Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold171
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: 2364178
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.28
Warning! 278680 characters in sequence are not A, C, G, or T
File 2 of 13
Found at i:183325 original size:34 final size:35
Alignment explanation
Indices: 183287--183353 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
183277 CCTTACAACA
183287 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
183321 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
183354 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:183987 original size:13 final size:13
Alignment explanation
Indices: 183969--183996 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
183959 ACTGCCAATG
183969 CTATGTATCGATA
1 CTATGTATCGATA
183982 CTATGTATCGATA
1 CTATGTATCGATA
183995 CT
1 CT
183997 TAGCAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (13 bp):
CTATGTATCGATA
Found at i:184116 original size:21 final size:21
Alignment explanation
Indices: 184076--184116 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
184066 GTCAACCTTG
*
184076 TGTATTGATACCAATAGTATA
1 TGTATTGATACCAACAGTATA
184097 TGTATTGATA-CAACACGTAT
1 TGTATTGATACCAACA-GTAT
184117 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (21 bp):
TGTATTGATACCAACAGTATA
Found at i:187233 original size:23 final size:20
Alignment explanation
Indices: 187164--187220 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
187154 GTAAAAAGAT
*
187164 AAAATGTATCGATACATTCA
1 AAAATGTATCGATACATTGA
* * *
187184 TACATATATCGATACATTGA
1 AAAATGTATCGATACATTGA
187204 AAAATGTATCGATACAT
1 AAAATGTATCGATACAT
187221 CTGGTAAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.32
Consensus pattern (20 bp):
AAAATGTATCGATACATTGA
Found at i:194328 original size:3 final size:3
Alignment explanation
Indices: 194314--194348 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
194304 CAAATCAATT
* *
194314 TCA TCA TTA TCA TCA TCA TCA TCA TCT TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
194349 TTTGATGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.40
Consensus pattern (3 bp):
TCA
Found at i:199699 original size:32 final size:31
Alignment explanation
Indices: 199663--199726 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 31
199653 TTACAAGCCA
* *
199663 ATGTATCGATACATTTTATGATGTATCGATAC
1 ATGTATCGATACATATTATG-TGTATCAATAC
*
199695 ATGTATCGATACATATTGTGTGTATCAATAC
1 ATGTATCGATACATATTATGTGTATCAATAC
199726 A
1 A
199727 AATTTAGCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 11 0.38
32 18 0.62
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (31 bp):
ATGTATCGATACATATTATGTGTATCAATAC
Found at i:199700 original size:12 final size:12
Alignment explanation
Indices: 199683--199708 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
199673 ACATTTTATG
199683 ATGTATCGATAC
1 ATGTATCGATAC
199695 ATGTATCGATAC
1 ATGTATCGATAC
199707 AT
1 AT
199709 ATTGTGTGTA
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:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:199786 original size:21 final size:21
Alignment explanation
Indices: 199760--199813 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
199750 CCAATGACCT
**
199760 GTATCGATACATTTTTTTCAA
1 GTATCGATACATTTTAGTCAA
*
199781 GTATCGATACA-TTTAGTCAT
1 GTATCGATACATTTTAGTCAA
199801 GTATCGATACATT
1 GTATCGATACATT
199814 GTATCGATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (21 bp):
GTATCGATACATTTTAGTCAA
Found at i:199856 original size:20 final size:20
Alignment explanation
Indices: 199833--199873 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
199823 CTGTGCAATT
199833 TGTATCGATACATTTAAGGG
1 TGTATCGATACATTTAAGGG
* *
199853 TGTATCGATACTTTTCAGGG
1 TGTATCGATACATTTAAGGG
199873 T
1 T
199874 TTTGACCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTTAAGGG
Found at i:201805 original size:21 final size:21
Alignment explanation
Indices: 201779--201826 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
201769 TGAATTGGAA
201779 GTGTTTTGGTACAAAACCAAG
1 GTGTTTTGGTACAAAACCAAG
*
201800 GTGTTTTGGTACAAAACCGAG
1 GTGTTTTGGTACAAAACCAAG
201821 GTGTTT
1 GTGTTT
201827 CGGATGTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.33
Consensus pattern (21 bp):
GTGTTTTGGTACAAAACCAAG
Found at i:201886 original size:20 final size:21
Alignment explanation
Indices: 201861--201902 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
201851 GGGGCTGCCC
201861 GGTTGCGACCT-GGGGGTGCT
1 GGTTGCGACCTAGGGGGTGCT
*
201881 GGTTGCGACCTAGTGGGTGCT
1 GGTTGCGACCTAGGGGGTGCT
201902 G
1 G
201903 CCTAGAGGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.07, C:0.19, G:0.48, T:0.26
Consensus pattern (21 bp):
GGTTGCGACCTAGGGGGTGCT
Found at i:202191 original size:20 final size:20
Alignment explanation
Indices: 202162--202202 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
202152 TGTTTTTGTT
202162 GATGATTTTG-ATGAAAAAC
1 GATGATTTTGAATGAAAAAC
202181 GATGTATTTTGAAATGAAAAAC
1 GATG-ATTTTG-AATGAAAAAC
202203 AAGAAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
22 9 0.47
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.32
Consensus pattern (20 bp):
GATGATTTTGAATGAAAAAC
Found at i:202352 original size:13 final size:13
Alignment explanation
Indices: 202334--202359 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
202324 ATAAACCCCT
202334 TGTATCGATACAG
1 TGTATCGATACAG
202347 TGTATCGATACAG
1 TGTATCGATACAG
202360 AGAATACTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:208545 original size:33 final size:32
Alignment explanation
Indices: 208508--208575 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
208498 CGTTACAAGC
*
208508 CAATGTATCGATACATTTTATGATGTATCGATA
1 CAATGTATCGATACATATTATG-TGTATCGATA
*
208541 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTATGTGTATCGATA
208573 CAA
1 CAA
208576 ATTTAGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
CAATGTATCGATACATATTATGTGTATCGATA
Found at i:208548 original size:13 final size:13
Alignment explanation
Indices: 208530--208555 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
208520 ACATTTTATG
208530 ATGTATCGATACA
1 ATGTATCGATACA
208543 ATGTATCGATACA
1 ATGTATCGATACA
208556 TATTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:214375 original size:42 final size:42
Alignment explanation
Indices: 214328--214446 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
214318 TTCTTCTTTC
* *
214328 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
214370 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* * *
214412 CTCCTCCTATAATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
214447 TTGAGGGCTA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.09, C:0.45, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:214388 original size:24 final size:24
Alignment explanation
Indices: 214352--214437 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
214342 CCTCCTCTCT
* *
214352 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
214376 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
214397 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
214418 CTATAATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
214438 TCTTTCTCTT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 13 0.27
22 5 0.10
24 21 0.44
ACGTcount: A:0.12, C:0.44, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:214412 original size:18 final size:18
Alignment explanation
Indices: 214343--214413 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
214333 CCTGTCATCC
* *
214343 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
214361 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
214383 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
214403 CTCCTGTCTCT
1 CTCCTGTCTCT
214414 CCTCCTATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:219064 original size:97 final size:96
Alignment explanation
Indices: 218883--219192 Score: 300
Period size: 97 Copynumber: 3.2 Consensus size: 96
218873 TTTGGGTAAG
* * * * * * * * *
218883 AAACAAGGCTAGAGTATCCCCTCGGAAGCATGGAGATGGAGTGTCCCCAATG-ATGATGACTTGA
1 AAACAAGGTTGGAGTATCCCCTCGAAAGAATGG-GGTTGAGTATCCCCAATGAATGATAAATT-A
* * * *
218947 GCAAAAACAAGGTTTAAATATTGACTACTTTAA
64 GGAAAAATAAGATTTAAATATTGACAACTTTAA
* * *
218980 AAATAGGGTTGGAGTATCCCCTCGAAAGAATGGGGCTTGAGTATCCCCGATGAATGATAAATTAG
1 AAACAAGGTTGGAGTATCCCCTCGAAAGAATGGGG-TTGAGTATCCCCAATGAATGATAAATTAG
* * *
219045 GAAAAATAAGATTTGAATATTGACAATTTTGA
65 GAAAAATAAGATTTAAATATTGACAACTTTAA
* * *
219077 AAACAAGGTTGGAGTATCCTCTC-AGAAGAATGAGGTTAGAGTATCCCTAATGAATGATAAATTA
1 AAACAAGGTTGGAGTATCCCCTCGA-AAGAATGGGGTT-GAGTATCCCCAATGAATGATAAATTA
* * * *
219141 GGCAAAATAAGATTTAAATATTGAAAATTTTGA
64 GGAAAAATAAGATTTAAATATTGACAACTTTAA
* **
219174 AAGCGGGGTTGGAGTATCC
1 AAACAAGGTTGGAGTATCC
219193 TAAGTGAATA
Statistics
Matches: 178, Mismatches: 31, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
96 4 0.02
97 166 0.93
98 8 0.04
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.26
Consensus pattern (96 bp):
AAACAAGGTTGGAGTATCCCCTCGAAAGAATGGGGTTGAGTATCCCCAATGAATGATAAATTAGG
AAAAATAAGATTTAAATATTGACAACTTTAA
Found at i:219193 original size:97 final size:97
Alignment explanation
Indices: 218921--219193 Score: 309
Period size: 97 Copynumber: 2.8 Consensus size: 97
218911 CATGGAGATG
* * * * * * ** * * *
218921 GAGTGTCCCCAATG-ATGATGACTTGAGCAAAAACAAGGTTTAAATATTGACTACTTTAAAAATA
1 GAGTATCCCCAATGAATGATAAATT-AGGAAAAATAAGATTTAAATATTGAAAATTTTGAAAACA
* *
218985 GGGTTGGAGTATCCCCTCGAAAGAATGGGGCTT
65 GGGTTGGAGTATCCTCTCGAAAGAATGAGGCTT
* * * *
219018 GAGTATCCCCGATGAATGATAAATTAGGAAAAATAAGATTTGAATATTGACAATTTTGAAAACAA
1 GAGTATCCCCAATGAATGATAAATTAGGAAAAATAAGATTTAAATATTGAAAATTTTGAAAACAG
219083 GGTTGGAGTATCCTCTC-AGAAGAATGAGG-TT
66 GGTTGGAGTATCCTCTCGA-AAGAATGAGGCTT
* * * *
219114 AGAGTATCCCTAATGAATGATAAATTAGGCAAAATAAGATTTAAATATTGAAAATTTTGAAAGCG
1 -GAGTATCCCCAATGAATGATAAATTAGGAAAAATAAGATTTAAATATTGAAAATTTTGAAAACA
219179 GGGTTGGAGTATCCT
65 GGGTTGGAGTATCCT
219194 AAGTGAATAA
Statistics
Matches: 150, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
96 3 0.02
97 139 0.93
98 8 0.05
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (97 bp):
GAGTATCCCCAATGAATGATAAATTAGGAAAAATAAGATTTAAATATTGAAAATTTTGAAAACAG
GGTTGGAGTATCCTCTCGAAAGAATGAGGCTT
Found at i:221399 original size:32 final size:32
Alignment explanation
Indices: 221348--221441 Score: 107
Period size: 32 Copynumber: 2.9 Consensus size: 32
221338 GTTATAAAAT
* * *
221348 TTTCGGGCTATTTTCGGGTTAAGGTCATTTTGGG
1 TTTCGGTC-ATTTT-GGGTTCAGGTCATTTTGGA
* *
221382 TTTCGTTCATTTTGGGTTCAGGTCACTTTGGA
1 TTTCGGTCATTTTGGGTTCAGGTCATTTTGGA
* *
221414 TTTGGGTCATTTTGAGTTCAGGTCATTT
1 TTTCGGTCATTTTGGGTTCAGGTCATTT
221442 CAGGTTTGGG
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
32 40 0.78
33 5 0.10
34 6 0.12
ACGTcount: A:0.13, C:0.13, G:0.28, T:0.47
Consensus pattern (32 bp):
TTTCGGTCATTTTGGGTTCAGGTCATTTTGGA
Found at i:221411 original size:16 final size:16
Alignment explanation
Indices: 221357--221441 Score: 82
Period size: 16 Copynumber: 5.2 Consensus size: 16
221347 TTTTCGGGCT
*
221357 ATTTTCGGGTTAAGGTC
1 ATTTT-GGGTTCAGGTC
*
221374 ATTTTGGGTTTC-GTTC
1 ATTTTGGG-TTCAGGTC
221390 ATTTTGGGTTCAGGTC
1 ATTTTGGGTTCAGGTC
* * **
221406 ACTTTGGATTTGGGTC
1 ATTTTGGGTTCAGGTC
*
221422 ATTTTGAGTTCAGGTC
1 ATTTTGGGTTCAGGTC
221438 ATTT
1 ATTT
221442 CAGGTTTGGG
Statistics
Matches: 54, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
