final size:33
Alignment explanation
Indices: 56720780--56720884 Score: 115
Period size: 33 Copynumber: 3.2 Consensus size: 33
56720770 GCCTTCTAAT
* *
56720780 ATAATCTTGAAAATCTTTATGAGCAGCTGCGAA
1 ATAATCTTGAAAATCTTTATGAGCATCTTCGAA
*
56720813 ATAATC-TGCAAAAT-TTTGATAAGCATCTTCGAA
1 ATAATCTTG-AAAATCTTT-ATGAGCATCTTCGAA
* * **
56720846 ATAATCTTCAAAATCCTCGTGAGCATCTTCGAA
1 ATAATCTTGAAAATCTTTATGAGCATCTTCGAA
56720879 ATAATC
1 ATAATC
56720885 ACCACCCCGC
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
32 5 0.08
33 53 0.88
34 2 0.03
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.31
Consensus pattern (33 bp):
ATAATCTTGAAAATCTTTATGAGCATCTTCGAA
Found at i:56724363 original size:16 final size:16
Alignment explanation
Indices: 56724324--56724390 Score: 55
Period size: 17 Copynumber: 4.1 Consensus size: 16
56724314 ATTTTATTTT
*
56724324 TATTTTATTA-TTTAA
1 TATTTTATCATTTTAA
* *
56724339 TATAATTATGATTTTAA
1 TAT-TTTATCATTTTAA
*
56724356 TATTTTATCATTTGTTA
1 TATTTTATCATTT-TAA
* *
56724373 TATATAATCATTTTAA
1 TATTTTATCATTTTAA
56724389 TA
1 TA
56724391 CAATGATGAT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
15 3 0.07
16 17 0.41
17 21 0.51
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (16 bp):
TATTTTATCATTTTAA
Found at i:56724733 original size:2 final size:2
Alignment explanation
Indices: 56724707--56724762 Score: 80
Period size: 2 Copynumber: 29.0 Consensus size: 2
56724697 TTAAATACAT
* *
56724707 TA TA T- TA TA -A TA TA CA TA AA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56724747 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
56724763 GAAGATAACA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:56724974 original size:15 final size:15
Alignment explanation
Indices: 56724954--56724985 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
56724944 AAATAATCTC
*
56724954 CAAAATCATCATCAT
1 CAAAATAATCATCAT
56724969 CAAAATAATCATCAT
1 CAAAATAATCATCAT
56724984 CA
1 CA
56724986 CCCCACATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (15 bp):
CAAAATAATCATCAT
Found at i:56726660 original size:13 final size:13
Alignment explanation
Indices: 56726644--56726707 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
56726634 TTTAAACCAA
56726644 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
*
56726657 ACTTCTT-AAAAGC
1 ACTT-TTCAAAAGT
56726670 ACTTTT-ACAAAGT
1 ACTTTTCA-AAAGT
*
56726683 AATTTTCAAAAGT
1 ACTTTTCAAAAGT
**
56726696 AAATTTCAAAAG
1 ACTTTTCAAAAG
56726708 CAATAAAGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
12 3 0.07
13 38 0.86
14 3 0.07
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:56731189 original size:35 final size:35
Alignment explanation
Indices: 56731143--56731212 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
56731133 GATTTTGGAA
56731143 GACAGCAAATATCATTTCAATTACAATCTCAATGT
1 GACAGCAAATATCATTTCAATTACAATCTCAATGT
56731178 GACAGCAAATATCATTTCAATTACAATCTCAATGT
1 GACAGCAAATATCATTTCAATTACAATCTCAATGT
56731213 TATCGGCTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (35 bp):
GACAGCAAATATCATTTCAATTACAATCTCAATGT
Found at i:56737650 original size:7 final size:7
Alignment explanation
Indices: 56737638--56737662 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
56737628 AGGTCTCCAA
56737638 TTTTTAT
1 TTTTTAT
56737645 TTTTTAT
1 TTTTTAT
56737652 TTTTTAT
1 TTTTTAT
56737659 TTTT
1 TTTT
56737663 GCTTTCCAAG
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:56749126 original size:26 final size:26
Alignment explanation
Indices: 56749084--56749135 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
56749074 TTTAAAGTTA
** *
56749084 ATTTTTTTTATTTTAAATA-TAAAAT
1 ATTTTTTTTATGATAAAAATTAAAAT
56749109 ATTTATTTTTATGATAAAAATTAAAAT
1 ATTT-TTTTTATGATAAAAATTAAAAT
56749136 TGTAAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 4 0.18
26 12 0.55
27 6 0.27
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
ATTTTTTTTATGATAAAAATTAAAAT
Found at i:56751334 original size:28 final size:29
Alignment explanation
Indices: 56751280--56751336 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
56751270 TTATAGGAAC
* *
56751280 TGGATCAAATTAGTCCCTCTATTATTAAA
1 TGGATCAAATTAGTCCCTATACTATTAAA
*
56751309 TGGATCAATTTAGT-CCTATACTATTAAA
1 TGGATCAAATTAGTCCCTATACTATTAAA
56751337 AAGAATCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (29 bp):
TGGATCAAATTAGTCCCTATACTATTAAA
Found at i:56773277 original size:105 final size:105
Alignment explanation
Indices: 56773095--56773308 Score: 428
Period size: 105 Copynumber: 2.0 Consensus size: 105
56773085 TATTGCAGCA
56773095 TTTCCTATAGAATCTCTTTCCCAGCTTCTAAAAATGGTAAAAGTTGATTTGGTTTAAAGCCTCCC
1 TTTCCTATAGAATCTCTTTCCCAGCTTCTAAAAATGGTAAAAGTTGATTTGGTTTAAAGCCTCCC
56773160 CAGGCCCCTACATTAAACCATGAAAGAACCCAGAGTTTGT
66 CAGGCCCCTACATTAAACCATGAAAGAACCCAGAGTTTGT
56773200 TTTCCTATAGAATCTCTTTCCCAGCTTCTAAAAATGGTAAAAGTTGATTTGGTTTAAAGCCTCCC
1 TTTCCTATAGAATCTCTTTCCCAGCTTCTAAAAATGGTAAAAGTTGATTTGGTTTAAAGCCTCCC
56773265 CAGGCCCCTACATTAAACCATGAAAGAACCCAGAGTTTGT
66 CAGGCCCCTACATTAAACCATGAAAGAACCCAGAGTTTGT
56773305 TTTC
1 TTTC
56773309 TTAAGGTATG
