Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 12 of 105
Found at i:2254113 original size:64 final size:64
Alignment explanation
Indices: 2253993--2254131 Score: 170
Period size: 64 Copynumber: 2.2 Consensus size: 64
2253983 GAAATTTTGA
* * * * **
2253993 ATTTTATTTTCAAACCTATGGTTCAATCTTAGTCATTCGTTTTGATCTCGACTCAGTCCAAATC
1 ATTTTATTTTTAAACCTACGGTTCAATCTTAGTCACTCATTTCAATCTCGACTCAGTCCAAATC
* * * * * *
2254057 ATTTTATTTTTAGATCTACGGTTCAATCTTGGTCACTCATTTCAATCTTGATTCAGTCCATATC
1 ATTTTATTTTTAAACCTACGGTTCAATCTTAGTCACTCATTTCAATCTCGACTCAGTCCAAATC
2254121 ATTTTATTTTT
1 ATTTTATTTTT
2254132 CTAACTCATG
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.24, C:0.19, G:0.10, T:0.47
Consensus pattern (64 bp):
ATTTTATTTTTAAACCTACGGTTCAATCTTAGTCACTCATTTCAATCTCGACTCAGTCCAAATC
Found at i:2254360 original size:64 final size:65
Alignment explanation
Indices: 2253993--2254392 Score: 161
Period size: 64 Copynumber: 6.2 Consensus size: 65
2253983 GAAATTTTGA
* * * ** * ** * *
2253993 ATTTTA-TTTTCAAACCTATGGTTCAATCTTAGTCATTCGTTTTGATCTCGACTCAGTCCAAATC
1 ATTTTATTTTTCTAACCTGTGATTCAATCTCGGTCACTCGTTTCAATCTCGACTCAATCCAAATT
* ** * * * * * * *
2254057 ATTTTA-TTTT-TAGATCTACGGTTCAATCTTGGTCACTCATTTCAATCTTGATTCAGTCCATAT
1 ATTTTATTTTTCTA-ACCTGTGATTCAATCTCGGTCACTCGTTTCAATCTCGACTCAATCCAAAT
*
2254120 C
65 T
* ** * * * * ** *
2254121 ATTTTATTTTTCTAA-CTCATGATTCAATCTCGGTCACCTATTTTTAGTCTCGGCTTAATTTAGA
1 ATTTTATTTTTCTAACCT-GTGATTCAATCTCGGTCA-CTCGTTTCAATCTCGACTCAATCCAAA
*
2254185 TC
64 TT
** * * * * * * * * *
2254187 ATTTTTACTTTTT-TGTCTTAT-AGTTTAATCTCGATCACT-TTTTCTGATCGCAACTCAGTCCA
1 A-TTTTA-TTTTTCTAACCTGTGA-TTCAATCTCGGTCACTCGTTTC-AATCTCGACTCAATCCA
2254249 AATT
62 AATT
* * * *
2254253 ATTTTATTTTTCTGACTTGTGGTTCAATCTCGGTCACTCGTTTCAATCTCGACTCAATCCAGATT
1 ATTTTATTTTTCTAACCTGTGATTCAATCTCGGTCACTCGTTTCAATCTCGACTCAATCCAAATT
* * * * * * *
2254318 ATTTTA-TTTTCTAACCTGTGATTTAATC-CTGGTCACTTGTTTCGATATCAACTCGATCCATAT
1 ATTTTATTTTTCTAACCTGTGATTCAATCTC-GGTCACTCGTTTCAATCTCGACTCAATCCAAAT
*
2254381 C
65 T
*
2254382 ATTTGATTTTT
1 ATTTTATTTTT
2254393 TTTGACTTAC
Statistics
Matches: 255, Mismatches: 66, Indels: 29
0.73 0.19 0.08
Matches are distributed among these distances:
63 2 0.01
64 114 0.45
65 75 0.29
66 38 0.15
67 20 0.08
68 6 0.02
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (65 bp):
ATTTTATTTTTCTAACCTGTGATTCAATCTCGGTCACTCGTTTCAATCTCGACTCAATCCAAATT
Found at i:2254497 original size:64 final size:64
Alignment explanation
Indices: 2254421--2254644 Score: 245
Period size: 64 Copynumber: 3.5 Consensus size: 64
2254411 TCCAATCATC
* **
2254421 ATCTCAGCTCAATCCAGATCATTTTATTTTCAGACATATGATTTAATCTTGATCACTCATTTCG
1 ATCTCAGCTCAATCCAAATCATTTTATTTTCAGACATATGATTTAATCCAGATCACTCATTTCG
* * * * *
2254485 ATCTCGGCTCAATCCAAATAATTTTATTTTCAAACATGTGATTTAATCCAGGTCACTCATTTCG
1 ATCTCAGCTCAATCCAAATCATTTTATTTTCAGACATATGATTTAATCCAGATCACTCATTTCG
* * * * * *
2254549 ATCTC-GACTCAGTTCAAATCATTTTATTTTTAGACCTATGGTTCAATCCCA-ATCACTCATTTC
1 ATCTCAG-CTCAATCCAAATCATTTTATTTTCAGACATATGATTTAAT-CCAGATCACTCATTTC
*
2254612 A
64 G
* * *
2254613 ATCTTAGTTCAATCTAAATCATTTTAATTTTC
1 ATCTCAGCTCAATCCAAATCATTTT-ATTTTC
2254645 TAACTCGCAG
Statistics
Matches: 131, Mismatches: 25, Indels: 7
0.80 0.15 0.04
Matches are distributed among these distances:
63 1 0.01
64 121 0.92
65 9 0.07
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (64 bp):
ATCTCAGCTCAATCCAAATCATTTTATTTTCAGACATATGATTTAATCCAGATCACTCATTTCG
Found at i:2254923 original size:3 final size:3
Alignment explanation
Indices: 2254917--2254942 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2254907 ATTATTATTA
2254917 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
2254943 ATTAAAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:2258762 original size:21 final size:22
Alignment explanation
Indices: 2258724--2258765 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2258714 TTTTTTTTTT
*
2258724 TGTTTAAGCTCTTTATATCAAA
1 TGTTGAAGCTCTTTATATCAAA
2258746 TGTTGAAGCTC-TTATATCAA
1 TGTTGAAGCTCTTTATATCAA
2258766 TTGCTATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (22 bp):
TGTTGAAGCTCTTTATATCAAA
Found at i:2259411 original size:151 final size:150
Alignment explanation
Indices: 2259136--2259432 Score: 436
Period size: 151 Copynumber: 1.9 Consensus size: 150
2259126 TTCAAGCTTG
* * * *
2259136 TACCAAATATTAAAGATACCATTTGTTAAAGATATGTTATCACAAATCATACTAATTTTTATCAC
1 TACCAAATATTAAAGATACCAATTGTTAAAGATAAGTTATCACAAATCATACCAATTGTTATCAC
*
2259201 AAAATGAATATTAATCTAAGCAAAATTATAAAATTTTTTCTCTTTTGAACAAAAGAAGAAGTGAA
66 AAAATAAATATTAATCTAAGCAAAATTATAAAATTTTTTCTCTTTTGAAC-AAAGAAGAAGTGAA
*
2259266 ATAATTTAAAGCACAAACTTA
130 ACAATTTAAAGCACAAACTTA
* *
2259287 TACCAAATATTAAGGATATCAATTGTTAAAGATAAGTTATCACAAATCATACCAATTGTTATCAC
1 TACCAAATATTAAAGATACCAATTGTTAAAGATAAGTTATCACAAATCATACCAATTGTTATCAC
*
2259352 AAAATAAATCATTTTAATCTAAGCAAAATTGT-AAATTTTTTCCTCCTTTT-AACAAAAGAAGAA
66 AAAATAAAT-A--TTAATCTAAGCAAAATTATAAAATTTTTT-CT-CTTTTGAAC-AAAGAAGAA
2259415 GTGAAACAATTTAAAGCA
125 GTGAAACAATTTAAAGCA
2259433 TGCAATTTTG
Statistics
Matches: 132, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
151 67 0.51
152 1 0.01
153 9 0.07
154 50 0.38
155 5 0.04
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (150 bp):
TACCAAATATTAAAGATACCAATTGTTAAAGATAAGTTATCACAAATCATACCAATTGTTATCAC
AAAATAAATATTAATCTAAGCAAAATTATAAAATTTTTTCTCTTTTGAACAAAGAAGAAGTGAAA
CAATTTAAAGCACAAACTTA
Found at i:2264621 original size:30 final size:30
Alignment explanation
Indices: 2264583--2264666 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 30
2264573 TCTTGTAGTT
* *
2264583 CAAAGAAGTGAAGGAAAATGGTGTTGCAGC
1 CAAAGAAGTGAAAGAAAATGGTGTGGCAGC
* *
2264613 CAACGAAGTGAAAGAAAATGGTGTGGCAGT
1 CAAAGAAGTGAAAGAAAATGGTGTGGCAGC
*
2264643 CAAAGAAGTGAAATAAAATGGTGT
1 CAAAGAAGTGAAAGAAAATGGTGT
2264667 AACCAATTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.43, C:0.08, G:0.31, T:0.18
Consensus pattern (30 bp):
CAAAGAAGTGAAAGAAAATGGTGTGGCAGC
Found at i:2265861 original size:17 final size:17
Alignment explanation
Indices: 2265839--2265876 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
2265829 TTTCAGTAGT
2265839 AGTAGTGAGGAAATTTC
1 AGTAGTGAGGAAATTTC
2265856 AGTAGTGAGGAAATTTC
1 AGTAGTGAGGAAATTTC
2265873 AGTA
1 AGTA
2265877 CCTATCTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.37, C:0.05, G:0.29, T:0.29
Consensus pattern (17 bp):
AGTAGTGAGGAAATTTC
Found at i:2270614 original size:61 final size:61
Alignment explanation
Indices: 2270519--2270644 Score: 153
Period size: 61 Copynumber: 2.1 Consensus size: 61
2270509 CTAATTCTTG
* * * *
2270519 TTGTACTAACAGATTTTAAATCATACTTTATCATAATATAAGAATCTCGCTCTATTACCAC
1 TTGTACTAACAGATCTTAAATCATACTTTATCATAAAATAAAAATCTCGCTCTAATACCAC
* * ** * * *
2270580 TTGTACTAATAGATCTTGAATTGTACTTTGTCATAAAATAAAAATTTCGTTCTAATACCAC
1 TTGTACTAACAGATCTTAAATCATACTTTATCATAAAATAAAAATCTCGCTCTAATACCAC
2270641 TTGT
1 TTGT
2270645 TAGAAAATCA
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.40
Consensus pattern (61 bp):
TTGTACTAACAGATCTTAAATCATACTTTATCATAAAATAAAAATCTCGCTCTAATACCAC
Found at i:2270729 original size:40 final size:40
Alignment explanation
Indices: 2270674--2270764 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
2270664 TGCAGTACTG
*
2270674 ACATACACAA-ACAATAGAGCAAGCCCAAAATAAGAATAA-A
1 ACATACA-AATACAATAGAGCAAG-CCAAAACAAGAATAAGA
**
2270714 ACATACAAATACAATAGAGCAAGCTTAAACAAGAATAAGA
1 ACATACAAATACAATAGAGCAAGCCAAAACAAGAATAAGA
*
2270754 ACATATAAATA
1 ACATACAAATA
2270765 TATTTGTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
39 14 0.31
40 31 0.69
ACGTcount: A:0.59, C:0.16, G:0.10, T:0.14
Consensus pattern (40 bp):
ACATACAAATACAATAGAGCAAGCCAAAACAAGAATAAGA
Found at i:2273481 original size:25 final size:25
Alignment explanation
Indices: 2273443--2273490 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
2273433 ATATATTTTA
2273443 TTTTAATTTAAAAAATTTAATAATT
1 TTTTAATTTAAAAAATTTAATAATT
* * * *
2273468 TTTTTATTTTAAAATTTTCATAA
1 TTTTAATTTAAAAAATTTAATAA
2273491 CAATAAAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTTAATTTAAAAAATTTAATAATT
Found at i:2273724 original size:7 final size:7
Alignment explanation
Indices: 2273712--2273737 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2273702 TTAAAATTTT
2273712 AATTAAA
1 AATTAAA
2273719 AATTAAA
1 AATTAAA
2273726 AATTAAA
1 AATTAAA
2273733 AATTA
1 AATTA
2273738 TAATTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
AATTAAA
Found at i:2273725 original size:27 final size:26
Alignment explanation
Indices: 2273691--2273792 Score: 73
Period size: 27 Copynumber: 3.6 Consensus size: 26
2273681 AATTAAAATG
* *
2273691 AAAATAAATACTT-AAAATTTTAATTA
1 AAAATAAA-AATTAAAAATTATAATTA
2273717 AAAATTAAAAATTAAAAATTATAATTA
1 AAAA-TAAAAATTAAAAATTATAATTA
*
2273744 ATTTAGAATAAAAATAAAAAATT-TAATTA
1 A---A-AATAAAAATTAAAAATTATAATTA
2273773 ATTATAATAAAACATTAAAA
1 A--A-AATAAAA-ATTAAAA
2273793 TTTTAAATAA
Statistics
Matches: 64, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
26 7 0.11
27 17 0.27
28 10 0.16
29 13 0.20
30 15 0.23
31 2 0.03
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (26 bp):
AAAATAAAAATTAAAAATTATAATTA
Found at i:2273805 original size:29 final size:28
Alignment explanation
Indices: 2273693--2273806 Score: 108
Period size: 29 Copynumber: 4.0 Consensus size: 28
2273683 TTAAAATGAA
*
2273693 AATAAATACTTAAAATTTTAATTAA--A-
1 AATAAA-AATTAAAATTTTAATTAATTAT
* *
2273719 AATTAAAAATTAAAAATTATAATTAATTTAG
1 AA-TAAAAATT-AAAATTTTAATTAA-TTAT
* *
2273750 AATAAAAATAAAAAATTTAATTAATTAT
1 AATAAAAATTAAAATTTTAATTAATTAT
*
2273778 AATAAAACATTAAAATTTTAAATAATTAT
1 AATAAAA-ATTAAAATTTTAATTAATTAT
2273807 CAAATTTTTC
Statistics
Matches: 72, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
26 5 0.07
27 17 0.24
28 10 0.14
29 30 0.42
30 8 0.11
31 2 0.03
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.38
Consensus pattern (28 bp):
AATAAAAATTAAAATTTTAATTAATTAT
Found at i:2274228 original size:6 final size:6
Alignment explanation
Indices: 2274217--2274241 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2274207 ATACATAAAA
2274217 ATTTAT ATTTAT ATTTAT ATTTAT A
1 ATTTAT ATTTAT ATTTAT ATTTAT A
2274242 AAATAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATTTAT
Found at i:2277412 original size:20 final size:20
Alignment explanation
Indices: 2277387--2277429 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
2277377 TCTATAGTGC
2277387 ACAGAATCTGATTAAAATGG
1 ACAGAATCTGATTAAAATGG
2277407 ACAGAATCTGATTAAAATGG
1 ACAGAATCTGATTAAAATGG
2277427 ACA
1 ACA
2277430 CAGCTATCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.23
Consensus pattern (20 bp):
ACAGAATCTGATTAAAATGG
Found at i:2280264 original size:11 final size:11
Alignment explanation
Indices: 2280234--2280291 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
2280224 TATATGTATT
**
2280234 ATATTAATAAA
1 ATATTAATTTA
2280245 ATATT-ATTTA
1 ATATTAATTTA
2280255 ATATTAATTT-
1 ATATTAATTTA
2280265 ATATATAA-TTA
1 ATAT-TAATTTA
2280276 ATATATAATTT-
1 ATAT-TAATTTA
2280287 ATATT
1 ATATT
2280292 TAAAAAATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
10 15 0.37
11 24 0.59
12 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATATTAATTTA
Found at i:2284399 original size:15 final size:15
Alignment explanation
Indices: 2284379--2284414 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2284369 ATGACCTATT
2284379 TTATTTTTAGTTTTA
1 TTATTTTTAGTTTTA
* *
2284394 TTATTTTTATTTTTG
1 TTATTTTTAGTTTTA
2284409 TTATTT
1 TTATTT
2284415 ATATATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (15 bp):
TTATTTTTAGTTTTA
Found at i:2284494 original size:28 final size:27
Alignment explanation
Indices: 2284448--2284537 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 27
2284438 ATATATTTAG
*