15 3 0.06
16 44 0.81
17 7 0.13
ACGTcount: A:0.14, C:0.12, G:0.27, T:0.47
Consensus pattern (16 bp):
ATTTTGGGTTCAGGTC
Found at i:221450 original size:32 final size:30
Alignment explanation
Indices: 221369--221452 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 30
221359 TTTCGGGTTA
* * *
221369 AGGTCATTTTGGGTTTCGTTCATTTTGGGTTC
1 AGGTCA-TTT-GGTTTGGGTCATTTTGAGTTC
221401 AGGTCACTTTGGATTTGGGTCATTTTGAGTTC
1 AGGTCA-TTTGG-TTTGGGTCATTTTGAGTTC
221433 AGGTCATTTCAGGTTTGGGT
1 AGGTCATTT--GGTTTGGGT
221453 TGTTTTAAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
31 5 0.11
32 38 0.84
33 2 0.04
ACGTcount: A:0.13, C:0.12, G:0.30, T:0.45
Consensus pattern (30 bp):
AGGTCATTTGGTTTGGGTCATTTTGAGTTC
Found at i:221464 original size:32 final size:32
Alignment explanation
Indices: 221369--221475 Score: 83
Period size: 32 Copynumber: 3.3 Consensus size: 32
221359 TTTCGGGTTA
* * * * **
221369 AGGTCATTTTGGGTTTCGTTCATTTTGGGTTC
1 AGGTCATTTCGGATTTGGGTCATTTTAAGTTC
*
221401 AGGTCACTTT-GGATTTGGGTCATTTTGAGTTC
1 AGGTCA-TTTCGGATTTGGGTCATTTTAAGTTC
**
221433 AGGTCATTTCAGG-TTTGGGTTGTTTTAAGTTC
1 AGGTCATTTC-GGATTTGGGTCATTTTAAGTTC
* *
221465 AAGTTATTTCG
1 AGGTCATTTCG
221476 CGTTCGGGTC
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
31 4 0.06
32 54 0.86
33 5 0.08
ACGTcount: A:0.15, C:0.11, G:0.27, T:0.47
Consensus pattern (32 bp):
AGGTCATTTCGGATTTGGGTCATTTTAAGTTC
Found at i:221521 original size:15 final size:15
Alignment explanation
Indices: 221501--221548 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
221491 GGTTTAATAC
221501 TCGGGTTAATCGGGT
1 TCGGGTTAATCGGGT
* * *
221516 TCGGGTCATTCTGGAT
1 TCGGGTTAATC-GGGT
*
221532 TCGAGTTAATCGGGT
1 TCGGGTTAATCGGGT
221547 TC
1 TC
221549 AAGTCATTCT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.15, C:0.17, G:0.33, T:0.35
Consensus pattern (15 bp):
TCGGGTTAATCGGGT
Found at i:221540 original size:31 final size:31
Alignment explanation
Indices: 221505--221578 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
221495 TAATACTCGG
** *
221505 GTTAATCGGGTTCGGGTCATTCTGGATTCGA
1 GTTAATCGGGTTCAAGTCATTCTAGATTCGA
*
221536 GTTAATCGGGTTCAAGTCATTCTAGATTCGG
1 GTTAATCGGGTTCAAGTCATTCTAGATTCGA
221567 GTTAATCGGGTT
1 GTTAATCGGGTT
221579 TAACATTTGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.19, C:0.15, G:0.30, T:0.36
Consensus pattern (31 bp):
GTTAATCGGGTTCAAGTCATTCTAGATTCGA
Found at i:222561 original size:16 final size:16
Alignment explanation
Indices: 222537--222613 Score: 118
Period size: 16 Copynumber: 4.8 Consensus size: 16
222527 CTTAATTTAA
222537 GTTCGGGTCATTTTGG
1 GTTCGGGTCATTTTGG
*
222553 GTTCAGGTCATTTTGG
1 GTTCGGGTCATTTTGG
222569 GTTCGGGTCATTTTGG
1 GTTCGGGTCATTTTGG
* * *
222585 ATTCGGGTCATTCTAG
1 GTTCGGGTCATTTTGG
222601 GTTCGGGTCATTT
1 GTTCGGGTCATTT
222614 CAGATTCAGG
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 54 1.00
ACGTcount: A:0.10, C:0.14, G:0.32, T:0.43
Consensus pattern (16 bp):
GTTCGGGTCATTTTGG
Found at i:222637 original size:32 final size:32
Alignment explanation
Indices: 222536--222680 Score: 123
Period size: 32 Copynumber: 4.5 Consensus size: 32
222526 ACTTAATTTA
** * *
222536 AGTTCGGGTCATTTTGGGTTCAGGTCATTTTG
1 AGTTCGGGTCATTTCAGATTCAGGTCATTTCG
* ** * *
222568 GGTTCGGGTCATTTTGGATTCGGGTCA-TTCT
1 AGTTCGGGTCATTTCAGATTCAGGTCATTTCG
*
222599 AGGTTCGGGTCATTTCAGATTCAGGTAATTTCG
1 A-GTTCGGGTCATTTCAGATTCAGGTCATTTCG
* ** *
222632 AGTTCGAGTCA-TTCTAGATTTGGGTCATTTCA
1 AGTTCGGGTCATTTC-AGATTCAGGTCATTTCG
*
222664 AGTTCGAGTCATTTCAG
1 AGTTCGGGTCATTTCAG
222681 GTTTGGGTTA
Statistics
Matches: 93, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
31 5 0.05
32 81 0.87
33 7 0.08
ACGTcount: A:0.17, C:0.15, G:0.28, T:0.40
Consensus pattern (32 bp):
AGTTCGGGTCATTTCAGATTCAGGTCATTTCG
Found at i:222660 original size:16 final size:15
Alignment explanation
Indices: 222538--222661 Score: 77
Period size: 16 Copynumber: 7.8 Consensus size: 15
222528 TTAATTTAAG
* *
222538 TTCGGGTCATTTTGGG
1 TTCGGGTCA-TTTAGA
* * *
222554 TTCAGGTCATTTTGGG
1 TTCGGGTCA-TTTAGA
*
222570 TTCGGGTCATTTTGGA
1 TTCGGGTCA-TTTAGA
*
222586 TTCGGGTCATTCTAGG
1 TTCGGGTCATT-TAGA
222602 TTCGGGTCATTTCAGA
1 TTCGGGTCATTT-AGA
* * *
222618 TTCAGGTAATTTCGA
1 TTCGGGTCATTTAGA
*
222633 GTTCGAGTCATTCTAGA
1 -TTCGGGTCATT-TAGA
*
222650 TTTGGGTCATTT
1 TTCGGGTCATTT
222662 CAAGTTCGAG
Statistics
Matches: 89, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
15 6 0.07
16 80 0.90
17 3 0.03
ACGTcount: A:0.15, C:0.15, G:0.28, T:0.42
Consensus pattern (15 bp):
TTCGGGTCATTTAGA
Found at i:222674 original size:16 final size:16
Alignment explanation
Indices: 222626--222679 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
222616 GATTCAGGTA
*
222626 ATTTCGAGTTCGAGTC
1 ATTTCAAGTTCGAGTC
* * *
222642 A-TTCTAGATTTGGGTC
1 ATTTCAAG-TTCGAGTC
222658 ATTTCAAGTTCGAGTC
1 ATTTCAAGTTCGAGTC
222674 ATTTCA
1 ATTTCA
222680 GGTTTGGGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 5 0.17
16 20 0.67
17 5 0.17
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (16 bp):
ATTTCAAGTTCGAGTC
Found at i:222678 original size:48 final size:47
Alignment explanation
Indices: 222569--222678 Score: 116
Period size: 48 Copynumber: 2.3 Consensus size: 47
222559 GTCATTTTGG
* * * *
222569 GTTCGGGTCATTTTGGATTCGGGTCATTCTAGGTTCGGGTCATTTCA
1 GTTCGAGTCATTTCGGATTCGAGTCATTCTAGATTCGGGTCATTTCA
* *
222616 GATTC-AGGTAATTTC-GAGTTCGAGTCATTCTAGATTTGGGTCATTTCAA
1 G-TTCGA-GTCATTTCGGA-TTCGAGTCATTCTAGATTCGGGTCATTTC-A
222665 GTTCGAGTCATTTC
1 GTTCGAGTCATTTC
222679 AGGTTTGGGT
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
47 3 0.06
48 45 0.88
49 3 0.06
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.40
Consensus pattern (47 bp):
GTTCGAGTCATTTCGGATTCGAGTCATTCTAGATTCGGGTCATTTCA
Found at i:223148 original size:20 final size:21
Alignment explanation
Indices: 223123--223174 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
223113 CATTTTAGGC
223123 ATGTATCGATACATTCACT-T
1 ATGTATCGATACATTCACTAT
* *
223143 ATGTATCAATACATTTACTAT
1 ATGTATCGATACATTCACTAT
*
223164 TTGTATCGATA
1 ATGTATCGATA
223175 TAAATTATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATTCACTAT
Found at i:223845 original size:52 final size:50
Alignment explanation
Indices: 223780--223934 Score: 175
Period size: 52 Copynumber: 3.0 Consensus size: 50
223770 TAAGGCCTGT
* * *
223780 GACACTGGACTTAATGATGATAACGATGCCAATGTGCCAATTCAAGGCCAAC
1 GACATTGG-CTTAAGGATGATAACGA-GCCAATGTGCCGATTCAAGGCCAAC
* * *
223832 GACATTGGTCTTAAGGATGATAAAGGAGCCAATGTGCCGATTCATGGCCAGC
1 GACATTGG-CTTAAGGATGAT-AACGAGCCAATGTGCCGATTCAAGGCCAAC
* *
223884 GACATTAGGCTTAAGGATGATAACAGAAGCCAATATGCTGATTCAAGGCCA
1 GACATT-GGCTTAAGGATGATAAC-G-AGCCAATGTGCCGATTCAAGGCCA
223935 GCAATATTGA
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
51 2 0.02
52 59 0.67
53 27 0.31
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.22
Consensus pattern (50 bp):
GACATTGGCTTAAGGATGATAACGAGCCAATGTGCCGATTCAAGGCCAAC
Found at i:223950 original size:53 final size:52
Alignment explanation
Indices: 223785--224059 Score: 252
Period size: 53 Copynumber: 5.3 Consensus size: 52
223775 CCTGTGACAC
* * * ** *
223785 TGGACTTAATGATGATAACGATGCCAATGTGCCAATTCAAGGCCAACGACAT
1 TGGACTTAAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACGATAT
* * * * * * *
223837 TGGTCTTAAGGATGATAAAGGA-GCCAATGTGCCGATTCATGGCCAGCGACAT
1 TGGACTTAAAGATGATAAA-GATGCCAATATGCTGATTCAAGGCCAACGATAT
* * * *
223889 TAGG-CTTAAGGATGATAACAGAAGCCAATATGCTGATTCAAGGCCAGCAATAT
1 T-GGACTTAAAGATGATAA-AGATGCCAATATGCTGATTCAAGGCCAACGATAT
* * * *
223942 TGAACTTAAAGATGAT--AGTTGCTAATATACTGATTCAAGGCCAACGATAT
1 TGGACTTAAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACGATAT
* * * * *
223992 TGGGCTTAAAGATAACAAGAGATGCCAATATACTGATTCACGGCCAACGATAT
1 TGGACTTAAAGATGATAA-AGATGCCAATATGCTGATTCAAGGCCAACGATAT
224045 TGGACTTAAAGATGA
1 TGGACTTAAAGATGA
224060 AGGGGTACCA
Statistics
Matches: 187, Mismatches: 28, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
50 40 0.21
52 61 0.33
53 86 0.46
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (52 bp):
TGGACTTAAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACGATAT
Found at i:224022 original size:103 final size:103
Alignment explanation
Indices: 223870--224059 Score: 254
Period size: 103 Copynumber: 1.8 Consensus size: 103
223860 CCAATGTGCC
* * * * * *
223870 GATTCATGGCCAGCGACATTAGGCTTAAGGATGATAACAGAAGCCAATATGCTGATTCAAGGCCA
1 GATTCAAGGCCAACGACATTAGGCTTAAAGATAACAACAGAAGCCAATATACTGATTCAAGGCCA
*
223935 GCAATATTGAACTTAAAGATGATAGTTGCTAATATACT
66 ACAATATTGAACTTAAAGATGATAGTTGCTAATATACT
* * * * *
223973 GATTCAAGGCCAACGATATTGGGCTTAAAGATAACAAGAGATGCCAATATACTGATTCACGGCCA
1 GATTCAAGGCCAACGACATTAGGCTTAAAGATAACAACAGAAGCCAATATACTGATTCAAGGCCA
* *
224038 ACGATATTGGACTTAAAGATGA
66 ACAATATTGAACTTAAAGATGA
224060 AGGGGTACCA
Statistics
Matches: 73, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
103 73 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.25
Consensus pattern (103 bp):
GATTCAAGGCCAACGACATTAGGCTTAAAGATAACAACAGAAGCCAATATACTGATTCAAGGCCA
ACAATATTGAACTTAAAGATGATAGTTGCTAATATACT
Found at i:224104 original size:51 final size:52
Alignment explanation
Indices: 223965--224104 Score: 158
Period size: 53 Copynumber: 2.7 Consensus size: 52
223955 GATAGTTGCT
*
223965 AATATACTGATTCAAGGCCAACGATATTGGGCTTAAAGATAACAAGAGATGCC
1 AATATACTGATTCAAGGCCAACGATATTGGGCTTAAAGAT-ACAAGAGATACC
* * * * *
224018 AATATACTGATTCACGGCCAACGATATTGGACTTAAAGAT-GAAGGGGTACC
1 AATATACTGATTCAAGGCCAACGATATTGGGCTTAAAGATACAAGAGATACC
* ** *
224069 AA-AGTGCTGATTCAAGGCCAGTGACATTGGGCTTAA
1 AATA-TACTGATTCAAGGCCAACGATATTGGGCTTAA
224105 GGAAAGAAGA
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
50 1 0.01
51 35 0.47
53 38 0.51
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.24
Consensus pattern (52 bp):
AATATACTGATTCAAGGCCAACGATATTGGGCTTAAAGATACAAGAGATACC
Found at i:224256 original size:34 final size:34
Alignment explanation
Indices: 224213--224358 Score: 197
Period size: 34 Copynumber: 4.4 Consensus size: 34
224203 TACCACTAAT
*
224213 TTGTGTGGGCTTTGAAAGAAAGGATGCCATCGAC
1 TTGTGTGGGCTTTGAAAGAAAGGATGCCACCGAC
*
224247 TTGTGTGGGCTTTGAAAAAAAGGATGCCACCGAC
1 TTGTGTGGGCTTTGAAAGAAAGGATGCCACCGAC
* * * * *
224281 TTATGTGGGCTTT-TAA-AAGGGTTGCCACCGAA
1 TTGTGTGGGCTTTGAAAGAAAGGATGCCACCGAC
* *
224313 TTGTGTGGGCTTTGAAAGAAAAGATGCCACCAAC
1 TTGTGTGGGCTTTGAAAGAAAGGATGCCACCGAC
224347 TTGTGTGGGCTT
1 TTGTGTGGGCTT
224359 AAAAGGATTA
Statistics
Matches: 96, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
32 25 0.26
33 4 0.04
34 67 0.70
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (34 bp):
TTGTGTGGGCTTTGAAAGAAAGGATGCCACCGAC
Found at i:224375 original size:100 final size:100
Alignment explanation
Indices: 224172--224358 Score: 268
Period size: 100 Copynumber: 1.9 Consensus size: 100
224162 AGAAGGAGAC
* *** * *
224172 GCCACCGACTTGTGTGGGCTTTGGGGAGGGTTACCACTAATTTGTGTGGGCTTTGAAAGAAAGGA
1 GCCACCGACTTATGTGGGCTTTGAAAAGGGTTACCACGAATTTGTGTGGGCTTTGAAAGAAAAGA
* *
224237 TGCCATCGACTTGTGTGGGCTTTGAAAAAAAGGAT
66 TGCCACCAACTTGTGTGGGCTTTGAAAAAAAGGAT
* *
224272 GCCACCGACTTATGTGGGCTTTTAAAAGGGTTGCCACCGAA-TTGTGTGGGCTTTGAAAGAAAAG
1 GCCACCGACTTATGTGGGCTTTGAAAAGGGTTACCA-CGAATTTGTGTGGGCTTTGAAAGAAAAG
224336 ATGCCACCAACTTGTGTGGGCTT
65 ATGCCACCAACTTGTGTGGGCTT
224359 AAAAGGATTA
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
100 73 0.96
101 3 0.04
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (100 bp):
