Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold305
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: 704983
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
File 5 of 5
Found at i:580393 original size:20 final size:20
Alignment explanation
Indices: 580368--580444 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
580358 AGTTACCCAG
*
580368 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTCTTCA
* * *
580388 ATGTATCGATATATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
*
580408 AGGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
580428 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
580445 ATCCTTTTAC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:583386 original size:16 final size:16
Alignment explanation
Indices: 583365--583409 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
583355 AAATTTTTAT
583365 AAATATTTTTTTAGAA
1 AAATATTTTTTTAGAA
583381 AAATATTTTTTTAGAA
1 AAATATTTTTTTAGAA
583397 AAATATTTTTTTA
1 AAATATTTTTTTA
583410 TATCTTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (16 bp):
AAATATTTTTTTAGAA
Found at i:584002 original size:27 final size:25
Alignment explanation
Indices: 583961--584052 Score: 69
Period size: 27 Copynumber: 3.5 Consensus size: 25
583951 TTTACAAAAA
*
583961 AATAAATCATGAATATATCATAATTT
1 AATAAAT-ATAAATATATCATAATTT
* *
583987 ATATAAATATATA-ATATCTTAAATTT
1 A-ATAAATATAAATATATCAT-AATTT
* * *
584013 AATATAATATAAAAATAACATAAATATA
1 AATA-AATATAAATATATCAT-AAT-TT
584041 AATAAATATAAA
1 AATAAATATAAA
584053 AAATTACATA
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
25 9 0.17
26 17 0.31
27 23 0.43
28 5 0.09
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (25 bp):
AATAAATATAAATATATCATAATTT
Found at i:584035 original size:11 final size:10
Alignment explanation
Indices: 584013--584056 Score: 54
Period size: 11 Copynumber: 4.3 Consensus size: 10
584003 TCTTAAATTT
584013 AATATAATATA
1 AATATAA-ATA
*
584024 AAAATAACATA
1 AATATAA-ATA
584035 AATATAAATA
1 AATATAAATA
584045 AATATAAA-A
1 AATATAAATA
584054 AAT
1 AAT
584057 TACATAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
9 4 0.13
10 11 0.37
11 15 0.50
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (10 bp):
AATATAAATA
Found at i:584502 original size:24 final size:24
Alignment explanation
Indices: 584474--584521 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
584464 TTAAAAATGG
* *
584474 GTTTTTTTCAT-AAAATTTTTGAT
1 GTTTTTTTAATAAAAATTATTGAT
584497 GTTTTTTTAATAAAAATTATTGAT
1 GTTTTTTTAATAAAAATTATTGAT
584521 G
1 G
584522 GAAATATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (24 bp):
GTTTTTTTAATAAAAATTATTGAT
Found at i:585233 original size:12 final size:11
Alignment explanation
Indices: 585214--585252 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
585204 TAATTATTTC
585214 AAAAATAAATA
1 AAAAATAAATA
585225 AATAAATAAATA
1 AA-AAATAAATA
*
585237 TAAAATAAAATA
1 AAAAAT-AAATA
585249 AAAA
1 AAAA
585253 TTGCATCTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 6 0.25
12 18 0.75
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAAATAAATA
Found at i:586392 original size:25 final size:25
Alignment explanation
Indices: 586364--586415 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
586354 TTTTATAGGA
* * *
586364 AATTTCTTCTGTAATGCTACTTAAT
1 AATTTCATCTCTAATACTACTTAAT
*
586389 AATTTCATCTCTAATACTATTTAAT
1 AATTTCATCTCTAATACTACTTAAT
586414 AA
1 AA
586416 CCAATTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.15, G:0.04, T:0.46
Consensus pattern (25 bp):
AATTTCATCTCTAATACTACTTAAT
Found at i:587007 original size:29 final size:27
Alignment explanation
Indices: 586969--587095 Score: 112
Period size: 29 Copynumber: 4.4 Consensus size: 27
586959 TATGCTCAAG
* *
586969 TAAAATTTTATATTTTTATTATATTTAAA
1 TAAATTTTTA-ATTTTAATT-TATTTAAA
*
586998 TAAATTTTTAATTCTTAATTTACATT-AA
1 TAAATTTTTAATT-TTAATTTA-TTTAAA
*
587026 TAAATTTTTTATTTTTAATTTATATTAAA
1 TAAA-TTTTTAATTTTAATTTAT-TTAAA
** *
587055 TAAATCATTAATTTTAATTTAAATTTTAA
1 TAAATTTTTAATTTTAATTT--ATTTAAA
587084 TAAATTTTTAAT
1 TAAATTTTTAAT
587096 ATAAATAATT
Statistics
Matches: 80, Mismatches: 11, Indels: 14
0.76 0.10 0.13
Matches are distributed among these distances:
28 34 0.43
29 44 0.55
30 2 0.03
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (27 bp):
TAAATTTTTAATTTTAATTTATTTAAA
Found at i:587027 original size:28 final size:27
Alignment explanation
Indices: 586996--587095 Score: 110
Period size: 28 Copynumber: 3.5 Consensus size: 27
586986 ATTATATTTA
*
586996 AATAAATTTTTAATTCTTAATTTACATT
1 AATAAATTTTTAATT-TTAATTTAAATT
* *
587024 AATAAATTTTTTATTTTTAATTTATATT
1 AATAAA-TTTTTAATTTTAATTTAAATT
**
587052 AAATAAATCATTAATTTTAATTTAAATTTT
1 -AATAAATTTTTAATTTTAATTTAAA--TT
587082 AATAAATTTTTAAT
1 AATAAATTTTTAAT
587096 ATAAATAATT
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
28 32 0.53
29 26 0.43
30 2 0.03
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (27 bp):
AATAAATTTTTAATTTTAATTTAAATT
Found at i:587036 original size:58 final size:58
Alignment explanation
Indices: 586974--587097 Score: 155
Period size: 58 Copynumber: 2.1 Consensus size: 58
586964 TCAAGTAAAA
* ** *
586974 TTTTATATTTTTA-TTATATTTAAATAAATTTTTAATTCTTAATTTACA-TTAATAAATT
1 TTTTATATTTTAATTTATA-TTAAATAAATCATTAATT-TTAATTTAAATTTAATAAATT
587032 TTTTAT-TTTTAATTTATATTAAATAAATCATTAATTTTAATTTAAATTTTAATAAATT
1 TTTTATATTTTAATTTATATTAAATAAATCATTAATTTTAATTTAAA-TTTAATAAATT
*
587090 TTTAATAT
1 TTTTATAT
587098 AAATAATTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
56 9 0.16
57 21 0.37
58 26 0.46
59 1 0.02
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (58 bp):
TTTTATATTTTAATTTATATTAAATAAATCATTAATTTTAATTTAAATTTAATAAATT
Found at i:587066 original size:57 final size:56
Alignment explanation
Indices: 586971--587092 Score: 158
Period size: 56 Copynumber: 2.1 Consensus size: 56
586961 TGCTCAAGTA
* ** *
586971 AAATTTTATATTTTTATTATATTTAAATAAATTTTTAATTCTTAATTTACA-TTAAT
1 AAATTTTTTATTTTTATTATATTTAAATAAATCATTAATT-TTAATTTAAATTTAAT
587027 AAATTTTTTATTTTTAATT-TATATTAAATAAATCATTAATTTTAATTTAAATTTTAAT
1 AAATTTTTTATTTTT-ATTATAT-TTAAATAAATCATTAATTTTAATTTAAA-TTTAAT
587085 AAATTTTT
1 AAATTTTT
587093 AATATAAATA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
56 26 0.45
57 19 0.33
58 13 0.22
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (56 bp):
AAATTTTTTATTTTTATTATATTTAAATAAATCATTAATTTTAATTTAAATTTAAT
Found at i:587093 original size:57 final size:55