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 109 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (105 bp):
TTTCCTATAGAATCTCTTTCCCAGCTTCTAAAAATGGTAAAAGTTGATTTGGTTTAAAGCCTCCC
CAGGCCCCTACATTAAACCATGAAAGAACCCAGAGTTTGT
Found at i:56786202 original size:32 final size:33
Alignment explanation
Indices: 56786141--56786207 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
56786131 ATTTGTGATT
* *
56786141 TAAAAATAATAATTTTAACTATATTTTAATTAA
1 TAAAAATAATAATTATAACTATATTTTAATAAA
56786174 TAAAAATAAGTAATTATAA-T-TATTTTAATAAA
1 TAAAAATAA-TAATTATAACTATATTTTAATAAA
56786206 TA
1 TA
56786208 CATATTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
32 13 0.42
33 10 0.32
34 8 0.26
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (33 bp):
TAAAAATAATAATTATAACTATATTTTAATAAA
Found at i:56786234 original size:21 final size:21
Alignment explanation
Indices: 56786197--56786247 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
56786187 TTATAATTAT
*
56786197 TTTAATAAATACATATTAAAA
1 TTTAATAAACACATATTAAAA
*
56786218 TTTAATAAACATC-TATTACAA
1 TTTAATAAACA-CATATTAAAA
*
56786239 TATAATAAA
1 TTTAATAAA
56786248 AACCATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (21 bp):
TTTAATAAACACATATTAAAA
Found at i:56790612 original size:10 final size:10
Alignment explanation
Indices: 56790597--56790621 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
56790587 AGAAATTGGC
56790597 GAGAGAGAGG
1 GAGAGAGAGG
56790607 GAGAGAGAGG
1 GAGAGAGAGG
56790617 GAGAG
1 GAGAG
56790622 CTAAACTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (10 bp):
GAGAGAGAGG
Found at i:56791179 original size:185 final size:186
Alignment explanation
Indices: 56790867--56791202 Score: 622
Period size: 185 Copynumber: 1.8 Consensus size: 186
56790857 GTTTACCATT
*
56790867 AATTAATAAAACTAAAACTCACGCATGATAACAACTCATGGTAGAACTTAATAATTTATATATTT
1 AATTAATAAAACTAAAACTCACACATGATAACAACTCATGGTAGAACTTAATAATTTATATATTT
* *
56790932 TGATTAAATATTATGGATCCCGGATTTAGATACTCAAAATCTATAACTTTCACCTTTATTAAT-A
66 TGATTAAATATTATGGATCCCGAACTTAGATACTCAAAATCTATAACTTTCACCTTTATTAATAA
56790996 TACCAAGATCTTTAATTATTAAAACTCTCGAATTGAAATCATCCAAACTATGAATA
131 TACCAAGATCTTTAATTATTAAAACTCTCGAATTGAAATCATCCAAACTATGAATA
56791052 AATTAATAAAACTAAAACTCACACATGATAACAACTCATGGTAGAACTTGAA-AATTTATATATT
1 AATTAATAAAACTAAAACTCACACATGATAACAACTCATGGTAGAACTT-AATAATTTATATATT
56791116 TTGATTAAATATTATGGATCCCGAACTTAGATACTCAAAATCTATAACTTTCACCTTTATTAATA
65 TTGATTAAATATTATGGATCCCGAACTTAGATACTCAAAATCTATAACTTTCACCTTTATTAATA
56791181 ATACCAAGATCTTTAATTATTA
130 ATACCAAGATCTTTAATTATTA
56791203 CTTTAAAAAA
Statistics
Matches: 146, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
185 122 0.84
186 24 0.16
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (186 bp):
AATTAATAAAACTAAAACTCACACATGATAACAACTCATGGTAGAACTTAATAATTTATATATTT
TGATTAAATATTATGGATCCCGAACTTAGATACTCAAAATCTATAACTTTCACCTTTATTAATAA
TACCAAGATCTTTAATTATTAAAACTCTCGAATTGAAATCATCCAAACTATGAATA
Found at i:56793277 original size:22 final size:24
Alignment explanation
Indices: 56793251--56793294 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
56793241 GAAAAATATT
56793251 AAATAT-AT-ATATTTTATTTTTA
1 AAATATAATAATATTTTATTTTTA
*
56793273 AAATATAATAATTTTTTATTTT
1 AAATATAATAATATTTTATTTT
56793295 AAGTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 2 0.11
24 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
AAATATAATAATATTTTATTTTTA
Found at i:56793424 original size:59 final size:59
Alignment explanation
Indices: 56793361--56793530 Score: 313
Period size: 59 Copynumber: 2.9 Consensus size: 59
56793351 TCAAGTTTGT
*
56793361 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
56793420 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
* *
56793479 TTTACTAATCAAATGTTAGATTTTATTACAACAATCAATACAATTAACAATT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATT
56793531 AATAATTTGA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 108 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
Found at i:56793562 original size:16 final size:16
Alignment explanation
Indices: 56793541--56793582 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
56793531 AATAATTTGA
*
56793541 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
56793557 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
56793573 TAGTTTTAAT
1 TAATTTTAAT
56793583 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:56793566 original size:22 final size:23
Alignment explanation
Indices: 56793556--56793617 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
56793546 TTACTAACAA
* * *
56793556 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
56793578 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
*
56793601 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
56793618 CGGGCCTGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.30
23 23 0.70
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:56804876 original size:5 final size:5
Alignment explanation
Indices: 56804866--56804905 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
56804856 GTACTTTAAT
*
56804866 ATTGA ATTGA ATTAA AGTTG- ATTGA ATTGA ATTGA ATTGA
1 ATTGA ATTGA ATTGA A-TTGA ATTGA ATTGA ATTGA ATTGA