GCCACCGACTTATGTGGGCTTTGAAAAGGGTTACCACGAATTTGTGTGGGCTTTGAAAGAAAAGA
TGCCACCAACTTGTGTGGGCTTTGAAAAAAAGGAT
Found at i:224406 original size:31 final size:32
Alignment explanation
Indices: 224350--224429 Score: 110
Period size: 31 Copynumber: 2.5 Consensus size: 32
224340 CACCAACTTG
*
224350 TGTGGGC-TTAAAAGGATTAGGTGCCATGGAGT
1 TGTGGGCTTTAAAAGGA-TAGGTGCCACGGAGT
224382 TGTGGGCTTTAAAAGGA-AGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATAGGTGCCACGGAGT
*
224413 TATGGGCTTTGAAAAGG
1 TGTGGGCTTT-AAAAGG
224430 GATGCCACGG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
31 22 0.50
32 13 0.30
33 9 0.20
ACGTcount: A:0.26, C:0.10, G:0.38, T:0.26
Consensus pattern (32 bp):
TGTGGGCTTTAAAAGGATAGGTGCCACGGAGT
Found at i:224438 original size:30 final size:30
Alignment explanation
Indices: 224371--224456 Score: 102
Period size: 30 Copynumber: 2.8 Consensus size: 30
224361 AAGGATTAGG
* * *
224371 TGCCATGGAGTTGTGGGCTTTAAAAGGAAGG
1 TGCCACGGAGTTATGGGCTTTAAAAGG-AGA
224402 TGCCACGGAGTTATGGGCTTTGAAAAGG-GA
1 TGCCACGGAGTTATGGGCTTT-AAAAGGAGA
* *
224432 TGCCACGGAGTCATGGACTTTAAAA
1 TGCCACGGAGTTATGGGCTTTAAAA
224457 AAGTTACTCT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 4 0.08
30 20 0.41
31 19 0.39
32 6 0.12
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.24
Consensus pattern (30 bp):
TGCCACGGAGTTATGGGCTTTAAAAGGAGA
Found at i:225785 original size:28 final size:27
Alignment explanation
Indices: 225729--225815 Score: 77
Period size: 28 Copynumber: 3.1 Consensus size: 27
225719 GACCATAGCC
* * *
225729 ATTGCAAGTTTCTTGATTCTAC-AAGGG
1 ATTGCAATTTTCTTGATTCCACTGA-GG
*
225756 ATTGCAATTTGTCTTTATTCCACTGAGG
1 ATTGCAATTT-TCTTGATTCCACTGAGG
* * *
225784 ATTGGCACTTTTCTTGATTCCATTGAAG
1 ATT-GCAATTTTCTTGATTCCACTGAGG
225812 ATTG
1 ATTG
225816 TAGGCTGCTC
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
27 10 0.20
28 32 0.65
29 7 0.14
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (27 bp):
ATTGCAATTTTCTTGATTCCACTGAGG
Found at i:226661 original size:12 final size:13
Alignment explanation
Indices: 226617--226665 Score: 64
Period size: 13 Copynumber: 3.6 Consensus size: 13
226607 AGAATACAAC
226617 TTTTTTTTGGTTG
1 TTTTTTTTGGTTG
226630 TTTTTTTTGTTGTTG
1 TTTTTTTTG--GTTG
226645 TTTTTTTTTGG-TG
1 -TTTTTTTTGGTTG
226658 TTTTTTTT
1 TTTTTTTT
226666 ACATTCGGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
12 8 0.24
13 11 0.33
14 1 0.03
15 4 0.12
16 9 0.27
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (13 bp):
TTTTTTTTGGTTG
Found at i:232640 original size:18 final size:19
Alignment explanation
Indices: 232598--232647 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
232588 TCCATCTTCT
232598 TCTCTCCTC-CTCTTGTCA
1 TCTCTCCTCTCTCTTGTCA
*
232616 TCCCTCCTCTCTCTAT-T-A
1 TCTCTCCTCTCTCT-TGTCA
*
232634 TCTCTCCTGTCTCT
1 TCTCTCCTCTCTCT
232648 CCTCCTATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 21 0.78
19 5 0.19
20 1 0.04
ACGTcount: A:0.06, C:0.44, G:0.04, T:0.46
Consensus pattern (19 bp):
TCTCTCCTCTCTCTTGTCA
Found at i:232659 original size:42 final size:42
Alignment explanation
Indices: 232604--232710 Score: 171
Period size: 42 Copynumber: 2.6 Consensus size: 42
232594 TTCTTCTCTC
* * *
232604 CTCCTCTTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
232646 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
232688 CTCCTCCTATCATCCCT-CTCTCT
1 CTCCTCCTATCATCCCTCCTCTCT
232711 TCTTTCTCTT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
41 5 0.08
42 55 0.92
ACGTcount: A:0.09, C:0.46, G:0.03, T:0.42
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:232688 original size:18 final size:18
Alignment explanation
Indices: 232619--232689 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
232609 CTTGTCATCC
* *
232619 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
232637 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
232659 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
232679 CTCCTGTCTCT
1 CTCCTGTCTCT
232690 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:237774 original size:42 final size:42
Alignment explanation
Indices: 237684--237803 Score: 186
Period size: 42 Copynumber: 2.8 Consensus size: 42
237674 TAGCCCTCAA
* *
237684 AGAGAAAGAAGAGAGAGGAGGGATGATAGGCAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGG-AGGAGAGACAGG
*
237727 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
237769 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
237804 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
42 44 0.62
43 27 0.38
ACGTcount: A:0.42, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:240776 original size:12 final size:12
Alignment explanation
Indices: 240746--240813 Score: 65
Period size: 12 Copynumber: 5.9 Consensus size: 12
240736 AAATGAAAGA
240746 AGAGATAGGAGG
1 AGAGATAGGAGG
*
240758 -GATGATAGAAGG
1 AGA-GATAGGAGG
*
240770 AGAGAT---AGT
1 AGAGATAGGAGG
240779 AGAGATAGGAGG
1 AGAGATAGGAGG
240791 -GATGATAGGAGG
1 AGA-GATAGGAGG
240803 AGAGATAGGAG
1 AGAGATAGGAG
240814 AGATAATAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
9 8 0.17
11 4 0.09
12 30 0.65
13 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.46, T:0.13
Consensus pattern (12 bp):
AGAGATAGGAGG
Found at i:240788 original size:33 final size:33
Alignment explanation
Indices: 240746--240818 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
240736 AAATGAAAGA
*
240746 AGAGATAGGAGGGATGATAGAAGGAGAGATAGT
1 AGAGATAGGAGGGATGATAGAAGGAGAGATAGG
*
240779 AGAGATAGGAGGGATGATAGGAGGAGAGATAGG
1 AGAGATAGGAGGGATGATAGAAGGAGAGATAGG
240812 AGAGATA
1 AGAGATA
240819 ATAGAGAGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.42, C:0.00, G:0.44, T:0.14
Consensus pattern (33 bp):
AGAGATAGGAGGGATGATAGAAGGAGAGATAGG
Found at i:240822 original size:12 final size:12
Alignment explanation
Indices: 240749--240827 Score: 53
Period size: 12 Copynumber: 6.9 Consensus size: 12
240739 TGAAAGAAGA
*
240749 GATAGGAGGGAT
1 GATAGGAGAGAT
*
240761 GATAGAAGGAGA-
1 GATAGGA-GAGAT
*
240773 GATA-G-TAGA-
1 GATAGGAGAGAT
*
240782 GATAGGAGGGAT
1 GATAGGAGAGAT
240794 GATAGGAGGAGA-
1 GATAGGA-GAGAT
240806 GATAGGAGAGAT
1 GATAGGAGAGAT
*
240818 AATA-GAGAGA
1 GATAGGAGAGA
240828 GGAGGGATGA
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
9 7 0.13
10 1 0.02
11 12 0.23
12 27 0.51
13 6 0.11
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.14
Consensus pattern (12 bp):
GATAGGAGAGAT
Found at i:240830 original size:18 final size:18
Alignment explanation
Indices: 240803--240852 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
240793 TGATAGGAGG
*
240803 AGAGATAGGAGAGATAAT
1 AGAGAGAGGAGAGATAAT
* *
240821 AGAGAGAGGAGGGATGAT
1 AGAGAGAGGAGAGATAAT
240839 AG-GAGGAGGAGAGA
1 AGAGA-GAGGAGAGA
240853 AGAAGATAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.44, C:0.00, G:0.46, T:0.10
Consensus pattern (18 bp):
AGAGAGAGGAGAGATAAT
Found at i:240846 original size:45 final size:44
Alignment explanation
Indices: 240749--240854 Score: 144
Period size: 42 Copynumber: 2.4 Consensus size: 44
240739 TGAAAGAAGA
* * * *
240749 GATAGGAGGGATGATAGAAGGAGAGATAGTAGAGATAGGAGGGAT
1 GATAGGA-GGAGGAGAGAAGGAGAGATAATAGAGAGAGGAGGGAT
*
240794 GATAGGAGGA-GAGA-TAGGAGAGATAATAGAGAGAGGAGGGAT
1 GATAGGAGGAGGAGAGAAGGAGAGATAATAGAGAGAGGAGGGAT
240836 GATAGGAGGAGGAGAGAAG
1 GATAGGAGGAGGAGAGAAG
240855 AAGATAGAAG
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
42 35 0.65
43 7 0.13
44 5 0.09
45 7 0.13
ACGTcount: A:0.42, C:0.00, G:0.46, T:0.12
Consensus pattern (44 bp):
GATAGGAGGAGGAGAGAAGGAGAGATAATAGAGAGAGGAGGGAT
Found at i:249012 original size:14 final size:13
Alignment explanation
Indices: 248988--249036 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
248978 ACTTAGTTTT
248988 TCTTTTTTTTCTC
1 TCTTTTTTTTCTC
*
249001 TC---TTTTTCTT
1 TCTTTTTTTTCTC
*
249011 TCTTTTATTTCTC
1 TCTTTTTTTTCTC
249024 TCTTTTTTTTCTC
1 TCTTTTTTTTCTC
249037 CAAGTTTCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
10 9 0.31
13 20 0.69
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (13 bp):
TCTTTTTTTTCTC
Found at i:249012 original size:23 final size:22
Alignment explanation
Indices: 248984--249035 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 22
248974 TTTGACTTAG
*
248984 TTTTTCTTTTTTTTCTCTCTTT
1 TTTTTCTTTTATTTCTCTCTTT
249006 TTCTTTCTTTTATTTCTCTCTTT
1 TT-TTTCTTTTATTTCTCTCTTT
249029 TTTTTCT
1 TTTTTCT
249036 CCAAGTTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 7 0.25
23 21 0.75
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTTCTTTTATTTCTCTCTTT
Found at i:249044 original size:23 final size:23
Alignment explanation
Indices: 248995--249045 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
248985 TTTTCTTTTT
***
248995 TTTCTCTCTTTTTCTTTCTTTTA
1 TTTCTCTCTTTTTCTTTCTCCAA
249018 TTTCTCTCTTTTT-TTTCTCCAA
1 TTTCTCTCTTTTTCTTTCTCCAA
249040 GTTTCT
1 -TTTCT
249046 AAAGCTTCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.06, C:0.24, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTCTCTCTTTTTCTTTCTCCAA
Found at i:249375 original size:17 final size:17
Alignment explanation
Indices: 249353--249385 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
249343 TATTTAGAAA
*
249353 AAATAAGTTAAATAAAT
1 AAATAAATTAAATAAAT
249370 AAATAAATTAAATAAA
1 AAATAAATTAAATAAA
249386 ATTTCCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (17 bp):
AAATAAATTAAATAAAT
Found at i:249385 original size:9 final size:9
Alignment explanation
Indices: 249353--249385 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
249343 TATTTAGAAA
*
249353 AAATAAGTT
1 AAATAAATT
249362 AAATAAA-T
1 AAATAAATT
249370 AAATAAATT
1 AAATAAATT
249379 AAATAAA
1 AAATAAA
249386 ATTTCCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (9 bp):
AAATAAATT
Found at i:249987 original size:165 final size:161
Alignment explanation
Indices: 249556--250134 Score: 476
Period size: 164 Copynumber: 3.5 Consensus size: 161
249546 AAAATTAATG
* * * *
249556 AAATAAATTGAATTTTTCAAAACTGATTTAATTTGATTTTAATGACAATATTAGATGAATTTTAA
1 AAATAAA-TGAATTTTTCAAAACTGATTT-ATATGAATTAAATGACAATATTTGATGAATTTTAA
* * * *
249621 AAATTTTAAACCT-ACAAAAATCCCCTTGGAAACATTTATGAAATAGAAAACTCGGTTTTTC-AA
64 AAATTATAAA-CTAAGAAAAATCCCC-TGAAAACATTTATGGAATAGAAAACTC-GTTTTTCGAA
* * * *
249684 AAATAGAGGAATTTCAAGAAAAAAATGAAAAACTTGTGA
126 AAA-GGA-AAATTTCAAG-AAAAAATAAAAAACTTATGA
* * * * * * * *
249723 AAATAAAT-AA-ATTTCCAAACTAATTTAAAGGGAGTCT-AATGACAATGTTGGATGAATTTTAA
1 AAATAAATGAATTTTTCAAAACTGATTTATA-TGAAT-TAAATGACAATATTTGATGAATTTTAA
* * *
249785 AAA-TATTAGA-TCGAGAAAAATACCCCTGAAAACATTTATGGACTAGAAAACTCGATTTTTCGA
64 AAATTA-TAAACT-AAGAAAAAT-CCCCTGAAAACATTTATGGAATAGAAAACTCG-TTTTTCGA
249848 AAAAGGAAAATTTCAAAGAAAAAATAAAAAACTTATGA
125 AAAAGGAAAATTTC-AAGAAAAAATAAAAAACTTATGA
* * **
249886 AAATAAATGAATTTTTCAAAATTTATTTACTATGAATTAAATGATGATATTTGATGAATTTTAAA
1 AAATAAATGAATTTTTCAAAACTGATTTA-TATGAATTAAATGACAATATTTGATGAATTTTAAA
** * * *
249951 AATTATAAACTAAGAAAAATCTCCCCAAAAACATTTACGGAATAGGAAACTCTGTATTTCGAAAA
65 AATTATAAACTAAGAAAAATC-CCCTGAAAACATTTATGGAATAGAAAACTC-GTTTTTCGAAAA
* * * *
250016 TAGAAAAATTTCAAG-GAAAATCAATAACTTATG-
128 -AGGAAAATTTCAAGAAAAAATAAAAAACTTATGA
* * ** * * * *
250049 AAATAAAAAGGATTTTTCAAAACTGATTTGATTAT-AATTAAACAATAATATTTGAAGAAGTTTG
1 AAAT-AAATGAATTTTTCAAAACTGATTT-A-TATGAATTAAATGACAATATTTGATGAATTTTA
*
250113 AAAATTATAAACTTAAAAAAAA
63 AAAATTATAAAC-TAAGAAAAA
250135 ATTTCTGAAA
Statistics
Matches: 337, Mismatches: 54, Indels: 44
0.77 0.12 0.10
Matches are distributed among these distances:
162 1 0.00
163 39 0.12