Alignment explanation
Indices: 586971--587093 Score: 151
Period size: 57 Copynumber: 2.2 Consensus size: 55
586961 TGCTCAAGTA
** *
586971 AAATTTTATATTTTTATTATATTTAAATAAATTTTTAATTCTTAATTTACATTAAT
1 AAATTTT-TATTTTTATTATATTTAAATAAATCATTAATTCTTAATTTAAATTAAT
587027 AAATTTTTTATTTTTAATT-TATATTAAATAAATCATTAATT-TTAATTTAAATTTTAAT
1 AAA-TTTTTATTTTT-ATTATAT-TTAAATAAATCATTAATTCTTAATTTAAA--TTAAT
587085 AAATTTTTA
1 AAATTTTTA
587094 ATATAAATAA
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
56 22 0.37
57 29 0.49
58 8 0.14
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (55 bp):
AAATTTTTATTTTTATTATATTTAAATAAATCATTAATTCTTAATTTAAATTAAT
Found at i:587274 original size:24 final size:26
Alignment explanation
Indices: 587246--587298 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
587236 TATTTATTTA
*
587246 TTTAATTATT-TTAATATAAA-ATAT
1 TTTAATTATTATTAATACAAATATAT
*
587270 TTTAATTATTATTTATACAAATATAT
1 TTTAATTATTATTAATACAAATATAT
587296 TTT
1 TTT
587299 TAAAATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 10 0.40
25 8 0.32
26 7 0.28
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTAATTATTATTAATACAAATATAT
Found at i:587311 original size:27 final size:24
Alignment explanation
Indices: 587246--587313 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 24
587236 TATTTATTTA
* * *
587246 TTTAATTATTTTAATATAAAATAT
1 TTTAAATATTTTTATACAAAATAT
*
587270 TTTAATTATTATTTATACAAATATATT
1 TTTAAATATT-TTTATACAAA-ATA-T
587297 TTTAAAATATTTTTATA
1 TTT-AAATATTTTTATA
587314 TTTAATATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 10 0.27
25 8 0.22
26 3 0.08
27 10 0.27
28 6 0.16
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTAAATATTTTTATACAAAATAT
Found at i:587341 original size:32 final size:34
Alignment explanation
Indices: 587305--587377 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 34
587295 TTTTTAAAAT
* *
587305 ATTTTTATAT-TTAATAT-ATAT-ATAATTTAATA
1 ATTTTTATATATAAATATAACATAATAATTTAA-A
*
587337 ATTTTTA-ATATAAATATAACATAATAATTTTAA
1 ATTTTTATATATAAATATAACATAATAATTTAAA
587370 ATTTTTAT
1 ATTTTTAT
587378 TCAAAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
31 2 0.06
32 13 0.38
33 11 0.32
34 8 0.24
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (34 bp):
ATTTTTATATATAAATATAACATAATAATTTAAA
Found at i:587343 original size:26 final size:26
Alignment explanation
Indices: 587314--587367 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
587304 TATTTTTATA
* **
587314 TTTAATATATATATAATTTAATAATT
1 TTTAATATAAATATAACATAATAATT
587340 TTTAATATAAATATAACATAATAATT
1 TTTAATATAAATATAACATAATAATT
587366 TT
1 TT
587368 AAATTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTAATATAAATATAACATAATAATT
Found at i:587441 original size:16 final size:17
Alignment explanation
Indices: 587411--587463 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 17
587401 TATTTTATTC
*
587411 TTTAATATAA-ATTAAT
1 TTTAATATAATTTTAAT
*
587427 TTTAATA-ATTTTTAA-
1 TTTAATATAATTTTAAT
*
587442 TATAATATAATTTT-AT
1 TTTAATATAATTTTAAT
587458 TTTAAT
1 TTTAAT
587464 CATTATTCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAATATAATTTTAAT
Found at i:589211 original size:16 final size:16
Alignment explanation
Indices: 589190--589222 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
589180 CTCAAGTCTC
*
589190 AAAAAACCCAAATTCA
1 AAAAAACCCAAACTCA
589206 AAAAAACCCAAACTCA
1 AAAAAACCCAAACTCA
589222 A
1 A
589223 GAGAACTCAA
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:0.64, C:0.27, G:0.00, T:0.09
Consensus pattern (16 bp):
AAAAAACCCAAACTCA
Found at i:589438 original size:22 final size:22
Alignment explanation
Indices: 589413--589455 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
589403 AAATAGTAAT
589413 TTAT-AAAAAAGTAAATTATATC
1 TTATCAAAAAA-TAAATTATATC
589435 TTATCAAAAAATAAATTATAT
1 TTATCAAAAAATAAATTATAT
589456 TATGAGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (22 bp):
TTATCAAAAAATAAATTATATC
Found at i:589959 original size:15 final size:17
Alignment explanation
Indices: 589916--589959 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
589906 GACAATTATT
589916 TTAT-TACATTAAAATA
1 TTATATACATTAAAATA
589932 TTATATA-ATTAAAA-A
1 TTATATACATTAAAATA
589947 -TATATACATTAAA
1 TTATATACATTAAA
589960 TCATAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.23
15 7 0.27
16 11 0.42
17 2 0.08
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
TTATATACATTAAAATA
Found at i:597302 original size:79 final size:78
Alignment explanation
Indices: 597219--597427 Score: 222
Period size: 79 Copynumber: 2.6 Consensus size: 78
597209 CTAATGCCTT
* * ** *
597219 TGTATCGATATGATAATGCCAACATGATCCCAAGAGCTTGAATTTATC-TTGAGAATCACTAAAG
1 TGTATTGATATGAAAATGCCAACATGATCCCAAGA-CTCAAATTTATCATT-AGAATCACTAAAA
* *
597283 CAACCCTACTGACCA
64 CAACCCAAATGACCA
* ** * *
597298 TGTATTGAAATGAAAATGCCAACATGATCTTGAAGACTCAAATTTATCATTAGAATTATTAAAAC
1 TGTATTGATATGAAAATGCCAACATGATC-CCAAGACTCAAATTTATCATTAGAATCACTAAAAC
*
597363 AACTCAAATGACCA
65 AACCCAAATGACCA
* * * *
597377 TTTATTGATATGAAAATGCCAACATGATCCTAAAGACTTAGATTTATCATT
1 TGTATTGATATGAAAATGCCAACATGATCC-CAAGACTCAAATTTATCATT
597428 GTTGCAATGT
Statistics
Matches: 108, Mismatches: 19, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
79 102 0.94
80 6 0.06
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (78 bp):
TGTATTGATATGAAAATGCCAACATGATCCCAAGACTCAAATTTATCATTAGAATCACTAAAACA
ACCCAAATGACCA
Found at i:598512 original size:79 final size:78
Alignment explanation
Indices: 598357--598502 Score: 190
Period size: 78 Copynumber: 1.9 Consensus size: 78
598347 ATGGAATATG
* * * * * *
598357 GGGTTGGAGTATCCCAAGATTGAAAAATTTAATATTTTTGAAATACAAATGGGGTTGGAGTTTCC
1 GGGTTGGAGTATCCCAAGATTGAAAAATTGAATATTTTGGAAATAAAAACGAGGTTGGAGTAT-C
598422 CTTCGGAAATAACA
65 CTTCGGAAATAACA
*
598436 GGGTTGGAGTATCCCCAAGA-TGAAAAA-TGAATATTTTGGAAGTAAAAACGAGGTTGGAGTAT-
1 GGGTTGGAGTAT-CCCAAGATTGAAAAATTGAATATTTTGGAAATAAAAACGAGGTTGGAGTATC
598498 CTTCG
65 CTTCG
598503 AGATGAATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
76 5 0.08
78 28 0.47
79 19 0.32
80 7 0.12
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (78 bp):
GGGTTGGAGTATCCCAAGATTGAAAAATTGAATATTTTGGAAATAAAAACGAGGTTGGAGTATCC
TTCGGAAATAACA
Found at i:598542 original size:51 final size:50
Alignment explanation
Indices: 598436--598544 Score: 137
Period size: 51 Copynumber: 2.2 Consensus size: 50
598426 GGAAATAACA
*
598436 GGGTTGGAGTATCCCCAAGATGAAAAATGAATATTTTGGAAGTAAAAACG