56804906 TATATATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 3 0.10
5 26 0.84
6 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
ATTGA
Found at i:56809544 original size:20 final size:20
Alignment explanation
Indices: 56809516--56809566 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
56809506 CACATATGTG
56809516 TATATATATAAGGTAT-ATAAA
1 TATATATATAA-GTATGA-AAA
56809537 TA-ATATATAAGTATGAAAA
1 TATATATATAAGTATGAAAA
56809556 TATATATATAA
1 TATATATATAA
56809567 ATAAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.32
20 17 0.61
21 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (20 bp):
TATATATATAAGTATGAAAA
Found at i:56809635 original size:26 final size:26
Alignment explanation
Indices: 56809582--56809635 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
56809572 TTTTAAAAAT
* * **
56809582 ATGTACGTATGTATATATATGACAAA
1 ATGTAAGTATGTACATATACAACAAA
*
56809608 ATGTAAGTATGTACATATACAACGAA
1 ATGTAAGTATGTACATATACAACAAA
56809634 AT
1 AT
56809636 TTGAAACTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.31
Consensus pattern (26 bp):
ATGTAAGTATGTACATATACAACAAA
Found at i:56810938 original size:8 final size:8
Alignment explanation
Indices: 56810927--56810953 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
56810917 GGCCTTTTAG
56810927 AAAATTTT
1 AAAATTTT
56810935 AAAATTTT
1 AAAATTTT
56810943 AAAATTTT
1 AAAATTTT
56810951 AAA
1 AAA
56810954 TTAATAAAGG
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
AAAATTTT
Found at i:56814855 original size:28 final size:28
Alignment explanation
Indices: 56814824--56814879 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
56814814 AAACTTTGTT
*
56814824 TTTTATTA-ATTTTTAA-TTTATTCAATTA
1 TTTTA-TAGATTTATAATTTTATT-AATTA
56814852 TTTTATAGATTTATAATTTTATTAATTA
1 TTTTATAGATTTATAATTTTATTAATTA
56814880 ATAATATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 2 0.08
28 17 0.68
29 6 0.24
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTTATAGATTTATAATTTTATTAATTA
Found at i:56824101 original size:28 final size:29
Alignment explanation
Indices: 56824061--56824118 Score: 100
Period size: 28 Copynumber: 2.0 Consensus size: 29
56824051 GAGTTTTAAT
*
56824061 ATTCTATAGGATTTTTTACCAAAAA-AAA
1 ATTCTATAAGATTTTTTACCAAAAATAAA
56824089 ATTCTATAAGATTTTTTACCAAAAATAAA
1 ATTCTATAAGATTTTTTACCAAAAATAAA
56824118 A
1 A
56824119 AGTATTATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.36
Consensus pattern (29 bp):
ATTCTATAAGATTTTTTACCAAAAATAAA
Found at i:56825354 original size:19 final size:18
Alignment explanation
Indices: 56825307--56825354 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
56825297 TTAAAAACGT
* *
56825307 TTTAATTAATATTTTTTA
1 TTTAATTAATATATTATA
**
56825325 TTTAAAAAATAGTATTATA
1 TTTAATTAATA-TATTATA
56825344 TTTAATTAATA
1 TTTAATTAATA
56825355 AATACTTTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
TTTAATTAATATATTATA
Found at i:56829332 original size:31 final size:31
Alignment explanation
Indices: 56829252--56829316 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
56829242 TATTTTGATC
* *
56829252 CAATTAAGCACATGAACTCGGCTTCTTAGTT
1 CAATTAAGCACATGAACTTGGCTGCTTAGTT
56829283 CAATTAAGCACATGAACTTGGCTGCTTAGTT
1 CAATTAAGCACATGAACTTGGCTGCTTAGTT
56829314 CAA
1 CAA
56829317 ATTGGCACCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (31 bp):
CAATTAAGCACATGAACTTGGCTGCTTAGTT
Found at i:56831256 original size:30 final size:31
Alignment explanation
Indices: 56831221--56831285 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
56831211 TAGTAATAAA
56831221 ATAAATTA-TTAATATAATTAATTAT-TTTTT
1 ATAAATTATTTAATATAA-TAATTATATTTTT
* *
56831251 ATAAATTATTTAATATTATAATTTTATTTTT
1 ATAAATTATTTAATATAATAATTATATTTTT
56831282 ATAA
1 ATAA
56831286 TAAATATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 14 0.45
31 17 0.55
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
ATAAATTATTTAATATAATAATTATATTTTT
Found at i:56831269 original size:17 final size:17
Alignment explanation
Indices: 56831221--56831271 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 17
56831211 TAGTAATAAA
*
56831221 ATAAATTA-TTAATATA
1 ATAAATTATTTAATATT
*
56831237 ATTAATTATTT--T-TT
1 ATAAATTATTTAATATT
56831251 ATAAATTATTTAATATT
1 ATAAATTATTTAATATT
56831268 ATAA
1 ATAA
56831272 TTTTATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.39
15 1 0.04
16 8 0.29
17 8 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATAAATTATTTAATATT
Found at i:56831289 original size:34 final size:31
Alignment explanation
Indices: 56831220--56831290 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 31
56831210 TTAGTAATAA
56831220 AATAAATTATTAATATAATTAATTATTTTTT
1 AATAAATTATTAATATAATTAATTATTTTTT
*
56831251 -ATAAATTATTTAATATTA-TAATTTTATTTTTAT
1 AATAAATTA-TTAATATAATTAA--TTATTTTT-T
56831284 AATAAAT
1 AATAAAT
56831291 ATACATTACA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
30 11 0.32
31 8 0.24
32 8 0.24
33 1 0.03
34 6 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
AATAAATTATTAATATAATTAATTATTTTTT
Found at i:56831560 original size:22 final size:22
Alignment explanation
Indices: 56831535--56831587 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