2284448 TTATCCATTAATATTA-TTTTTTATTAT
1 TTATCTATTAATATTATTTTTTTA-TAT
*
2284475 TTATCTATTAATGTATATTTTTTTATAT
1 TTATCTATTAATAT-TATTTTTTTATAT
*
2284503 TTATCTATTATTATTATTATTATTT-TGAT
1 TTATCTATTAATATTATT-TT-TTTAT-AT
2284532 TTATCT
1 TTATCT
2284538 GTTCTGAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
27 16 0.30
28 20 0.37
29 18 0.33
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (27 bp):
TTATCTATTAATATTATTTTTTTATAT
Found at i:2285313 original size:19 final size:19
Alignment explanation
Indices: 2285276--2285313 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2285266 TTTTTTTTTC
*
2285276 TTATTTATTATTATTATTA
1 TTATTTATTATTATGATTA
2285295 TTATTTATTGATTA-GATTA
1 TTATTTATT-ATTATGATTA
2285314 GAATTATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
TTATTTATTATTATGATTA
Found at i:2285432 original size:57 final size:57
Alignment explanation
Indices: 2285370--2285660 Score: 347
Period size: 58 Copynumber: 5.1 Consensus size: 57
2285360 GATTTTGTTT
* *
2285370 AAATAAAATTCTAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTA
1 AAATAAATTTCTAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTA
* * * * *
2285427 AAATAAGTTTTTTTAAAAAATATTTTTTAGAAAAAGTTGAAAGTATCAATTTTCCTTGA
1 AAATAA-ATTTCTAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT-A
* *
2285486 AAATAAGTTTTCT-AAAAAATATTTTTGAGAAAAAATTGAAAGTATCAA-TTTTCTTTAA
1 AAATAA-ATTTCTAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTC-TT-A
* * * *
2285544 AAATAATTTTCTAAAAAAATGTTTTTGAGAAAAAGTTGAAAATATCAATTTTTCTCA
1 AAATAAATTTCTAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTA
* * *
2285601 AAATTAAAGTTTC-AGAAAAATA-TTTTGAGAAAAAGTTGAAAGTACCAATTTTTCTAA
1 AAA-TAAA-TTTCTAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTA
2285658 AAA
1 AAA
2285661 GAAAAAAACA
Statistics
Matches: 205, Mismatches: 22, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
57 55 0.27
58 128 0.62
59 22 0.11
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (57 bp):
AAATAAATTTCTAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTA
Found at i:2285442 original size:15 final size:14
Alignment explanation
Indices: 2285418--2285464 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 14
2285408 AAAGTATCAA
2285418 TTTTTCTTAAAATAAG
1 TTTTT-TTAAAA-AAG
2285434 TTTTTTTAAAAAA-
1 TTTTTTTAAAAAAG
2285447 TATTTTTTAGAAAAAG
1 T-TTTTTTA-AAAAAG
2285463 TT
1 TT
2285465 GAAAGTATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
13 1 0.04
14 9 0.32
15 12 0.43
16 6 0.21
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.51
Consensus pattern (14 bp):
TTTTTTTAAAAAAG
Found at i:2297146 original size:15 final size:15
Alignment explanation
Indices: 2297126--2297161 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2297116 ATGGCCTATT
2297126 TTATTTTTAGTTTTA
1 TTATTTTTAGTTTTA
* *
2297141 TTATTTTTATTTTTG
1 TTATTTTTAGTTTTA
2297156 TTATTT
1 TTATTT
2297162 ATATATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (15 bp):
TTATTTTTAGTTTTA
Found at i:2297239 original size:28 final size:27
Alignment explanation
Indices: 2297193--2297267 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 27
2297183 ATATATTTAG
*
2297193 TTATCCATTAATATTA-TTTTTTATTAT
1 TTATCTATTAATATTATTTTTTTA-TAT
*
2297220 TTATCTATTAATGTATATTTTTTTATAT
1 TTATCTATTAATAT-TATTTTTTTATAT
*
2297248 TTATCTATTATTATTATTTT
1 TTATCTATTAATATTATTTT
2297268 GATTTATCCG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 18 0.43
28 17 0.40
29 7 0.17
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.65
Consensus pattern (27 bp):
TTATCTATTAATATTATTTTTTTATAT
Found at i:2298059 original size:22 final size:22
Alignment explanation
Indices: 2298019--2298068 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2298009 TTTTTTTTTC
* **
2298019 TTATTTATTATTATTATTATTA
1 TTATTTATTATTATGATTAGAA
2298041 TTATTTATTTATTA-GATTAGAA
1 TTATTTA-TTATTATGATTAGAA
2298063 TTATTT
1 TTATTT
2298069 GATATTCCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
TTATTTATTATTATGATTAGAA
Found at i:2301133 original size:19 final size:15
Alignment explanation
Indices: 2301090--2301135 Score: 83
Period size: 15 Copynumber: 3.1 Consensus size: 15
2301080 TTTACATACA
2301090 TGCATTTTCATTCAT
1 TGCATTTTCATTCAT
2301105 TGCATTTTCATTCAT
1 TGCATTTTCATTCAT
*
2301120 TGCATTCTCATTCAT
1 TGCATTTTCATTCAT
2301135 T
1 T
2301136 ACACTTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.20, C:0.22, G:0.07, T:0.52
Consensus pattern (15 bp):
TGCATTTTCATTCAT
Found at i:2309490 original size:45 final size:44
Alignment explanation
Indices: 2309419--2309607 Score: 245
Period size: 44 Copynumber: 4.3 Consensus size: 44
2309409 AAGTTATGGT
* * *
2309419 GCCTTTGTTTAAAAGAGCTTTATTTATTTTTTCAAAGTCGTTGA
1 GCCTTTATTTAGAGGAGCTTTATTTATTTTTTCAAAGTCGTTGA
* * * *
2309463 GCCTTCTGTTTAGAGGAGCTTTGTTTATCTTTCCAAAGTCGTTGA
1 GCCTT-TATTTAGAGGAGCTTTATTTATTTTTTCAAAGTCGTTGA
* * * *
2309508 ACCTTTATTTAGAGGATCTTTATCTATTTTTTCAAAGTCATTGA
1 GCCTTTATTTAGAGGAGCTTTATTTATTTTTTCAAAGTCGTTGA
*
2309552 GCCTCTATTTAGAGGAGCTTTATTTA-TTTTTCAAAGTCGTTGA
1 GCCTTTATTTAGAGGAGCTTTATTTATTTTTTCAAAGTCGTTGA
*
2309595 GCTTTTATTTAGA
1 GCCTTTATTTAGA
2309608 AGAGTTTTGA
Statistics
Matches: 124, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
43 27 0.22
44 59 0.48
45 38 0.31
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.46
Consensus pattern (44 bp):
GCCTTTATTTAGAGGAGCTTTATTTATTTTTTCAAAGTCGTTGA
Found at i:2309536 original size:89 final size:87
Alignment explanation
Indices: 2309436--2309607 Score: 263
Period size: 89 Copynumber: 2.0 Consensus size: 87
2309426 TTTAAAAGAG
* * * *
2309436 CTTTATTTATTTTTTCAAAGTCGTTGAGCCTTCTGTTTAGAGGAGCTTTGTTTATCTTTCCAAAG
1 CTTTATCTATTTTTTCAAAGTCATTGAGCC-TCTATTTAGAGGAGCTTTATTTAT-TTTCCAAAG
2309501 TCGTTGAACCTTTATTTAGAGGAT
64 TCGTTGAACCTTTATTTAGAGGAT
*
2309525 CTTTATCTATTTTTTCAAAGTCATTGAGCCTCTATTTAGAGGAGCTTTATTTATTTTTCAAAGTC
1 CTTTATCTATTTTTTCAAAGTCATTGAGCCTCTATTTAGAGGAGCTTTATTTATTTTCCAAAGTC
* *
2309590 GTTGAGCTTTTATTTAGA
66 GTTGAACCTTTATTTAGA
2309608 AGAGTTTTGA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
87 26 0.34
88 22 0.29
89 28 0.37
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.47
Consensus pattern (87 bp):
CTTTATCTATTTTTTCAAAGTCATTGAGCCTCTATTTAGAGGAGCTTTATTTATTTTCCAAAGTC
GTTGAACCTTTATTTAGAGGAT
Found at i:2309815 original size:7 final size:6
Alignment explanation
Indices: 2309794--2309836 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
2309784 AAATGGCCCA
* * *
2309794 TTTTAT TTTTAT TTTTAG TTTTAT TATTTAT ATATAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT T-TTTAT TTTTAT TTTTAT
2309837 CTAATAATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (6 bp):
TTTTAT
Found at i:2309860 original size:24 final size:22
Alignment explanation
Indices: 2309822--2309880 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
2309812 TTTTATTATT
*
2309822 TATATATATTTTTATCTAATAA
1 TATATATATTTTTATCCAATAA
*
2309844 TATATATATTTAGTTATCCATTAA
1 TATATATATTT--TTATCCAATAA
2309868 TAT-TAT-TTTTTAT
1 TATATATATTTTTAT
2309881 TATTTATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 4 0.12
22 14 0.42
23 3 0.09
24 12 0.36
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.58
Consensus pattern (22 bp):
TATATATATTTTTATCCAATAA
Found at i:2309886 original size:31 final size:28
Alignment explanation
Indices: 2309848--2309917 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 28
2309838 TAATAATATA
2309848 TATATTTAGTTATCCATTAATAT-TATTTTT
1 TATATTTA-TTAT--ATTAATATATATTTTT
*
2309878 TATTATTTA-TATATTAATGTATATTTTT
1 TA-TATTTATTATATTAATATATATTTTT
2309906 TATATTTATTAT
1 TATATTTATTAT
2309918 TTTTTTTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
27 13 0.36
28 12 0.33
29 3 0.08
30 2 0.06
31 6 0.17
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (28 bp):
TATATTTATTATATTAATATATATTTTT
Found at i:2309920 original size:16 final size:16
Alignment explanation
Indices: 2309899--2309931 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2309889 TATTAATGTA
2309899 TATTTTTTATATTTAT
1 TATTTTTTATATTTAT
*
2309915 TATTTTTTTTATTTAT
1 TATTTTTTATATTTAT
2309931 T
1 T
2309932 TGTTCTACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
TATTTTTTATATTTAT
Found at i:2309922 original size:18 final size:18
Alignment explanation
Indices: 2309871--2309926 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
2309861 CCATTAATAT
* * *
2309871 TATTTTTTATTATTTATA
1 TATTTATTATTTTTTTTA
* *
2309889 TATTAATGTATATTTTTTA
1 TATTTAT-TATTTTTTTTA
2309908 TATTTATTATTTTTTTTA
1 TATTTATTATTTTTTTTA
2309926 T
1 T
2309927 TTATTTGTTC
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
18 16 0.53
19 14 0.47
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (18 bp):
TATTTATTATTTTTTTTA
Found at i:2310707 original size:9 final size:10
Alignment explanation
Indices: 2310681--2310717 Score: 53
Period size: 9 Copynumber: 4.0 Consensus size: 10
2310671 CCAAAGGTTT
2310681 TTATTTA-T-
1 TTATTTATTA
2310689 TTATTTATTA
1 TTATTTATTA
2310699 TTA-TTATTA
1 TTATTTATTA
2310708 TTATTTATTA
1 TTATTTATTA
2310718 GATTAGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 7 0.27
9 10 0.38
10 9 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTATTTATTA
Found at i:2310775 original size:16 final size:16
Alignment explanation
Indices: 2310744--2310773 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2310734 TATTCCTTAT
2310744 TTTATTTTTATTTTTA
1 TTTATTTTTATTTTTA
2310760 TTTA-TTTTATTTTT
1 TTTATTTTTATTTTT
2310774 TAAATGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTATTTTTATTTTTA
Found at i:2315756 original size:971 final size:972
Alignment explanation
Indices: 2313600--2316519 Score: 5012
Period size: 971 Copynumber: 3.0 Consensus size: 972
2313590 TGGGATACAA
*
2313600 GACAAACTTTCACTCTTATAACTTTACTAACTTTCAATGATGGATTATGAGATTCAAAGTACATC
1 GACAAACTTTCACTCTTATAACTTTACTAACTTTCAATGATGGATTATGAGATTCAAAGTAAATC
* *
2313665 CCTACAAATCCTCTCTTGATTTGAATCTCTAAACACTTCAATAGTATCTGTAAAGTTAACATGCT
66 CCTGCAAATCCTCTCTTGATTTGAATCTCTAAACACTTCAATAGTATCTGTAAAGTTGACATGCT
* ** * *
2313730 TACCTTTTTTCTTTTCCTTTATCATAAAAATCTCAATAACTGAGCCTCCATCAAGCATGTGCAAG
131 TACCCTTTTTCTTTT-CTTCGTCATAAAAATCTCAACAACTGAGCCTCCATCAAGCATGTACAAG
* *
2313795 TGATTTTTGACCTTATTCATTTATAGAATAACACTACCATTCTTGTACACTTTCTACCAATCATT
195 TGATTTTTGACCATATTCATTTATAGAATAACACTACCATTCTTGTACACTTTCAACCAATCATT
*
2313860 ACTATCATAGTATGTGTACCTTTGAAAAGCTAATTCATTCAAAGCAATCAAATTGTAACTATAAC
260 ACTATCATAGTATGTGTACCCTTGAAAAGCTAATTCATTCAAAGCAATCAAATTGTAACTATAAC
* *
2313925 TTAGTACATACTTTACATGACGAAGTGTTCTAACAACTCCATTATGAGATTTAATGTGAACACTC
325 TTAGTACATACTTTACATGACGAAGCGTCCTAACAACTCCATTATGAGATTTAATGTGAACACTC
* *
2313990 TCAATGTTTTGAATCTATACTTTTTCTTTGTTGGCAACCATAATATCTCCATACTTCTTATTTTT
390 TCAATGCTTTGAATCTACACTTTTTCTTTGTTGGCAACCATAATATCTCCATACTTCTT-TTTTT
2314055 TTCAACTTCATAAAGTAACTCCTATCATTATAGACATGAACTATAGTAATTGAATCTAAAACCTA
454 TTCAACTTCATAAAGTAACTCCTATCATTATAGACATGAACTATAGTAATTGAATCTAAAACCTA
2314120 ACCTTTATCACATTTCAAAGTCTGAGTCTTATCCACACAAGTAATCAAAATAACATCATTATCAT
519 ACCTTTATCACATTTCAAAGTCTGAGTCTTATCCACACAAGTAATCAAAATAACATCATTATCAT
* *
2314185 CAGATACAACAACAATAGTATCACTTTTTTCTTCATTTCATTTTTTTTTATCATTTATCCTTTTG
584 CAGATACATCAACAATAGTATCACTTTTTTCTTCATTT-ATTTTTTTTTATCATTTGTCCTTTTG
* * *
2314250 AAAATAACCATATCCCCTCTCAGCTTCTTGCAGTGCACTTGGATATATTCTTTTTCATTACAATA
648 AAAATAGCCATAT-CCCTCTCAGCTTCTTGCAGTGCACTTAGATATGTTCTTTTTCATTACAATA
2314315 ATAACATTCTATATTACTTTAATCTTTGTTTCTTAACTTAGATCTCCTTCTTAATCCATCAATCT
712 ATAACATTCTATATTACTTTAATCTTTGTTTCTTAACTTAGATCTCCTTCTTAATCCATCAATCT
* *
2314380 TTTTTGAGTTATTCGATTAAAACCCTTTACAGCTAGTGCACTTCCTCCAGGTGATGAGTTATATG
777 TTTTTGAGTTATTCGATCAAAACCCTTTACAACTAGTGCACTTCCTCCAGGTGATGAGTTATATG
*
2314445 TTCCCATAAACCTTTCATTCTCATGCAATAGGGCAGTCACATCATCCAACTTCAAAATAGACTTA