1 GGGTTGGAGTATCCCCAAGATGAAAAATGAATATTTTGGAAATAAAAACG
* ** * * * *
598486 AGGTTGGAGTATCTTCGAGATGAATAATTTAATATTTTTGAAATAAAAACG
1 GGGTTGGAGTATCCCCAAGATGAA-AAATGAATATTTTGGAAATAAAAACG
598537 GGGTTGGA
1 GGGTTGGA
598545 CTATTCCCTC
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
50 20 0.41
51 29 0.59
ACGTcount: A:0.38, C:0.07, G:0.26, T:0.29
Consensus pattern (50 bp):
GGGTTGGAGTATCCCCAAGATGAAAAATGAATATTTTGGAAATAAAAACG
Found at i:598588 original size:129 final size:130
Alignment explanation
Indices: 598358--598606 Score: 353
Period size: 129 Copynumber: 1.9 Consensus size: 130
598348 TGGAATATGG
* * *
598358 GGTTGGAGTATCCCAAGATTGAAAAATTTAATATTTTTGAAATACAAATGGGGTTGGAGTTTCCC
1 GGTTGGAGTATCCCAAGATTGAAAAATTTAATATTTTTGAAATAAAAACGGGGTTGGACTTTCCC
*
598423 TTCGGAAATAACAGGGTTGGAGTATCCCCAAGATGAAAAAT-GA-ATATTTTGGAAGTAAAAACG
66 TTCGGAAATAACAGGGTTGAAGTATCCCCAAGATGAAAAATCGATAT-TTTTGGAAGTAAAAACG
598486 A
130 A
* * *
598487 GGTTGGAGTATCTTCGAGA-TGAATAATTTAATATTTTTGAAATAAAAACGGGGTTGGACTATTC
1 GGTTGGAGTATC-CCAAGATTGAAAAATTTAATATTTTTGAAATAAAAACGGGGTTGGACT-TTC
** *
598551 CC-TCGGAAATAACTTGGTTGAAGTATTCCCAAGATGAAAAATCGATATTTTTGGAA
64 CCTTCGGAAATAACAGGGTTGAAGTATCCCCAAGATGAAAAATCGATATTTTTGGAA
598607 AGACAAATTT
Statistics
Matches: 106, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
129 85 0.80
130 19 0.18
131 2 0.02
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (130 bp):
GGTTGGAGTATCCCAAGATTGAAAAATTTAATATTTTTGAAATAAAAACGGGGTTGGACTTTCCC
TTCGGAAATAACAGGGTTGAAGTATCCCCAAGATGAAAAATCGATATTTTTGGAAGTAAAAACGA
Found at i:601114 original size:20 final size:21
Alignment explanation
Indices: 601089--601135 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
601079 TAGACATGTA
601089 GATACATTCACT-TCTGTATC
1 GATACATTCACTGTCTGTATC
* * *
601109 GATACATTTACTGTTTGTATT
1 GATACATTCACTGTCTGTATC
601130 GATACA
1 GATACA
601136 AATTGCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.43
Consensus pattern (21 bp):
GATACATTCACTGTCTGTATC
Found at i:601472 original size:40 final size:40
Alignment explanation
Indices: 601422--601545 Score: 103
Period size: 40 Copynumber: 3.1 Consensus size: 40
601412 GAAAAGCCAG
601422 AATGATCCTAAAGACTCAGATTTATCATGAAAATTATCAA
1 AATGATCCTAAAGACTCAGATTTATCATGAAAATTATCAA
* * ** **
601462 AATGACCCTAATGACT-ATGTATCGAT-ATGAAAA-TGCCAA
1 AATGATCCTAAAGACTCA-G-ATTTATCATGAAAATTATCAA
* * * *
601501 CATGATCCTAAAGATTCAAATTTATCA-CATAAATTATCAA
1 AATGATCCTAAAGACTCAGATTTATCATGA-AAATTATCAA
601541 AATGA
1 AATGA
601546 ACTTAATAGG
Statistics
Matches: 61, Mismatches: 17, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
38 5 0.08
39 21 0.34
40 31 0.51
41 4 0.07
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.29
Consensus pattern (40 bp):
AATGATCCTAAAGACTCAGATTTATCATGAAAATTATCAA
Found at i:601704 original size:48 final size:46
Alignment explanation
Indices: 601644--601733 Score: 117
Period size: 48 Copynumber: 1.9 Consensus size: 46
601634 TAAAATAATG
*
601644 AAAATTACAAAATGATAGTGGATTATATTAAATAACCTTAAATCATA
1 AAAATTACAAAATGATAGTAGATTATATTAAATAA-CTTAAATCATA
** * *
601691 AAAATTACTAAAATGATTTTATATTATGTTAAATAACTTAAAT
1 AAAATTAC-AAAATGATAGTAGATTATATTAAATAACTTAAAT
601734 AGCTTTAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
47 15 0.41
48 22 0.59
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (46 bp):
AAAATTACAAAATGATAGTAGATTATATTAAATAACTTAAATCATA
Found at i:602573 original size:11 final size:10
Alignment explanation
Indices: 602557--602619 Score: 64
Period size: 9 Copynumber: 6.7 Consensus size: 10
602547 TAGAACAAAG
602557 CTTTCTTCTTT
1 CTTTCTT-TTT
602568 CTTTCTTTTT
1 CTTTCTTTTT
*
602578 TTTTCTTTTT
1 CTTTCTTTTT
602588 -TTTC-TTTT
1 CTTTCTTTTT
602596 -TTTCTTTTT
1 CTTTCTTTTT
*
602605 -TTCCTTTTT
1 CTTTCTTTTT
602614 -TTTCTT
1 CTTTCTT
602620 GGTTAAAGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
8 8 0.17
9 21 0.44
10 12 0.25
11 7 0.15
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:604567 original size:25 final size:22
Alignment explanation
Indices: 604537--604594 Score: 64
Period size: 25 Copynumber: 2.5 Consensus size: 22
604527 TTTTTCTCCG
604537 TTCTTTTTTTTCTCTCTCTTTCTCT
1 TTCTTTTTTTTCT-T-TC-TTCTCT
604562 TTCTTTTTCCTTTCTTTCTTCTCT
1 TTCTTTTT--TTTCTTTCTTCTCT
604586 TT-TTTTTTT
1 TTCTTTTTTT
604595 CTCATCAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
21 2 0.06
23 5 0.16
24 8 0.26
25 10 0.32
26 1 0.03
27 5 0.16
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (22 bp):
TTCTTTTTTTTCTTTCTTCTCT
Found at i:604576 original size:11 final size:12
Alignment explanation
Indices: 604538--604592 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
604528 TTTTCTCCGT
604538 TCTTT-TTTTTC
1 TCTTTCTTTTTC
*
604549 TC--TCTCTTTC
1 TCTTTCTTTTTC
604559 TCTTTCTTTTTC
1 TCTTTCTTTTTC
604571 -CTTTCTTTCTTC
1 TCTTTCTTT-TTC
604583 TCTTT-TTTTT
1 TCTTTCTTTTT
604593 TTCTCATCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 1 0.03
10 7 0.19
11 12 0.32
12 13 0.35
13 4 0.11
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (12 bp):
TCTTTCTTTTTC
Found at i:604595 original size:25 final size:23
Alignment explanation
Indices: 604540--604593 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
604530 TTCTCCGTTC
604540 TTTTTTTT-CTCTCTCTTTCTCT
1 TTTTTTTTCCTCTCTCTTTCTCT
* * *
604562 TTCTTTTTCCTTTCTTTCTTCTCT
1 TTTTTTTTCCTCTCTCT-TTCTCT
604586 TTTTTTTT
1 TTTTTTTT
604594 TCTCATCAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 7 0.27
23 6 0.23
24 13 0.50
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTTTTTCCTCTCTCTTTCTCT
Found at i:605002 original size:24 final size:24
Alignment explanation
Indices: 604974--605022 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
604964 AGGTTTATAT
*
604974 TAAAAATCATATCATTTAATTAAA
1 TAAAAATCATATCATTTAATAAAA
604998 TAAAAATCATATCATTTAATAAAA
1 TAAAAATCATATCATTTAATAAAA
605022 T
1 T
605023 TTATTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (24 bp):
TAAAAATCATATCATTTAATAAAA
Found at i:614355 original size:20 final size:20
Alignment explanation
Indices: 614330--614370 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
614320 TTGATCAAGG
*
614330 TACCAAAAGTT-ATTCTTTGA
1 TACCAAAAATTAATT-TTTGA
614350 TACCAAAAATTAATTTTTGA
1 TACCAAAAATTAATTTTTGA
614370 T
1 T
614371 TCCTTTGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.41
Consensus pattern (20 bp):
TACCAAAAATTAATTTTTGA
Found at i:615181 original size:21 final size:21
Alignment explanation
Indices: 615157--615196 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