56831525 CATTTTAAAT
* * *
56831535 TAAAATTAAAATTATTTTTTAA
1 TAAAATTAAAACTACTTGTTAA
*
56831557 TAAAATTAAAACTACTTGTTAT
1 TAAAATTAAAACTACTTGTTAA
56831579 TAAAATTAA
1 TAAAATTAA
56831588 TTGTTAGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAAATTAAAACTACTTGTTAA
Found at i:56831580 original size:16 final size:16
Alignment explanation
Indices: 56831561--56831599 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
56831551 TTTTAATAAA
*
56831561 ATTAAAACTACTTGTT
1 ATTAAAACTAATTGTT
*
56831577 ATTAAAATTAATTGTT
1 ATTAAAACTAATTGTT
*
56831593 AGTAAAA
1 ATTAAAA
56831600 TTATCAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (16 bp):
ATTAAAACTAATTGTT
Found at i:56831600 original size:16 final size:16
Alignment explanation
Indices: 56831572--56831602 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56831562 TTAAAACTAC
*
56831572 TTGTTATTAAAATTAA
1 TTGTTAGTAAAATTAA
56831588 TTGTTAGTAAAATTA
1 TTGTTAGTAAAATTA
56831603 TCAAATTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (16 bp):
TTGTTAGTAAAATTAA
Found at i:56831708 original size:9 final size:9
Alignment explanation
Indices: 56831675--56831702 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
56831665 TTTATCAAAT
56831675 TATTAATTG
1 TATTAATTG
56831684 TATTAATTG
1 TATTAATTG
56831693 TATTAATTG
1 TATTAATTG
56831702 T
1 T
56831703 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:56831712 original size:68 final size:68
Alignment explanation
Indices: 56831591--56831800 Score: 379
Period size: 68 Copynumber: 3.1 Consensus size: 68
56831581 AAATTAATTG
*
56831591 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
56831654 TGA
66 TGA
56831657 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
56831722 TGA
66 TGA
* *
56831725 TTAGTATATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
56831790 TGA
66 TGA
56831793 TTAGTAAA
1 TTAGTAAA
56831801 ACAAACTTGA
Statistics
Matches: 138, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
66 26 0.19
68 112 0.81
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:56831757 original size:9 final size:9
Alignment explanation
Indices: 56831743--56831770 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
56831733 TTTATCAAAT
56831743 TATTAATTG
1 TATTAATTG
56831752 TATTAATTG
1 TATTAATTG
56831761 TATTAATTG
1 TATTAATTG
56831770 T
1 T
56831771 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:56831908 original size:22 final size:24
Alignment explanation
Indices: 56831868--56831911 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
56831858 AAATAAACTT
56831868 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
56831892 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
56831912 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:56832218 original size:18 final size:17
Alignment explanation
Indices: 56832195--56832229 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
56832185 TATGATATTG
*
56832195 ATTATTATAAAATATTTT
1 ATTATTA-AAAAAATTTT
56832213 ATTATTAAAAAAATTTT
1 ATTATTAAAAAAATTTT
56832230 TGATGGTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTATTAAAAAAATTTT
Found at i:56833041 original size:36 final size:36
Alignment explanation
Indices: 56832991--56833077 Score: 88
Period size: 36 Copynumber: 2.4 Consensus size: 36
56832981 TTTCTTTTTT
* * **
56832991 TATTGTTGTT-TTGTTGTTATTTCGTTATTATATTGC
1 TATTGTT-TTATTGTTATTATTTCGATATTATATAAC
* *
56833027 TATTGTTTTATTGTTATTGTTTGGATATTATATAAC
1 TATTGTTTTATTGTTATTATTTCGATATTATATAAC
*
56833063 TCTTG-TTTATTGTTA
1 TATTGTTTTATTGTTA
56833078 ATTTTCCTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
35 12 0.28
36 31 0.72
ACGTcount: A:0.18, C:0.05, G:0.15, T:0.62
Consensus pattern (36 bp):
TATTGTTTTATTGTTATTATTTCGATATTATATAAC
Found at i:56841889 original size:41 final size:41
Alignment explanation
Indices: 56841827--56841908 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
56841817 AGTTTAGTCC
*
56841827 TAATTTTAAGTAAATCGATAAATATATAAAATTGTTCAATT
1 TAATTTTAAGTAAATCAATAAATATATAAAATTGTTCAATT
56841868 TAATTTTAAGTAAATCAATAAATATATAAAATTGTTCAATT
1 TAATTTTAAGTAAATCAATAAATATATAAAATTGTTCAATT
56841909 AGATAAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (41 bp):
TAATTTTAAGTAAATCAATAAATATATAAAATTGTTCAATT
Found at i:56844378 original size:2 final size:2
Alignment explanation
Indices: 56844371--56844404 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
56844361 AAATCTTTAA
56844371 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56844405 CAGTAAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:56852627 original size:28 final size:29
Alignment explanation
Indices: 56852591--56852650 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
56852581 ATTGAAAATA
56852591 TTTAATTTT-AGAATTTAGTCCATTTACT
1 TTTAATTTTAAGAATTTAGTCCATTTACT
* * * *
56852619 TTTATTTTTAAGAATTTATTCCTTTTATT
1 TTTAATTTTAAGAATTTAGTCCATTTACT
56852648 TTT
1 TTT
56852651 CAAATTTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.25, C:0.08, G:0.05, T:0.62
Consensus pattern (29 bp):
TTTAATTTTAAGAATTTAGTCCATTTACT
Found at i:56852783 original size:31 final size:30
Alignment explanation