842 TTCCCATAAACCTTTCATTCTCACGCAATAGGGCAGTCACATCATCCAACTTCAAAATAGACTTA
* *
2314510 TCCACCAATAAAGTTTGAATTAAAGGTTTATAGGACTTCGGCAAAAATGACAATAAAATTAAAGA
907 TCCACCAACAAAGTTTGAATTAAAGGTTTATAGGACTTCGGCAAAGATGACAATAAAATTAAAGA
2314575 T
972 T
2314576 GACAAACTTTCACTCTTATAACTTTACTAACTTTCAATGATGGATTATGAGATTCAAAGTAAATC
1 GACAAACTTTCACTCTTATAACTTTACTAACTTTCAATGATGGATTATGAGATTCAAAGTAAATC
*
2314641 CCTGTAAATCCTCTCTTGATTTGAATCTCTAAACACTTCAATAGTATCTGTAAAGTTGACATGCT
66 CCTGCAAATCCTCTCTTGATTTGAATCTCTAAACACTTCAATAGTATCTGTAAAGTTGACATGCT
2314706 TA-CCTTTTTCTTTTCTTTCGTCATAAAAATCTCAACAACTGAGCCTCCATCAAGCATGTACAAG
131 TACCCTTTTTCTTTTC-TTCGTCATAAAAATCTCAACAACTGAGCCTCCATCAAGCATGTACAAG
2314770 TGATTTTTGACCATATTCATTTATAGAATAACACTACCATTCTTGTACACTTTCAACCAATCATT
195 TGATTTTTGACCATATTCATTTATAGAATAACACTACCATTCTTGTACACTTTCAACCAATCATT
2314835 ACTATCATAGTATGTGTACCCTTGAAAAGCTAATTCATTCAAAGCAATCAAATTGTAACTATAAC
260 ACTATCATAGTATGTGTACCCTTGAAAAGCTAATTCATTCAAAGCAATCAAATTGTAACTATAAC
2314900 TTAGTACATACTTTACATGACGAAGCGTCCTAACAACTCCATTATGAGATTTAATGTGAACACTC
325 TTAGTACATACTTTACATGACGAAGCGTCCTAACAACTCCATTATGAGATTTAATGTGAACACTC
2314965 TCAATGCTTTGAATCTACACTTTTTCTTTGTTGGCAACCATAATATCTCCATACTT-TTTTTTTT
390 TCAATGCTTTGAATCTACACTTTTTCTTTGTTGGCAACCATAATATCTCCATACTTCTTTTTTTT
*
2315029 TCCAACTTCATAAAGTAACTCATATCATTATAGACATGAACTATAGTAATTGAATCTAAAACCTA
455 T-CAACTTCATAAAGTAACTCCTATCATTATAGACATGAACTATAGTAATTGAATCTAAAACCTA
*
2315094 ACCTTTATCACATTTCAAAGTCTGAGTCTTATCCACACAAGTAATCAAAATAACATCATTATTAT
519 ACCTTTATCACATTTCAAAGTCTGAGTCTTATCCACACAAGTAATCAAAATAACATCATTATCAT
*
2315159 CAGATACATCAACAATAGTATCA-TTTTTT-TTCATTTGA-TTTTTTTTAACATTTGTCCTTTTG
584 CAGATACATCAACAATAGTATCACTTTTTTCTTCATTT-ATTTTTTTTTATCATTTGTCCTTTTG
*
2315221 AAAATAGCTATATCCCT-TCAGCTTCTTGCAGTGCACTTAGATATGTTCTTTTTCATTACAATAA
648 AAAATAGCCATATCCCTCTCAGCTTCTTGCAGTGCACTTAGATATGTTCTTTTTCATTACAATAA
2315285 TAACATTCTATATTACTTTAATCTTTGTTTCTTAACTTAGATCTCCTTCTTAATCCATCAATCTT
713 TAACATTCTATATTACTTTAATCTTTGTTTCTTAACTTAGATCTCCTTCTTAATCCATCAATC-T
* * *
2315350 TTTTTGAGTTATTCGATCAAAATCATTTACAACTAGTGCACTTCCTCTAGGTGATGAGTTATATG
777 TTTTTGAGTTATTCGATCAAAACCCTTTACAACTAGTGCACTTCCTCCAGGTGATGAGTTATATG
* *
2315415 TTCCCATAAACCTTTTATTCTCACGCAATAGGGCAGTCACATCATCCAACTTCAAAATAAACTTA
842 TTCCCATAAACCTTTCATTCTCACGCAATAGGGCAGTCACATCATCCAACTTCAAAATAGACTTA
* * *
2315480 TCCACCAACAAAGTTTGAATTAAAAGGTTTATAGGACTTTGACAAAGATGATAATAAAATTAAAG
907 TCCACCAACAAAGTTTGAATT-AAAGGTTTATAGGACTTCGGCAAAGATGACAATAAAATTAAAG
2315545 AT
971 AT
*
2315547 GACAAACTTTCACTCTTATAACTTTACTAACTTTCAATGTTGGATTATGAGATTCAAAGTAAATC
1 GACAAACTTTCACTCTTATAACTTTACTAACTTTCAATGATGGATTATGAGATTCAAAGTAAATC
*
2315612 CCTGCAAATCTTCTCTTGATTTGAATCTCTAAACACTTCAATAGTATCTGTAAAGTTGACATGCT
66 CCTGCAAATCCTCTCTTGATTTGAATCTCTAAACACTTCAATAGTATCTGTAAAGTTGACATGCT
* *
2315677 TACCCTTCTTCTTTTCTTCGTCATAAAAATCTCAACAACTAAGCCTCCATCAAGCATGTACAAGT
131 TACCCTTTTTCTTTTCTTCGTCATAAAAATCTCAACAACTGAGCCTCCATCAAGCATGTACAAGT
* * * * *
2315742 AATTTTTTACCATATTCATTTGTAGAATAACACTACTATTCTTGTACATTTTCAACCAATCATTA
196 GATTTTTGACCATATTCATTTATAGAATAACACTACCATTCTTGTACACTTTCAACCAATCATTA
* * * *
2315807 CTATCATAGTATGTGTACCCCTAAAAAGCTAACTCATTCAAAGCAATCAAATTATAACTATAACT
261 CTATCATAGTATGTGTACCCTTGAAAAGCTAATTCATTCAAAGCAATCAAATTGTAACTATAACT
*
2315872 TAGTACATACTTTACATGACGAAGCGTCCTAACAACTCCATTATGAGATTTAATGCGAACACTCT
326 TAGTACATACTTTACATGACGAAGCGTCCTAACAACTCCATTATGAGATTTAATGTGAACACTCT
* * *
2315937 CAGTGCTTTGAATCTACACTTTTT-TTTGTTGGTAACCATAATATCTCCATACTTCTCATTTTTT
391 CAATGCTTTGAATCTACACTTTTTCTTTGTTGGCAACCATAATATCTCCATACTTCT-TTTTTTT
2316001 TCAACTTCATAAAGTAACTCCTATCATTATAGACATGAACTATAGTAATTGAATCTAAAACCTAA
455 TCAACTTCATAAAGTAACTCCTATCATTATAGACATGAACTATAGTAATTGAATCTAAAACCTAA
*
2316066 CCTTTATCACATTTCAAAGTCTGAGTCTCATCCACACAAGTAATCAAAATAACATCATTATCATC
520 CCTTTATCACATTTCAAAGTCTGAGTCTTATCCACACAAGTAATCAAAATAACATCATTATCATC
* *
2316131 AGATACAAT-AACAATAGTATCACTTTTTTCTTCATCTATTTTTTTCTTATCATTTGTCCTTTTA
585 AGATAC-ATCAACAATAGTATCACTTTTTTCTTCATTTATTTTTTT-TTATCATTTGTCCTTTTG
2316195 AAAATAGCCATATCCTCTCTCAGCTTCTTGCAGTGCACTTAGATATG-TCATTTTTCATTACAAT
648 AAAATAGCCATATCC-CTCTCAGCTTCTTGCAGTGCACTTAGATATGTTC-TTTTTCATTACAAT
* * * * * *
2316259 AATAATATTATATATTACTTTAATCTTAGTTTTTTAATTTAGATCTCCTTCTTAATTCATCAATC
711 AATAACATTCTATATTACTTTAATCTTTGTTTCTTAACTTAGATCTCCTTCTTAATCCATCAAT-
* *
2316324 CTTTTTTAAGTTATTCGATCAAAACCCTTTATAACTAGTGCACTTCCTCCAGGTGATGAGTTATA
775 CTTTTTTGAGTTATTCGATCAAAACCCTTTACAACTAGTGCACTTCCTCCAGGTGATGAGTTATA
* * * *
2316389 TGTTCCCATAAACCTTTCATTCTCACGCAATAGGACAATCACATCATTCAATTTCAAAATAGACT
840 TGTTCCCATAAACCTTTCATTCTCACGCAATAGGGCAGTCACATCATCCAACTTCAAAATAGACT
2316454 TATCCACCAACAAAGTTTGAATTAAAGGTTTATAGGACTTCGGCAAAGATGACAATAAAATTAAA
905 TATCCACCAACAAAGTTTGAATTAAAGGTTTATAGGACTTCGGCAAAGATGACAATAAAATTAAA
2316519 G
970 G
2316520 TCTTCTCTTT
Statistics
Matches: 1844, Mismatches: 84, Indels: 33
0.94 0.04 0.02
Matches are distributed among these distances:
969 108 0.06
970 176 0.10
971 605 0.33
972 36 0.02
973 25 0.01
974 181 0.10
975 343 0.19
976 369 0.20
977 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.37
Consensus pattern (972 bp):
GACAAACTTTCACTCTTATAACTTTACTAACTTTCAATGATGGATTATGAGATTCAAAGTAAATC
CCTGCAAATCCTCTCTTGATTTGAATCTCTAAACACTTCAATAGTATCTGTAAAGTTGACATGCT
TACCCTTTTTCTTTTCTTCGTCATAAAAATCTCAACAACTGAGCCTCCATCAAGCATGTACAAGT
GATTTTTGACCATATTCATTTATAGAATAACACTACCATTCTTGTACACTTTCAACCAATCATTA
CTATCATAGTATGTGTACCCTTGAAAAGCTAATTCATTCAAAGCAATCAAATTGTAACTATAACT
TAGTACATACTTTACATGACGAAGCGTCCTAACAACTCCATTATGAGATTTAATGTGAACACTCT
CAATGCTTTGAATCTACACTTTTTCTTTGTTGGCAACCATAATATCTCCATACTTCTTTTTTTTT
CAACTTCATAAAGTAACTCCTATCATTATAGACATGAACTATAGTAATTGAATCTAAAACCTAAC
CTTTATCACATTTCAAAGTCTGAGTCTTATCCACACAAGTAATCAAAATAACATCATTATCATCA
GATACATCAACAATAGTATCACTTTTTTCTTCATTTATTTTTTTTTATCATTTGTCCTTTTGAAA
ATAGCCATATCCCTCTCAGCTTCTTGCAGTGCACTTAGATATGTTCTTTTTCATTACAATAATAA
CATTCTATATTACTTTAATCTTTGTTTCTTAACTTAGATCTCCTTCTTAATCCATCAATCTTTTT
TGAGTTATTCGATCAAAACCCTTTACAACTAGTGCACTTCCTCCAGGTGATGAGTTATATGTTCC
CATAAACCTTTCATTCTCACGCAATAGGGCAGTCACATCATCCAACTTCAAAATAGACTTATCCA
CCAACAAAGTTTGAATTAAAGGTTTATAGGACTTCGGCAAAGATGACAATAAAATTAAAGAT
Found at i:2317413 original size:506 final size:508
Alignment explanation
Indices: 2316454--2317732 Score: 1472
Period size: 506 Copynumber: 2.5 Consensus size: 508
2316444 AAAATAGACT
* * *
2316454 TATCCACCAACAAAGTTTGAATTAAAGGTTTATAGGACTTCGGCAAAGATGACAATAAAATTAAA
1 TATCCACCAACAAAGTTTGAACTAAAGGTTTATAGAACTTCGGCAAAGATGACAATAGAATTAAA
* * * * * * *
2316519 GTCTTCTCTTTATCTTC-AACTCATTAACAGAAATTGTTAGCAATTGAGAAACTAACTTATTAAA
66 GCCTTCTCTTTATTTTCTAACTCATCAACAGAAATTATCAGCAATTGAAAAACTAACCTATTAAA
* * * * *
2316583 CTCATTCAGGTGATTATGAAGACTAGCACATTATTCCATCTTTAGAGAATATAAATCCA-CTTTC
131 CTCATTCAGGTGATTATGAAGACTAGCACTTTCTTTCATCTTTAAAGAATATAGATCCATC-TTC
* ** * * *
2316647 AAACATAGTCTGTTAGTCAACAACTTTGAAGCGTAAATACCCTCAAGCTTATCCTACAAATTCTT
195 AAACATAATCTGTTAGTCAATGACTTTGAAGCGTAAATACTCTCAAGCTTATCCCACAAACTCTT
** * * * *
2316712 CAAAGTATTCTTAATCAACATATAATACTTTACCTTTAAGGCTAGCACTAATCTAATAGTATAAA
260 TGAAGTATTCTTAATCAACACATAATACTTTACCTCTAAGGCTAGCACTAATCTAATAATACAAA
* * * *
2316777 CTATTTTTTTTAAAATTTGATTTCAATTACTATTAGACATTCCCTCTAACTTACTACTCTCTAAT
325 CTATTTTTCTTAAAATTTGATTTCAATTACTATCAAACATTCCATCTAACTTACTACTCTCTAAT
* ** * *
2316842 GTTTGCCTTCAAGCTTACTACTCTCTAATGTCTGATCAGGTTTATTACTCTCTAATGCCTGATCC
390 GCTACCCTTCAAGCTTACTACTCTCTAATGTCTGATCAGGTTAACTACTCTCTAATGCCTGATCC
* * * * * * *
2316907 AATATTTGTTGTACTAATAGATCTTGAATTGTATTTTGTCATAACATAAAAACC
455 AACACTTATTGTACTAACAAATCTTGAATCGTATTTTATCATAACATAAAAACC
* * *
2316961 TATCCACCAACAAAGTTTGAACTAAAGGTCTATAGAATTTTGGCAAAGATGA-AATAGAATTAAA
1 TATCCACCAACAAAGTTTGAACTAAAGGTTTATAGAACTTCGGCAAAGATGACAATAGAATTAAA
* *
2317025 GCCTTCTCTTCATTTTCTAACTCATCAACAGAAATTACCAGCAATTGAAAAACTAACCTATTAAA
66 GCCTTCTCTTTATTTTCTAACTCATCAACAGAAATTATCAGCAATTGAAAAACTAACCTATTAAA
* * * *
2317090 TTAATTCAGGTGATTATGAA-AC-ATGCCCTTTCTTTCATCTTTAAAGAATACAGATCCATCTTC
131 CTCATTCAGGTGATTATGAAGACTA-GCACTTTCTTTCATCTTTAAAGAATATAGATCCATCTTC
* * *** *
2317153 AAACATAATTTGTTAGTCAATGACTTTAAAATATAAATATTCTCAAGCTTATCCCACAAACTCTT
195 AAACATAATCTGTTAGTCAATGACTTTGAAGCGTAAATACTCTCAAGCTTATCCCACAAACTCTT
* * * * ** * ** *
2317218 TGGAGTATTTTTAGTTAACACATTGTACTTTACCTCTAGGGCTAGCGTTAATCTAATAATACGAA
260 TGAAGTATTCTTAATCAACACATAATACTTTACCTCTAAGGCTAGCACTAATCTAATAATACAAA
* * *
2317283 -TAACTTTTTCTT-GAATTCT-A-TTCTAATTACTGTCAAACATTCCATC-AGACTTACTATTCT
325 CT-A-TTTTTCTTAAAATT-TGATTTC-AATTACTATCAAACATTCCATCTA-ACTTACTACTCT
* *
2317343 TTAATGCCTACCCTT-AAGCTTACTACTCTCTAATG-CTTGATCAGGTTAACTACTCTTTAATGC
385 CTAATG-CTACCCTTCAAGCTTACTACTCTCTAATGTC-TGATCAGGTTAACTACTCTCTAATGC
* * * * *
2317406 TTGATCCAACACTTATTGTATTAACAAATCTTGAATCGTATTTTATCATTATATAAGAACC
448 CTGATCCAACACTTATTGTACTAACAAATCTTGAATCGTATTTTATCATAACATAAAAACC
* * * * * *
2317467 TA-CCTACTAACAAAGTCTAAACTAAAGGTTTATA-AGACTTCAGTAAAGATAACAATAGAATTA
1 TATCC-ACCAACAAAGTTTGAACTAAAGGTTTATAGA-ACTTCGGCAAAGATGACAATAGAATTA
* * * * *
2317530 AAGCCTTATCTTTATCTTT-TAACTCATCAATAAAAATTTTCAACAATTGAAAAACTAACCTATT
64 AAGCCTTCTCTTTAT-TTTCTAACTCATCAACAGAAATTATCAGCAATTGAAAAACTAACCTATT
* * **
2317594 AAACTCATTCAGGTGATTATGAAGACTCGCACTTTCTTTCATCTTTAAAAAATATAGATCTGTCT
128 AAACTCATTCAGGTGATTATGAAGACTAGCACTTTCTTTCATCTTTAAAGAATATAGATCCATCT
* * * *
2317659 TCAAATATAATCCGTTAGTCAATGACTTTGAAGCGTAAATACTCTCAAGCTTATTCCACAAACTT
193 TCAAACATAATCTGTTAGTCAATGACTTTGAAGCGTAAATACTCTCAAGCTTATCCCACAAACTC
2317724 TTTGAAGTA
258 TTTGAAGTA
2317733 CCTTATTTTA
Statistics
Matches: 643, Mismatches: 113, Indels: 31
0.82 0.14 0.04
Matches are distributed among these distances:
505 10 0.02
506 329 0.51
507 204 0.32
508 100 0.16
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (508 bp):
TATCCACCAACAAAGTTTGAACTAAAGGTTTATAGAACTTCGGCAAAGATGACAATAGAATTAAA
GCCTTCTCTTTATTTTCTAACTCATCAACAGAAATTATCAGCAATTGAAAAACTAACCTATTAAA
CTCATTCAGGTGATTATGAAGACTAGCACTTTCTTTCATCTTTAAAGAATATAGATCCATCTTCA
AACATAATCTGTTAGTCAATGACTTTGAAGCGTAAATACTCTCAAGCTTATCCCACAAACTCTTT
GAAGTATTCTTAATCAACACATAATACTTTACCTCTAAGGCTAGCACTAATCTAATAATACAAAC
TATTTTTCTTAAAATTTGATTTCAATTACTATCAAACATTCCATCTAACTTACTACTCTCTAATG
CTACCCTTCAAGCTTACTACTCTCTAATGTCTGATCAGGTTAACTACTCTCTAATGCCTGATCCA
ACACTTATTGTACTAACAAATCTTGAATCGTATTTTATCATAACATAAAAACC
Found at i:2318076 original size:95 final size:95
Alignment explanation
Indices: 2317911--2318096 Score: 295
Period size: 95 Copynumber: 2.0 Consensus size: 95
2317901 ACAATAGAGC
* *
2317911 AAGCCTAAAATAAGAATAAAAATATACAAATATATTTATTTCAACCTAACCCAAAATGGCTTACT
1 AAGCCTAAAATAAGAATAAAAATACACAAATATATTTATTTCAACCTAACCCAAAATGACTTACT
*
2317976 TCAAACCGAATCCACTAACAAATAAAAAGT
66 TCAAACCCAATCCACTAACAAATAAAAAGT
* *
2318006 AAGCCTAAAATAAGAATAAAAATACATAAATATATTTATTTCAATCC-AACCCAAAATTACTTA-
1 AAGCCTAAAATAAGAATAAAAATACACAAATATATTTATTTCAA-CCTAACCCAAAATGACTTAC
2318069 TTCCAAACCCAATCCACTAACAAATAAA
65 TT-CAAACCCAATCCACTAACAAATAAA
2318097 TATTTATAAT
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
94 2 0.02
95 80 0.95
96 2 0.02
ACGTcount: A:0.51, C:0.20, G:0.04, T:0.25
Consensus pattern (95 bp):
AAGCCTAAAATAAGAATAAAAATACACAAATATATTTATTTCAACCTAACCCAAAATGACTTACT
TCAAACCCAATCCACTAACAAATAAAAAGT
Found at i:2321172 original size:29 final size:28
Alignment explanation
Indices: 2321080--2321173 Score: 107
Period size: 29 Copynumber: 3.2 Consensus size: 28
2321070 AAATACTTAA
*
2321080 AATTTTAATTAAAAATTTAAAATTTTAATT
1 AATTATAA-TAAAAA-TTAAAATTTTAATT
* * *
2321110 AATTTAGAATAAAAATAAAAAATTTAATT
1 AA-TTATAATAAAAATTAAAATTTTAATT
*
2321139 AATTATAATAAAACATTAAAATTTTAAAT
1 AATTATAATAAAA-ATTAAAATTTTAATT
2321168 AATTAT
1 AATTAT
2321174 CAAATTTTAC
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 10 0.19
29 32 0.59
30 8 0.15
31 4 0.07
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (28 bp):
AATTATAATAAAAATTAAAATTTTAATT