615147 ACCATCTTGC
615157 AATTCAATTATCTTCTTTTCT
1 AATTCAATTATCTTCTTTTCT
* *
615178 AATTCACTTATTTTCTTTT
1 AATTCAATTATCTTCTTTT
615197 AAGCACATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (21 bp):
AATTCAATTATCTTCTTTTCT
Found at i:617264 original size:20 final size:20
Alignment explanation
Indices: 617256--617309 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
617246 GATACTTTTC
617256 ACTATGTATCGATACAATGT
1 ACTATGTATCGATACAATGT
*
617276 ACCATGTATCGATACAATGT
1 ACTATGTATCGATACAATGT
617296 ACTATGTATCGATA
1 ACTATGTATCGATA
617310 TATTTCACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (20 bp):
ACTATGTATCGATACAATGT
Found at i:617777 original size:31 final size:31
Alignment explanation
Indices: 617739--617811 Score: 119
Period size: 31 Copynumber: 2.3 Consensus size: 31
617729 AGCTTGAAGT
* *
617739 TAATATAACAGTATTGAAACTAAAGTAAACA
1 TAATATAACAATATTGAAAATAAAGTAAACA
617770 TAATATAACAATATTGAAAATAAAGTAAACA
1 TAATATAACAATATTGAAAATAAAGTAAACA
617801 TAATAATAACA
1 TAAT-ATAACA
617812 TGAGCATAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 33 0.85
32 6 0.15
ACGTcount: A:0.59, C:0.08, G:0.07, T:0.26
Consensus pattern (31 bp):
TAATATAACAATATTGAAAATAAAGTAAACA
Found at i:619139 original size:79 final size:78
Alignment explanation
Indices: 619039--619253 Score: 243
Period size: 78 Copynumber: 2.7 Consensus size: 78
619029 GGGGCTAGAA
* * * *
619039 TATCCCCGATTATAGAAAATCGGTGTTTTAAAAATAAAATCGGGGTTAGAGTATCCCCTCAAAAA
1 TATCCCCGATTATGGAAAATCGGT-TTTTAGAAATAAAATCGGGGTTGGAGTATCCCCACAAAAA
619104 TAAC-GGAGTTGGAG
65 TAACAGG-GTTGGAG
* * ** * **
619118 TATCCCCGATTATGGAAAATCGATCTTTAGAAATAAGGTCGGGGTTGGAGTAGCTTCACAAAAAT
1 TATCCCCGATTATGGAAAATCGGTTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCACAAAAAT
619183 AACAGGGTTGGAG
66 AACAGGGTTGGAG
* * * * * *
619196 TATCCTCGATTGTGAAAAATTAGGATTTTAGAAATAAAATAGGGGTTGGAGTATCCCC
1 TATCCCCGATTATGGAAAA-TCGGTTTTTAGAAATAAAATCGGGGTTGGAGTATCCCC
619254 GATTGTGAGA
Statistics
Matches: 110, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
78 58 0.53
79 52 0.47
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (78 bp):
TATCCCCGATTATGGAAAATCGGTTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCACAAAAAT
AACAGGGTTGGAG
Found at i:619257 original size:51 final size:51
Alignment explanation
Indices: 619183--619304 Score: 174
Period size: 51 Copynumber: 2.4 Consensus size: 51
619173 TCACAAAAAT
* *
619183 AACA-GGGTTGGAGTATCCTCGATTGTGAAAAATTAGGATTTTAGAAATAA
1 AACAGGGGTTGGAGTATCCCCGATTGTGAAAAATTAAGATTTTAGAAATAA
* * *
619233 AATAGGGGTTGGAGTATCCCCGATTGTGAGAAATTAATATTTTAGAAATAA
1 AACAGGGGTTGGAGTATCCCCGATTGTGAAAAATTAAGATTTTAGAAATAA
* *
619284 AGCCGGGGTTGGAGTATCCCC
1 AACAGGGGTTGGAGTATCCCC
619305 TCAGAAATAA
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
50 3 0.05
51 60 0.95
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (51 bp):
AACAGGGGTTGGAGTATCCCCGATTGTGAAAAATTAAGATTTTAGAAATAA
Found at i:619413 original size:131 final size:130
Alignment explanation
Indices: 619111--619511 Score: 456
Period size: 131 Copynumber: 3.1 Consensus size: 130
619101 AAATAACGGA
* * * * * * *
619111 GTTGGAGTATCCCCGATTATG-GAAAATCGAT-CTTTAGAAATAAGGTCGGGGTTGGAGTAGCTT
1 GTTGGAGTATCCCCGATTGTGAG-AAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCTC
* * * *
619174 CACAAAAATAACAGGGTTGGAGTAT-CCTCGATTGTGAAAAATTAGG-ATTTTAGAAATAAAATA
65 CTCAGAAATAACAGGATTGGAGTATCCCT-GATTGTGAAAAATT-GGTGTTTTAGAAATAAAATA
619237 GGG
128 GGG
* *
619240 GTTGGAGTATCCCCGATTGTGAGAAATTAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCTCC
* *
619305 TCAGAAATAAC-GAGATTGGAGTATCCCTGATTGTGAAAAGATTGGTGTTTTAAAAATAAAATTG
66 TCAGAAATAACAG-GATTGGAGTATCCCTGATTGTGAAAA-ATTGGTGTTTTAGAAATAAAATAG
619369 GG
129 GG
* * * *
619371 TTTGGAGTATCCCAGATTGTGAGAAATCAATATTTTAGAAATAAAACCGGGGTTAGAGTATCTCC
1 GTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCTCC
* * * * * **
619436 TC-GAAAATAAAAGGATTGGAGTATCTCC-GATTATGAAAAATTGATGCTTTGGAAATAAAACCG
66 TCAG-AAATAACAGGATTGGAGTATC-CCTGATTGTGAAAAATTGGTGTTTTAGAAATAAAATAG
619499 GG
129 GG
619501 GTTGGAGTATC
1 GTTGGAGTATC
619512 GTCAAGATGA
Statistics
Matches: 233, Mismatches: 30, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
129 27 0.12
130 91 0.39
131 112 0.48
132 3 0.01
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (130 bp):
GTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCTCC
TCAGAAATAACAGGATTGGAGTATCCCTGATTGTGAAAAATTGGTGTTTTAGAAATAAAATAGGG
Found at i:621866 original size:29 final size:29
Alignment explanation
Indices: 621824--621917 Score: 89
Period size: 29 Copynumber: 3.6 Consensus size: 29
621814 GATACATTGA
* *
621824 AAAATATACCGATACATCTGAGTAAACCC
1 AAAATGTATCGATACATCTGAGTAAACCC
*
621853 AAAATGTATTGATACAT-T--G---A---
1 AAAATGTATCGATACATCTGAGTAAACCC
621873 AAAATGTATCGATACATCTGAGTAAACCC
1 AAAATGTATCGATACATCTGAGTAAACCC
*
621902 AGAATGTATCGATACA
1 AAAATGTATCGATACA
621918 ATTAACAGTG
Statistics
Matches: 51, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
20 16 0.31
21 1 0.02
23 2 0.04
26 2 0.04
28 1 0.02
29 29 0.57
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.26
Consensus pattern (29 bp):
AAAATGTATCGATACATCTGAGTAAACCC
Found at i:621930 original size:49 final size:49
Alignment explanation
Indices: 621805--621937 Score: 196
Period size: 49 Copynumber: 2.7 Consensus size: 49
621795 AAAAATGCAT
* *
621805 GAATGTATCGATACATTGAAAAATATACCGATACATCTGAGTAAACCCA
1 GAATGTATCGATACATTGAAAAATGTATCGATACATCTGAGTAAACCCA
* *
621854 AAATGTATTGATACATTGAAAAATGTATCGATACATCTGAGTAAACCCA
1 GAATGTATCGATACATTGAAAAATGTATCGATACATCTGAGTAAACCCA
* *
621903 GAATGTATCGATACAATT-AACAGTGTATCGATACA
1 GAATGTATCGATAC-ATTGAAAAATGTATCGATACA
621938 ATGAATAATG
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
49 72 0.96
50 3 0.04
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (49 bp):
GAATGTATCGATACATTGAAAAATGTATCGATACATCTGAGTAAACCCA
Found at i:621931 original size:20 final size:20
Alignment explanation
Indices: 621906--622026 Score: 107
Period size: 20 Copynumber: 5.6 Consensus size: 20
621896 AAACCCAGAA
* *
621906 TGTATCGATACAATTAACAG
1 TGTATCGATACAATGAATAG
*
621926 TGTATCGATACAATGAATAA
1 TGTATCGATACAATGAATAG
* *
621946 TGTATCGATACATCTGAGTAAACCCAG
1 TGTATCGATACA----A-TGAA--TAG
621973 AATGTATCGATACAATGAATAG
1 --TGTATCGATACAATGAATAG
*
621995 TGTATCGATACAATGAATAA
1 TGTATCGATACAATGAATAG
622015 TGTATCGATACA
1 TGTATCGATACA
622027 TCTGGGTAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 18