Indices: 56852719--56852784 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
56852709 ATTTCATTAC
*
56852719 AATTTTTTTAGTCAAATTGCTACCAAATGA
1 AATTTTTTTAGTCAAAATGCTACCAAATGA
*
56852749 AATTTTTTTATTTCAAAATGTCATACC-AAT-A
1 AATTTTTTTA-GTCAAAATG-C-TACCAAATGA
56852780 AATTT
1 AATTT
56852785 AACAAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 10 0.32
31 13 0.42
32 4 0.13
33 4 0.13
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (30 bp):
AATTTTTTTAGTCAAAATGCTACCAAATGA
Found at i:56852871 original size:23 final size:22
Alignment explanation
Indices: 56852845--56852889 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
56852835 AAAATAAATT
56852845 ACTAGAAATAAAAATATAAAAAA
1 ACTA-AAATAAAAATATAAAAAA
* * *
56852868 ACTAAATTCAAAATTTAAAAAA
1 ACTAAAATAAAAATATAAAAAA
56852890 GCCTACATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.22
Consensus pattern (22 bp):
ACTAAAATAAAAATATAAAAAA
Found at i:56854040 original size:15 final size:14
Alignment explanation
Indices: 56854010--56854047 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
56854000 ACCCGATTGA
56854010 TTTCTATTTTAGTTT
1 TTTCT-TTTTAGTTT
*
56854025 TTTCTTTTTAGCTT
1 TTTCTTTTTAGTTT
56854039 TTT-TTTTTA
1 TTTCTTTTTA
56854048 AAGTTGACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.27
14 11 0.50
15 5 0.23
ACGTcount: A:0.11, C:0.08, G:0.05, T:0.76
Consensus pattern (14 bp):
TTTCTTTTTAGTTT
Found at i:56854807 original size:10 final size:11
Alignment explanation
Indices: 56854781--56854806 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
56854771 GAAAAAATAA
56854781 AAAAATATTTT
1 AAAAATATTTT
56854792 AAAAATATTTT
1 AAAAATATTTT
56854803 AAAA
1 AAAA
56854807 TTAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:56854813 original size:37 final size:41
Alignment explanation
Indices: 56854753--56854831 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 41
56854743 ATAAACACTA
56854753 AAAAATTATTTTAAAAATGAAAAAATAAAAA-A-ATATTTT
1 AAAAATTATTTTAAAAATGAAAAAATAAAAATATATATTTT
*
56854792 AAAAA-TATTTT-AAAATTAAAAAATAAAAATATATATTTT
1 AAAAATTATTTTAAAAATGAAAAAATAAAAATATATATTTT
56854831 A
1 A
56854832 TCCAAACAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
37 17 0.46
38 7 0.19
39 13 0.35
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (41 bp):
AAAAATTATTTTAAAAATGAAAAAATAAAAATATATATTTT
Found at i:56860853 original size:162 final size:161
Alignment explanation
Indices: 56860514--56861003 Score: 547
Period size: 163 Copynumber: 3.0 Consensus size: 161
56860504 ATTGAGTCGA
* * * *
56860514 GGCAAGG-GGATTTTATCTAAAACCGCCCCCAAT-ATGCCCTGAAAA-TTCAGCCAAGTAACTAA
1 GGCAAGGTGGATTTTATCTAGAACCGCCCCC-ATCATG-CCTGAAAATTTCAGCTAAGAAACCAA
* * * **
56860576 CATGCCTAGCCTCTGAACTCGATTGTTAGATAAAAGAAAGACCTATAAGGTGAGGTTGAAACCTG
64 CATGCCTAGCCTCCGAACTCGATTGTCAGATAAAAGAAAGACCTATAGGGTGAGGTTGAAACCCA
* * *
56860641 AAAAGTTAGGTTATTTTTCCTCATATATGTTCGG
129 AAAAGTTCGGTTATTTCTCC-CATATAAGTTCGG
* * * *
56860675 GGCAAGGTGGATTTTATCTAGAACCACTCCCATCCTGCCATGAAAATTTCAGCTATGAAACCAAC
1 GGCAAGGTGGATTTTATCTAGAACCGCCCCCATCATGCC-TGAAAATTTCAGCTAAGAAACCAAC
*
56860740 ATGCCTAGCCTCCGAACTCGATTGTCAGATAAAAGAAAGCCCTATAGGGTGAGGTTGAAACCCAA
65 ATGCCTAGCCTCCGAACTCGATTGTCAGATAAAAGAAAGACCTATAGGGTGAGGTTGAAACCCAA
* *
56860805 AAAGTTCGATTGTTTCTCCCATATAAGTTCGG
130 AAAGTTCGGTTATTTCTCCCATATAAGTTCGG
* * * * * *
56860837 GGCAAGGTGGATTTTATCTAGAACTGCCCCACAACTTGTCCCGAAAATTTCAGATAAGAAATCAA
1 GGCAAGGTGGATTTTATCTAGAACCGCCCC-CATCATG-CCTGAAAATTTCAGCTAAGAAACCAA
* * * * * *
56860902 CATGCCTAGCCTCCGAACTCAATTGTGAGAAAAAAAAAAAAAAGACTTAATAGGGGGAGGTTGAA
64 CATGCCTAGCCTCCGAACTCGATTGTCAG----ATAAAAGAAAGACCT-ATAGGGTGAGGTTGAA
* * *
56860967 ACCCAAAAATTTCGGTTTTTTC-CCCATGTAAGTTCGG
124 ACCCAAAAAGTTCGGTTATTTCTCCCATATAAGTTCGG
56861004 TTGAAACTCG
Statistics
Matches: 279, Mismatches: 39, Indels: 16
0.84 0.12 0.05
Matches are distributed among these distances:
161 11 0.04
162 67 0.24
163 140 0.50
164 2 0.01
167 25 0.09
168 34 0.12
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (161 bp):
GGCAAGGTGGATTTTATCTAGAACCGCCCCCATCATGCCTGAAAATTTCAGCTAAGAAACCAACA
TGCCTAGCCTCCGAACTCGATTGTCAGATAAAAGAAAGACCTATAGGGTGAGGTTGAAACCCAAA
AAGTTCGGTTATTTCTCCCATATAAGTTCGG
Found at i:56862698 original size:20 final size:21
Alignment explanation
Indices: 56862670--56862708 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
56862660 ATTTCTAATT
56862670 TATACTTTAA-AATTATTTGA
1 TATACTTTAACAATTATTTGA
*
56862690 TATATTTTAACAATTATTT
1 TATACTTTAACAATTATTT
56862709 ATTTTACTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (21 bp):
TATACTTTAACAATTATTTGA
Found at i:56871632 original size:3 final size:3
Alignment explanation
Indices: 56871624--56871654 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
56871614 GTCAAACATA
56871624 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
56871655 NNNNNNNNNN
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:56873671 original size:2 final size:2
Alignment explanation
Indices: 56873664--56873700 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
56873654 GTCCTACCAT
56873664 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