164 161 0.48
165 113 0.34
166 16 0.05
167 7 0.02
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.31
Consensus pattern (161 bp):
AAATAAATGAATTTTTCAAAACTGATTTATATGAATTAAATGACAATATTTGATGAATTTTAAAA
ATTATAAACTAAGAAAAATCCCCTGAAAACATTTATGGAATAGAAAACTCGTTTTTCGAAAAAGG
AAAATTTCAAGAAAAAATAAAAAACTTATGA
Found at i:251001 original size:13 final size:13
Alignment explanation
Indices: 250983--251008 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
250973 CTATTTATGA
250983 TGTATCGATACAC
1 TGTATCGATACAC
250996 TGTATCGATACAC
1 TGTATCGATACAC
251009 ACAAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:251148 original size:10 final size:10
Alignment explanation
Indices: 251129--251179 Score: 84
Period size: 10 Copynumber: 5.1 Consensus size: 10
251119 GTATCGATAC
*
251129 ATGAACAGTG
1 ATGAATAGTG
251139 ATGAATAGTG
1 ATGAATAGTG
251149 ATGAATAGTG
1 ATGAATAGTG
251159 ATGAATAGTG
1 ATGAATAGTG
*
251169 ATGAACAGTG
1 ATGAATAGTG
251179 A
1 A
251180 AAATGAGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 39 1.00
ACGTcount: A:0.41, C:0.04, G:0.29, T:0.25
Consensus pattern (10 bp):
ATGAATAGTG
Found at i:251158 original size:20 final size:20
Alignment explanation
Indices: 251076--251179 Score: 95
Period size: 20 Copynumber: 5.0 Consensus size: 20
251066 TAGTGATACG
*
251076 TGAACAGTG-TGAACAGTGA
1 TGAATAGTGATGAACAGTGA
251095 TGAATAGTGATACATGAA-AGTGA
1 TGAATAGTG----ATGAACAGTGA
* * *
251118 TGTATCGATACATGAACAGTGA
1 TGAATAG-T-GATGAACAGTGA
*
251140 TGAATAGTGATGAATAGTGA
1 TGAATAGTGATGAACAGTGA
251160 TGAATAGTGATGAACAGTGA
1 TGAATAGTGATGAACAGTGA
251180 AAATGAGATT
Statistics
Matches: 68, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
19 8 0.12
20 29 0.43
21 6 0.09
22 10 0.15
23 10 0.15
24 5 0.07
ACGTcount: A:0.39, C:0.07, G:0.28, T:0.26
Consensus pattern (20 bp):
TGAATAGTGATGAACAGTGA
Found at i:251267 original size:53 final size:53
Alignment explanation
Indices: 251203--251339 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
251193 CTACTTCCAA
251203 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
251256 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
251309 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
251340 TATGCAATTT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 67 0.84
54 13 0.16
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:251372 original size:20 final size:20
Alignment explanation
Indices: 251309--251379 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
251299 GCCAATGTCC
**
251309 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
251329 TGTATCGATAC-TATGCAATT
1 TGTATCGATACATAT-TAATG
251349 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
251369 TGTATCGATAC
1 TGTATCGATAC
251380 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:251445 original size:21 final size:21
Alignment explanation
Indices: 251419--251459 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
251409 GTCAACCTTG
251419 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
251440 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
251460 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:257216 original size:23 final size:23
Alignment explanation
Indices: 257173--257218 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
257163 CTTTAACAAG
*
257173 AAACAAAAGAAAAAGGAAGATGA
1 AAACAAAAGAAAAAAGAAGATGA
257196 AAACAAAAGAAAAATAG-AGATGA
1 AAACAAAAGAAAAA-AGAAGATGA
257219 TGATTTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (23 bp):
AAACAAAAGAAAAAAGAAGATGA
Found at i:257805 original size:56 final size:56
Alignment explanation
Indices: 257729--257999 Score: 199
Period size: 56 Copynumber: 4.9 Consensus size: 56
257719 AATGTAGTTG
* * *
257729 GCAGAGTTAAGCCTAGTGAAATTGGCAGCTAGATGAGATTAAGCCCAAGGTAGCTA
1 GCAGGGTTAAGCCTAATGAAATTGGCAGCTAGATGAGATTAAGCCCAACGTAGCTA
* * * * * * * *
257785 GCAGGGTTAAACCTAATGAAATTGGCATCTAAATGATATTAAGTCCAACATAACCA
1 GCAGGGTTAAGCCTAATGAAATTGGCAGCTAGATGAGATTAAGCCCAACGTAGCTA
* * * * * * * * * *
257841 GTAGAGCTAAGCCAAATGAAATTAGCACCTAAATGATATTAAGCCCAATGTTGCTA
1 GCAGGGTTAAGCCTAATGAAATTGGCAGCTAGATGAGATTAAGCCCAACGTAGCTA
* * * * * * * * * *
257897 GCAAGATTAA-CC-CATGAAATTGGTATCAAGATGAGATTATGCCTAACGTAGATG
1 GCAGGGTTAAGCCTAATGAAATTGGCAGCTAGATGAGATTAAGCCCAACGTAGCTA
* *
257951 GGAAGGTTAAGCTCT-ATGAAATTGGCATG-TAGATGAGATTAAGCCCAAC
1 GCAGGGTTAAGC-CTAATGAAATTGGCA-GCTAGATGAGATTAAGCCCAAC
258000 ATAGTTGGCC
Statistics
Matches: 162, Mismatches: 49, Indels: 8
0.74 0.22 0.04
Matches are distributed among these distances:
54 37 0.23
55 3 0.02
56 122 0.75
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.24
Consensus pattern (56 bp):
GCAGGGTTAAGCCTAATGAAATTGGCAGCTAGATGAGATTAAGCCCAACGTAGCTA
Found at i:258016 original size:56 final size:55
Alignment explanation
Indices: 257910--258031 Score: 129
Period size: 56 Copynumber: 2.2 Consensus size: 55
257900 AGATTAACCC
* * * * * *
257910 ATGAAATTGGTATCAAGATGAGATTATGCCTAACGTAGATGGGAAGGTTAAGCTCT
1 ATGAAATTGGCATCAAGATGAGATTAAGCCCAACATAGATGGCAAGGTTAAG-ACT
** *
257966 ATGAAATTGGCATGTAGATGAGATTAAGCCCAACATAGTTGGCCAA-GTTAAGACT
1 ATGAAATTGGCATCAAGATGAGATTAAGCCCAACATAGATGG-CAAGGTTAAGACT
258021 AGTGAAATTGG
1 A-TGAAATTGG
258032 AGGTTAAGTC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
55 3 0.05
56 50 0.91
57 2 0.04
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.27
Consensus pattern (55 bp):
ATGAAATTGGCATCAAGATGAGATTAAGCCCAACATAGATGGCAAGGTTAAGACT
Found at i:258755 original size:10 final size:10
Alignment explanation
Indices: 258736--258770 Score: 54
Period size: 9 Copynumber: 3.5 Consensus size: 10
258726 TAAATCAAAG
258736 AAAAAGGGATT
1 AAAAA-GGATT
258747 AAAAAGGATT
1 AAAAAGGATT
258757 -AAAAGGATT
1 AAAAAGGATT
258766 AAAAA
1 AAAAA
258771 TGCATTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.39
10 9 0.39
11 5 0.22
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (10 bp):
AAAAAGGATT
Found at i:260713 original size:19 final size:20
Alignment explanation
Indices: 260668--260719 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
260658 TTACAAGCCA
*
260668 ATGTATCGATACATTTTGGG
1 ATGTATCGATACATATTGGG
*
260688 ATGTATCGATACATATTGTG
1 ATGTATCGATACATATTGGG
260708 -TGTATCGATACA
1 ATGTATCGATACA
260720 AATTTGGCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATATTGGG
Found at i:263113 original size:20 final size:21
Alignment explanation
Indices: 263084--263124 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
263074 TGTTTTTGTT
263084 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
263103 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
263125 AAGAAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:269132 original size:20 final size:21
Alignment explanation
Indices: 269085--269139 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
269075 GCCAATGACC
**
269085 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
269106 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
269126 TGTATCGATACATT
1 TGTATCGATACATT
269140 GTATCGATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:273268 original size:20 final size:20
Alignment explanation
Indices: 273255--273329 Score: 59
Period size: 19 Copynumber: 3.9 Consensus size: 20
273245 ATTTCATGCA
*
273255 TTTTGATGTCATTTAGGTCAT
1 TTTTGATGTCATTTAGG-CAC
* * *
273276 TTTTCATG--ATGTAGGAAC
1 TTTTGATGTCATTTAGGCAC
*
273294 TTTT-ATGTCATTTCATGCA-
1 TTTTGATGTCATTT-AGGCAC
273313 TTTTGATGTCATTTAGG
1 TTTTGATGTCATTTAGG
273330 TCATTTTCCA
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
17 3 0.07
18 5 0.12
19 15 0.36
20 12 0.29
21 7 0.17
ACGTcount: A:0.21, C:0.11, G:0.19, T:0.49
Consensus pattern (20 bp):
TTTTGATGTCATTTAGGCAC
Found at i:273275 original size:29 final size:29
Alignment explanation
Indices: 273243--273335 Score: 93
Period size: 29 Copynumber: 3.2 Consensus size: 29
273233 GACTTTTAAA
273243 TCATTTCATGCATTTTGATGTCATTTAGG
1 TCATTTCATGCATTTTGATGTCATTTAGG
* * * * *
273272 TCATTTTTCATG-A-TGT-AGGAACTTTTATG
1 TCA--TTTCATGCATTTTGATG-TCATTTAGG
273301 TCATTTCATGCATTTTGATGTCATTTAGG
1 TCATTTCATGCATTTTGATGTCATTTAGG
273330 TCATTT
1 TCATTT
273336 TCCATGATCC
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
27 7 0.15
28 3 0.06
29 28 0.58
30 3 0.06
31 7 0.15
ACGTcount: A:0.22, C:0.13, G:0.16, T:0.49
Consensus pattern (29 bp):
TCATTTCATGCATTTTGATGTCATTTAGG
Found at i:273334 original size:20 final size:19
Alignment explanation
Indices: 273252--273336 Score: 68
Period size: 20 Copynumber: 4.4 Consensus size: 19
273242 ATCATTTCAT
273252 GCATTTTGATGTCATTTAG
1 GCATTTTGATGTCATTTAG
* *
273271 GTCATTTTTCATG--ATGTAG
1 G-CA-TTTTGATGTCATTTAG
* *
273290 GAACTTTT-ATGTCATTTCAT
1 GCA-TTTTGATGTCATTT-AG
273310 GCATTTTGATGTCATTTAG
1 GCATTTTGATGTCATTTAG
273329 GTCATTTT
1 G-CATTTT
273337 CCATGATCCA
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
17 3 0.06
18 5 0.10
19 16 0.31
20 20 0.39
21 7 0.14
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.49
Consensus pattern (19 bp):
GCATTTTGATGTCATTTAG
Found at i:273465 original size:58 final size:58
Alignment explanation
Indices: 273156--273467 Score: 288
Period size: 58 Copynumber: 5.4 Consensus size: 58
273146 ATATTTTGAT
* * *
273156 GTCATTTACCGTGATCTAGGGACTTAGATGTAATTTTGTGAATTTTGAT-TCCATTTAG
1 GTCATTTTCCATGATCTAGGGACTTGGATGTAATTTTGTGAATTTTGATGT-CATTTAG
* * * ** ** * ** *
273214 GT-ATTTTTCATGATGTAAGGACTTTTAAATCATTTCATGCATTTTGATGTCATTTAG
1 GTCATTTTCCATGATCTAGGGACTTGGATGTAATTTTGTGAATTTTGATGTCATTTAG
* * * ** * ** *
273271 GTCATTTTTCATGATGTAGGAACTTTTATGTCATTTCATGCATTTTGATGTCATTTAG
1 GTCATTTTCCATGATCTAGGGACTTGGATGTAATTTTGTGAATTTTGATGTCATTTAG
* * * *
273329 GTCATTTTCCATGATCCAGGAACTTGGATGCAATTTTGTGAAATTTGATGTCATTTAG
1 GTCATTTTCCATGATCTAGGGACTTGGATGTAATTTTGTGAATTTTGATGTCATTTAG
* * * * *
273387 GTCATATAT-CATTATCTAGGGACTTGGATTTAATTTTGTGAATTTTGATTTTATTTAG
1 GTCAT-TTTCCATGATCTAGGGACTTGGATGTAATTTTGTGAATTTTGATGTCATTTAG
*
273445 GTCATTGTCCATGATCTAGGGAC
1 GTCATTTTCCATGATCTAGGGAC
273468 ATTTATCCAA
Statistics
Matches: 211, Mismatches: 39, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
57 44 0.21
58 165 0.78
59 2 0.01
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.45
Consensus pattern (58 bp):
GTCATTTTCCATGATCTAGGGACTTGGATGTAATTTTGTGAATTTTGATGTCATTTAG
Found at i:274858 original size:13 final size:13
Alignment explanation
Indices: 274840--274864 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
274830 TATTCAATAA
274840 ATCGATACATTGT
1 ATCGATACATTGT
274853 ATCGATACATTG
1 ATCGATACATTG
274865 ATCTTTGTAT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
ATCGATACATTGT
Found at i:290283 original size:18 final size:18
Alignment explanation
Indices: 290260--290367 Score: 58
Period size: 21 Copynumber: 5.3 Consensus size: 18
290250 ATCTTCTTCT
290260 CTCCTCCTCCTATCATCC
1 CTCCTCCTCCTATCATCC
*
290278 CTCCT-CTCTCTATTATCTCTC
1 CTCCTCCTC-CTATCA--TC-C
290299 CTGTCTCTCCTCCTATCATCC
1 C--TC-CTCCTCCTATCATCC
*
290320 CTCCTATCTCTACTATC-TCTC
1 CTCC--TC-CTCCTATCATC-C
290341 CTGTCTCTCCTCCTATCATCC
1 C--TC-CTCCTCCTATCATCC
290362 CTCCTC
1 CTCCTC
290368 TCTCTTCTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 32
0.66 0.04 0.30
Matches are distributed among these distances:
17 3 0.04
18 14 0.20
19 4 0.06
20 6 0.09
21 22 0.31
22 6 0.09
23 4 0.06
24 8 0.11
25 3 0.04
ACGTcount: A:0.10, C:0.48, G:0.02, T:0.40
Consensus pattern (18 bp):
CTCCTCCTCCTATCATCC
Found at i:290315 original size:42 final size:42
Alignment explanation
Indices: 290263--290381 Score: 202