0.75 0.08 0.16
Matches are distributed among these distances:
20 60 0.72
22 2 0.02
24 4 0.05
25 4 0.05
27 1 0.01
29 12 0.14
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (20 bp):
TGTATCGATACAATGAATAG
Found at i:621936 original size:69 final size:69
Alignment explanation
Indices: 621857--622077 Score: 352
Period size: 69 Copynumber: 3.2 Consensus size: 69
621847 AAACCCAAAA
* * * *
621857 TGTATTGATACATTGAAAAATGTATCGATACATCTGAGTAAACCCAGAATGTATCGATACAATTA
1 TGTATCGATACAATGAATAATGTATCGATACATCTGAGTAAACCCAGAATGTATCGATACAATAA
621922 ACAG
66 ACAG
*
621926 TGTATCGATACAATGAATAATGTATCGATACATCTGAGTAAACCCAGAATGTATCGATACAATGA
1 TGTATCGATACAATGAATAATGTATCGATACATCTGAGTAAACCCAGAATGTATCGATACAATAA
*
621991 ATAG
66 ACAG
* *
621995 TGTATCGATACAATGAATAATGTATCGATACATCTGGGTAAAACCCAAAATGTATCGATACAATA
1 TGTATCGATACAATGAATAATGTATCGATACATCTGAGT-AAACCCAGAATGTATCGATACAATA
*
622060 AACAA
65 AACAG
622065 TGTATCGATACAA
1 TGTATCGATACAA
622078 ATTGTGAAAA
Statistics
Matches: 141, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
69 102 0.72
70 39 0.28
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.28
Consensus pattern (69 bp):
TGTATCGATACAATGAATAATGTATCGATACATCTGAGTAAACCCAGAATGTATCGATACAATAA
ACAG
Found at i:622728 original size:15 final size:15
Alignment explanation
Indices: 622709--622745 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
622699 AAGATTCTCC
622709 CTTTTTCTTT-TC-TT
1 CTTTTT-TTTGTCTTT
622723 CTTTTTTTTGTCTTT
1 CTTTTTTTTGTCTTT
622738 CTTTTTTT
1 CTTTTTTT
622746 AAGTTTAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.14
14 8 0.38
15 10 0.48
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (15 bp):
CTTTTTTTTGTCTTT
Found at i:623292 original size:40 final size:40
Alignment explanation
Indices: 623237--623315 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
623227 ATGTGCAATA
* *
623237 AAAAAGTTAAATTAAAAATTGTCTATGAAAAAAGTCTAAC
1 AAAAAGTTAAATTAAAAATTCTATATGAAAAAAGTCTAAC
* * * *
623277 AAAAGGTTTAATTAAAAATTCTATATGCAAAAATTCTAA
1 AAAAAGTTAAATTAAAAATTCTATATGAAAAAAGTCTAA
623316 TGAAAAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.53, C:0.08, G:0.09, T:0.30
Consensus pattern (40 bp):
AAAAAGTTAAATTAAAAATTCTATATGAAAAAAGTCTAAC
Found at i:623316 original size:28 final size:27
Alignment explanation
Indices: 623283--623479 Score: 171
Period size: 28 Copynumber: 7.1 Consensus size: 27
623273 TAACAAAAGG
**
623283 TTTAATTAAAAATTCTATATGCAAAAA
1 TTTAATTAAAAATTCTATATATAAAAA
* *
623310 TTCTAATGAAAAAAATT-TATATATAATAAG
1 TT-TAAT--TAAAAATTCTATATATAA-AAA
** * * *
623340 TTTAATTGGAAATTTTATATGTAAAAG
1 TTTAATTAAAAATTCTATATATAAAAA
623367 TTTAATTAAAAATTCTATATATAAAAAA
1 TTTAATTAAAAATTCTATATAT-AAAAA
** * *
623395 TTTAATTGGAAATTCTTTATGTAAAAA
1 TTTAATTAAAAATTCTATATATAAAAA
* * *
623422 GTTTAGTTAAAACTTTTATATATAAAAA
1 -TTTAATTAAAAATTCTATATATAAAAA
*
623450 GTTTAATTAAAAATTTTATATATAAAAA
1 -TTTAATTAAAAATTCTATATATAAAAA
623478 TT
1 TT
623480 GTTGACAACT
Statistics
Matches: 137, Mismatches: 26, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
27 35 0.26
28 80 0.58
29 11 0.08
30 11 0.08
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.42
Consensus pattern (27 bp):
TTTAATTAAAAATTCTATATATAAAAA
Found at i:623326 original size:15 final size:15
Alignment explanation
Indices: 623290--623323 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
623280 AGGTTTAATT
*
623290 AAAAATTCTATATGC
1 AAAAATTCTATATGA
623305 AAAAATTCTA-ATGA
1 AAAAATTCTATATGA
623319 AAAAA
1 AAAAA
623324 ATTTATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.59, C:0.09, G:0.06, T:0.26
Consensus pattern (15 bp):
AAAAATTCTATATGA
Found at i:623370 original size:84 final size:83
Alignment explanation
Indices: 623277--623479 Score: 223
Period size: 84 Copynumber: 2.4 Consensus size: 83
623267 AAAGTCTAAC
* **
623277 AAAAGGTTTAATTAAAAATTCTATATGCAAAAATTCTAA-TGAAAAAAATTTATATATAATAAGT
1 AAAAAGTTTAATTAAAAATTCTATATAAAAAAATT-TAATTGAAAAAAATTTATATA-AA-AAGT
* *
623341 TTAATTGGAAA-TTTTATATGT
63 TTAATT-AAAACTTTTATATAT
* *** *
623362 -AAAAGTTTAATTAAAAATTCTATATATAAAAAATTTAATTGGAAATTCTTTATGTAAAAAGTTT
1 AAAAAGTTTAATTAAAAATTCTATATA-AAAAAATTTAATTGAAAAAAATTTATATAAAAAGTTT
*
623426 AGTTAAAACTTTTATATAT
65 AATTAAAACTTTTATATAT
* *
623445 AAAAAGTTTAATTAAAAATTTTATATATAAAAATT
1 AAAAAGTTTAATTAAAAATTCTATATAAAAAAATT
623480 GTTGACAACT
Statistics
Matches: 101, Mismatches: 13, Indels: 10
0.81 0.10 0.08
Matches are distributed among these distances:
82 3 0.03
83 25 0.25
84 54 0.53
85 19 0.19
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.40
Consensus pattern (83 bp):
AAAAAGTTTAATTAAAAATTCTATATAAAAAAATTTAATTGAAAAAAATTTATATAAAAAGTTTA
ATTAAAACTTTTATATAT
Found at i:623432 original size:13 final size:13
Alignment explanation
Indices: 623416--623477 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
623406 ATTCTTTATG
*
623416 TAAAAAGTTTAGT
1 TAAAAAGTTTAAT
**
623429 TAAAACTTTTATAT
1 TAAAAAGTTTA-AT
623443 ATAAAAAGTTTAAT
1 -TAAAAAGTTTAAT
*
623457 TAAAAATTTTATAT
1 TAAAAAGTTTA-AT
623471 ATAAAAA
1 -TAAAAA
623478 TTGTTGACAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 19 0.49
14 5 0.13
15 15 0.38
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (13 bp):
TAAAAAGTTTAAT
Found at i:623477 original size:56 final size:56
Alignment explanation
Indices: 623277--623477 Score: 219
Period size: 56 Copynumber: 3.6 Consensus size: 56
623267 AAAGTCTAAC
* ** * * * *
623277 AAAAGGTTTAATTAAAAATTCTATATGCAAAAA-TTCTAATGAAAAAAATTTATATAT
1 AAAAAGTTTAATTGGAAATTTTATATGTAAAAAGTT-TAAT-TAAAAATTTTATATAT
* *
623334 AATAAGTTTAATTGGAAATTTTATATGT-AAAAGTTTAATTAAAAATTCTATATAT
1 AAAAAGTTTAATTGGAAATTTTATATGTAAAAAGTTTAATTAAAAATTTTATATAT
* * *
623389 AAAAAATTTAATTGGAAATTCTT-TATGTAAAAAGTTTAGTTAAAACTTTTATATAT
1 AAAAAGTTTAATTGGAAATT-TTATATGTAAAAAGTTTAATTAAAAATTTTATATAT
** *
623445 AAAAAGTTTAATTAAAAATTTTATATATAAAAA
1 AAAAAGTTTAATTGGAAATTTTATATGTAAAAA
623478 TTGTTGACAA
Statistics
Matches: 122, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
55 38 0.31
56 60 0.49
57 24 0.20
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (56 bp):
AAAAAGTTTAATTGGAAATTTTATATGTAAAAAGTTTAATTAAAAATTTTATATAT
Found at i:623892 original size:18 final size:18
Alignment explanation
Indices: 623857--623895 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
623847 AATTTTTTTG
623857 TATTAGTTTATTCTTAAT
1 TATTAGTTTATTCTTAAT
*
623875 TATTA-TTTATTGTGTAAT
1 TATTAGTTTATTCT-TAAT
623893 TAT
1 TAT