Found at i:2328775 original size:14 final size:13
Alignment explanation
Indices: 2328745--2328780 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
2328735 CTAAAATTAA
2328745 AATTA-TATTGTT
1 AATTATTATTGTT
2328757 AATTATTATTGTT
1 AATTATTATTGTT
2328770 ATATTATTATT
1 A-ATTATTATT
2328781 ATATTCAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 5 0.23
13 8 0.36
14 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (13 bp):
AATTATTATTGTT
Found at i:2329754 original size:127 final size:128
Alignment explanation
Indices: 2329604--2329858 Score: 422
Period size: 127 Copynumber: 2.0 Consensus size: 128
2329594 GCTCATAAAA
*
2329604 ATATATTTATGGTTCAAGATCGTTAGTAAATGTATATATATTGGTATAGTACCTATTATGTGTTT
1 ATATATTTATGGTTCAAGATCGTTAGTAAATGTATATATATTGGTATAGCACCTATTATGTGTTT
* *
2329669 CACTATTATACCTTTTACCAATGGTTAATACCTATTAGTATAGACTTATATGTTTTAATTTTT
66 CACTATTATACCTTTTACCAATGGTTAATACCTATCAGTATAGACTTATATATTTTAATTTTT
* * * *
2329732 ATATTTTTAT-GTTCAAGATCGTTAGTAAATGTATATTTATTGGTATAGCATCTATTGTGTGTTT
1 ATATATTTATGGTTCAAGATCGTTAGTAAATGTATATATATTGGTATAGCACCTATTATGTGTTT
**
2329796 CACTATTATACCTTTTACTGATGGTTAATACCTATCAGTATAGACTTATATATTTTAATTTTT
66 CACTATTATACCTTTTACCAATGGTTAATACCTATCAGTATAGACTTATATATTTTAATTTTT
2329859 CTTTCTTATA
Statistics
Matches: 118, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
127 109 0.92
128 9 0.08
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (128 bp):
ATATATTTATGGTTCAAGATCGTTAGTAAATGTATATATATTGGTATAGCACCTATTATGTGTTT
CACTATTATACCTTTTACCAATGGTTAATACCTATCAGTATAGACTTATATATTTTAATTTTT
Found at i:2333081 original size:19 final size:18
Alignment explanation
Indices: 2333057--2333119 Score: 59
Period size: 19 Copynumber: 3.8 Consensus size: 18
2333047 ATCCAAACAA
2333057 TAAACAATTATATATAAT
1 TAAACAATTATATATAAT
2333075 GTAAAC----A-ATAT-A-
1 -TAAACAATTATATATAAT
2333087 TAAACAATTATATATAAT
1 TAAACAATTATATATAAT
2333105 CTAAACAATTATATA
1 -TAAACAATTATATA
2333120 AATCTTATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 16
0.69 0.00 0.31
Matches are distributed among these distances:
11 5 0.14
13 1 0.03
14 4 0.11
15 2 0.06
16 4 0.11
17 1 0.03
19 19 0.53
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.35
Consensus pattern (18 bp):
TAAACAATTATATATAAT
Found at i:2333092 original size:30 final size:31
Alignment explanation
Indices: 2333056--2333121 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 31
2333046 AATCCAAACA
*
2333056 ATAAACAATTATATATAATGTAAACAA-TAT
1 ATAAACAATTATATATAATCTAAACAATTAT
2333086 ATAAACAATTATATATAATCTAAACAATTAT
1 ATAAACAATTATATATAATCTAAACAATTAT
2333117 ATAAA
1 ATAAA
2333122 TCTTATTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 26 0.76
31 8 0.24
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.33
Consensus pattern (31 bp):
ATAAACAATTATATATAATCTAAACAATTAT
Found at i:2333303 original size:30 final size:30
Alignment explanation
Indices: 2333269--2333387 Score: 157
Period size: 30 Copynumber: 3.9 Consensus size: 30
2333259 CAATAAATAG
2333269 TTATATATAATCTAAACAATATATAAACAA
1 TTATATATAATCTAAACAATATATAAACAA
* * * * *
2333299 TTATATATAATTTAAATAGTATGTAAATAA
1 TTATATATAATCTAAACAATATATAAACAA
* * *
2333329 TTATATATAATTTAAACAGTATGTAAACAA
1 TTATATATAATCTAAACAATATATAAACAA
2333359 TTATATATAATCTAAACAATTATATAAAC
1 TTATATATAATCTAAACAA-TATATAAAC
2333388 CTTATTATGT
Statistics
Matches: 78, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
30 70 0.90
31 8 0.10
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (30 bp):
TTATATATAATCTAAACAATATATAAACAA
Found at i:2333337 original size:60 final size:60
Alignment explanation
Indices: 2333262--2333374 Score: 181
Period size: 60 Copynumber: 1.9 Consensus size: 60
2333252 AGCCAAACAA
* *
2333262 TAAATAGTTATATATAATCTAAACAATATATAAACAATTATATATAATTTAAATAGTATG
1 TAAATAATTATATATAATCTAAACAATATATAAACAATTATATATAATCTAAATAGTATG
* * *
2333322 TAAATAATTATATATAATTTAAACAGTATGTAAACAATTATATATAATCTAAA
1 TAAATAATTATATATAATCTAAACAATATATAAACAATTATATATAATCTAAA
2333375 CAATTATATA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.38
Consensus pattern (60 bp):
TAAATAATTATATATAATCTAAACAATATATAAACAATTATATATAATCTAAATAGTATG
Found at i:2336126 original size:23 final size:23
Alignment explanation
Indices: 2336096--2336139 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2336086 ATAATTCATG
2336096 GATTATTTAAGGTATTTTTGACA
1 GATTATTTAAGGTATTTTTGACA
*
2336119 GATTATTTAAGGTGTTTTTGA
1 GATTATTTAAGGTATTTTTGA
2336140 TAAAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.02, G:0.20, T:0.50
Consensus pattern (23 bp):
GATTATTTAAGGTATTTTTGACA
Found at i:2336841 original size:2 final size:2
Alignment explanation
Indices: 2336834--2336868 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2336824 ATTTATTTGA
2336834 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2336869 CACACACACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2337095 original size:15 final size:15
Alignment explanation
Indices: 2337072--2337103 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2337062 TCTTCAAAAG
*
2337072 AAATGAAAGAAAGGA
1 AAATAAAAGAAAGGA
2337087 AAATAAAAGAAAGGA
1 AAATAAAAGAAAGGA
2337102 AA
1 AA
2337104 CCTGTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (15 bp):
AAATAAAAGAAAGGA
Found at i:2344198 original size:5 final size:5
Alignment explanation
Indices: 2344169--2344285 Score: 78
Period size: 5 Copynumber: 22.4 Consensus size: 5
2344159 TTAGTTTGTG
* * * * *
2344169 TATTA TTATTA TATAA TATAA TATTA TATTA TCTTA CTATTA TAGTA TAGTA
1 TATTA -TATTA TATTA TATTA TATTA TATTA TATTA -TATTA TATTA TATTA
* *
2344221 TATTA TATGATA TAGTG TATTA TA-T- TATTA TCATTA TTATTA TTATT-
1 TATTA TAT--TA TATTA TATTA TATTA TATTA T-ATTA -TATTA -TATTA
2344268 TATTA TATTA TTATTA TA
1 TATTA TATTA -TATTA TA
2344286 CTTTACTATT
Statistics
Matches: 92, Mismatches: 10, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
3 2 0.02
4 6 0.07
5 52 0.57
6 27 0.29
7 5 0.05
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.56
Consensus pattern (5 bp):
TATTA
Found at i:2344236 original size:17 final size:16
Alignment explanation
Indices: 2344206--2344245 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
2344196 ATTATCTTAC
2344206 TATTATA-GTATAGTA
1 TATTATATGTATAGTA
*
2344221 TATTATATGATATAGTG
1 TATTATATG-TATAGTA
2344238 TATTATAT
1 TATTATAT
2344246 TATTATCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.32
16 1 0.05
17 14 0.64
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (16 bp):
TATTATATGTATAGTA
Found at i:2344298 original size:3 final size:3
Alignment explanation
Indices: 2344238--2344284 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
2344228 TGATATAGTG
*
2344238 TAT TA- TAT TAT TAT CAT TAT TAT TAT TATT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
2344282 TAT
1 TAT
2344285 ACTTTACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 4 0.10
3 32 0.82
4 3 0.08
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2344298 original size:27 final size:30
Alignment explanation
Indices: 2344238--2344295 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
2344228 TGATATAGTG
* *
2344238 TATTATATTATTATCATTATTATTATTATT
1 TATTATATTATTATCATTACTATTACTATT
*
2344268 TATTATATTATTATTA-TACT-TTACTATT
1 TATTATATTATTATCATTACTATTACTATT
2344296 ATTTTTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.28
29 3 0.12
30 15 0.60
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (30 bp):
TATTATATTATTATCATTACTATTACTATT
Found at i:2344826 original size:12 final size:12
Alignment explanation
Indices: 2344809--2344833 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2344799 GATGAACGTA
2344809 AATTTTTTGATG
1 AATTTTTTGATG
2344821 AATTTTTTGATG
1 AATTTTTTGATG
2344833 A
1 A
2344834 TTGATTGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (12 bp):
AATTTTTTGATG
Found at i:2345231 original size:5 final size:5
Alignment explanation
Indices: 2345221--2345284 Score: 51
Period size: 5 Copynumber: 12.4 Consensus size: 5
2345211 TATTTTAAAC
* * *
2345221 TTTAT TTTAT TTTCAGT TTT-T TTTAT CTTAT CTTAT TTTACT TGTTTT
1 TTTAT TTTAT TTT-A-T TTTAT TTTAT TTTAT TTTAT TTTA-T T-TTAT
2345269 TTTA- TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TT
2345285 AGTAATTCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
4 8 0.16
5 30 0.61
6 5 0.10
7 6 0.12
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:2345251 original size:26 final size:26
Alignment explanation
Indices: 2345221--2345284 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
2345211 TATTTTAAAC
2345221 TTTATTTTATTTT-CAGT-TTTTTTTA
1 TTTATTTTATTTTAC-GTGTTTTTTTA
* *
2345246 TCTTATCTTATTTTACTTGTTTTTTTA
1 T-TTATTTTATTTTACGTGTTTTTTTA
2345273 TTTATTTTATTT
1 TTTATTTTATTT
2345285 AGTAATTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 1 0.03
26 22 0.67
27 10 0.30
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (26 bp):
TTTATTTTATTTTACGTGTTTTTTTA
Found at i:2346686 original size:33 final size:32
Alignment explanation
Indices: 2346637--2346701 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
2346627 TGGAATGAAG
*
2346637 TCCCCTTCAATTTCTTCCATCATGGTGAATAC
1 TCCCCTTCAATTTCTTCCATCAAGGTGAATAC
* *
2346669 TCCCCTTTCAGTTTCTTCCATTAAGGTGAATAC
1 TCCCC-TTCAATTTCTTCCATCAAGGTGAATAC
2346702 ATTGTACTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 5 0.17
33 24 0.83
ACGTcount: A:0.22, C:0.29, G:0.11, T:0.38
Consensus pattern (32 bp):
TCCCCTTCAATTTCTTCCATCAAGGTGAATAC
Found at i:2348375 original size:7 final size:7
Alignment explanation
Indices: 2348363--2348395 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
2348353 ACAATTCATT
2348363 AAAAATG
1 AAAAATG
2348370 AAAAATG
1 AAAAATG
2348377 AAAAATG
1 AAAAATG
2348384 AAAAATG
1 AAAAATG
2348391 AAAAA
1 AAAAA
2348396 AGGAATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:2348408 original size:21 final size:21
Alignment explanation
Indices: 2348360--2348408 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2348350 AATACAATTC
*
2348360 ATTAAAAATGAAAAATGAAAA
1 ATTAAAAATGAAAAAAGAAAA
* * *
2348381 ATGAAAAATGAAAAAAGGAAT
1 ATTAAAAATGAAAAAAGAAAA
2348402 ATTAAAA
1 ATTAAAA
2348409 GAAAGGAAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.18
Consensus pattern (21 bp):
ATTAAAAATGAAAAAAGAAAA
Found at i:2350971 original size:4 final size:4
Alignment explanation
Indices: 2350964--2351009 Score: 51
Period size: 4 Copynumber: 11.5 Consensus size: 4
2350954 TTGGATTTTT
*
2350964 TTTA TTTA -TTA -TTA TTTA TTTA TTTA TTGGTA ATTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT--TA TTTA TTTA TTTA TT
2351010 GTTAGGTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
3 6 0.16
4 28 0.76
6 3 0.08
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:2350989 original size:22 final size:22
Alignment explanation
Indices: 2350964--2351009 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
2350954 TTGGATTTTT
* *
2350964 TTTATTTATTATTATTTATTTA
1 TTTATTGATAATTATTTATTTA
*
2350986 TTTATTGGTAATTATTTATTTA
1 TTTATTGATAATTATTTATTTA
2351008 TT
1 TT
2351010 GTTAGGTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (22 bp):
TTTATTGATAATTATTTATTTA
Found at i:2351010 original size:18 final size:18
Alignment explanation
Indices: 2350964--2351010 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
2350954 TTGGATTTTT
** *
2350964 TTTATTTATTATTATTTA
1 TTTATTTATTGGTAATTA
2350982 TTTATTTATTGGTAATTA
1 TTTATTTATTGGTAATTA
2351000 TTTATTTATTG
1 TTTATTTATTG
2351011 TTAGGTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (18 bp):
TTTATTTATTGGTAATTA
Found at i:2353617 original size:25 final size:25
Alignment explanation
Indices: 2353587--2353637 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2353577 CCGACGGATC
2353587 GACCTCAGGCAGTGGTGGGCGACTG
1 GACCTCAGGCAGTGGTGGGCGACTG
2353612 GACCTCAGGCAGTGGTGGGCGACTG