56873701 TATTATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:56873706 original size:3 final size:3
Alignment explanation
Indices: 56873698--56873722 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
56873688 TATATATATA
56873698 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
56873723 TTAGAGTGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:56876087 original size:15 final size:16
Alignment explanation
Indices: 56876067--56876105 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
56876057 TCCAATCTTG
*
56876067 AACCCTAAAAAC-TCA
1 AACCCTAAAAACATAA
56876082 AACCCTAAAAACATAA
1 AACCCTAAAAACATAA
56876098 AACCCTAA
1 AACCCTAA
56876106 CTCTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.56, C:0.31, G:0.00, T:0.13
Consensus pattern (16 bp):
AACCCTAAAAACATAA
Found at i:56882763 original size:52 final size:53
Alignment explanation
Indices: 56882667--56882772 Score: 128
Period size: 52 Copynumber: 2.0 Consensus size: 53
56882657 TCTAGATATG
* *
56882667 TATATAAAGGGATTACATCAGTTTCGACTGAATAAGTTTGTTTGAACAGACTT
1 TATATAAAGGGATTACATCAGTTTCGACAGAATAAGATTGTTTGAACAGACTT
* * *
56882720 TATA-AAAGGGATTACATCAGTTTGGGTCAG-ATAA-ATTGATTTGAATAGACTT
1 TATATAAAGGGATTACATCAGTTT-CGACAGAATAAGATTG-TTTGAACAGACTT
56882772 T
1 T
56882773 TATGCATTCC
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
51 3 0.07
52 36 0.78
53 7 0.15
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.36
Consensus pattern (53 bp):
TATATAAAGGGATTACATCAGTTTCGACAGAATAAGATTGTTTGAACAGACTT
Found at i:56884475 original size:29 final size:29
Alignment explanation
Indices: 56884443--56884500 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
56884433 TTAATTAAAA
*
56884443 AAATGAAACTAATATAAAAGTAGACATTT
1 AAATAAAACTAATATAAAAGTAGACATTT
* * *
56884472 AAATAAAACTAATGTAAATGTAGATATTT
1 AAATAAAACTAATATAAAAGTAGACATTT
56884501 CATGAATTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.31
Consensus pattern (29 bp):
AAATAAAACTAATATAAAAGTAGACATTT
Found at i:56892659 original size:20 final size:18
Alignment explanation
Indices: 56892626--56892669 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
56892616 AACATACACC
56892626 TAATTATTTTTATTTCAT
1 TAATTATTTTTATTTCAT
*
56892644 TAATTATATATTTATTTTAT
1 TAATTAT-T-TTTATTTCAT
56892664 TAATTA
1 TAATTA
56892670 GTGTATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
19 1 0.04
20 15 0.65
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TAATTATTTTTATTTCAT
Found at i:56892683 original size:20 final size:20
Alignment explanation
Indices: 56892626--56892685 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
56892616 AACATACACC
56892626 TAATTAT-T-TTTAT-TTCAT
1 TAATTATATATTTATATT-AT
*
56892644 TAATTATATATTTATTTTAT
1 TAATTATATATTTATATTAT
*
56892664 TAATTAGTGTATTTA-ATTAT
1 TAATTA-TATATTTATATTAT
56892684 TA
1 TA
56892686 TTTAAAGATA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
18 7 0.19
19 1 0.03
20 19 0.53
21 9 0.25
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (20 bp):
TAATTATATATTTATATTAT
Found at i:56895232 original size:45 final size:47
Alignment explanation
Indices: 56895178--56895288 Score: 118
Period size: 49 Copynumber: 2.4 Consensus size: 47
56895168 TCCATATAGA
* *
56895178 ACTACACTTCTTTTATTT-TATT-TTAAAATAAGGTTTTTCAACCTT
1 ACTACACTTCTTTTATTTATATTATTAAAATAAGATGTTTCAACCTT
* * * * *
56895223 ATTACACTTCATCTATTTGATATTGATTAGAATTAGATGTTTCAACCTT
1 ACTACACTTCTTTTATTT-ATATT-ATTAAAATAAGATGTTTCAACCTT
*
56895272 ACTACACTCCTTTTATT
1 ACTACACTTCTTTTATT
56895289 AGAATATGGG
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
45 15 0.29
47 4 0.08
49 32 0.63
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.48
Consensus pattern (47 bp):
ACTACACTTCTTTTATTTATATTATTAAAATAAGATGTTTCAACCTT
Found at i:56900982 original size:2 final size:2
Alignment explanation
Indices: 56900975--56901009 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
56900965 GTGTAAGTGA
56900975 AT 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 AT A
56901010 ATGAAAATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:56904476 original size:14 final size:15
Alignment explanation
Indices: 56904450--56904480 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
56904440 TCCGGGTTCA
56904450 TCAACACATTTTTCT
1 TCAACACATTTTTCT
56904465 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
56904479 TC
1 TC
56904481 CCATTTCTTG
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:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:56908396 original size:20 final size:18
Alignment explanation
Indices: 56908363--56908406 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
56908353 AACATACATC
56908363 TAATTATTTTTATTTCAT
1 TAATTATTTTTATTTCAT
*
56908381 TAATTATATATTTATTTTAT
1 TAATTAT-T-TTTATTTCAT
56908401 TAATTA
1 TAATTA
56908407 GTGTATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
19 1 0.04
20 15 0.65
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TAATTATTTTTATTTCAT
Found at i:56908420 original size:20 final size:20
Alignment explanation
Indices: 56908363--56908422 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
56908353 AACATACATC
56908363 TAATTAT-T-TTTAT-TTCAT
1 TAATTATATATTTATATT-AT