623896 AAATACTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.62
Consensus pattern (18 bp):
TATTAGTTTATTCTTAAT
Found at i:625382 original size:12 final size:12
Alignment explanation
Indices: 625335--625383 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
625325 TTATCACGTG
625335 TAAAATTTTAAT
1 TAAAATTTTAAT
*
625347 TAACATTTTAAGT
1 TAAAATTTTAA-T
*
625360 ATATGAATTTTAAT
1 -TA-AAATTTTAAT
625374 TAAAATTTTA
1 TAAAATTTTA
625384 TTTGTTACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
12 17 0.57
13 3 0.10
14 3 0.10
15 7 0.23
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (12 bp):
TAAAATTTTAAT
Found at i:629377 original size:257 final size:254
Alignment explanation
Indices: 628916--629462 Score: 650
Period size: 257 Copynumber: 2.1 Consensus size: 254
628906 TTATGAGATA
* * * *
628916 CATGAAGGCATGTAACCTTAATACCTTAAATATTTAGGTGCATTGGTATTTAATTTTGGTGCGCT
1 CATGAAGGCATGTATCCTTAATGCCTTAAATATTTAGGTGCATTGGTATTTAATTTTGGTGCACC
* * * * ** *
628981 TTTTTTATAAAGTTTAGGGAAAAGATGTGCCTTCTAACACCATCTAAACGTGCCTAAATGATTTA
66 TATTTTAGAAAGTTTAGGGAAAAGATATGCCTCCTAACACCATCTAAACACGCCTAAAAGATTTA
* ** *
629046 TAGAAATATCTCCAAAATACATACATGAAATAGGTGCACTAGTATGAAATTTAGGTGCATTATTT
131 AAGAAATATCTCCAAAATACATACATGAAATAGGCACACTAGTATGAAATTTAGGTACATTATTT
* * ***
629111 TACTAAAGTT-TAGAGAAAAGGTTTGATTTTTCAATCCATTTAAGCGTGCCTAAATGCTATAC
196 TACTAAAGTTCT--A-AAAAGG-TTGACTTTTCAATCCATCTAAGCACACCTAAATGCTATAC
* *
629173 CATGAAGGCAAGTATCCTTAGTGCCTTAAATATTTAGGTGCATTGGTATTTAATTTTGGTGCACC
1 CATGAAGGCATGTATCCTTAATGCCTTAAATATTTAGGTGCATTGGTATTTAATTTTGGTGCACC
* * * * * * *
629238 TATTTTGGAAAGTTTGGGGAAAAGGTAT-CCTCCTAATACCTTTTAAACACGCCTAAAAGCTTTA
66 TATTTTAGAAAGTTTAGGGAAAAGATATGCCTCCTAACACCATCTAAACACGCCTAAAAGATTTA
* * * ** *
629302 AATAAACTATCTGCAAAATACATACATGAAATAGGCACAC-CGTTATGAAATTTAGGTATGTTGT
131 AAGAAA-TATCTCCAAAATACATACATGAAATAGGCACACTAG-TATGAAATTTAGGTACATTAT
* * * *
629366 TTTATTAAAGTTCTAAAAAGGTTGGCTTTTCGATCTATCTAAGCACACCTAAATGCTATAC
194 TTTACTAAAGTTCTAAAAAGGTTGACTTTTCAATCCATCTAAGCACACCTAAATGCTATAC
* *
629427 CATAAAGGCATGTATCCTTAATGTCTTAAATATTTA
1 CATGAAGGCATGTATCCTTAATGCCTTAAATATTTA
629463 TACGCGCCAC
Statistics
Matches: 244, Mismatches: 43, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
254 64 0.26
255 6 0.02
256 34 0.14
257 139 0.57
258 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (254 bp):
CATGAAGGCATGTATCCTTAATGCCTTAAATATTTAGGTGCATTGGTATTTAATTTTGGTGCACC
TATTTTAGAAAGTTTAGGGAAAAGATATGCCTCCTAACACCATCTAAACACGCCTAAAAGATTTA
AAGAAATATCTCCAAAATACATACATGAAATAGGCACACTAGTATGAAATTTAGGTACATTATTT
TACTAAAGTTCTAAAAAGGTTGACTTTTCAATCCATCTAAGCACACCTAAATGCTATAC
Found at i:630050 original size:73 final size:73
Alignment explanation
Indices: 629936--630072 Score: 177
Period size: 73 Copynumber: 1.9 Consensus size: 73
629926 GTGTACTAGC
* * * * *
629936 AATGACCAATTGCAATTTCCATTAGACCAAACATGAGTGTAATAATATTAAGTATATATTCAATC
1 AATGACCAATTGCAATTTCAATTAGACCAAACACGAATGTAATAACACTAAGTATATATTCAATC
630001 ATACAAGT
66 ATACAAGT
* * * *
630009 AATGACCAATTTCAATTTCAATTAGTCTAATA-ACGAATGTAATAACCCTAAGTATATATTCAAT
1 AATGACCAATTGCAATTTCAATTAGACCAA-ACACGAATGTAATAACACTAAGTATATATTCAAT
630073 TGTACTAATA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
73 53 0.98
74 1 0.02
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.33
Consensus pattern (73 bp):
AATGACCAATTGCAATTTCAATTAGACCAAACACGAATGTAATAACACTAAGTATATATTCAATC
ATACAAGT
Found at i:630171 original size:185 final size:189
Alignment explanation
Indices: 629927--630380 Score: 569
Period size: 185 Copynumber: 2.4 Consensus size: 189
629917 TATATTCGAG
* * * * * *
629927 TGTACTAGCAATGACCAATTGCAATTTCCATTAGACCAAACATGAGTGTAATAATATTAAGTATA
1 TGTACTAGTAATGACCAATTTCAATTTCCATTAGTCTAAATATGAATGTAATAATATTAAGTATA
*
629992 TATTCAATCATACA-AGTAATGACCAATTTCAATTTCAATTAGTCT-AATAACGAATGTAATAAC
66 TATTCAATCATA-ATAGTAATAACCAATTTCAATTTCAATTAGTCTAAAT-ACGAATGTAATAAC
* *
630055 CCTAAGTATATATTCAATTGTACTAATAAT-A-A-TAAATTTTAATTAGTTTAAG-TCAAT
129 ACTAAGTATATAGTCAATTGTACTAATAATGATATTAAATTTTAATTAGTTTAAGATCAAT
* * * *
630112 TGTACTAGTAATGACCTATTTAAATTTCCATTAGTCTAAATATGAATATAAAAATATTAAGTATA
1 TGTACTAGTAATGACCAATTTCAATTTCCATTAGTCTAAATATGAATGTAATAATATTAAGTATA
* * * * *
630177 TATACAATCATAATAGTAATAACCAATTTCATTTTCATTTAGTCTAAATACGAATGTAATAGCAT
66 TATTCAATCATAATAGTAATAACCAATTTCAATTTCAATTAGTCTAAATACGAATGTAATAACAC
* * * *
630242 TTAGTATATAGTCAATTGTATTAGTAATGATCTATTTCAATTTTAATTAGTTTAAGTACATTCAA
131 TAAGTATATAGTCAATTGTACTAATAATGA--TA-TTAAATTTTAATTAGTTTAAG---A-TCAA
630307 T
189 T
* *
630308 TATACTAGTAATGACCAATTTCAATTTCTATTAGTCTAAATATGAATGTAATAATATTAAGTATA
1 TGTACTAGTAATGACCAATTTCAATTTCCATTAGTCTAAATATGAATGTAATAATATTAAGTATA
630373 TATTCAAT
66 TATTCAAT
630381 TGTGCTAGAA
Statistics
Matches: 227, Mismatches: 29, Indels: 15
0.84 0.11 0.06
Matches are distributed among these distances:
184 1 0.00
185 131 0.58
186 4 0.02
189 1 0.00
191 19 0.08
196 71 0.31
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (189 bp):
TGTACTAGTAATGACCAATTTCAATTTCCATTAGTCTAAATATGAATGTAATAATATTAAGTATA
TATTCAATCATAATAGTAATAACCAATTTCAATTTCAATTAGTCTAAATACGAATGTAATAACAC
TAAGTATATAGTCAATTGTACTAATAATGATATTAAATTTTAATTAGTTTAAGATCAAT
Found at i:630279 original size:73 final size:72
Alignment explanation
Indices: 630097--630292 Score: 189
Period size: 73 Copynumber: 2.7 Consensus size: 72
630087 TAAATTTTAA
* * * * *
630097 TTAGTTTA-AGTCAATTGTACTAGTAATGACCTATTTAAATTTCCATTAGTCTAAATATGAATAT
1 TTAGTATATAGTCAATTGTAATAGTAATGACCTATTT-CATTTTCATTAGTCTAAATACGAATAT
*
630161 AAAAATAT
65 AAAAACAT
* ** * * *
630169 TAAGTATATA-TACAATCATAATAGTAATAACCAATTTCATTTTCATTTAGTCTAAATACGAATG
1 TTAGTATATAGT-CAATTGTAATAGTAATGACCTATTTCATTTTCA-TTAGTCTAAATACGAATA
* *
630233 TAATAGCAT
64 TAAAAACAT
* * *
630242 TTAGTATATAGTCAATTGTATTAGTAATGATCTATTTCAATTTTAATTAGT
1 TTAGTATATAGTCAATTGTAATAGTAATGACCTATTTC-ATTTTCATTAGT
630293 TTAAGTACAT
Statistics
Matches: 97, Mismatches: 22, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
72 13 0.13
73 77 0.79
74 7 0.07
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (72 bp):
TTAGTATATAGTCAATTGTAATAGTAATGACCTATTTCATTTTCATTAGTCTAAATACGAATATA
AAAACAT
Found at i:630434 original size:123 final size:123
Alignment explanation
Indices: 630181--630404 Score: 297
Period size: 123 Copynumber: 1.8 Consensus size: 123
630171 AGTATATATA
* * * * *
630181 CAATCATAATAGTAATAACCAATTTCATTTTCATTTAGTCTAAATACGAATGTAATAGCATTTAG
1 CAATTATACTAGTAATAACCAATTTCAATTTCATTTAGTCTAAATACGAATGTAATAACATTAAG
* * * **