1 GACCTCAGGCAGTGGTGGGCGACTG
2353637 G
1 G
2353638 TTGGAACAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.16, C:0.24, G:0.45, T:0.16
Consensus pattern (25 bp):
GACCTCAGGCAGTGGTGGGCGACTG
Found at i:2353706 original size:79 final size:79
Alignment explanation
Indices: 2353612--2353821 Score: 366
Period size: 79 Copynumber: 2.6 Consensus size: 79
2353602 TGGGCGACTG
*
2353612 GACCTCAGGCAGTGGTGGGCGACTGGTTGGAACAGATTTGGGCGCATCCAGTTCTGGGCGTAGTC
1 GACCTCAAGCAGTGGTGGGCGACTGGTTGGAACAGATTTGGGCGCATCCAGTTCTGGGCGTAGTC
2353677 CCTTCCGACGGATC
66 CCTTCCGACGGATC
*
2353691 GACCTCAAGCAGTGGTAGGCGACTGGTTGGAACAGATTTGGGCGCATCCAGTTCTGGGCGTAGTC
1 GACCTCAAGCAGTGGTGGGCGACTGGTTGGAACAGATTTGGGCGCATCCAGTTCTGGGCGTAGTC
2353756 CCTTCCGACGGATC
66 CCTTCCGACGGATC
* * *
2353770 AACCTCAAGCAGTGGTGGGCGACTGGTTAGAACCAGATTCGGGCGCATCCAG
1 GACCTCAAGCAGTGGTGGGCGACTGGTTGGAA-CAGATTTGGGCGCATCCAG
2353822 ACTGAGGGTC
Statistics
Matches: 124, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
79 106 0.85
80 18 0.15
ACGTcount: A:0.20, C:0.25, G:0.34, T:0.21
Consensus pattern (79 bp):
GACCTCAAGCAGTGGTGGGCGACTGGTTGGAACAGATTTGGGCGCATCCAGTTCTGGGCGTAGTC
CCTTCCGACGGATC
Found at i:2353887 original size:118 final size:118
Alignment explanation
Indices: 2353716--2353939 Score: 396
Period size: 118 Copynumber: 1.9 Consensus size: 118
2353706 TAGGCGACTG
2353716 GTTGGAACAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGACGGATCAACCTCAAGCA
1 GTTGGAACAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGACGGATCAACCTCAAGCA
2353781 GTGGTGGGCGACTGGTTAGAACCAGATTCGGGCGCATCCAGACTGAGGGTCTT
66 GTGGTGGGCGACTGGTTAGAACCAGATTCGGGCGCATCCAGACTGAGGGTCTT
* *
2353834 GTTGGAACCAGATTTGGGCGCATCCAGTTCT-GGCGTAGTCCCTTCCGACGGATCGACCTCAGGC
1 GTTGGAA-CAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGACGGATCAACCTCAAGC
* *
2353898 AGTGGTGGGCGACTGGTTGGAACCAGATTTGGGCGCATCCAG
65 AGTGGTGGGCGACTGGTTAGAACCAGATTCGGGCGCATCCAG
2353940 TTCTGGGCGT
Statistics
Matches: 101, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
118 78 0.77
119 23 0.23
ACGTcount: A:0.19, C:0.25, G:0.33, T:0.23
Consensus pattern (118 bp):
GTTGGAACAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGACGGATCAACCTCAAGCA
GTGGTGGGCGACTGGTTAGAACCAGATTCGGGCGCATCCAGACTGAGGGTCTT
Found at i:2353978 original size:198 final size:198
Alignment explanation
Indices: 2353637--2354333 Score: 1240
Period size: 198 Copynumber: 3.5 Consensus size: 198
2353627 TGGGCGACTG
* *
2353637 GTTGGAA-CAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGACGGATCGACCTCAAGC
1 GTTGGAACCAGATTTGGGCGCATCCAGTTCT-GGCGTAATCCCTTCCGACGGATCGACCTCAGGC
* *
2353701 AGTGGTAGGCGACTGGTTGGAA-CAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGAC
65 AGTGGTGGGCGACTGGTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGAC
* * *
2353765 GGATCAACCTCAAGCAGTGGTGGGCGACTGGTTAGAACCAGATTCGGGCGCATCCAGACTGAGGG
130 GGATCAACTTCAAGCAGTGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGGGGG
2353830 TCTT
195 TCTT
*
2353834 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGCGTAGTCCCTTCCGACGGATCGACCTCAGGCA
1 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGCGTAATCCCTTCCGACGGATCGACCTCAGGCA
2353899 GTGGTGGGCGACTGGTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACG
66 GTGGTGGGCGACTGGTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACG
*
2353964 GATCAACTTCAAGCAGTGGTGGGCGACTGGTTGGAACCAGATTAGGGCGCATCCAGACTGGGGGT
131 GATCAACTTCAAGCAGTGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGGGGGT
2354029 CTT
196 CTT
2354032 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGCGTAATCCCTTCCGACGGATCGACCTCAGGCA
1 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGCGTAATCCCTTCCGACGGATCGACCTCAGGCA
* *
2354097 GTGGTGGGCGACTAGTTGGAACCAAATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACG
66 GTGGTGGGCGACTGGTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACG
*
2354162 GGTCAACTTCAAGCAGTGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGGGGGT
131 GATCAACTTCAAGCAGTGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGGGGGT
2354227 CTT
196 CTT
2354230 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGCGTAATCCCTTCCGACGGATCGACCTCAGGCA
1 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGCGTAATCCCTTCCGACGGATCGACCTCAGGCA
*
2354295 --GGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAG
66 GTGGTGGGCGACTGGTTGGAACCAGATTTGGGCGCATCCAG
2354334 ACTGGGGGTC
Statistics
Matches: 483, Mismatches: 15, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
196 36 0.07
197 60 0.12
198 387 0.80
ACGTcount: A:0.19, C:0.25, G:0.33, T:0.23
Consensus pattern (198 bp):
GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGCGTAATCCCTTCCGACGGATCGACCTCAGGCA
GTGGTGGGCGACTGGTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACG
GATCAACTTCAAGCAGTGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGGGGGT
CTT
Found at i:2353986 original size:80 final size:79
Alignment explanation
Indices: 2353834--2354019 Score: 318
Period size: 80 Copynumber: 2.3 Consensus size: 79
2353824 TGAGGGTCTT
* *
2353834 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGCGTAGTCCCTTCCGACGGATCGACCTCAGGCA
1 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGCGTAGTCCCTTCCGACGGATCAACCTCAAGCA
2353899 GTGGTGGGCGACTG
66 GTGGTGGGCGACTG
* *
2353913 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACGGATCAACTTCAAGC
1 GTTGGAACCAGATTTGGGCGCATCCAGTTCT-GGCGTAGTCCCTTCCGACGGATCAACCTCAAGC
2353978 AGTGGTGGGCGACTG
65 AGTGGTGGGCGACTG
*
2353993 GTTGGAACCAGATTAGGGCGCATCCAG
1 GTTGGAACCAGATTTGGGCGCATCCAG
2354020 ACTGGGGGTC
Statistics
Matches: 101, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
79 31 0.31
80 70 0.69
ACGTcount: A:0.19, C:0.25, G:0.33, T:0.23
Consensus pattern (79 bp):
GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGCGTAGTCCCTTCCGACGGATCAACCTCAAGCA
GTGGTGGGCGACTG
Found at i:2354130 original size:118 final size:119
Alignment explanation
Indices: 2353913--2354137 Score: 371
Period size: 118 Copynumber: 1.9 Consensus size: 119
2353903 TGGGCGACTG
* * *
2353913 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACGGATCAACTTCAAGC
1 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAATCCCTTCCGACGGATCAACCTCAAGC
* *
2353978 AGTGGTGGGCGACTGGTTGGAACCAGATTAGGGCGCATCCAGACTGGGGGTCTT
66 AGTGGTGGGCGACTAGTTGGAACCAAATTAGGGCGCATCCAGACTGGGGGTCTT
* *
2354032 GTTGGAACCAGATTTGGGCGCATCCAGTTCT-GGCGTAATCCCTTCCGACGGATCGACCTCAGGC
1 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAATCCCTTCCGACGGATCAACCTCAAGC
*
2354096 AGTGGTGGGCGACTAGTTGGAACCAAATTTGGGCGCATCCAG
66 AGTGGTGGGCGACTAGTTGGAACCAAATTAGGGCGCATCCAG
2354138 TTCTGGGCGT
Statistics
Matches: 98, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
118 67 0.68
119 31 0.32
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.24
Consensus pattern (119 bp):
GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAATCCCTTCCGACGGATCAACCTCAAGC
AGTGGTGGGCGACTAGTTGGAACCAAATTAGGGCGCATCCAGACTGGGGGTCTT
Found at i:2354187 original size:80 final size:79
Alignment explanation
Indices: 2354032--2354217 Score: 282
Period size: 80 Copynumber: 2.3 Consensus size: 79
2354022 TGGGGGTCTT
* *
2354032 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGCGTAATCCCTTCCGACGGATCGACCTCAGGCA
1 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGCGTAATCCCTTCCGACGGATCAACCTCAAGCA
2354097 GTGGTGGGCGACTA
66 GTGGTGGGCGACTA
* * * * *
2354111 GTTGGAACCAAATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACGGGTCAACTTCAAGC
1 GTTGGAACCAGATTTGGGCGCATCCAGTTCT-GGCGTAATCCCTTCCGACGGATCAACCTCAAGC
*
2354176 AGTGGTGGGCGACTG
65 AGTGGTGGGCGACTA
*
2354191 GTTGGAACCAGATTCGGGCGCATCCAG
1 GTTGGAACCAGATTTGGGCGCATCCAG
2354218 ACTGGGGGTC
Statistics
Matches: 96, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
79 30 0.31
80 66 0.69
ACGTcount: A:0.19, C:0.25, G:0.32, T:0.23
Consensus pattern (79 bp):
GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGCGTAATCCCTTCCGACGGATCAACCTCAAGCA
GTGGTGGGCGACTA
Found at i:2354326 original size:116 final size:116
Alignment explanation
Indices: 2354111--2354450 Score: 536
Period size: 116 Copynumber: 2.9 Consensus size: 116
2354101 TGGGCGACTA
* * * *
2354111 GTTGGAACCAAATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACGGGTCAACTTCAAGC
1 GTTGGAACCAGATTTGGGCGCATCCAGTTCT-GGCGTAGTCCCTTCTGACGGATCGACTTCAGGC
2354176 AGTGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGGGGGTCTT
65 A--GGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGGGGGTCTT
* * *
2354230 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGCGTAATCCCTTCCGACGGATCGACCTCAGGCA
1 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGCGTAGTCCCTTCTGACGGATCGACTTCAGGCA
2354295 GGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGGGGGTCTT
66 GGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGGGGGTCTT
* * * *
2354346 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGACATAGTCCCTTCTGACGAATCGATTTCAGAC
1 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGG-CGTAGTCCCTTCTGACGGATCGACTTCAGGC
*
2354411 AGGTGGGCGACTGGTTAGAACCAGATTCGGGCGCATCCAG
65 AGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAG
2354451 TTCTGAGGGT
Statistics
Matches: 205, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
116 84 0.41
117 63 0.31
118 28 0.14
119 30 0.15
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.24
Consensus pattern (116 bp):
GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGCGTAGTCCCTTCTGACGGATCGACTTCAGGCA
GGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGGGGGTCTT
Found at i:2354495 original size:78 final size:78
Alignment explanation
Indices: 2354350--2354500 Score: 191
Period size: 78 Copynumber: 1.9 Consensus size: 78
2354340 GGTCTTGTTG
* * *
2354350 GAACCAGATTTGGGCGCATCCAGTTCTGGACATAGTCCCTTCTGACGAATCGATTTCAGACAGGT
1 GAACCAGATTCGGGCGCATCCAGTTCTGGACATAGTCCCTTCCGACGAATCGACTTCAGACAGGT
2354415 GGGCGACTGGTTA
66 GGGCGACTGGTTA
** *
2354428 GAACCAGATTCGGGCGCATCCAGTTCT-GAGGGTAGTCCCTTCCGACTG-ATCGACCTT-AGGCA
1 GAACCAGATTCGGGCGCATCCAGTTCTGGA-CATAGTCCCTTCCGAC-GAATCGA-CTTCAGACA
*
2354490 TGTGGGCGACT
63 GGTGGGCGACT
2354501 ATGTGTTTGT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
77 2 0.03
78 58 0.92
79 3 0.05
ACGTcount: A:0.21, C:0.25, G:0.29, T:0.25
Consensus pattern (78 bp):
GAACCAGATTCGGGCGCATCCAGTTCTGGACATAGTCCCTTCCGACGAATCGACTTCAGACAGGT
GGGCGACTGGTTA
Found at i:2357454 original size:16 final size:13
Alignment explanation
Indices: 2357423--2357476 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 13
2357413 GGTAAATAAT
2357423 ATTATT-TTTTTA
1 ATTATTATTTTTA
2357435 ATTAATTCATTTTTA
1 ATT-ATT-ATTTTTA
2357450 TATTATTATTTTTAA
1 -ATTATTATTTTT-A
2357465 ATATATTATTTT
1 AT-TATTATTTT
2357477 ATGAGATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.08
13 3 0.08
14 8 0.22
15 19 0.53
16 3 0.08
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTATTATTTTTA
Found at i:2357478 original size:28 final size:28
Alignment explanation
Indices: 2357421--2357476 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
2357411 TTGGTAAATA
*
2357421 ATATTATTTTTTTAATTAATTCATTTTT
1 ATATTATTTTTTTAAATAATTCATTTTT
2357449 ATATTATTATTTTTAAATATATT-ATTTT
1 ATATTATT-TTTTTAAATA-ATTCATTTT
2357477 ATGAGATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 8 0.32
29 14 0.56
30 3 0.12
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (28 bp):
ATATTATTTTTTTAAATAATTCATTTTT
Found at i:2363962 original size:19 final size:19
Alignment explanation
Indices: 2363938--2363981 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
2363928 CATATATAGT
2363938 TATATT-AAAAGTTTTGAAA-
1 TATATTGAAAA-TTTT-AAAG
2363957 TATATTGAAAATTTTAAAG
1 TATATTGAAAATTTTAAAG
2363976 TATATT
1 TATATT
2363982 TACTTTGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.13
19 16 0.70