*
56908381 TAATTATATATTTATTTTAT
1 TAATTATATATTTATATTAT
*
56908401 TAATTAGTGTATTTA-ATTAT
1 TAATTA-TATATTTATATTAT
56908421 TA
1 TA
56908423 TTTAAAGATA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
18 7 0.19
19 1 0.03
20 19 0.53
21 9 0.25
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (20 bp):
TAATTATATATTTATATTAT
Found at i:56909262 original size:3 final size:3
Alignment explanation
Indices: 56909247--56909302 Score: 96
Period size: 3 Copynumber: 18.7 Consensus size: 3
56909237 TAAATAATAA
56909247 ATT A-T ATT AATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
56909292 ATT ATT ATT AT
1 ATT ATT ATT AT
56909303 GAAATAAGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:56909757 original size:12 final size:13
Alignment explanation
Indices: 56909727--56909751 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56909717 AGTAAAAATT
56909727 AAAGAAACAAAAA
1 AAAGAAACAAAAA
56909740 AAAGAAACAAAA
1 AAAGAAACAAAA
56909752 GAAGAACAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAGAAACAAAAA
Found at i:56910168 original size:22 final size:24
Alignment explanation
Indices: 56910140--56910183 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
56910130 TATGGCAAGA
56910140 AATTAAG-TAGAAAAG-AAGTATG
1 AATTAAGCTAGAAAAGTAAGTATG
56910162 AATTAAGCTAGAAAAGTAAGTA
1 AATTAAGCTAGAAAAGTAAGTA
56910184 AGCTCAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.55, C:0.02, G:0.20, T:0.23
Consensus pattern (24 bp):
AATTAAGCTAGAAAAGTAAGTATG
Found at i:56910568 original size:37 final size:36
Alignment explanation
Indices: 56910508--56910599 Score: 98
Period size: 37 Copynumber: 2.5 Consensus size: 36
56910498 ATATGTGTGG
* *
56910508 AATTGAAATGAATAT-TGACTTGAAAATGGAAAAGTGA
1 AATTGAATTGAA-ATGTGA-TTGAAAATGAAAAAGTGA
* *
56910545 ATTTTGAATT-AAATTGTGATTGAAAGTGAAAAAGTGA
1 A-ATTGAATTGAAA-TGTGATTGAAAATGAAAAAGTGA
56910582 AATTGAATTGAAATGTGA
1 AATTGAATTGAAATGTGA
56910600 ATTTGGAGAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
36 13 0.28
37 24 0.52
38 9 0.20
ACGTcount: A:0.46, C:0.01, G:0.22, T:0.32
Consensus pattern (36 bp):
AATTGAATTGAAATGTGATTGAAAATGAAAAAGTGA
Found at i:56912911 original size:26 final size:26
Alignment explanation
Indices: 56912881--56912943 Score: 63
Period size: 32 Copynumber: 2.2 Consensus size: 26
56912871 TAAGAAGGAC
56912881 AGTTCTAAATGTATTAACATCTGTTA
1 AGTTCTAAATGTATTAACATCTGTTA
*
56912907 AGTTCCTACACTAAATGTATTGACATCTGTTA
1 AG-T--T---CTAAATGTATTAACATCTGTTA
56912939 AGTTC
1 AGTTC
56912944 CCGCAGGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 12
0.70 0.02 0.28
Matches are distributed among these distances:
26 3 0.10
27 1 0.03
29 2 0.07
31 1 0.03
32 23 0.77
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.40
Consensus pattern (26 bp):
AGTTCTAAATGTATTAACATCTGTTA
Found at i:56920294 original size:9 final size:9
Alignment explanation
Indices: 56920282--56920308 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
56920272 CAGAACAATG
56920282 AAGCAAGAT
1 AAGCAAGAT
56920291 AAGCAAGAT
1 AAGCAAGAT
56920300 AAGCAAGAT
1 AAGCAAGAT
56920309 GCAAGAGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.22, T:0.11
Consensus pattern (9 bp):
AAGCAAGAT
Found at i:56921077 original size:29 final size:29
Alignment explanation
Indices: 56921045--56921101 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
56921035 AATTTGACAG
*
56921045 GCTCACACTTTGCTTACTGTCTTTAACAA
1 GCTCACACTTTGCTTACTGTCTTCAACAA
*
56921074 GCTCGCACTTTGCTTACTGTCTTCAACA
1 GCTCACACTTTGCTTACTGTCTTCAACA
56921102 GGCTTGCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.37
Consensus pattern (29 bp):
GCTCACACTTTGCTTACTGTCTTCAACAA
Found at i:56921229 original size:26 final size:26
Alignment explanation
Indices: 56921199--56921249 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
56921189 CTTTGACATC
56921199 TTGCTAAGCTTGCACCTTGCACATTT
1 TTGCTAAGCTTGCACCTTGCACATTT
* * *
56921225 TTGCTGAGGTTGCAGCTTGCACATT
1 TTGCTAAGCTTGCACCTTGCACATT
56921250 GGAAAGCTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.37
Consensus pattern (26 bp):
TTGCTAAGCTTGCACCTTGCACATTT
Found at i:56924269 original size:2 final size:2
Alignment explanation
Indices: 56924262--56924290 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
56924252 ATGTAAGTGA
56924262 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 A
56924291 GTGAAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56927949 original size:14 final size:15
Alignment explanation
Indices: 56927923--56927953 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
56927913 TCCGGGTTCA
56927923 TCAACACATTTTTCT
1 TCAACACATTTTTCT
56927938 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
56927952 TC
1 TC
56927954 CCATTTCTTG
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:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:56933050 original size:21 final size:21
Alignment explanation
Indices: 56933024--56933066 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
56933014 TTATTAAATG
56933024 TGTCGTATTTATATCAAGGAT
1 TGTCGTATTTATATCAAGGAT
56933045 TGTCGTATTTATATCAAGGAT
1 TGTCGTATTTATATCAAGGAT
56933066 T
1 T