Period size: 42 Copynumber: 2.8 Consensus size: 42
290253 TTCTTCTCTC
*
290263 CTCCTCCTATCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
290305 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
290347 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
290382 TTGAGGGCTA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.09, C:0.46, G:0.02, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:290322 original size:12 final size:11
Alignment explanation
Indices: 290296--290371 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
290286 TCTATTATCT
*
290296 CTCCTGTCTCTC
1 CTCCTATCTC-C
290308 CTCCTATCATCC
1 CTCCTATC-TCC
290320 CTCCTATCT--
1 CTCCTATCTCC
*
290329 CTACTATCT--
1 CTCCTATCTCC
*
290338 CTCCTGTCTCTC
1 CTCCTATCTC-C
290350 CTCCTATCATCC
1 CTCCTATC-TCC
*
290362 CTCCTCTCTC
1 CTCCTATCTC
290372 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:294350 original size:24 final size:23
Alignment explanation
Indices: 294317--294425 Score: 78
Period size: 21 Copynumber: 5.1 Consensus size: 23
294307 AGAGAAAGAA
294317 GAGAGA-GGAGGGATGATAGGAG
1 GAGAGACGGAGGGATGATAGGAG
*
294339 GAGAGACCGGA--GA-GATAGTA-
1 GAGAGA-CGGAGGGATGATAGGAG
*
294359 GAGATA-GGAGGGATGATAGGAG
1 GAGAGACGGAGGGATGATAGGAG
**
294381 GAGAGAC--AGGAGA-GATAATA-
1 GAGAGACGGAGG-GATGATAGGAG
*
294401 GAGAGA-GGAGGGATGACAGGAG
1 GAGAGACGGAGGGATGATAGGAG
294423 GAG
1 GAG
294426 GAGAGAAGAA
Statistics
Matches: 66, Mismatches: 9, Indels: 24
0.67 0.09 0.24
Matches are distributed among these distances:
18 3 0.05
20 15 0.23
21 27 0.41
22 18 0.27
24 3 0.05
ACGTcount: A:0.39, C:0.04, G:0.48, T:0.09
Consensus pattern (23 bp):
GAGAGACGGAGGGATGATAGGAG
Found at i:294368 original size:42 final size:42
Alignment explanation
Indices: 294307--294425 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
294297 TAGCCCTCAA
* * *
294307 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACCGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
294349 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
294391 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
294426 GAGAGAAGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.42, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:304514 original size:1 final size:1
Alignment explanation
Indices: 304508--304577 Score: 50
Period size: 1 Copynumber: 70.0 Consensus size: 1
304498 CGTCCTTCGC
* * * * * * * * * *
304508 AAAAAAAAAAGAAAAAAAAAAGAGAGAGACAAAAACAAAAAAAAAAAAAAAGAAAAAAAACAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
304573 AAAAA
1 AAAAA
304578 GGGTCCGGAT
Statistics
Matches: 49, Mismatches: 20, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.86, C:0.06, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:305420 original size:17 final size:17
Alignment explanation
Indices: 305398--305431 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
305388 CCCCTATGTG
305398 CTGGACTTTATGTCATA
1 CTGGACTTTATGTCATA
305415 CTGGACTTTATGTCATA
1 CTGGACTTTATGTCATA
305432 TCCCAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (17 bp):
CTGGACTTTATGTCATA
Found at i:305652 original size:37 final size:37
Alignment explanation
Indices: 305611--305695 Score: 170
Period size: 37 Copynumber: 2.3 Consensus size: 37
305601 TGCCATAATC
305611 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
1 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
305648 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
1 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
305685 ATGCATTTGTG
1 ATGCATTTGTG
305696 CTTCATCTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (37 bp):
ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
Found at i:306097 original size:28 final size:28
Alignment explanation
Indices: 306055--306166 Score: 163
Period size: 28 Copynumber: 4.0 Consensus size: 28
306045 GGTATTCTTC
*
306055 ACCTTC-AGAGCCCACAAGTCAGTGGCA
1 ACCTTCAAAAGCCCACAAGTCAGTGGCA
*
306082 ACCTTCAAAAGCCCACAAGTTAGTGGCA
1 ACCTTCAAAAGCCCACAAGTCAGTGGCA
* * *
306110 TCTTTTCAAAAGCCCACAAGTCAGTGGTA
1 AC-CTTCAAAAGCCCACAAGTCAGTGGCA
306139 ACCTTCAAAAGCCCACAAGTCAGTGGCA
1 ACCTTCAAAAGCCCACAAGTCAGTGGCA
306167 TCTTTTCTTC
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
27 6 0.08
28 44 0.59
29 24 0.32
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (28 bp):
ACCTTCAAAAGCCCACAAGTCAGTGGCA
Found at i:306151 original size:57 final size:58
Alignment explanation
Indices: 306063--306235 Score: 222
Period size: 57 Copynumber: 2.9 Consensus size: 58
306053 TCACCTTCAG
306063 AGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCATCTTTTC-AAA
1 AGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCATCTTTTCTAAA
* * *
306120 AGCCCACAAGTCAGTGGTAACCTTCAAAAGCCCACAAGTCAGTGGCATCTTTTCTTCAA
1 AGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCATCTTTTC-TAAA
* * * * * *
306179 AGTCCACGAGTCAGTGGCAATCTCTTCTCAAAGTCCACGACTTAGTGGCATCTTTTC
1 AGCCCACAAGTCAGTGGCAA-C-CTTC-AAAAGCCCACAAGTTAGTGGCATCTTTTC
306236 CCAAAGTCCA
Statistics
Matches: 100, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
57 52 0.52
59 19 0.19
60 1 0.01
61 4 0.04
62 24 0.24
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (58 bp):
AGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTTAGTGGCATCTTTTCTAAA
Found at i:306193 original size:31 final size:31
Alignment explanation
Indices: 306158--306488 Score: 146
Period size: 34 Copynumber: 10.5 Consensus size: 31
306148 AGCCCACAAG
*
306158 TCAGTGGCATCTTTTCTTCAAAGTCCACGAG
1 TCAGTGGCATCTTTTCTTCAAAGTCCACGAC
*
306189 TCAGTGGCAATCTCTTC-TCAAAGTCCACGAC
1 TCAGTGGC-ATCTTTTCTTCAAAGTCCACGAC
* *
306220 TTAGTGGCATCTTTTC-CCAAAGTCCACGAC
1 TCAGTGGCATCTTTTCTTCAAAGTCCACGAC
* *
306250 TCTA-TGGCACCTTTTTCTTTTCAAAGTCCACAAC
1 TC-AGTGGCATC-TTTTC--TTCAAAGTCCACGAC
* ** *
306284 TCTGTGGCA-CCCTT-TT--AAGTCCACAAC
1 TCAGTGGCATCTTTTCTTCAAAGTCCACGAC
* * * * *
306311 TCCGTGGCACCTTTTTCTTTTTAAAGCCCACAAC
1 TCAGTGGCATC-TTTTC--TTCAAAGTCCACGAC
* ** *
306345 TCTGTGGCACTCTTTTTCCTTTTAAGTCCACAAC
1 TCAGTGGCA-TC-TTTT-CTTCAAAGTCCACGAC
* ** *
306379 TCCGTGGCA-CCCTT-TT--AAGTCCACAAC
1 TCAGTGGCATCTTTTCTTCAAAGTCCACGAC
* ** *
306406 TCCGTGGCATCTTTTTCCTTTTAAGTCCACAAC
1 TCAGTGGCATC-TTTT-CTTCAAAGTCCACGAC
* * *
306439 TCCGTGGCACCTTTTTCCTTTTAAA-TCCACGAC
1 TCAGTGGCATC-TTTT-C-TTCAAAGTCCACGAC
*
306472 TCCGTGGCATTCTTTTC
1 TCAGTGGCA-TCTTTTC
306489 CCTTTTAAGC
Statistics
Matches: 247, Mismatches: 29, Indels: 47
0.76 0.09 0.15
Matches are distributed among these distances:
27 39 0.16
28 2 0.01
29 8 0.03
30 27 0.11
31 38 0.15
32 13 0.05
33 49 0.20
34 64 0.26
35 6 0.02
36 1 0.00
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.34
Consensus pattern (31 bp):
TCAGTGGCATCTTTTCTTCAAAGTCCACGAC
Found at i:306243 original size:30 final size:30
Alignment explanation
Indices: 306160--306264 Score: 131
Period size: 30 Copynumber: 3.4 Consensus size: 30
306150 CCCACAAGTC
* *
306160 AGTGGCATCTTTTCTTCAAAGTCCACGAGTC
1 AGTGGCATCTTTTC-TCAAAGTCCACGACTT
*
306191 AGTGGCAATCTCTTCTCAAAGTCCACGACTT
1 AGTGGC-ATCTTTTCTCAAAGTCCACGACTT
*
306222 AGTGGCATCTTTTCCCAAAGTCCACGACTCT
1 AGTGGCATCTTTTCTCAAAGTCCACGACT-T
*
306253 A-TGGCACCTTTT
1 AGTGGCATCTTTT
306265 TCTTTTCAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
30 31 0.47
31 28 0.42
32 7 0.11
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (30 bp):
AGTGGCATCTTTTCTCAAAGTCCACGACTT
Found at i:306280 original size:34 final size:33
Alignment explanation
Indices: 306238--306553 Score: 288
Period size: 34 Copynumber: 9.8 Consensus size: 33
306228 ATCTTTTCCC
* **
306238 AAAGTCCACGACTCTATGGCACCTTTTTCTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTT
*
306271 CAAAGTCCACAACTCTGTGGCACC-----CTTTT
1 -AAAGTCCACAACTCCGTGGCACCTTTTTCTTTT
306300 -AAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTTTC-TTTT
* *
306333 AAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTT
1 AAAGTCCACAACTCCGTGGCAC-CTTTTT-CTTTT
306368 -AAGTCCACAACTCCGTGGCACC-----CTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTT
*
306395 -AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTTT-CTTTT
306428 -AAGTCCACAACTCCGTGGCACCTTTTTCCTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTTT-CTTTT
* * *
306461 AAA-TCCACGACTCCGTGGCATTCTTTTCCCTTTT
1 AAAGTCCACAACTCCGTGGCA-CCTTTT-TCTTTT
* * * *
306495 -AAGCCCACACCTCCGTGGCATCCTTTTTTCCTGT
1 AAAGTCCACAACTCCGTGGCA-CC-TTTTTCTTTT
*
306529 -AAGTCCACAACTCCATGGCACCTTT
1 AAAGTCCACAACTCCGTGGCACCTTT
306554 AAGTCCAATA
Statistics
Matches: 240, Mismatches: 22, Indels: 42
0.79 0.07 0.14
Matches are distributed among these distances:
27 47 0.20
29 5 0.02
32 4 0.02
33 62 0.26
34 107 0.45
35 14 0.06
36 1 0.00
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (33 bp):
AAAGTCCACAACTCCGTGGCACCTTTTTCTTTT
Found at i:306304 original size:61 final size:61
Alignment explanation
Indices: 306239--306360 Score: 190
Period size: 61 Copynumber: 2.0 Consensus size: 61
306229 TCTTTTCCCA
* * *
306239 AAGTCCACGACTCTATGGCACCTTTTTCTTTTCAAAGTCCACAACTCTGTGGCACCCTTTT
1 AAGTCCACAACTCCATGGCACCTTTTTCTTTTCAAAGCCCACAACTCTGTGGCACCCTTTT
* * *
306300 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTT
1 AAGTCCACAACTCCATGGCACCTTTTTCTTTTCAAAGCCCACAACTCTGTGGCACCCTTTT
306361 TCCTTTTAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.34
Consensus pattern (61 bp):
AAGTCCACAACTCCATGGCACCTTTTTCTTTTCAAAGCCCACAACTCTGTGGCACCCTTTT
Found at i:306306 original size:27 final size:27
Alignment explanation
Indices: 306273--306454 Score: 148
Period size: 27 Copynumber: 6.0 Consensus size: 27
306263 TTTCTTTTCA
*
306273 AAGTCCACAACTCTGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
306300 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACC-----C-TTTT
* *
306333 AAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTT
1 -AAGTCCACAACTCCGTGGCA--C-----CCTTTT
306368 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
306395 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCA-C-----CCTTTT
*
306428 AAGTCCACAACTCCGTGGCACCTTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
306455 CCTTTTAAAT
Statistics
Matches: 129, Mismatches: 6, Indels: 40
0.74 0.03 0.23
Matches are distributed among these distances:
27 52 0.40
28 1 0.01
32 3 0.02
33 30 0.23
34 36 0.28
35 4 0.03
36 2 0.02
41 1 0.01
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.34
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCACCCTTTT
Found at i:306347 original size:95 final size:95
Alignment explanation
Indices: 306238--306553 Score: 374
Period size: 95 Copynumber: 3.3 Consensus size: 95
306228 ATCTTTTCCC
* * *
306238 AAAGTCCACGACTCTATGGCACCTTTTT-CTTTTCAAAGTCCACAACTCTGTGGCACCCTTTTAA
1 AAAGTCCACAACTCTGTGGCACCTTTTTCCTTTT-AAAGTCCACAACTCCGTGGCACCCTTTTAA
*
306302 GTCCACAACTCCGTGGCACCTTTTTCTTTTT
65 GTCCACAACTCCGTGGCACCTTTTTCCTTTT
*
306333 AAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAA
1 AAAGTCCACAACTCTGTGGCAC-CTTTTTCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAA
*
306397 GTCCACAACTCCGTGGCATCTTTTTCCTTTT
65 GTCCACAACTCCGTGGCACCTTTTTCCTTTT
* *
306428 -AAGTCCACAACTCCGTGGCACCTTTTTCCTTTTAAA-TCCACGACTCCGTGGCATTCTTTTCCC
1 AAAGTCCACAACTCTGTGGCACCTTTTTCCTTTTAAAGTCCACAACTCCGTGGCA-------CCC
* * *
306491 TTTTAAGCCCACACCTCCGTGGCATCCTTTTTTCC-TGT
59 TTTTAAGTCCACAACTCCGTGGCA-CC-TTTTTCCTTTT
**
306529 -AAGTCCACAACTCCATGGCACCTTT
1 AAAGTCCACAACTCTGTGGCACCTTT
306554 AAGTCCAATA
Statistics
Matches: 195, Mismatches: 14, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
93 28 0.14
94 21 0.11