630246 TATATAGTCAATTGTATTAGTAATGATCTATTTCAATTTTAATTAGTTTAAGTACATT
66 TATATAGTCAATTGTACTAGAAATGATCAATTTCAATTTTAATTAGACTAAGTACATT
* * *
630304 CAATTATACTAGTAATGACCAATTTCAATTTC-TATTAGTCTAAATATGAATGTAATAATATTAA
1 CAATTATACTAGTAATAACCAATTTCAATTTCAT-TTAGTCTAAATACGAATGTAATAACATTAA
* *
630368 GTATATATTCAATTGTGCTAGAAATGATCAATTTCAA
65 GTATATAGTCAATTGTACTAGAAATGATCAATTTCAA
630405 ATAGTTTATG
Statistics
Matches: 87, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
122 1 0.01
123 86 0.99
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.41
Consensus pattern (123 bp):
CAATTATACTAGTAATAACCAATTTCAATTTCATTTAGTCTAAATACGAATGTAATAACATTAAG
TATATAGTCAATTGTACTAGAAATGATCAATTTCAATTTTAATTAGACTAAGTACATT
Found at i:633601 original size:19 final size:19
Alignment explanation
Indices: 633570--633619 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 19
633560 AAATACAAAT
633570 ATAAT-AATATTCAATTGTA
1 ATAATCAAT-TTCAATTGTA
*
633589 ATAATCAATTTCAATTTTA
1 ATAATCAATTTCAATTGTA
633608 ATTAATCTAATT
1 A-TAATC-AATT
633620 AATAATTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 15 0.56
20 8 0.30
21 4 0.15
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (19 bp):
ATAATCAATTTCAATTGTA
Found at i:633625 original size:16 final size:16
Alignment explanation
Indices: 633606--633638 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
633596 ATTTCAATTT
633606 TAATTAATCTA-ATTAA
1 TAATTAAT-TACATTAA
633622 TAATTAATTACATTAA
1 TAATTAATTACATTAA
633638 T
1 T
633639 CATGATTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 14 0.88
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATTAATTACATTAA
Found at i:637602 original size:3 final size:3
Alignment explanation
Indices: 637594--637631 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
637584 ATTTAAATAG
637594 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
637632 CCTTTAAGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:637843 original size:20 final size:18
Alignment explanation
Indices: 637791--637861 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 18
637781 AATTTTCATT
*
637791 ATAAAATATTTTAATATTA
1 ATAAAA-ATTTTAATTTTA
637810 ATAAGAAATATTTAATTTATA
1 ATAA-AAAT-TTTAATTT-TA
637831 AGTAAAAATTTTAATTTTA
1 A-TAAAAATTTTAATTTTA
*
637850 TTAAAAAGTTTT
1 ATAAAAA-TTTT
637862 TTTAAAAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
18 6 0.13
19 12 0.27
20 17 0.38
21 7 0.16
22 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (18 bp):
ATAAAAATTTTAATTTTA
Found at i:639489 original size:11 final size:11
Alignment explanation
Indices: 639457--639495 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
639447 AATTTTAATA
639457 TTTTATATTAT
1 TTTTATATTAT
**
639468 TAGTA-ATTAT
1 TTTTATATTAT
639478 TTTTATATTAT
1 TTTTATATTAT
639489 TTTTATA
1 TTTTATA
639496 AATATATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (11 bp):
TTTTATATTAT
Found at i:639809 original size:18 final size:17
Alignment explanation
Indices: 639770--639806 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
639760 TGAAAAATTT
639770 ATTATTGATGTGTAAAA
1 ATTATTGATGTGTAAAA
*
639787 ATTATTGATGTGTTAAA
1 ATTATTGATGTGTAAAA
639804 ATT
1 ATT
639807 TATATAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.46
Consensus pattern (17 bp):
ATTATTGATGTGTAAAA
Found at i:640902 original size:17 final size:19
Alignment explanation
Indices: 640870--640904 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
640860 AAAAATATGA
640870 TTTAAGAAAACAATAATTT
1 TTTAAGAAAACAATAATTT
640889 TTTAA-AAAAC-ATAATT
1 TTTAAGAAAACAATAATT
640905 ACTGACCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (19 bp):
TTTAAGAAAACAATAATTT
Found at i:640956 original size:25 final size:25
Alignment explanation
Indices: 640928--640979 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
640918 TTTTATAGGA
* *
640928 AATTTCATCTTTAATACTCTTTAAT
1 AATTTCATCTGTAATACTATTTAAT
640953 AATTTCATCTGTAATACTATTTAAT
1 AATTTCATCTGTAATACTATTTAAT
640978 AA
1 AA
640980 CGAATTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.37, C:0.13, G:0.02, T:0.48
Consensus pattern (25 bp):
AATTTCATCTGTAATACTATTTAAT
Found at i:641530 original size:29 final size:29
Alignment explanation
Indices: 641498--641553 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
641488 TTTATTACAT
* * *
641498 TTAAATTAATTTTTAATTTTTAATTTATA
1 TTAAATAAATTATTAACTTTTAATTTATA
641527 TTAAATAAATTATTAACTTTTAATTTA
1 TTAAATAAATTATTAACTTTTAATTTA
641554 AATTTTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (29 bp):
TTAAATAAATTATTAACTTTTAATTTATA
Found at i:641754 original size:25 final size:27
Alignment explanation
Indices: 641712--641777 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 27
641702 TATTTATTTA
641712 ATTAATAATTTTTAATATAAA-ATATT
1 ATTAATAATTTTTAATATAAATATATT
*
641738 -TTAATTATTATTT-ATATAAATATATT
1 ATTAATAATT-TTTAATATAAATATATT
641764 ATTAA-ACATTTTTA
1 ATTAATA-ATTTTTA
641778 TTATTTAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
25 15 0.45
26 11 0.33
27 7 0.21
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (27 bp):
ATTAATAATTTTTAATATAAATATATT
Found at i:641777 original size:26 final size:24
Alignment explanation
Indices: 641719--641778 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 24
641709 TTAATTAATA
**
641719 ATTTTTAATATAAAATATTTTAATT
1 ATTTTT-ATATAAAATATTTTAAAC
641744 ATTATTTATATAAATATATTATTAAAC
1 ATT-TTTATATAAA-ATATT-TTAAAC
641771 ATTTTTAT
1 ATTTTTAT
641779 TATTTAGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 10 0.33
26 13 0.43
27 7 0.23
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTTTATATAAAATATTTTAAAC
Found at i:641924 original size:26 final size:27
Alignment explanation
Indices: 641879--641935 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
641869 TTATATTTTC
* *
641879 TTTTTTAATATAAATTTAATTTAAAAA
1 TTTTTAAATATAAATATAATTTAAAAA
* *
641906 TTTTTAAATAT-AATATAATTTTAATA
1 TTTTTAAATATAAATATAATTTAAAAA
641932 TTTT
1 TTTT
641936 AATTATTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTTTAAATATAAATATAATTTAAAAA
Found at i:641954 original size:97 final size:96
Alignment explanation
Indices: 641773--642028 Score: 277
Period size: 97 Copynumber: 2.6 Consensus size: 96
641763 TATTAAACAT
* * * * * *
641773 TTTTATTATTTAGTATAAATATAATTTTGATAATTTTTTAATATTAATATAACATTAGTAAT-TT
1 TTTTATTATTTAATATAAATTTAATTTTAAAAATTTTTAAATA-TAATAT-A-ATT-TTAATATT
*
641837 TTAATTATTATTCAAAATAAATATAATTTCCTTTATA
62 TTAATTATTATTCAAAATAAATAAAATTT--TTTATA
* *