20 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (19 bp):
TATATTGAAAATTTTAAAG
Found at i:2368496 original size:19 final size:20
Alignment explanation
Indices: 2368455--2368505 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
2368445 ACCCGAAATT
*
2368455 AATAAAATATTATTTTTTAA
1 AATATAATATTATTTTTTAA
2368475 AATATAATATTATTTTTT-A
1 AATATAATATTATTTTTTAA
2368494 AATATAAATATT
1 AATAT-AATATT
2368506 TAAAAAATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATATAATATTATTTTTTAA
Found at i:2368542 original size:24 final size:22
Alignment explanation
Indices: 2368498--2368563 Score: 78
Period size: 24 Copynumber: 2.9 Consensus size: 22
2368488 TTTTTAAATA
*
2368498 TAAATATTTAAAAAATCATTAAT
1 TAAATA-TTAAAAAATAATTAAT
*
2368521 TAAATATATATATAAATAATTAAT
1 TAAATAT-TA-AAAAATAATTAAT
*
2368545 TAATTATTAAAAAATAATT
1 TAAATATTAAAAAATAATT
2368564 TTTATATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 10 0.27
23 10 0.27
24 17 0.46
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAATATTAAAAAATAATTAAT
Found at i:2368814 original size:14 final size:13
Alignment explanation
Indices: 2368795--2368833 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
2368785 GCAATTCTTC
*
2368795 AAAAAAGAAAAAT
1 AAAAAAAAAAAAT
*
2368808 AAAAAAAAAATATT
1 AAAAAAAAAA-AAT
2368822 AAAAAAAAAAAA
1 AAAAAAAAAAAA
2368834 ACTTTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (13 bp):
AAAAAAAAAAAAT
Found at i:2371721 original size:13 final size:11
Alignment explanation
Indices: 2371687--2371726 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
2371677 TTATATTTTT
2371687 TATTTATATCA
1 TATTTATATCA
*
2371698 TATTCATATCA
1 TATTTATATCA
2371709 TATCATTATATCA
1 TAT--TTATATCA
2371722 TATTT
1 TATTT
2371727 TAGACATTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 15 0.60
13 10 0.40
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (11 bp):
TATTTATATCA
Found at i:2373294 original size:19 final size:18
Alignment explanation
Indices: 2373270--2373315 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
2373260 AAAAGTGAAG
*
2373270 AAAGAAAATAGAAGATACA
1 AAAGAAAATAGAA-AAACA
*
2373289 AAAGAAAA-AGAAAAATA
1 AAAGAAAATAGAAAAACA
2373306 AAAGAAAATA
1 AAAGAAAATA
2373316 AAAGGAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 11 0.46
18 5 0.21
19 8 0.33
ACGTcount: A:0.76, C:0.02, G:0.13, T:0.09
Consensus pattern (18 bp):
AAAGAAAATAGAAAAACA
Found at i:2373315 original size:10 final size:10
Alignment explanation
Indices: 2373294--2373349 Score: 53
Period size: 10 Copynumber: 5.4 Consensus size: 10
2373284 ATACAAAAGA
2373294 AAAAGAAAAAT
1 AAAAG-AAAAT
2373305 AAAAGAAAAT
1 AAAAGAAAAT
2373315 AAAAGGAAGAA-
1 AAAA-GAA-AAT
2373326 AAATA-AAAAT
1 AAA-AGAAAAT
*
2373336 AAAATAAAAT
1 AAAAGAAAAT
2373346 AAAA
1 AAAA
2373350 TTTAATTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
9 3 0.08
10 23 0.57
11 11 0.28
12 3 0.08
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (10 bp):
AAAAGAAAAT
Found at i:2373324 original size:25 final size:26
Alignment explanation
Indices: 2373296--2373344 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
2373286 ACAAAAGAAA
2373296 AAGAAAAAT-AAAAGAAAATAAAAGG
1 AAGAAAAATAAAAAGAAAATAAAAGG
*
2373321 AAGAAAAATAAAAATAAAATAAAA
1 AAGAAAAATAAAAAGAAAATAAAA
2373345 TAAAATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (26 bp):
AAGAAAAATAAAAAGAAAATAAAAGG
Found at i:2373328 original size:31 final size:31
Alignment explanation
Indices: 2373290--2373349 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
2373280 GAAGATACAA
2373290 AAGAAAAAGAAAAATAAAAGAAAATAAAAGG
1 AAGAAAAAGAAAAATAAAAGAAAATAAAAGG
* *
2373321 AAGAAAAATAAAAATAAAATAAAATAAAA
1 AAGAAAAAGAAAAATAAAAGAAAATAAAA
2373350 TTTAATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (31 bp):
AAGAAAAAGAAAAATAAAAGAAAATAAAAGG
Found at i:2373333 original size:5 final size:5
Alignment explanation
Indices: 2373300--2373350 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
2373290 AAGAAAAAGA
* * *
2373300 AAAAT AAAAG AAAAT AAAAGG AAGA- AAAAT AAAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT
2373351 TTAATTTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
4 3 0.08
5 27 0.71
6 8 0.21
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:2379324 original size:387 final size:387
Alignment explanation
Indices: 2378604--2379369 Score: 1212
Period size: 387 Copynumber: 2.0 Consensus size: 387
2378594 GAAGGATCCC
* * * *
2378604 TAAAAGAATAGGTTTGAGTCTACTAACCAAAACAAGGTTCAGGAGTCGTTTACATGTGGAGAAGG
1 TAAAAAAATAGGTTCGAGTCTACTAACCAAAACAAGGTTCAGAAGTCGATTACATGTGGAGAAGG
* *
2378669 TTATAGCACCCCTATATGCCTATCCAAAGGATGGTACCATTTTATTTTAAATTTATCCTAGGATC
66 TTATAGCACCCCCACATGCCTATCCAAAGGATGGTACCATTTTATTTTAAATTTATCCTAGGATC
* * *
2378734 TCGATTCTAATGGTTTTAAGTTTATATGTTAAATATTAAAAATAATTTATAAGATTCTTCCATCA
131 TCGACTCTAATGGTTTAAAGTTTATATGTTAAATATTAAAAATAATTTATAAGATTATTCCATCA
* * **
2378799 ATCTGGTAGAACTCTTTAAAATATTTTCTCACCTCAAGAGTATTAAAGGATCTTGTTGGATTTCT
196 ATCTGATAGAACTCTTTAAAATATTTTCTCACCTCAAAAGTATTAAAGGATCCAGTTGGATTTCT
*
2378864 TGAAGAGGCTCCGTCATCGGAAAAGCTTTTGTTAGTTCTATTTTTTTGTTGAAAATATATCTAAT
261 TGAAGAGGCTCCGTCATCGGAAAAGCTTTTGTTAGTTCTATTTTTTTGTTAAAAATATATCTAAT
2378929 TATTCCACCATTTGGACCAAATTAGAAATATTTTCTTATTTTGAATTTCTAAATAGGCCCTT
326 TATTCCACCATTTGGACCAAATTAGAAATATTTTCTTATTTTGAATTTCTAAATAGGCCCTT
* * * *
2378991 TAAAAAAATAGGTTCGAGTCTACTAACCAGAATAAGGTTC-GAAAGTCGATTACATGTGGGGGAG
1 TAAAAAAATAGGTTCGAGTCTACTAACCAAAACAAGGTTCAG-AAGTCGATTACATGTGGAGAAG
*
2379055 GTTATAGCACCCCCACATGCCTATCCAAAGGATGGTACCATTTTATTTTAAATTTATCCTAGGGT
65 GTTATAGCACCCCCACATGCCTATCCAAAGGATGGTACCATTTTATTTTAAATTTATCCTAGGAT
* **
2379120 TTCGACTCTAATGGTTTAAAGTTTATATGTTAAATATTGGAAATAATTTATAAGATTATTCCATC
130 CTCGACTCTAATGGTTTAAAGTTTATATGTTAAATATTAAAAATAATTTATAAGATTATTCCATC
* * *
2379185 AATCTGATAGAACT-TTTAAAAATATTTTTTCACCTTAAAAGTATTCAAGGATCCAGTTGGATTT
195 AATCTGATAGAACTCTTT-AAAATATTTTCTCACCTCAAAAGTATTAAAGGATCCAGTTGGATTT
* * * * *
2379249 CTTGGAGAGGCTCTGTCGTCGGAAAAGTTTTTGTTAGTTTTATTTTTTTGTTAAAAATATATCTA
259 CTTGAAGAGGCTCCGTCATCGGAAAAGCTTTTGTTAGTTCTATTTTTTTGTTAAAAATATATCTA
* *
2379314 ATTATTCCACCATTTGGGCCAAATTAGAAATATTTTTTTATTTTGAATTTCTAAAT
324 ATTATTCCACCATTTGGACCAAATTAGAAATATTTTCTTATTTTGAATTTCTAAAT
2379370 TTTTTCACCA
Statistics
Matches: 345, Mismatches: 32, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
386 4 0.01
387 341 0.99
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (387 bp):
TAAAAAAATAGGTTCGAGTCTACTAACCAAAACAAGGTTCAGAAGTCGATTACATGTGGAGAAGG
TTATAGCACCCCCACATGCCTATCCAAAGGATGGTACCATTTTATTTTAAATTTATCCTAGGATC
TCGACTCTAATGGTTTAAAGTTTATATGTTAAATATTAAAAATAATTTATAAGATTATTCCATCA
ATCTGATAGAACTCTTTAAAATATTTTCTCACCTCAAAAGTATTAAAGGATCCAGTTGGATTTCT
TGAAGAGGCTCCGTCATCGGAAAAGCTTTTGTTAGTTCTATTTTTTTGTTAAAAATATATCTAAT
TATTCCACCATTTGGACCAAATTAGAAATATTTTCTTATTTTGAATTTCTAAATAGGCCCTT
Found at i:2379771 original size:18 final size:17
Alignment explanation
Indices: 2379745--2379785 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
2379735 AATTCCAAAA
*
2379745 TTTTATATTGTTTTATGT
1 TTTTTTATTGTTTTAT-T
*
2379763 TTTTTTATTTTTTTATT
1 TTTTTTATTGTTTTATT
2379780 TTTTTT
1 TTTTTT
2379786 GGTTTGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.12, C:0.00, G:0.05, T:0.83
Consensus pattern (17 bp):
TTTTTTATTGTTTTATT
Found at i:2380068 original size:16 final size:16
Alignment explanation
Indices: 2380017--2380065 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
2380007 TAAATAACAC
*
2380017 ATAAAAAAATAAATTAA
1 ATAAACAAATAAA-TAA
*
2380034 TTAAACAAATAAATAA
1 ATAAACAAATAAATAA
2380050 ATAAACAAAT-AATAA
1 ATAAACAAATAAATAA
2380065 A
1 A
2380066 ATACAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 6 0.21
16 12 0.41
17 11 0.38
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (16 bp):
ATAAACAAATAAATAA
Found at i:2380982 original size:42 final size:43
Alignment explanation
Indices: 2380912--2381086 Score: 241
Period size: 44 Copynumber: 4.1 Consensus size: 43
2380902 TTTGTTTAAA
*
2380912 GCTCCTCTAAATAGAGGCTCAAC-G-ACTTTG-AGAAAATAAATT
1 GCTCCTCTAAATAGAGG--CAACAGAACTTTGAAAAAAATAAATT
* *
2380954 GCTCCTCTAAATAGAGACAACAGAACTTTGAAAAAAATAAAAT
1 GCTCCTCTAAATAGAGGCAACAGAACTTTGAAAAAAATAAATT
*
2380997 GCTCCTCTAAATAGAGGCAACAAAACTTTTGAAAAAAATAAATT
1 GCTCCTCTAAATAGAGGCAACAGAAC-TTTGAAAAAAATAAATT
* *
2381041 GCTCCTTTAAATAGAGGCAATAGAACTTTG-AAAAAATAAATT
1 GCTCCTCTAAATAGAGGCAACAGAACTTTGAAAAAAATAAATT
2381083 GCTC
1 GCTC
2381087 ATCAACAATC
Statistics
Matches: 120, Mismatches: 9, Indels: 8
0.88 0.07 0.06
Matches are distributed among these distances:
40 4 0.03
41 1 0.01
42 38 0.32
43 38 0.32
44 39 0.32
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.25
Consensus pattern (43 bp):
GCTCCTCTAAATAGAGGCAACAGAACTTTGAAAAAAATAAATT
Found at i:2381044 original size:44 final size:42
Alignment explanation
Indices: 2380912--2381086 Score: 226
Period size: 43 Copynumber: 4.1 Consensus size: 42
2380902 TTTGTTTAAA
* * *
2380912 GCTCCTCTAAATAGAGGC-TCAACGACTTTGAGAAAATAAATT
1 GCTCCTCTAAATAGAGGCAACAA-AACTTTGAAAAAATAAATT
* * *
2380954 GCTCCTCTAAATAGAGACAACAGAACTTTGAAAAAAATAAAAT
1 GCTCCTCTAAATAGAGGCAACAAAACTTTG-AAAAAATAAATT
2380997 GCTCCTCTAAATAGAGGCAACAAAACTTTTGAAAAAAATAAATT
1 GCTCCTCTAAATAGAGGCAACAAAAC-TTTG-AAAAAATAAATT
* * *
2381041 GCTCCTTTAAATAGAGGCAATAGAACTTTGAAAAAATAAATT
1 GCTCCTCTAAATAGAGGCAACAAAACTTTGAAAAAATAAATT
2381083 GCTC
1 GCTC
2381087 ATCAACAATC
Statistics
Matches: 118, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
42 39 0.33
43 40 0.34
44 39 0.33
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.25
Consensus pattern (42 bp):
GCTCCTCTAAATAGAGGCAACAAAACTTTGAAAAAATAAATT
Found at i:2393141 original size:28 final size:27
Alignment explanation
Indices: 2393090--2393142 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
2393080 TATTTAATTC
*
2393090 TAAAATTTTATATTGTTTTATGTTTTT
1 TAAAATTTTATATTATTTTATGTTTTT
* *
2393117 TAAAATTTTTTAATTATTTTTTGTTT
1 TAAAATTTTAT-ATTATTTTATGTTT
2393143 GAAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (27 bp):
TAAAATTTTATATTATTTTATGTTTTT
Found at i:2393297 original size:27 final size:27
Alignment explanation
Indices: 2393262--2393315 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
2393252 TGAAATTTCT
2393262 ATAAATTCTATAATTGGATTATTAATA
1 ATAAATTCTATAATTGGATTATTAATA
2393289 ATAAATTCTATAATTGGATTATTAATA
1 ATAAATTCTATAATTGGATTATTAATA
2393316 TTCATTCTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (27 bp):
ATAAATTCTATAATTGGATTATTAATA
Found at i:2396608 original size:18 final size:21
Alignment explanation
Indices: 2396590--2396629 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2396580 TTTTGAAATT
2396590 TTGG-AATT-TTTATTTATTTA
1 TTGGTAATTATTTATTTA-TTA
2396610 TTGGTAATTATTTATTTATT
1 TTGGTAATTATTTATTTATT
2396630 GTAAGGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 6 0.33
22 8 0.44
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (21 bp):
TTGGTAATTATTTATTTATTA
Found at i:2398650 original size:14 final size:14
Alignment explanation
Indices: 2398631--2398685 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
2398621 AAAATTAATA
* *
2398631 AAATATTATTTTTT
1 AAATATTAATATTT
2398645 AAATATTAATATTT
1 AAATATTAATATTT
*
2398659 AAATATATAATTATAT
1 AAATAT-TAA-TATTT
2398675 AAATATATAAT
1 AAATAT-TAAT
2398686 TAAAAAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
14 18 0.50
15 4 0.11
16 14 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AAATATTAATATTT
Found at i:2398677 original size:16 final size:16
Alignment explanation
Indices: 2398623--2398687 Score: 66
Period size: 16 Copynumber: 4.3 Consensus size: 16
2398613 CCCTACCCAA
2398623 AATTA-ATAAA-ATAT
1 AATTATATAAATATAT
* * *
2398637 TATTTTTTAAATAT-T
1 AATTATATAAATATAT
*
2398652 AA-TATTTAAATATAT
1 AATTATATAAATATAT
2398667 AATTATATAAATATAT