95 76 0.39
96 6 0.03
97 5 0.03
100 25 0.13
101 27 0.14
102 7 0.04
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (95 bp):
AAAGTCCACAACTCTGTGGCACCTTTTTCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAG
TCCACAACTCCGTGGCACCTTTTTCCTTTT
Found at i:306431 original size:33 final size:33
Alignment explanation
Indices: 306294--306553 Score: 309
Period size: 34 Copynumber: 7.9 Consensus size: 33
306284 TCTGTGGCAC
*
306294 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
* * *
306327 CTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
1 CCTTTT-AAGTCCACAACTCCGTGGCA-TCTTTTT
306362 CCTTTTAAGTCCACAACTCCGTGGCA-C-----
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
306389 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
*
306422 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
* * *
306455 CCTTTTAAATCCACGACTCCGTGGCATTCTTTTC
1 CCTTTTAAGTCCACAACTCCGTGGCA-TCTTTTT
* *
306489 CCTTTTAAGCCCACACCTCCGTGGCATCCTTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCAT-C-TTTTT
* * *
306524 CC-TGTAAGTCCACAACTCCATGGCACCTTT
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTT
306554 AAGTCCAATA
Statistics
Matches: 194, Mismatches: 22, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
27 26 0.13
28 1 0.01
32 4 0.02
33 63 0.32
34 83 0.43
35 17 0.09
ACGTcount: A:0.19, C:0.33, G:0.12, T:0.35
Consensus pattern (33 bp):
CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
Found at i:306623 original size:49 final size:49
Alignment explanation
Indices: 306550--307213 Score: 530
Period size: 49 Copynumber: 13.8 Consensus size: 49
306540 TCCATGGCAC
* * * *
306550 CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCATCTTTAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
306599 CTTTAAGACCAATGTCGCTGGCCTTGAATCAACACATTGG------CA-
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
** * * **
306641 ---TAAG-CCTAATATCATTGGCCTTAAATCAGCATATTGGCACC-TCGC
1 CTTTAAGTCC-AATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * *
306686 CTTTAAGACCAATGTTGCTGGCTTTGAATTAGCACATTGG------CA-
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
306728 C---AAGCCCAATATCACTAGCCTTGAATCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * *
306774 CTTTAAGACCGATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTAACTAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT--C-AT
*
306826 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTAGCACCTTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
306875 CTTTAAGTCCGATATCGCTAGCCTTGAATCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * *
306924 CTTTAAGACCGATGTCGTTGGCCTTGAATCAGCACATTGACACCTTAACCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT---CAT
* ** * *
306976 CTTTAAGTCCAATGTCATTGGCCTTGAATCAGCACCTTGGCACATTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
307025 CTTTAAGTCCGATATCGCTAGCCTTGAATCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * * * * *
307074 CTTTAAGTCCGATATCGTTGGCCTTGAATTAGCATATTATAGCATCTTTAA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACA-T-TGGCACCTTCAT
* * * ** *
307125 CATTCCTAGGCCCAATGTCGCTGGCCTTGTCTCAGCACATTGGCA--TTCTT
1 C-TT--TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * *
307175 CTTCAAGTCTAATGTCGCTGGCCATGAATCAGCACATTG
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTG
307214 TCATTCTTCG
Statistics
Matches: 494, Mismatches: 89, Indels: 66
0.76 0.14 0.10
Matches are distributed among these distances:
38 2 0.00
39 57 0.12
42 1 0.00
43 2 0.00
44 1 0.00
45 2 0.00
46 1 0.00
47 29 0.06
48 26 0.05
49 241 0.49
50 5 0.01
51 10 0.02
52 92 0.19
53 1 0.00
54 24 0.05
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (49 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
Found at i:306714 original size:87 final size:87
Alignment explanation
Indices: 306558--306816 Score: 347
Period size: 87 Copynumber: 3.0 Consensus size: 87
306548 ACCTTTAAGT
* * *
306558 CCAATATCGCTAGCCTTGAATCAGCATATTGGCATCTTTATCTTTAAGACCAATGTCGCTGGCCT
1 CCAATATCACTAGCCTTGAATCAGCATATTGGCA-CCTCATCTTTAAGACCAATGTCGCTGGCCT
* *
306623 TGAATCAACACATTGGCATAAGC
65 TGAATCAGCACATTGGCACAAGC
* * * * ** * *
306646 CTAATATCATTGGCCTTAAATCAGCATATTGGCACCTCGCCTTTAAGACCAATGTTGCTGGCTTT
1 CCAATATCACTAGCCTTGAATCAGCATATTGGCACCTCATCTTTAAGACCAATGTCGCTGGCCTT
*
306711 GAATTAGCACATTGGCACAAGC
66 GAATCAGCACATTGGCACAAGC
* * *
306733 CCAATATCACTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCT
1 CCAATATCACTAGCCTTGAATCAGCATATTGGCACC-TCATCTTTAAGACCAATGTCGCTGGCCT
306798 TGAATCAGCACATTGGCAC
65 TGAATCAGCACATTGGCAC
306817 CTTAACTATC
Statistics
Matches: 144, Mismatches: 26, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
87 75 0.52
88 69 0.48
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (87 bp):
CCAATATCACTAGCCTTGAATCAGCATATTGGCACCTCATCTTTAAGACCAATGTCGCTGGCCTT
GAATCAGCACATTGGCACAAGC
Found at i:306908 original size:101 final size:98
Alignment explanation
Indices: 306733--307107 Score: 516
Period size: 101 Copynumber: 3.8 Consensus size: 98
306723 TGGCACAAGC
* * *
306733 CCAATATCACTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCT
1 CCAATATCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCGATATCGTTGGCCT
306798 TGAATCAGCACATTGGCACCTTAACTATCTTTAAGT
66 TGAATCAGCACATTGGCACCTT--C-ATCTTTAAGT
* * * *
306834 CCAATATCGCTGGCCTTGAATCAGCACATTAGCACCTTCATCTTTAAGTCCGATATCGCTAGCCT
1 CCAATATCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCGATATCGTTGGCCT
*
306899 TGAATCAGCACATTGGCACCTTCATCTTTAAGA
66 TGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * * * * * * *
306932 CCGATGTCGTTGGCCTTGAATCAGCACATTGACACCTTAACCATCTTTAAGTCCAATGTCATTGG
1 CCAATATCGCTAGCCTTGAATCAGCACATTGGCACCTT---CATCTTTAAGTCCGATATCGTTGG
* *
306997 CCTTGAATCAGCACCTTGGCACATTCATCTTTAAGT
63 CCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
*
307033 CCGATATCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCGATATCGTTGGCCT
1 CCAATATCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCGATATCGTTGGCCT
*
307098 TGAATTAGCA
66 TGAATCAGCA
307108 TATTATAGCA
Statistics
Matches: 242, Mismatches: 29, Indels: 9
0.86 0.10 0.03
Matches are distributed among these distances:
98 75 0.31
99 1 0.00
101 166 0.69
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.31
Consensus pattern (98 bp):
CCAATATCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCGATATCGTTGGCCT
TGAATCAGCACATTGGCACCTTCATCTTTAAGT
Found at i:307007 original size:150 final size:150
Alignment explanation
Indices: 306736--307107 Score: 636
Period size: 150 Copynumber: 2.5 Consensus size: 150
306726 CACAAGCCCA
*
306736 ATATCACTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCTTGA
1 ATATCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCTTGA
* * *
306801 ATCAGCACATTGGCACCTTAACTATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTAG
66 ATCAGCACATTGACACCTTAACCATCTTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTAG
*
306866 CACCTTCATCTTTAAGTCCG
131 CACATTCATCTTTAAGTCCG
306886 ATATCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCTTGA
1 ATATCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCTTGA
* * * *
306951 ATCAGCACATTGACACCTTAACCATCTTTAAGTCCAATGTCATTGGCCTTGAATCAGCACCTTGG
66 ATCAGCACATTGACACCTTAACCATCTTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTAG
307016 CACATTCATCTTTAAGTCCG
131 CACATTCATCTTTAAGTCCG
* *
307036 ATATCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCGATATCGTTGGCCTTGA
1 ATATCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCTTGA
*
307101 ATTAGCA
66 ATCAGCA
307108 TATTATAGCA
Statistics
Matches: 210, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
150 210 1.00
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.31
Consensus pattern (150 bp):
ATATCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCTTGA
ATCAGCACATTGACACCTTAACCATCTTTAAGTCCAATATCACTGGCCTTGAATCAGCACATTAG
CACATTCATCTTTAAGTCCG
Found at i:307172 original size:150 final size:149
Alignment explanation
Indices: 306736--307213 Score: 624
Period size: 150 Copynumber: 3.2 Consensus size: 149
306726 CACAAGCCCA
*
306736 ATATCACTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCTTGA
1 ATATCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCTTGA
* *
306801 ATCAGCACA-TTGGCACCTTAAC-TATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT
66 ATCAGCACATTTAGCACCTTAACAT-TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATT
*
306864 AGCACCTTCATCTTTAAGTCCG
130 GGCA--TTCATCTTTAAGTCCG
306886 ATATCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCTTGA
1 ATATCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCTTGA
* ** *
306951 ATCAGCACATTGA-CACCTTAACCA-TCTTTAAGTCCAATGTCATTGGCCTTGAATCAGCACCTT
66 ATCAGCACATTTAGCACCTTAA-CATTCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATT
307014 GGCACATTCATCTTTAAGTCCG
130 GG--CATTCATCTTTAAGTCCG
* *
307036 ATATCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCGATATCGTTGGCCTTGA
1 ATATCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCTTGA
* * * * * * **
307101 ATTAGCATATTATAGCATCTTTAACATTC-CTAGGCCCAATGTCGCTGGCCTTGTCTCAGCACAT
66 ATCAGCACATT-TAGCA-CCTTAACATTCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACAT
* * **
307165 TGGCATTCTTCTTCAAGTCTA
129 TGGCATTCATCTTTAAGTCCG
* * *
307186 ATGTCGCTGGCCATGAATCAGCACATTG
1 ATATCGCTAGCCTTGAATCAGCACATTG
307214 TCATTCTTCG
Statistics
Matches: 290, Mismatches: 29, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
150 244 0.84
151 3 0.01
152 36 0.12
153 7 0.02
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (149 bp):
ATATCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCTTGA
ATCAGCACATTTAGCACCTTAACATTCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTG
GCATTCATCTTTAAGTCCG
Found at i:308020 original size:20 final size:20
Alignment explanation
Indices: 307995--308049 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
307985 CTGCCAAGGA
307995 AATGTATCGATACATT-ATTC
1 AATGTATCGATACATTGA-TC
308015 AATGTATCGATACATTGATC
1 AATGTATCGATACATTGATC
**
308035 TTTGTATCGATACAT
1 AATGTATCGATACAT
308050 CTGAGAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTGATC
Found at i:318122 original size:12 final size:11
Alignment explanation
Indices: 318100--318175 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
318090 AGAGAAAGAA
*
318100 GAGAGAGGAGG
1 GAGATAGGAGG
318111 GATGATAGGAGG
1 GA-GATAGGAGG
*
318123 AGAGACAGGA--
1 -GAGATAGGAGG
*
318133 GAGATAGTA--
1 GAGATAGGAGG
318142 GAGATAGGAGG
1 GAGATAGGAGG
318153 GATGATAGGAGG
1 GA-GATAGGAGG
*
318165 AGAGACAGGAG
1 -GAGATAGGAG
318176 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:318132 original size:24 final size:24
Alignment explanation
Indices: 318099--318184 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
318089 AAGAGAAAGA
*
318099 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
318123 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
318141 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
318165 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
318185 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:318151 original size:42 final size:42
Alignment explanation
Indices: 318090--318208 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
318080 TAGCCCTCAA
* *
318090 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
318132 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
318174 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
318209 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:323641 original size:155 final size:154