56933067 TTATTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (21 bp):
TGTCGTATTTATATCAAGGAT
Found at i:56940609 original size:13 final size:13
Alignment explanation
Indices: 56940591--56940615 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56940581 CTTTAAAATA
56940591 TTTTTATTTTTAT
1 TTTTTATTTTTAT
56940604 TTTTTATTTTTA
1 TTTTTATTTTTA
56940616 AAATATTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:56952808 original size:16 final size:16
Alignment explanation
Indices: 56952787--56952819 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
56952777 AAAGTTATAA
56952787 AAAAAATT-AAAACAAT
1 AAAAAATTCAAAA-AAT
56952803 AAAAAATTCAAAAAAT
1 AAAAAATTCAAAAAAT
56952819 A
1 A
56952820 TATAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAAAATTCAAAAAAT
Found at i:56952827 original size:29 final size:30
Alignment explanation
Indices: 56952794--56952867 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 30
56952784 TAAAAAAAAT
56952794 TAAAACAA-TAAAAAATTCAAAAAATATATA
1 TAAAA-AAGTAAAAAATTCAAAAAATATATA
*
56952824 -AAAATAAGT-AAGAATTCAAAAAATATATA
1 TAAAA-AAGTAAAAAATTCAAAAAATATATA
*
56952853 TAAAAAATTAAAAAA
1 TAAAAAAGTAAAAAA
56952868 ATGATGAGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
29 28 0.76
30 9 0.24
ACGTcount: A:0.70, C:0.04, G:0.03, T:0.23
Consensus pattern (30 bp):
TAAAAAAGTAAAAAATTCAAAAAATATATA
Found at i:56952925 original size:17 final size:18
Alignment explanation
Indices: 56952905--56952944 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
56952895 AAAAAACTTC
*
56952905 AAAATTTTTAAAAATA-A
1 AAAATTGTTAAAAATATA
*
56952922 AAAATTGTTAAAATTATA
1 AAAATTGTTAAAAATATA
56952940 AAAAT
1 AAAAT
56952945 CAGTAGCCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
AAAATTGTTAAAAATATA
Found at i:56962416 original size:87 final size:87
Alignment explanation
Indices: 56962254--56962424 Score: 252
Period size: 87 Copynumber: 2.0 Consensus size: 87
56962244 TTCTTTCAGC
* **
56962254 AGTGTTAATGCATTCATATTCTCGGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCACCCTTATC
1 AGTGTTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCACCCGAATC
*** **
56962319 TGTTCTATTGCATACTTCACGT
66 CACTAAATTGCATACTTCACGT
* *
56962341 AGTGTTAATGCATTGATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCAGCCGAATC
1 AGTGTTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCACCCGAATC
56962406 CACTAAATTGCATACTTCA
66 CACTAAATTGCATACTTCA
56962425 AGTGAAGAAC
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (87 bp):
AGTGTTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCACCCGAATC
CACTAAATTGCATACTTCACGT
Found at i:56962775 original size:153 final size:153
Alignment explanation
Indices: 56962494--56962795 Score: 428
Period size: 153 Copynumber: 2.0 Consensus size: 153
56962484 TTTAAGCATC
** * *
56962494 TTGCAATATGACAATCCAAGAAACTGAAGCTTGGATAGTCCAGTAAGAGATGCAGGTATGCTGAT
1 TTGCAATATGACAATCCAAGAAACCCAAGCTTCGAGAGTCCAGTAAGAGATGCAGGTATGCTGAT
* *
56962559 GACATTGTTACCACAAAGACCAAGATGTACCAAAGAGGATAGACCAGAAATATAACTATGAATAT
66 GAAATTGTTACCACAAAGACCAAGATGTACCAAAGAGGATAGACCAGAAATATAACTAGGAATAT
* *
56962624 CTGCTTCACCAAGAGTGCACATG
131 CTCCTTCACAAAGAGTGCACATG
* *
56962647 TTGCAATTTGACAAGT-CAAGAAACCCAAGCTTCGAGAGTCGAGTAAGAGATGCAGGTATGCTGA
1 TTGCAATATGACAA-TCCAAGAAACCCAAGCTTCGAGAGTCCAGTAAGAGATGCAGGTATGCTGA
* * ** *
56962711 TGAAATTGTTACCACGAAGATCAAGATGTTTCAAAGAGGATAGACCAGAAATATCACGT-GGAAT
65 TGAAATTGTTACCACAAAGACCAAGATGTACCAAAGAGGATAGACCAGAAATATAAC-TAGGAAT
*
56962775 ATCTCCTTCACAAAGATTGCA
129 ATCTCCTTCACAAAGAGTGCA
56962796 GTCCCTTAGA
Statistics
Matches: 131, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
153 129 0.98
154 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.23
Consensus pattern (153 bp):
TTGCAATATGACAATCCAAGAAACCCAAGCTTCGAGAGTCCAGTAAGAGATGCAGGTATGCTGAT
GAAATTGTTACCACAAAGACCAAGATGTACCAAAGAGGATAGACCAGAAATATAACTAGGAATAT
CTCCTTCACAAAGAGTGCACATG
Found at i:56963900 original size:20 final size:21
Alignment explanation
Indices: 56963875--56963915 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
56963865 GGAAATATAT
*
56963875 TTTCCATTCAA-TTTTCCATC
1 TTTCCAATCAAGTTTTCCATC
56963895 TTTCCAATCAAGTTTTCCATC
1 TTTCCAATCAAGTTTTCCATC
56963916 CCCACAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.22, C:0.29, G:0.02, T:0.46
Consensus pattern (21 bp):
TTTCCAATCAAGTTTTCCATC
Found at i:56964523 original size:14 final size:15
Alignment explanation
Indices: 56964497--56964527 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
56964487 TCCAGGTTCA
56964497 TCAACACATTTTTCT
1 TCAACACATTTTTCT
56964512 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
56964526 TC
1 TC
56964528 CCATTTCTTG
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:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:56967420 original size:16 final size:16
Alignment explanation
Indices: 56967401--56967433 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
56967391 TATTTCATAA
*
56967401 ATTTTATAATAGTTTT
1 ATTTTATAATACTTTT
56967417 ATTTTATAATACTTTT
1 ATTTTATAATACTTTT
56967433 A
1 A
56967434 AAAATTCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (16 bp):
ATTTTATAATACTTTT
Done.