1 AATTATATAAATATAT
2398683 AATTA
1 AATTA
2398688 AAAAATTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
14 13 0.32
15 9 0.22
16 19 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTATATAAATATAT
Found at i:2399739 original size:96 final size:92
Alignment explanation
Indices: 2399631--2399992 Score: 387
Period size: 96 Copynumber: 3.8 Consensus size: 92
2399621 TAAATTCATA
* *
2399631 AATTCTACCAAACTATTGCCAGATTTAAATTTCAAAATTAAATGTTACCAAATTATTAGAAGGTT
1 AATTCTACCAAACTATTG--AGATTTAAATTTCAAAATTAAATGTTACCAAACTATT-GAAAGTT
* *
2399696 TAATTATTTTTGTTTAAAAAATAAAATTTTT
63 TAATTATTTTT-TTTAAAAAACAAAATTTTC
* *
2399727 AATTCTACCAAACTATTGGTAGGTTTAAATCTCAAAATTAAATGTTACCAAACTATTGGAAAGTT
1 AATTCTACCAAACTATT-G-AGATTTAAATTTCAAAATTAAATGTTACCAAACTATT-GAAAGTT
*
2399792 TAATTATTTTTATTTAAAAAACCAAATTTTC
63 TAATTATTTTT-TTTAAAAAACAAAATTTTC
* *
2399823 AATTCTACCAAATTATTAGATGATTT-AATCTT-AAAATTAAATCTTACCAAACTATTGAAAAGT
1 AATTCTACCAAACTATT-GA-GATTTAAAT-TTCAAAATTAAATGTTACCAAACTATTG-AAAGT
2399886 TTAATTA--TTTTTT-AAAAACAAAATTTTC
62 TTAATTATTTTTTTTAAAAAACAAAATTTTC
* * * *
2399914 AATCCTACCAAACTATTGGAGAATTTAAATCTT-AGAGTTAAAAT-TTACCAAACTATTGAAAAA
1 AATTCTACCAAACTATT-GAG-ATTTAAAT-TTCAAAATT-AAATGTTACCAAACTATTG-AAAG
**
2399977 TTTAACGATTTTTTTT
61 TTTAATTATTTTTTTT
2399993 TCTTAAGCTG
Statistics
Matches: 233, Mismatches: 24, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
90 1 0.00
91 35 0.15
92 37 0.16
93 7 0.03
94 7 0.03
95 39 0.17
96 106 0.45
97 1 0.00
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (92 bp):
AATTCTACCAAACTATTGAGATTTAAATTTCAAAATTAAATGTTACCAAACTATTGAAAGTTTAA
TTATTTTTTTTAAAAAACAAAATTTTC
Found at i:2399964 original size:187 final size:190
Alignment explanation
Indices: 2399631--2399981 Score: 450
Period size: 187 Copynumber: 1.9 Consensus size: 190
2399621 TAAATTCATA
* * *
2399631 AATTCTACCAAACTATTGCCAGATTTAAATTTCAAAATTAAATGTTACCAAATTATTAGAAGGTT
1 AATTCTACCAAACTATTG-CAGATTTAAATTTCAAAATTAAATCTTACCAAACTATTAGAAAGTT
* * * *
2399696 TAATTATTTTTGTTTAAAAAATAAAATTTTTAATTCTACCAAACTATTGGTAGGTTTAAATCTCA
65 TAATTA-TTTTGTTTAAAAAACAAAATTTTCAATCCTACCAAACTATTGGTAGATTTAAATCTCA
* *
2399761 AAATTAAATGTTACCAAACTATTGGAAAGTTTAATTATTTTTATTTAAAAAACCAAATTTTC
129 AAATTAAATGTTACCAAACTATTGAAAAATTTAATTATTTTTATTTAAAAAACCAAATTTTC
*
2399823 AATTCTACCAAATTATTAG-ATGATTT-AATCTT-AAAATTAAATCTTACCAAACTATT-GAAAA
1 AATTCTACCAAACTATT-GCA-GATTTAAAT-TTCAAAATTAAATCTTACCAAACTATTAG-AAA
2399884 GTTTAATTA-TTT-TTT-AAAAACAAAATTTTCAATCCTACCAAACTATTGG-AGAATTTAAATC
62 GTTTAATTATTTTGTTTAAAAAACAAAATTTTCAATCCTACCAAACTATTGGTAG-ATTTAAATC
* * *
2399945 TTAGAGTTAAAAT-TTACCAAACTATTGAAAAATTTAA
126 TCAAAATT-AAATGTTACCAAACTATTGAAAAATTTAA
2399982 CGATTTTTTT
Statistics
Matches: 140, Mismatches: 13, Indels: 17
0.82 0.08 0.10
Matches are distributed among these distances:
186 2 0.01
187 66 0.47
188 7 0.05
189 3 0.02
190 1 0.01
191 37 0.26
192 23 0.16
193 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (190 bp):
AATTCTACCAAACTATTGCAGATTTAAATTTCAAAATTAAATCTTACCAAACTATTAGAAAGTTT
AATTATTTTGTTTAAAAAACAAAATTTTCAATCCTACCAAACTATTGGTAGATTTAAATCTCAAA
ATTAAATGTTACCAAACTATTGAAAAATTTAATTATTTTTATTTAAAAAACCAAATTTTC
Found at i:2400536 original size:167 final size:168
Alignment explanation
Indices: 2400327--2400658 Score: 528
Period size: 167 Copynumber: 2.0 Consensus size: 168
2400317 GCTACGCTCA
* *
2400327 TTCGAATGAGTGTTATAACATTTCTCATATATTACCATGCTCTCAGACTT-AATTCTAGTTTCAT
1 TTCGAATGAGTGCTATAACATTTCTCATATATAACCATGCTCTCAGACTTAAATT-TAGTTTCAT
* *
2400391 GGATTAGAATTTAAATTTTAAATATATTTGAGTCAAGCTTAAAAC-TTTTTTTTAAAATAATACA
65 GGATTAAAATTTAAATTTTAAAGATATTTGAGTCAAGCTTAAAACTTTTTTTTTAAAATAATACA
2400455 GATTTAGTTA-AGTGACTAATCGCGCCTAAACAAAAATCC
130 GATTTAGTTAGA-TGACTAATCGCGCCTAAACAAAAATCC
* *
2400494 TTCGAAT-AGGTGCTATAACCTTTCTCATATATAACCATGCTCTCAGACTTAAATTTAGTTTCGT
1 TTCGAATGA-GTGCTATAACATTTCTCATATATAACCATGCTCTCAGACTTAAATTTAGTTTCAT
* *
2400558 GGATTAAAATTTAAATTTTAAAGATATTTGAGTCAAGCTTAAAACTTTTTTTTTAGAATAGTACA
65 GGATTAAAATTTAAATTTTAAAGATATTTGAGTCAAGCTTAAAACTTTTTTTTTAAAATAATACA
*
2400623 GATTTAGTTAGATGACTAATCGTGCCTAAACAAAAA
130 GATTTAGTTAGATGACTAATCGCGCCTAAACAAAAA
2400659 AAGATTGATT
Statistics
Matches: 152, Mismatches: 9, Indels: 7
0.90 0.05 0.04
Matches are distributed among these distances:
166 1 0.01
167 96 0.63
168 54 0.36
169 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (168 bp):
TTCGAATGAGTGCTATAACATTTCTCATATATAACCATGCTCTCAGACTTAAATTTAGTTTCATG
GATTAAAATTTAAATTTTAAAGATATTTGAGTCAAGCTTAAAACTTTTTTTTTAAAATAATACAG
ATTTAGTTAGATGACTAATCGCGCCTAAACAAAAATCC
Found at i:2408518 original size:29 final size:30
Alignment explanation
Indices: 2408467--2408527 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
2408457 AAATAGTAAT
* *
2408467 AATAATATTAAAAAGAATAAAAA-ATAAAA
1 AATAATATTAAAAAGAAAAAAAAGAGAAAA
2408496 AATAATATTAAAAA-AAAAGAAAAGAGAAAA
1 AATAATATTAAAAAGAAAA-AAAAGAGAAAA
2408526 AA
1 AA
2408528 GGAATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 3 0.11
29 18 0.64
30 7 0.25
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (30 bp):
AATAATATTAAAAAGAAAAAAAAGAGAAAA
Found at i:2410885 original size:37 final size:39
Alignment explanation
Indices: 2410844--2410947 Score: 99
Period size: 39 Copynumber: 2.7 Consensus size: 39
2410834 TTTTGTATTT
* *
2410844 TATGTATTGTATTATTTATTATTATTATG-TATTA-ATA
1 TATGTATTATATTATTTATTATTATTATGTTAATATATA
* *
2410881 TATGTA-TATATTTATTTATTTATT-TTTTGTTAATATTTA
1 TATGTATTATA-TTATTTA-TTATTATTATGTTAATATATA
* *
2410920 TGTGTATTTTATTATTTATGTATTATTA
1 TATGTATTATATTATTTAT-TATTATTA
2410948 CTAATATGTA
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
36 3 0.06
37 17 0.32
38 10 0.19
39 18 0.34
40 5 0.09
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (39 bp):
TATGTATTATATTATTTATTATTATTATGTTAATATATA
Found at i:2410987 original size:69 final size:70
Alignment explanation
Indices: 2410832--2410990 Score: 170
Period size: 69 Copynumber: 2.3 Consensus size: 70
2410822 TTTTTCTTCT
* *
2410832 TCTTTTGTATTTTATGTATTGTATTATTTATTATTATTATGTATTAATATATGTATATATTTATT
1 TCTTTTTTATTTTATTTATTGTATTATTTATTATTATTATGTATTAATATATGTATATA-TTATT
2410897 TATTTA
65 TATTTA
** *
2410903 T-TTTTTGT-TAATATTTATGTGTA-T-TTTATTATTTATGTAT-TATTACTAATATGTATATA-
1 TCTTTTT-TATTTTATTTAT-TGTATTATTTATTA-TTAT-TATGTATTAAT-ATATGTATATAT
2410962 TATTT-TTTA
61 TATTTATTTA
2410971 TCTTTTTTATTTTATTTATT
1 TCTTTTTTATTTTATTTATT
2410991 TTTGTATTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
68 7 0.09
69 25 0.34
70 22 0.30
71 20 0.27
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.65
Consensus pattern (70 bp):
TCTTTTTTATTTTATTTATTGTATTATTTATTATTATTATGTATTAATATATGTATATATTATTT
ATTTA
Found at i:2410991 original size:73 final size:67
Alignment explanation
Indices: 2410858--2411000 Score: 157
Period size: 71 Copynumber: 2.0 Consensus size: 67
2410848 TATTGTATTA
2410858 TTTATTATTATTATGTATTAATATATGTATATATTTATTTATTTATTTTTTGTTAATATTTATGT
1 TTTATTATTATTATGTATTAATATATGTATATATTTATTTATTTATTTTTTGTTAATATTT-T-T
2410923 GTAT
64 GTAT
* * *
2410927 TTTATTATTTATGTAT-TATTACTAATATGTATATATATTTTTTATCTT-TTTTATT-TTATTTA
1 TTTATTA-TTAT-TATGTATTAAT-ATATGTATATAT-TTATTTAT-TTATTTT-TTGTTA-ATA
2410989 TTTTTGTAT
59 TTTTTGTAT
2410998 TTT
1 TTT
2411001 TACTTATCTA
Statistics
Matches: 64, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
69 7 0.11
70 10 0.16
71 23 0.36
72 15 0.23
73 9 0.14
ACGTcount: A:0.27, C:0.01, G:0.06, T:0.66
Consensus pattern (67 bp):
TTTATTATTATTATGTATTAATATATGTATATATTTATTTATTTATTTTTTGTTAATATTTTTGT
AT
Found at i:2411002 original size:18 final size:18
Alignment explanation
Indices: 2410967--2411000 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2410957 ATATATATTT
*
2410967 TTTATCTTTTTTATTTTA
1 TTTATCTTTTGTATTTTA
2410985 TTTAT-TTTTGTATTTT
1 TTTATCTTTTGTATTTT
2411001 TACTTATCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTATCTTTTGTATTTTA
Found at i:2411954 original size:12 final size:11
Alignment explanation
Indices: 2411934--2412079 Score: 50
Period size: 12 Copynumber: 12.4 Consensus size: 11
2411924 TTTTTTGGAA
2411934 TATTTTTTATT
1 TATTTTTTATT
2411945 TATTTGTTTATT
1 TATTT-TTTATT
*
2411957 TGTTTTATTATT
1 TATTTT-TTATT
*
2411969 TCATTTATT-TT
1 T-ATTTTTTATT
**
2411980 T-TTTTAGATT
1 TATTTTTTATT
* *
2411990 AGATTTATTTA-A
1 -TATTT-TTTATT
2412002 TATTTTTTATCTT
1 TATTTTTTA--TT
*
2412015 TATCTTATT-TT
1 TAT-TTTTTATT
2412026 TATTTTTGT-TT
1 TATTTTT-TATT
2412037 TACCTTTCTTTATAT
1 TA--TTT-TTTAT-T
*
2412052 TTTATTTTTATT
1 TAT-TTTTTATT
2412064 TATTTCTTTATT
1 TATTT-TTTATT
2412076 TATT
1 TATT
2412080 CTATTTTCTT
Statistics
Matches: 100, Mismatches: 16, Indels: 37
0.65 0.10 0.24
Matches are distributed among these distances:
9 3 0.03
10 9 0.09
11 25 0.25
12 34 0.34
13 18 0.18
14 9 0.09
15 2 0.02
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (11 bp):
TATTTTTTATT
Found at i:2412065 original size:17 final size:17
Alignment explanation
Indices: 2412005--2412076 Score: 56
Period size: 17 Copynumber: 4.2 Consensus size: 17
2411995 TATTTAATAT
*
2412005 TTTTTATCTT-TATCTTA
1 TTTTTAT-TTATATTTTA
* *
2412022 TTTTTATTTTTGTTTTA
1 TTTTTATTTATATTTTA
** *
2412039 CCTTTCTTTATATTTTA
1 TTTTTATTTATATTTTA
*
2412056 TTTTTATTTATTTCTTTA
1 TTTTTATTTATAT-TTTA
2412074 TTT
1 TTT
2412077 ATTCTATTTT
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
16 2 0.05
17 33 0.79
18 7 0.17
ACGTcount: A:0.15, C:0.08, G:0.01, T:0.75
Consensus pattern (17 bp):
TTTTTATTTATATTTTA
Found at i:2412079 original size:27 final size:27
Alignment explanation
Indices: 2411993--2412086 Score: 75
Period size: 27 Copynumber: 3.3 Consensus size: 27
2411983 TTAGATTAGA
* *
2411993 TTTATTTAATATTTTTTATCTTTATCTTATT
1 TTTATTT-TTATTTATT-TCTTTAT-TTA-T
*
2412024 TTTATTTTTGTTTTACCTTTCTTTA--TAT
1 TTTATTTTT-ATTTA--TTTCTTTATTTAT
2412052 TTTATTTTTATTTATTTCTTTATTTAT
1 TTTATTTTTATTTATTTCTTTATTTAT
*
2412079 TCTATTTT
1 TTTATTTT
2412087 CTTTAAATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
25 8 0.15
27 14 0.26
28 10 0.19
29 2 0.04
30 1 0.02
31 10 0.19
32 6 0.11
33 2 0.04
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.73
Consensus pattern (27 bp):
TTTATTTTTATTTATTTCTTTATTTAT
Found at i:2412379 original size:59 final size:59
Alignment explanation
Indices: 2412094--2412511 Score: 574
Period size: 61 Copynumber: 7.0 Consensus size: 59
2412084 TTTCTTTAAA
** *
2412094 TAAAAATCAAAATTTCCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAAT-AAAATTT-CAAAAAAAGGAT-TTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCT
* **
2412157 TGAAAATCAAAATTTTCAAAAAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAAT-AAAA-TTTCAAAAAAAGGATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCT
2412218 TAAAAATAAAATTTCAAAAAAAAGAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAATAAAATTTC-AAAAAAAG-GATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
*
2412279 TAAAAATAAAATTTCAAAAAAAGAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCT
1 TAAAAATAAAATTTCAAAAAAAG-GATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
* * *
2412339 TAAAAATAAATTTTCAGAAAAAGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCT
1 TAAAAATAAAATTTCAAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
*
2412398 TAAAAATAAAATTTC-AAAAAAGGATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAATAAAATTTCAAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
** * * *
2412456 CGAAATTAAAA-TTCAAAAAAA-TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 TAAAAATAAAATTTCAAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
2412512 CTGAACAAGA
Statistics
Matches: 334, Mismatches: 16, Indels: 16
0.91 0.04 0.04
Matches are distributed among these distances:
57 37 0.11
58 54 0.16
59 54 0.16
60 76 0.23
61 83 0.25
62 5 0.01
63 22 0.07
64 3 0.01
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (59 bp):
TAAAAATAAAATTTCAAAAAAAGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
Found at i:2416400 original size:16 final size:16
Alignment explanation
Indices: 2416343--2416417 Score: 61
Period size: 16 Copynumber: 4.8 Consensus size: 16
2416333 ACAATGGATG
2416343 AAAAATGAGAAAAGA-GA
1 AAAAATGA-AAAA-ATGA
*
2416360 AAAAA--AAAAAA-AA
1 AAAAATGAAAAAATGA
* *
2416373 AAAAAGGGAAAAAT-A
1 AAAAATGAAAAAATGA
2416388 AGAAAATGAAAAAATGA
1 A-AAAATGAAAAAATGA
2416405 AAAAATGAAAAAA
1 AAAAATGAAAAAA
2416418 GAGATCCAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
13 7 0.14
14 4 0.08
15 8 0.16
16 23 0.47
17 7 0.14
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.07
Consensus pattern (16 bp):
AAAAATGAAAAAATGA
Found at i:2417743 original size:42 final size:41
Alignment explanation
Indices: 2417660--2418475 Score: 1079
Period size: 41 Copynumber: 20.1 Consensus size: 41
2417650 ATGATTGTCA
2417660 AGGAGCAATTTAC-TTT-CAAAGTCCGT-TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCCAAAGT-CGTGTGCCTCTGTTTAG
* *
2417699 AGGAGCTATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAG
1 AGGAGCAATTTACTTTTCCAAAGTCGT-GTGCCTCTGTTTAG
2417741 AGGAGCAATTTACTTTT-CAAAGTTCGT-TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCCAAAG-TCGTGTGCCTCTGTTTAG
*
2417781 AGGAGCAATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAG
1 AGGAGCAATTTACTTTTCCAAAGTCGT-GTGCCTCTGTTTAG
*
2417823 AGGAGCAATTTACTTTTCCAAAGTCGTGGTACCTCT-TTTAG
1 AGGAGCAATTTACTTTTCCAAAGTCGT-GTGCCTCTGTTTAG
2417864 AGGAGGCAATTT-CTTTT-CAAAGTTCGT-TGCCTCTGTTTAG
1 AGGA-GCAATTTACTTTTCCAAAG-TCGTGTGCCTCTGTTTAG
*
2417904 AGGAGCAATTTACTTTTTCCAAAGTCGTGGTACCTCCTGTTTAG
1 AGGAGCAATTTAC-TTTTCCAAAGTCGT-GTGCCT-CTGTTTAG
*
2417948 AGGAGCAATTTACTTTTCAAAAGTTCGT-TGCC-CTTGTTCTAG
1 AGGAGCAATTTACTTTTCCAAAG-TCGTGTGCCTC-TGTT-TAG
2417990 AGGAGCAATTTACTTTTCC-AAGTCGT-TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCCAAAGTCGTGTGCCTCTGTTTAG
*
2418029 AGGAGCAATTTAC--TTCAAAAGTC--GTG-----GTTTAG
1 AGGAGCAATTTACTTTTCCAAAGTCGTGTGCCTCTGTTTAG
2418061 AGGAGCAATTTAC-TTTCCAAAGTCGTG-GTCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCCAAAGTCGTGTG-CCTCTGTTTAG
2418101 AGGAGCAATTTACTTTTCCAAAGTCGTGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCCAAAGTCGTGTGCCTCTGTTTAG
2418142 AGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCCAAAGTCGT-GTGCCTCTGTTTAG
2418183 AGGAGCAATTTAC-TTT-CAAAGTTCGT-TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCCAAAG-TCGTGTGCCTCTGTTTAG
2418222 AGGAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTG-TTAG
1 AGGAGCAATTTACTTTTCCAAAGTCGT-GTGCCTCTGTTTAG
2418263 AGGAGCAATTTACTTTTCC-AAGTCGT-TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCCAAAGTCGTGTGCCTCTGTTTAG
*
2418302 AGGAGCAATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAG
1 AGGAGCAATTTACTTTTCCAAAGTCGT-GTGCCTCTGTTTAG
*
2418344 AGGAGCAATTTAC-TTTCCAAAAGTCGTGTACCTCTGTTTAG
1 AGGAGCAATTTACTTTTCC-AAAGTCGTGTGCCTCTGTTTAG
*
2418385 AGGAGCAATTTAC-TTTCCAAAAGTCGTGGTGCCTCTATTTAG
1 AGGAGCAATTTACTTTTCC-AAAGTCGT-GTGCCTCTGTTTAG
*
2418427 AGGAGCAATTTA-TGTTTCTCAAAGTCGTTGAGCCTCTGTTTAG
1 AGGAGCAATTTACT-TTTC-CAAAGTCG-TGTGCCTCTGTTTAG
2418470 AGGAGC
1 AGGAGC
2418476 TTTGGTAAAA
Statistics
Matches: 710, Mismatches: 17, Indels: 96
0.86 0.02 0.12
Matches are distributed among these distances:
32 19 0.03
33 9 0.01
34 1 0.00
35 1 0.00
37 5 0.01
38 13 0.02
39 90 0.13
40 124 0.17
41 197 0.28
42 182 0.26
43 42 0.06
44 27 0.04
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCCAAAGTCGTGTGCCTCTGTTTAG
Found at i:2418498 original size:11 final size:11
Alignment explanation
Indices: 2418482--2418516 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
2418472 GAGCTTTGGT
2418482 AAAAAAAAA-A
1 AAAAAAAAACA
2418492 AAAAAAAAACA
1 AAAAAAAAACA
2418503 AAAAAAAAACA
1 AAAAAAAAACA
2418514 AAA
1 AAA
2418517 TAACCAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:2418507 original size:19 final size:19
Alignment explanation
Indices: 2418483--2418527 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
2418473 AGCTTTGGTA
2418483 AAAAAAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAAAAAC
* *
2418502 AAAAAAAAAACAAAATAAC
1 AAAAAAAAAAAAAAAAAAC
*
2418521 CAAAAAA
1 AAAAAAA
2418528 TGTTGAGTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.89, C:0.09, G:0.00, T:0.02
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAAAAC
Found at i:2418507 original size:20 final size:20
Alignment explanation
Indices: 2418482--2418527 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2418472 GAGCTTTGGT
2418482 AAAAAAAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAAAAAAC
* * *
2418502 AAAAAAAAAACAAAATAACC
1 AAAAAAAAAAAAAAAAAAAC
2418522 AAAAAA
1 AAAAAA
2418528 TGTTGAGTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.89, C:0.09, G:0.00, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAAAAAC
Found at i:2418527 original size:1 final size:1
Alignment explanation
Indices: 2418482--2418516 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
2418472 GAGCTTTGGT
* *
2418482 AAAAAAAAAAAAAAAAAAACAAAAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2418517 TAACCAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2418653 original size:20 final size:21
Alignment explanation
Indices: 2418615--2418653 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2418605 CTGTAGACAC
2418615 TCAATTGGGTCCAGGCCCAGA
1 TCAATTGGGTCCAGGCCCAGA
*
2418636 TCAATTGGG-CCTGGCCCA
1 TCAATTGGGTCCAGGCCCA
2418654 AATGGGTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.21, C:0.31, G:0.28, T:0.21
Consensus pattern (21 bp):
TCAATTGGGTCCAGGCCCAGA
Found at i:2418775 original size:35 final size:36
Alignment explanation
Indices: 2418759--2418844 Score: 72
Period size: 35 Copynumber: 2.5 Consensus size: 36
2418749 ATATATGTAT
* * * *
2418759 ATATT-TATTTATTTATTTTTTGTTAATATTTATGT
1 ATATTATATTTATTTATGTATTATTAATAATTATGT
* * *
2418794 GTATTTTA-TTATTTATGTATTATTACTAA-TATGT
1 ATATTATATTTATTTATGTATTATTAATAATTATGT
2418828 ATATATATATTT-TTTAT
1 ATAT-TATATTTATTTAT
2418845 CTTTTTTATT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
34 8 0.20
35 28 0.70
36 4 0.10
ACGTcount: A:0.29, C:0.01, G:0.06, T:0.64
Consensus pattern (36 bp):
ATATTATATTTATTTATGTATTATTAATAATTATGT
Found at i:2418814 original size:16 final size:16
Alignment explanation
Indices: 2418710--2418814 Score: 60
Period size: 16 Copynumber: 6.6 Consensus size: 16
2418700 TCTTTTGTAT
*
2418710 TTTATGTATTGTATTA
1 TTTATGTATTTTATTA
2418726 TTTAT-TA--TTATTA
1 TTTATGTATTTTATTA
*
2418739 -TTATGTA-TTAATATA
1 TTTATGTATTTTAT-TA
* *
2418754 TGTATATA-TTTATTTA
1 TTTATGTATTTTA-TTA
* * *
2418770 TTTATTTTTTGTTAATA
1 TTTATGTATT-TTATTA
2418787 TTTATGTGTATTTTATTA
1 TTTA--TGTATTTTATTA
2418805 TTTATGTATT
1 TTTATGTATT
2418815 ATTACTAATA
Statistics
Matches: 68, Mismatches: 12, Indels: 18
0.69 0.12 0.18
Matches are distributed among these distances:
12 4 0.06
13 7 0.10
14 3 0.04
15 4 0.06
16 26 0.38
17 8 0.12
18 12 0.18
19 4 0.06
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.65
Consensus pattern (16 bp):
TTTATGTATTTTATTA
Found at i:2418860 original size:71 final size:74
Alignment explanation
Indices: 2418700--2418863 Score: 182
Period size: 71 Copynumber: 2.3 Consensus size: 74
2418690 TTTTTCTTCT
* * * *
2418700 TCTTTTGTATTTTATGTATTGTATTATTTATTATTATTATTATGTATTAATATATGTATATATTT
1 TCTTTTTTATTTTATTTATTGTATTATTTATTATTATTATTATGTACTAATATATGTATATATAT
2418765 ATTTATTTA
66 ATTTATTTA
**
2418774 T-TTTTTGT-TAATATTTATGTGTA-T-TTTATTATTTATGTATTAT-TACT-A-ATATGTATAT
1 TCTTTTT-TATTTTATTTAT-TGTATTATTTATTA-TTAT-TATTATGTACTAATATATGTATAT
2418832 ATATATTT-TTTA
62 ATATATTTATTTA
2418844 TCTTTTTTATTTTATTTATT
1 TCTTTTTTATTTTATTTATT
2418864 TTTGTATTTT
Statistics
Matches: 76, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
70 7 0.09
71 30 0.39
72 8 0.11
73 19 0.25
74 12 0.16
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (74 bp):
TCTTTTTTATTTTATTTATTGTATTATTTATTATTATTATTATGTACTAATATATGTATATATAT
ATTTATTTA
Found at i:2418872 original size:83 final size:76
Alignment explanation
Indices: 2418702--2418873 Score: 177
Period size: 83 Copynumber: 2.1 Consensus size: 76
2418692 TTTCTTCTTC
2418702 TTTTGTATTTTATGTATTGTATTATTTATTATTATTATTATGTATTAATATATGTATATATTTAT
1 TTTTGTATTTTATGTATTGTATTATTTATTATTATTATTATGTATTAATATATGTATATATTTAT
2418767 TTATTTATTTT
66 TTATTTATTTT
* * * *
2418778 TTGTTAATATTTATGTGTATTTTATTATTTATGTATTATTACTAATATGTA-TATATATAT-TTT
1 TT-TT-GTATTT-TATGTATTGTATTATTTAT-TATTATTA-T--TATGTATTA-ATATATGTAT
* *
2418841 TTATCTTTTTTATTTTATTTAT
58 ATAT-TTATTTA-TTTATTT-T
2418863 TTTTGTATTTT
1 TTTTGTATTTT
2418874 TACTTATCTA
Statistics
Matches: 78, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
76 2 0.03
77 2 0.03
78 5 0.06
79 17 0.22
80 8 0.10
81 1 0.01
82 8 0.10
83 23 0.29
84 9 0.12
85 3 0.04
ACGTcount: A:0.26, C:0.01, G:0.06, T:0.66
Consensus pattern (76 bp):
TTTTGTATTTTATGTATTGTATTATTTATTATTATTATTATGTATTAATATATGTATATATTTAT
TTATTTATTTT
Found at i:2418875 original size:18 final size:18
Alignment explanation
Indices: 2418840--2418873 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2418830 ATATATATTT
*
2418840 TTTATCTTTTTTATTTTA
1 TTTATCTTTTGTATTTTA
2418858 TTTAT-TTTTGTATTTT
1 TTTATCTTTTGTATTTT
2418874 TACTTATCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTATCTTTTGTATTTTA
Found at i:2418890 original size:53 final size:55
Alignment explanation
Indices: 2418795--2418918 Score: 137
Period size: 53 Copynumber: 2.3 Consensus size: 55
2418785 TATTTATGTG
* * * * * *
2418795 TATTTTATTATTTATGTATTATTACTAATATGTATATATATATTTTTTATCTTTTT
1 TATTTTATTATTTTTGTATTATTACT-ATATCTATATATATATATCTGATATTTTT
*
2418851 TATTTTATTTATTTTTGTATTTTTACT-TATCTA-AT-TATATATCTGATATTTTT
1 TATTTTA-TTATTTTTGTATTATTACTATATCTATATATATATATCTGATATTTTT
*
2418904 TTTTTTATTATTTTT
1 TATTTTATTATTTTT
2418919 ATCCTATAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
52 8 0.14
53 20 0.34
54 2 0.03
55 5 0.08
56 7 0.12
57 17 0.29
ACGTcount: A:0.25, C:0.04, G:0.03, T:0.68
Consensus pattern (55 bp):
TATTTTATTATTTTTGTATTATTACTATATCTATATATATATATCTGATATTTTT
Found at i:2419365 original size:31 final size:31
Alignment explanation
Indices: 2419330--2419422 Score: 123
Period size: 31 Copynumber: 3.0 Consensus size: 31
2419320 AGATTCCGGC
* *
2419330 GAAAATTTCGGCAAAGTTTGAATTTTTCGAT
1 GAAAATTTCGACGAAGTTTGAATTTTTCGAT
**
2419361 GAAAATTTCGACGAAGTTTGAATTTTTCGGC
1 GAAAATTTCGACGAAGTTTGAATTTTTCGAT
* * *
2419392 AAAAATTCCAACGAAGTTTGAATTTTTCGAT
1 GAAAATTTCGACGAAGTTTGAATTTTTCGAT
2419423 TAACATTCCG
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (31 bp):
GAAAATTTCGACGAAGTTTGAATTTTTCGAT
Found at i:2419431 original size:31 final size:31
Alignment explanation
Indices: 2419343--2419431 Score: 115
Period size: 31 Copynumber: 2.9 Consensus size: 31
2419333 AATTTCGGCA
* * *
2419343 AAGTTTGAATTTTTCGATGAAAATTTCGACG
1 AAGTTTGAATTTTTCGATAAAAATTCCAACG
**
2419374 AAGTTTGAATTTTTCGGCAAAAATTCCAACG
1 AAGTTTGAATTTTTCGATAAAAATTCCAACG
* *
2419405 AAGTTTGAATTTTTCGATTAACATTCC
1 AAGTTTGAATTTTTCGATAAAAATTCC
2419432 GGCCAACCTT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (31 bp):
AAGTTTGAATTTTTCGATAAAAATTCCAACG
Found at i:2420029 original size:17 final size:17
Alignment explanation
Indices: 2419969--2420040 Score: 56
Period size: 17 Copynumber: 4.2 Consensus size: 17
2419959 TATTTAATAT
*
2419969 TTTTTATCTT-TATCTTA
1 TTTTTAT-TTATATTTTA
* *
2419986 TTTTTATTTTTGTTTTA
1 TTTTTATTTATATTTTA
** *
2420003 CCTTTCTTTATATTTTA
1 TTTTTATTTATATTTTA
*
2420020 TTTTTATTTATTTCTTTA
1 TTTTTATTTATAT-TTTA
2420038 TTT
1 TTT
2420041 ATTCTATTTT
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
16 2 0.05
17 33 0.79
18 7 0.17
ACGTcount: A:0.15, C:0.08, G:0.01, T:0.75
Consensus pattern (17 bp):
TTTTTATTTATATTTTA
Done.