Alignment explanation
Indices: 323445--323801 Score: 373
Period size: 154 Copynumber: 2.3 Consensus size: 154
323435 TTGGTGTAAG
* * * *
323445 GGTGACAACCTAAGACTCGATCTTAAAAAAATTATGAAAATGCCCCTAAAGG-TTACCTTCGACG
1 GGTGACAACCTAGGACTCGAT-TTTAGAAAATTATGAAAATGCCCCTAAAGGAATACCTTCGACG
* ** *
323509 TAAAAGTACCCGATGCCCCTTAAAAGACTTAAAAAGATTATAGATGGGATGAACCAATCA-ATAA
65 TAAAAGTACCCAATAACCC-TAAAAGACTTAAAAACATTATAGATGGGATGAACCAATCATA-AA
* *
323573 TACCCACCTTCGGCATAAAAGC-GAACTT
128 TACCAACCTT-GGCATAAAAGCAG-ACTC
* * * * * * * *
323601 GGTGATAACCTAGGACTCGATTTTGGAAAATTATAAAAATG-CCCTTAGGGAATATCTTTGACTT
1 GGTGACAACCTAGGACTCGATTTTAGAAAATTATGAAAATGCCCCTAAAGGAATACCTTCGACGT
* * * * ** *
323665 AGAAGTGCCCAATAACCCTAAAGGACTTAAAAACTTTATAGATGGGATGAACTTATCCTAAATAC
66 AAAAGTACCCAATAACCCTAAAAGACTTAAAAACATTATAGATGGGATGAACCAATCATAAATAC
323730 CAACCTTGGCATAAAAGCAGACTC
131 CAACCTTGGCATAAAAGCAGACTC
* * *
323754 AGTGACAACCTAGGATTC-AGTTTTAGAAAATTATGAAAATGCTCCTAA
1 GGTGACAACCTAGGACTCGA-TTTTAGAAAATTATGAAAATGCCCCTAA
323802 GATACACCTT
Statistics
Matches: 164, Mismatches: 32, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
152 1 0.01
153 48 0.29
154 57 0.35
155 39 0.24
156 19 0.12
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (154 bp):
GGTGACAACCTAGGACTCGATTTTAGAAAATTATGAAAATGCCCCTAAAGGAATACCTTCGACGT
AAAAGTACCCAATAACCCTAAAAGACTTAAAAACATTATAGATGGGATGAACCAATCATAAATAC
CAACCTTGGCATAAAAGCAGACTC
Found at i:323813 original size:153 final size:154
Alignment explanation
Indices: 323446--323813 Score: 343
Period size: 153 Copynumber: 2.4 Consensus size: 154
323436 TGGTGTAAGG
* * * * * * *** * *
323446 GTGACAACCTAAGACTCGATCTTAAAAAAATTATGAAAATGCCCCTAAAGGTTACCTTCGACGTA
1 GTGACAACCTAGGACTCGAT-TTTAGAAAATTATAAAAATGCCCTTAGAGAACACCTTTGACTTA
* * * ** *
323511 AAAGTACCCGATGCCCCTTAAAAGACTTAAAAAGATTATAGATGGGATGAACCAATCAATAATAC
65 GAAGTGCCCAATAACCC-TAAAAGACTTAAAAACATTATAGATGGGATGAACCAATCAATAATAC
* **
323576 CCACCTTCGGCATAAAAGCGAACTTG
129 CAACCTTCGGCATAAAAGCGAACTCA
* * * * *
323602 GTGATAACCTAGGACTCGATTTTGGAAAATTATAAAAATGCCCTTAGGGAATATCTTTGACTTAG
1 GTGACAACCTAGGACTCGATTTTAGAAAATTATAAAAATGCCCTTAGAGAACACCTTTGACTTAG
* * ** *
323667 AAGTGCCCAATAACCCTAAAGGACTTAAAAACTTTATAGATGGGATGAACTTATC-CTAAATACC
66 AAGTGCCCAATAACCCTAAAAGACTTAAAAACATTATAGATGGGATGAACCAATCAAT-AATACC
323731 AACCTT-GGCATAAAAGC-AGACTCA
130 AACCTTCGGCATAAAAGCGA-ACTCA
* *
323755 GTGACAACCTAGGATTC-AGTTTTAGAAAATTATGAAAATGCTCC-TA-AGATACACCTTTG
1 GTGACAACCTAGGACTCGA-TTTTAGAAAATTATAAAAATGC-CCTTAGAGA-ACACCTTTG
323814 GCGTGAAAGT
Statistics
Matches: 172, Mismatches: 35, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
152 4 0.02
153 59 0.34
154 47 0.27
155 44 0.26
156 18 0.10
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.26
Consensus pattern (154 bp):
GTGACAACCTAGGACTCGATTTTAGAAAATTATAAAAATGCCCTTAGAGAACACCTTTGACTTAG
AAGTGCCCAATAACCCTAAAAGACTTAAAAACATTATAGATGGGATGAACCAATCAATAATACCA
ACCTTCGGCATAAAAGCGAACTCA
Found at i:323830 original size:28 final size:28
Alignment explanation
Indices: 323798--323853 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
323788 GAAAATGCTC
* *
323798 CTAAGATACACCTTTGGCGTGAAAGTAT
1 CTAAGATACACCTTCGACGTGAAAGTAT
* * *
323826 CTAAGGTATACCTTCGATGTGAAAGTAT
1 CTAAGATACACCTTCGACGTGAAAGTAT
323854 TTTGGTAACC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.30
Consensus pattern (28 bp):
CTAAGATACACCTTCGACGTGAAAGTAT
Found at i:324303 original size:138 final size:142
Alignment explanation
Indices: 324030--324343 Score: 397
Period size: 138 Copynumber: 2.2 Consensus size: 142
324020 TTTGTGAATC
* * * *
324030 TCTATACTCATATGGATGACCATAGGAATGA-TAGAAGTCTTGAAAAATTAAGATAATAATTTTT
1 TCTATACCCCTATGGATAACCATAGGAAT-ATTAGAAATCTTGAAAAATTAAGATAATAATTTTT
* * * * * *
324094 ATTTAATTTTTAATTTCCAAAAGAATTCATTTCGTACCTTAATGGAGAACCAAAAAGATACGAAA
65 ACTTAATTTTTAATTTCAAAAAAAAATCATTTCGTAACTTAATGAAGAACCAAAAAGATACGAAA
324159 AATTTTGAAGATT
130 AATTTTGAAGATT
* *
324172 TCTTTA-CCCTATGGATAACCATAGGAATATTAGAAATCTTGAAAAATTAAGATAATGA-TTTT-
1 TCTATACCCCTATGGATAACCATAGGAATATTAGAAATCTTGAAAAATTAAGATAATAATTTTTA
* * *
324234 CTTATTTTTTAATTT-AAAAAAAAATCATTTCGTATAC-TAATGAAGAACCGAAAAGATATGAAA
66 CTTAATTTTTAATTTCAAAAAAAAATCATTTCGTA-ACTTAATGAAGAACCAAAAAGATACGAAA
*
324297 AGTTTTGAAGATT
130 AATTTTGAAGATT
* * *
324310 TCTATACCCCTACGGAAAACCAGAGGAATATTAG
1 TCTATACCCCTATGGATAACCATAGGAATATTAG
324344 TGATGACAAC
Statistics
Matches: 149, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
138 56 0.38
139 38 0.26
140 5 0.03
141 45 0.30
142 5 0.03
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.33
Consensus pattern (142 bp):
TCTATACCCCTATGGATAACCATAGGAATATTAGAAATCTTGAAAAATTAAGATAATAATTTTTA
CTTAATTTTTAATTTCAAAAAAAAATCATTTCGTAACTTAATGAAGAACCAAAAAGATACGAAAA
ATTTTGAAGATT
Found at i:325956 original size:10 final size:10
Alignment explanation
Indices: 325937--325973 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
325927 TTTGGCTAGA
325937 TTTCTC-TTT
1 TTTCTCTTTT
325946 TTTCTCTTTT
1 TTTCTCTTTT
325956 TTTCTCTCTTT
1 TTTCTCT-TTT
325967 TTT-TCTT
1 TTTCTCTT
325974 CACTTGCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 7 0.27
10 13 0.50
11 6 0.23
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTCTCTTTT
Found at i:325963 original size:12 final size:12
Alignment explanation
Indices: 325943--325972 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
325933 TAGATTTCTC
325943 TTTTT-TCTCTT
1 TTTTTCTCTCTT
325954 TTTTTCTCTCTT
1 TTTTTCTCTCTT
325966 TTTTTCT
1 TTTTTCT
325973 TCACTTGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTCTCTCTT
Found at i:336919 original size:12 final size:13
Alignment explanation
Indices: 336898--336942 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
336888 TTATTTTTGA
336898 TATT-TTTGATTT
1 TATTATTTGATTT
336910 T-TTATTTGATTAT
1 TATTATTTGATT-T
*
336923 TATTTTTTG-TTT
1 TATTATTTGATTT
336935 TATTATTT
1 TATTATTT
336943 TTTAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 2 0.07
12 16 0.57
13 4 0.14
14 6 0.21
ACGTcount: A:0.18, C:0.00, G:0.07, T:0.76
Consensus pattern (13 bp):
TATTATTTGATTT
Found at i:336927 original size:18 final size:18
Alignment explanation
Indices: 336906--336945 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
336896 GATATTTTTG
336906 ATTTTTTATTTGATTATT
1 ATTTTTTATTTGATTATT
* *
336924 ATTTTTTGTTTTATTATT
1 ATTTTTTATTTGATTATT
336942 -TTTT
1 ATTTT
336946 AATTTTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (18 bp):
ATTTTTTATTTGATTATT
Found at i:337597 original size:44 final size:44
Alignment explanation
Indices: 337518--338975 Score: 1292
Period size: 44 Copynumber: 33.6 Consensus size: 44
337508 AGAAAGTTTT
* * * * * *
337518 CAGGGTCAAAACCGATAGGCAAACTTAAAGATAAAGGAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * *
337562 CAAGGTCAAAGCCAACAGGTAGACTTGAGGGTAAAGGAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * * * * *
337606 TAGGGACAAAGCTGACTGGCAGACTTGAGGGTAAAAGAAGTCTT
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * * * *
337650 CAGGGACAAAGTCGACTAGGCAAACTT-AAGG-AAATGAAGTCTC
1 CAGGGTCAAAGCCGAC-AGGCAGACTTGAGGGTAAAGGAAGTCTC
*
337693 CAGGGTCAAAGCTGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * * * *
337737 TAGGGAT-AAAGTCGACAGGTAGAGTTGAGGGTAAAAGAAGTCTC
1 CAGGG-TCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* ** * * * * *
337781 TACAGACAAAGCCGACAGACAGACTT-AAGGAAAAGAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * *
337824 CAGGGTCAAAGCCGACAGGAAAACTTAAGGGTAAAGGAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * * * * *
337868 TAGGGACAAAGCTGACAGGCAGACTTGAGGGCAAAAGAAGTCTT
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * * * * *
337912 CAAGGACAAAACCGACAAGCATACTTGAGGGTAAAAGAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * * * *
337956 CAAGGACAAAGCCGACAGGTAGACTTGAGGGAAAAAGAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * *
338000 CAGGGTCAAAGCTGACAAGTAGACTTGAGGGTAAAGGAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * * * *
338044 CAAGGACAAAGCTGACAGGCAGACTTGAGGGAAAAAGAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * * *
338088 TAGGGACAAAGCCGACAGGTAGACTTGAGGGTAAAAGAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * * * *
338132 CAAGGACAAAGCCAACAGGCAGACTT-AAGG-AAAGAAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * * *
338174 CAAGGTCAAAGTCGATAGGCAGACTTGAGGGAAAAGGAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * * * * *
338218 AAGGGACAAAGTCGACAGGTAGACTTAAGGGTAAAAGAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* *
338262 CAGGGACAAAGCCGACAGGCAGACTT-AAGG-AAAGGAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
** * * * *
338304 CAAAGTTAAAGCCGACAAGCAGACTTGAGGATAAA-AAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* ** * * *
338347 CAGGGACAAAGTTGACAGGTAGACTTGAGGGAAAAAGAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* *
338391 CAGGGAT-AAAACCGACAGGCAGACTT-AAGG-AAAGGAAGTCTC
1 CAGGG-TCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * * * * *
338433 CAGGGTCAAAGTCGACAAGCAAACTTAAAGATAAAGGAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* ** * * *
338477 TAGGGTCAAAGCTAACAGGTAAACTTGAGGGAAAAGGAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * * * * *
338521 CAAGGACAAAGCTGATAGGCAGACTT-AAGG-AAAAGAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * * *
338563 CAAGGTCAAAGTCAACAGGCAGACTT-AAGG-AAAGGAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * *
338605 CAAGGTCAAAGCCGACAGACAGACTTGAGGGAAAAGGAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* *
338649 CAGGGAT-AAAACCGACAGGCAGACTT-AAGG-AAAGGAAGTCTC
1 CAGGG-TCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * * * * * *
338691 CAGGGTCAAAGTCGACAAGCAAACTTAAAGATAAAGGAAGTCTT
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * ** * *
338735 TAAGGTCAAAGCTAACAGGTAGACTTGAGGGAAAAGGAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * * * * *
338779 CAAGGACAAAGCTGATAGGCAGACTT-AAGG-AAAAGAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * *
338821 CAAGGTCAAAGTCGACAGGCAGACTT-AAGG-AAAGGAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * * *
338863 CAAGGTCAAAGCCGACAGACAGACTTAAGGATAAAGGAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * *
338907 CAGGGTCAGAGCCGACAAGCAGACTTAAGGGTAAA-GAAGTCTC
1 CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
* * *
338950 TAGGGAT-AAAGCCAACAAGCAGACTT
1 CAGGG-TCAAAGCCGACAGGCAGACTT
338976 AAAAAAAAGA
Statistics
Matches: 1159, Mismatches: 231, Indels: 49
0.81 0.16 0.03
Matches are distributed among these distances:
41 2 0.00
42 278 0.24
43 153 0.13
44 716 0.62
45 10 0.01
ACGTcount: A:0.40, C:0.17, G:0.28, T:0.15
Consensus pattern (44 bp):
CAGGGTCAAAGCCGACAGGCAGACTTGAGGGTAAAGGAAGTCTC
Found at i:338228 original size:130 final size:129
Alignment explanation
Indices: 337475--338949 Score: 1374
Period size: 130 Copynumber: 11.3 Consensus size: 129
337465 AAGAATCTTA
* * * * * * * ** *
337475 CCAGGGACAAAGCTGACAGGTAAAC-AAAGGGAAAGAAAGTTTTCAGGGTCAAAACCGATAGGCA
1 CCAGGGACAAAGCCGACAGGCAGACTTAA-GGAAAGAAAGTCTCCAAGGTCAAAGTCGACAGGCA
* * * *
337539 AACTTAAAGATAAAGGAAGTCTCCAA-GGTCAAAGCCAACAGGTAGACTTGAGGGTAAAGGAAGT
65 GACTTAAGGA-AAAGGAAGTCT-CAAGGGTCAAAGCCGACAGGTAGACTTGAGGGTAAAAGAAGT
337603 CT
128 CT
* * * * * * *
337605 CTAGGGACAAAGCTGACTGGCAGACTTGAGGGTAAA-AGAAGTCTTCAGGGACAAAGTCGACTAG
1 CCAGGGACAAAGCCGACAGGCAGACTT-AAGG-AAAGA-AAGTCTCCAAGGTCAAAGTCGAC-AG
* * * * * *
337669 GCAAACTTAAGG-AAATGAAGTCTCCAGGGTCAAAGCTGACAGGCAGACTTGAGGGTAAAGGAAG
62 GCAGACTTAAGGAAAAGGAAGTCTCAAGGGTCAAAGCCGACAGGTAGACTTGAGGGTAAAAGAAG
337733 TCT
127 TCT
* * * * * * * * *
337736 CTAGGGATAAAGTCGACAGGTAGAGTTGAGGGTAAA-AGAAGTCTCTACA-GACAAAGCCGACAG
1 CCAGGGACAAAGCCGACAGGCAGACTT-AAGG-AAAGA-AAGTCTCCA-AGGTCAAAGTCGACAG
* * * * * * *
337799 ACAGACTTAAGGAAAAGAAAGTCTCCAGGGTCAAAGCCGACAGGAAAACTTAAGGGTAAAGGAAG
62 GCAGACTTAAGGAAAAGGAAGTCTCAAGGGTCAAAGCCGACAGGTAGACTTGAGGGTAAAAGAAG
337864 TCT
127 TCT
* * * * * ** *
337867 CTAGGGACAAAGCTGACAGGCAGACTTGAGGGCAAA-AGAAGTCTTCAAGGACAAAACCGACAAG
1 CCAGGGACAAAGCCGACAGGCAGACTT-AAGG-AAAGA-AAGTCTCCAAGGTCAAAGTCGACAGG
* * * *
337931 CATACTTGAGGGTAAAA-GAAGTCTCCAA-GGACAAAGCCGACAGGTAGACTTGAGGGAAAAAGA
63 CAGACTT-AAGG-AAAAGGAAGTCT-CAAGGGTCAAAGCCGACAGGTAGACTTGAGGGTAAAAGA
337994 AGTCT
125 AGTCT
* * * * * * *
337999 CCAGGGTCAAAGCTGACAAGTAGACTTGAGGGTAAAGGAAGTCTCCAAGGACAAAG-CTGACAGG
1 CCAGGGACAAAGCCGACAGGCAGACTT-AAGG-AAAGAAAGTCTCCAAGGTCAAAGTC-GACAGG
* * * *
338063 CAGACTTGAGGGAAAAAGAAGTCTCTAGGGACAAAGCCGACAGGTAGACTTGAGGGTAAAAGAAG
63 CAGACTT-AAGGAAAAGGAAGTCTCAAGGGTCAAAGCCGACAGGTAGACTTGAGGGTAAAAGAAG
338128 TCT
127 TCT
* * *
338131 CCAAGGACAAAGCCAACAGGCAGACTTAAGGAAAGAAAGTCTCCAAGGTCAAAGTCGATAGGCAG
1 CCAGGGACAAAGCCGACAGGCAGACTTAAGGAAAGAAAGTCTCCAAGGTCAAAGTCGACAGGCAG
* * * *
338196 ACTTGAGGGAAAAGGAAGTCTCAAGGGACAAAGTCGACAGGTAGACTTAAGGGTAAAAGAAGTCT
66 ACTT-AAGGAAAAGGAAGTCTCAAGGGTCAAAGCCGACAGGTAGACTTGAGGGTAAAAGAAGTCT
* * * * *
338261 CCAGGGACAAAGCCGACAGGCAGACTTAAGGAAAGGAAGTCTCCAAAGTTAAAGCCGACAAGCAG
1 CCAGGGACAAAGCCGACAGGCAGACTTAAGGAAAGAAAGTCTCCAAGGTCAAAGTCGACAGGCAG
* * * * ** *
338326 ACTTGAGGATAAA-AAAGTCTCCAGGGACAAAGTTGACAGGTAGACTTGAGGGAAAAAGAAGTCT
66 ACTTAAGGA-AAAGGAAGTCTCAAGGGTCAAAGCCGACAGGTAGACTTGAGGGTAAAAGAAGTCT
* * * * * *
338390 CCAGGGATAAAACCGACAGGCAGACTTAAGGAAAGGAAGTCTCCAGGGTCAAAGTCGACAAGCAA
1 CCAGGGACAAAGCCGACAGGCAGACTTAAGGAAAGAAAGTCTCCAAGGTCAAAGTCGACAGGCAG
* * ** *
338455 ACTTAAAGATAAAGGAAGTCTCTAGGGTCAAAGCTAACAGGTAAACTTGAGGG-AAAAGGAAGTC
66 ACTTAAGGA-AAAGGAAGTCTCAAGGGTCAAAGCCGACAGGTAGACTTGAGGGTAAAA-GAAGTC
338519 T
129 T
* * * *
338520 CCAAGGACAAAGCTGATAGGCAGACTTAAGGAAA-AGAAGTCTCCAAGGTCAAAGTCAACAGGCA
1 CCAGGGACAAAGCCGACAGGCAGACTTAAGGAAAGA-AAGTCTCCAAGGTCAAAGTCGACAGGCA
**
338584 GACTTAAGG-AAAGGAAGTCTCCAA-GGTCAAAGCCGACAGACAGACTTGAGGG-AAAAGGAAGT
65 GACTTAAGGAAAAGGAAGTCT-CAAGGGTCAAAGCCGACAGGTAGACTTGAGGGTAAAA-GAAGT
338646 CT
128 CT
* * * * * *
338648 CCAGGGATAAAACCGACAGGCAGACTTAAGGAAAGGAAGTCTCCAGGGTCAAAGTCGACAAGCAA
1 CCAGGGACAAAGCCGACAGGCAGACTTAAGGAAAGAAAGTCTCCAAGGTCAAAGTCGACAGGCAG
* * **
338713 ACTTAAAGATAAAGGAAGTCTTTAA-GGTCAAAGCTAACAGGTAGACTTGAGGG-AAAAGGAAGT
66 ACTTAAGGA-AAAGGAAGTC-TCAAGGGTCAAAGCCGACAGGTAGACTTGAGGGTAAAA-GAAGT
338776 CT
128 CT
* * *
338778 CCAAGGACAAAGCTGATAGGCAGACTTAAGGAAA-AGAAGTCTCCAAGGTCAAAGTCGACAGGCA
1 CCAGGGACAAAGCCGACAGGCAGACTTAAGGAAAGA-AAGTCTCCAAGGTCAAAGTCGACAGGCA
** * * *
338842 GACTTAAGG-AAAGGAAGTCTCCAA-GGTCAAAGCCGACAGACAGACTTAAGGATAAAGGAAGTC
65 GACTTAAGGAAAAGGAAGTCT-CAAGGGTCAAAGCCGACAGGTAGACTTGAGGGTAAAAGAAGTC
338905 T
129 T
* * *
338906 CCAGGGTCAGAGCCGACAAGCAGACTTAAGGGTAAAG-AAGTCTC
1 CCAGGGACAAAGCCGACAGGCAGACTTAA-GG-AAAGAAAGTCTC
338950 TAGGGATAAA
Statistics
Matches: 1144, Mismatches: 169, Indels: 65
0.83 0.12 0.05
Matches are distributed among these distances:
127 1 0.00
128 171 0.15
129 136 0.12
130 404 0.35
131 218 0.19
132 195 0.17
133 19 0.02
ACGTcount: A:0.40, C:0.17, G:0.28, T:0.15
Consensus pattern (129 bp):
CCAGGGACAAAGCCGACAGGCAGACTTAAGGAAAGAAAGTCTCCAAGGTCAAAGTCGACAGGCAG
ACTTAAGGAAAAGGAAGTCTCAAGGGTCAAAGCCGACAGGTAGACTTGAGGGTAAAAGAAGTCT
Found at i:338702 original size:258 final size:259
Alignment explanation
Indices: 337475--339020 Score: 1564
Period size: 258 Copynumber: 5.9 Consensus size: 259
337465 AAGAATCTTA
* * * * * * * * *
337475 CCAGGGACAAAGCTGACAGGTAAAC-AAAGGGAAAGAAAGTTTTCAGGGTCAAAACCGATAGGCA
1 CCAGGGACAAAGCTGACAGGCAGACTTAAGGAAAAG-AAGTCTCCAAGGTCAAAGCCGACAGGCA
* * * * *
337539 AACTTAAAGATAAAGGAAGTCTCCAAGGTCAAAGCCAACAGGTAGACTTGAGGGTAAAGGAAGTC
65 GACTT-AAG-GAAAGGAAGTCTCCAAGGTCAAAGCCGACAGATAGACTTGAGGGAAAAGGAAGTC
* * * * * * * *
337604 TCTAGGGACAAAGCTGACTGGCAGACTTGAGGGTAAAAGAAGTCTTCAGGGACAAAGTCGACTAG
128 TCCAGGGACAAAGCCGACAGGCAGACTT-AAGGTAAAGGAAGTCTCCAGGGTCAAAGTCGAC-AA
* * * * * * *
337669 GCAAACTT-AAG-GAAATGAAGTCTCCAGGGTCAAAGCTGACAGGCAGACTTGAGGGTAAAGGAA
191 GCAAACTTAAAGATAAAGGAAGTCTCTAAGGTCAAAGCTAACAGGTAGACTTGAGGGAAAAGGAA
337732 GTCT
256 GTCT
* * * * * * *
337736 CTAGGGATAAAG-TCGACAGGTAGAGTTGAGGGTAAAAGAAGTCTCTACA-GACAAAGCCGACAG
1 CCAGGGACAAAGCT-GACAGGCAGACTT-AAGG-AAAAGAAGTCTCCA-AGGTCAAAGCCGACAG
* * * * * *
337799 ACAGACTTAAGGAAAAGAAAGTCTCCAGGGTCAAAGCCGACAGGA-AAACTTAAGGGTAAAGGAA
62 GCAGACTTAAGG-AAAGGAAGTCTCCAAGGTCAAAGCCGACA-GATAGACTTGAGGGAAAAGGAA
* * * * * * * * **
337863 GTCTCTAGGGACAAAGCTGACAGGCAGACTTGAGGGCAAAAGAAGTCTTCAAGGACAAAACCGAC
125 GTCTCCAGGGACAAAGCCGACAGGCAGACTT-AAGGTAAAGGAAGTCTCCAGGGTCAAAGTCGAC
* * * * * * * ** *
337928 AAGCATACTTGAGGGTAAAAGAAGTCTCCAAGGACAAAGCCGACAGGTAGACTTGAGGGAAAAAG
189 AAGCAAACTTAAAGATAAAGGAAGTCTCTAAGGTCAAAGCTAACAGGTAGACTTGAGGGAAAAGG
337993 AAGTCT
254 AAGTCT
* * * * * * *
337999 CCAGGGTCAAAGCTGACAAGTAGACTTGAGGGTAAAGGAAGTCTCCAAGGACAAAGCTGACAGGC
1 CCAGGGACAAAGCTGACAGGCAGACTT-AAGG-AAAAGAAGTCTCCAAGGTCAAAGCCGACAGGC
* * * * * *
338064 AGACTTGAGGGAAAAAGAAGTCTCTAGGGACAAAGCCGACAGGTAGACTTGAGGGTAAAA-GAAG
64 AGACTT-AAGG-AAAGGAAGTCTCCAAGGTCAAAGCCGACAGATAGACTTGAGGG-AAAAGGAAG
* * * * * *
338128 TCTCCAAGGACAAAGCCAACAGGCAGACTTAAGG-AAAGAAAGTCTCCAAGGTCAAAGTCGATAG
126 TCTCCAGGGACAAAGCCGACAGGCAGACTTAAGGTAAAGGAAGTCTCCAGGGTCAAAGTCGACAA
* ** * * *
338192 GCAGACTTGAGGGA-AAAGGAAGTCTC-AAGGGACAAAG-TCGACAGGTAGACTTAAGGGTAAAA
191 GCAAACTT-AAAGATAAAGGAAGTCTCTAA-GGTCAAAGCT-AACAGGTAGACTTGAGGG-AAAA
338254 -GAAGTCT
252 GGAAGTCT
* * * * *
338261 CCAGGGACAAAGCCGACAGGCAGACTTAAGGAAAGGAAGTCTCCAAAGTTAAAGCCGACAAGCAG
1 CCAGGGACAAAGCTGACAGGCAGACTTAAGGAAAAGAAGTCTCCAAGGTCAAAGCCGACAGGCAG
* ** * * ** * *
338326 ACTTGAGGATAAAAAAGTCTCCAGGGACAAAGTTGACAGGTAGACTTGAGGGAAAAAGAAGTCTC
66 ACTTAAGGA-AAGGAAGTCTCCAAGGTCAAAGCCGACAGATAGACTTGAGGGAAAAGGAAGTCTC
* *
338391 CAGGGATAAAACCGACAGGCAGACTTAAGG-AAAGGAAGTCTCCAGGGTCAAAGTCGACAAGCAA
130 CAGGGACAAAGCCGACAGGCAGACTTAAGGTAAAGGAAGTCTCCAGGGTCAAAGTCGACAAGCAA
* *
338455 ACTTAAAGATAAAGGAAGTCTCTAGGGTCAAAGCTAACAGGTAAACTTGAGGGAAAAGGAAGTCT
195 ACTTAAAGATAAAGGAAGTCTCTAAGGTCAAAGCTAACAGGTAGACTTGAGGGAAAAGGAAGTCT
* * * *
338520 CCAAGGACAAAGCTGATAGGCAGACTTAAGGAAAAGAAGTCTCCAAGGTCAAAGTCAACAGGCAG
1 CCAGGGACAAAGCTGACAGGCAGACTTAAGGAAAAGAAGTCTCCAAGGTCAAAGCCGACAGGCAG
*
338585 ACTTAAGGAAAGGAAGTCTCCAAGGTCAAAGCCGACAGACAGACTTGAGGGAAAAGGAAGTCTCC
66 ACTTAAGGAAAGGAAGTCTCCAAGGTCAAAGCCGACAGATAGACTTGAGGGAAAAGGAAGTCTCC
* *
338650 AGGGATAAAACCGACAGGCAGACTTAAGG-AAAGGAAGTCTCCAGGGTCAAAGTCGACAAGCAAA
131 AGGGACAAAGCCGACAGGCAGACTTAAGGTAAAGGAAGTCTCCAGGGTCAAAGTCGACAAGCAAA
*
338714 CTTAAAGATAAAGGAAGTCTTTAAGGTCAAAGCTAACAGGTAGACTTGAGGGAAAAGGAAGTCT
196 CTTAAAGATAAAGGAAGTCTCTAAGGTCAAAGCTAACAGGTAGACTTGAGGGAAAAGGAAGTCT
* * *
338778 CCAAGGACAAAGCTGATAGGCAGACTTAAGGAAAAGAAGTCTCCAAGGTCAAAGTCGACAGGCAG
1 CCAGGGACAAAGCTGACAGGCAGACTTAAGGAAAAGAAGTCTCCAAGGTCAAAGCCGACAGGCAG
* *
338843 ACTTAAGGAAAGGAAGTCTCCAAGGTCAAAGCCGACAGACAGACTT-AAGGATAAAGGAAGTCTC
66 ACTTAAGGAAAGGAAGTCTCCAAGGTCAAAGCCGACAGATAGACTTGAGGGA-AAAGGAAGTCTC
* * * * * *
338907 CAGGGTCAGAGCCGACAAGCAGACTTAAGGGTAAA-GAAGTCTCTAGGGAT-AAAGCCAACAAGC
130 CAGGGACAAAGCCGACAGGCAGACTTAA-GGTAAAGGAAGTCTCCAGGG-TCAAAGTCGACAAGC
* * * * **
338970 AGACTTAAA-A-AAAAGAAGTCTTTAAGGTCAAAGCTAATAGACAGACTTGAG
193 AAACTTAAAGATAAAGGAAGTCTCTAAGGTCAAAGCTAACAGGTAGACTTGAG
339021 AATGCATGAT
Statistics
Matches: 1111, Mismatches: 146, Indels: 60
0.84 0.11 0.05
Matches are distributed among these distances:
257 41 0.04
258 330 0.30
259 245 0.22
260 40 0.04
261 32 0.03
262 204 0.18
263 143 0.13
264 73 0.07
265 3 0.00
ACGTcount: A:0.40, C:0.17, G:0.28, T:0.15
Consensus pattern (259 bp):
CCAGGGACAAAGCTGACAGGCAGACTTAAGGAAAAGAAGTCTCCAAGGTCAAAGCCGACAGGCAG
ACTTAAGGAAAGGAAGTCTCCAAGGTCAAAGCCGACAGATAGACTTGAGGGAAAAGGAAGTCTCC
AGGGACAAAGCCGACAGGCAGACTTAAGGTAAAGGAAGTCTCCAGGGTCAAAGTCGACAAGCAAA
CTTAAAGATAAAGGAAGTCTCTAAGGTCAAAGCTAACAGGTAGACTTGAGGGAAAAGGAAGTCT
Found at i:351684 original size:7 final size:7
Alignment explanation
Indices: 351672--351717 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
351662 TGAAAAAGAA
351672 TTTATTT
1 TTTATTT
351679 TTTATTT
1 TTTATTT
*
351686 TAT-TTT
1 TTTATTT
351692 TTTATTTT
1 TTTA-TTT
351700 TTTATTTT
1 TTTA-TTT
351708 TTTATTT
1 TTTATTT
351715 TTT
1 TTT
351718 TAAATTTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 5 0.14
7 15 0.43
8 15 0.43
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTATTT
Found at i:351696 original size:8 final size:8
Alignment explanation
Indices: 351683--351719 Score: 74
Period size: 8 Copynumber: 4.6 Consensus size: 8
351673 TTATTTTTTA
351683 TTTTATTT
1 TTTTATTT
351691 TTTTATTT
1 TTTTATTT
351699 TTTTATTT
1 TTTTATTT
351707 TTTTATTT
1 TTTTATTT
351715 TTTTA
1 TTTTA
351720 AATTTTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTATTT
Found at i:351725 original size:16 final size:16
Alignment explanation
Indices: 351690--351730 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
351680 TTATTTTATT
**
351690 TTTTTATTTTTTTATT
1 TTTTTATTTTTTTAAA
351706 TTTTTATTTTTTTAAA
1 TTTTTATTTTTTTAAA
*
351722 TTTTAATTT
1 TTTTTATTT
351731 CATACCTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTATTTTTTTAAA
Found at i:351725 original size:24 final size:24
Alignment explanation
Indices: 351683--351730 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
351673 TTATTTTTTA
** *
351683 TTTTATTTTTTTATTTTTTTATTT
1 TTTTATTTTTTTAAATTTTAATTT
351707 TTTTATTTTTTTAAATTTTAATTT
1 TTTTATTTTTTTAAATTTTAATTT
351731 CATACCTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (24 bp):
TTTTATTTTTTTAAATTTTAATTT
Found at i:352416 original size:13 final size:13
Alignment explanation
Indices: 352392--352432 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
352382 TCTTCCCTTT
352392 TGCTCATCCTTTGC
1 TGCTC-TCCTTTGC
352406 TGCTCTCCTTTGC
1 TGCTCTCCTTTGC
*
352419 TACTCTCCTTTGC
1 TGCTCTCCTTTGC
352432 T
1 T
352433 CGTATTGCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 21 0.81
14 5 0.19
ACGTcount: A:0.05, C:0.37, G:0.12, T:0.46
Consensus pattern (13 bp):
TGCTCTCCTTTGC
Found at i:354082 original size:8 final size:8
Alignment explanation
Indices: 354079--354111 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
354069 TCTTTTTTAA
354079 TTTTTGAT
1 TTTTTGAT
354087 TTTTTGA-
1 TTTTTGAT
354094 TTTTTGAT
1 TTTTTGAT
*
354102 TTTTTTAT
1 TTTTTGAT
354110 TT
1 TT
354112 GATTATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (8 bp):
TTTTTGAT
Found at i:354089 original size:15 final size:15
Alignment explanation
Indices: 354071--354111 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
354061 TTTCTTTTTC
354071 TTTTTTAATTTTTGA
1 TTTTTTAATTTTTGA
*
354086 TTTTTTGATTTTTGA
1 TTTTTTAATTTTTGA
*
354101 TTTTTTTATTT
1 TTTTTTAATTT
354112 GATTATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (15 bp):
TTTTTTAATTTTTGA
Found at i:354118 original size:8 final size:7
Alignment explanation
Indices: 354072--354105 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
354062 TTCTTTTTCT
*
354072 TTTTTAA
1 TTTTTGA
354079 TTTTTGA
1 TTTTTGA
354086 TTTTTTGA
1 -TTTTTGA
354094 TTTTTGA
1 TTTTTGA
354101 TTTTT
1 TTTTT
354106 TTATTTGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (7 bp):
TTTTTGA
Done.