641874 TTTTCTTTTTTAATATAAATTTAA-TTTAAAAATTTTTAAATATAATATAATTTTAATATTTTAA
1 TTTTATTATTTAATATAAATTTAATTTTAAAAATTTTTAAATATAATATAATTTTAATATTTTAA
* *
641938 TTATTGTTCAACATAAATAAAATTTTTTATA
66 TTATTATTCAAAATAAATAAAATTTTTTATA
* * * *
641969 TTTTATTATTTAATATAAATATAAATTTTAAGAATTTATTATATATAA-A-CATTTTAATAT
1 TTTTATTATTTAATATAAAT-TTAATTTTAAAAATTT-TTAAATATAATATAATTTTAATAT
642029 ATTATTTTTA
Statistics
Matches: 134, Mismatches: 17, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
95 24 0.18
96 17 0.13
97 42 0.31
98 10 0.07
99 6 0.04
100 15 0.11
101 20 0.15
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (96 bp):
TTTTATTATTTAATATAAATTTAATTTTAAAAATTTTTAAATATAATATAATTTTAATATTTTAA
TTATTATTCAAAATAAATAAAATTTTTTATA
Found at i:642011 original size:26 final size:26
Alignment explanation
Indices: 641976--642025 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
641966 ATATTTTATT
641976 ATTTAATATAAATATAA-ATTTTAAGA
1 ATTTAATATAAATA-AACATTTTAAGA
* *
642002 ATTTATTATATATAAACATTTTAA
1 ATTTAATATAAATAAACATTTTAA
642026 TATATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.10
26 19 0.90
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (26 bp):
ATTTAATATAAATAAACATTTTAAGA
Found at i:643244 original size:22 final size:23
Alignment explanation
Indices: 643205--643247 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
643195 AAATTATAAA
643205 TATTGTAATTTAGATTTTAAATT
1 TATTGTAATTTAGATTTTAAATT
643228 TATTG-AATATTA-ATTTTAAA
1 TATTGTAAT-TTAGATTTTAAA
643248 AATAATAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (23 bp):
TATTGTAATTTAGATTTTAAATT
Found at i:643593 original size:8 final size:8
Alignment explanation
Indices: 643580--643615 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
643570 CTTGATTTGA
643580 TTAAAAAT
1 TTAAAAAT
643588 TT-AAAAT
1 TTAAAAAT
*
643595 TTAAAATT
1 TTAAAAAT
643603 TTAAAAAT
1 TTAAAAAT
643611 TTAAA
1 TTAAA
643616 CTTGAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
TTAAAAAT
Found at i:643857 original size:22 final size:22
Alignment explanation
Indices: 643832--643884 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
643822 ATATATGATG
*
643832 AAATAATAAT-TTATAAAAAATT
1 AAATAAT-ATCTTATAAAAAAGT
* *
643854 AAATTATATCTTATCAAAAAGT
1 AAATAATATCTTATAAAAAAGT
*
643876 AAATTATAT
1 AAATAATAT
643885 TATGAGCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 2 0.07
22 25 0.93
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (22 bp):
AAATAATATCTTATAAAAAAGT
Found at i:647221 original size:51 final size:50
Alignment explanation
Indices: 647159--647257 Score: 162
Period size: 51 Copynumber: 2.0 Consensus size: 50
647149 AAACTTTAGG
* *
647159 AAAAAAAAGATTTAAACCTTGACAAGTTTCACAATAGGGTTAGAGTATGA
1 AAAAAAAAGATTTAAACCTTGACAAGTTTAAAAATAGGGTTAGAGTATGA
*
647209 AAAAAATAAGATTTAAACCTTGACAAGTTTAAAAATAGGGTTGGAGTAT
1 AAAAAA-AAGATTTAAACCTTGACAAGTTTAAAAATAGGGTTAGAGTAT
647258 CCCCTTGGAG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
50 6 0.13
51 39 0.87
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.27
Consensus pattern (50 bp):
AAAAAAAAGATTTAAACCTTGACAAGTTTAAAAATAGGGTTAGAGTATGA
Found at i:649262 original size:13 final size:13
Alignment explanation
Indices: 649244--649273 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
649234 ACAATTCATC
649244 ATGTATCGATACA
1 ATGTATCGATACA
649257 ATGTATCGATACA
1 ATGTATCGATACA
649270 ATGT
1 ATGT
649274 GCCATGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:649363 original size:19 final size:19
Alignment explanation
Indices: 649319--649391 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
649309 TTGCCAGTTT
**
649319 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
649339 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
649358 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
649379 -ATGTATCGATACA
1 CATGTATCGATACA
649392 TCTGGGTGTG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 18 0.38
20 29 0.60
21 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:649980 original size:21 final size:19
Alignment explanation
Indices: 649942--649983 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
649932 AAGGCTCTCA
*
649942 AAAAAATTTTCCCTTTGAT
1 AAAAAATTTTCCCCTTGAT
649961 AAAAAATTTCTCCCCCTTGAT
1 AAAAAATTT-T-CCCCTTGAT
649982 AA
1 AA
649984 TCGATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 1 0.05
21 10 0.50
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (19 bp):
AAAAAATTTTCCCCTTGAT
Found at i:651887 original size:13 final size:13
Alignment explanation
Indices: 651869--651894 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
651859 TAGTAACCCT
651869 TGTATCGATACAA
1 TGTATCGATACAA
651882 TGTATCGATACAA
1 TGTATCGATACAA
651895 AGAATATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:658561 original size:51 final size:51
Alignment explanation
Indices: 658455--658584 Score: 145
Period size: 51 Copynumber: 2.5 Consensus size: 51
658445 TGGATGTATG
* * * **
658455 ATACATTGAACAATGTATCGATATATTTGGTTCAAAACCAAAAATGCATGG
1 ATACAATGAAAAATGTATCGATATATTTGGGTCAAAACCAAAAATGCATCA
* * * * * *
658506 ATACAGT-AAATAATGTATTGATACATTTGGGTCAAAACCCAGAATGTATCA
1 ATACAATGAAA-AATGTATCGATATATTTGGGTCAAAACCAAAAATGCATCA
658557 ATACAATGAAAAATGTATCGATATATTT
1 ATACAATGAAAAATGTATCGATATATTT
658585 TCATTCCATA
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
50 2 0.03
51 59 0.92
52 3 0.05
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (51 bp):
ATACAATGAAAAATGTATCGATATATTTGGGTCAAAACCAAAAATGCATCA
Found at i:658663 original size:20 final size:20
Alignment explanation
Indices: 658619--658693 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
658609 TAACATGGTC
* *
658619 ATGTATCGATACATTTCAGAC
1 ATGTATCGATACA-TTCACAT
*
658640 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACAT
* * *
658660 ATGTATCAATACGTT-ACCCT
1 ATGTATCGATACATTCA-CAT
658680 ATTGTATCGATACA
1 A-TGTATCGATACA
658694 ATTTGTTGAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 20 0.45
21 23 0.52
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTCACAT
Found at i:661967 original size:85 final size:85
Alignment explanation
Indices: 661818--662000 Score: 201
Period size: 85 Copynumber: 2.1 Consensus size: 85
661808 AGATTAAGAA
* * *
661818 AGAATTTAGTAACAGAAAAAGTCATGAAATTTATACAAAACAAGAATTTGTGATAATCTATTTGT
1 AGAATTTAGTAACAGAAAAAGTCATGAAATTTATACAAAACAAAAAATTGTGATAATCAATTTGT
*
661883 GACAAAATTTTAATTTGT-GAT
66 GACAAAA-TTTAATTT-TAAAT
* * ** * * *
661904 AGAATTTAGTAACAG-AATAGTGATGAAATTTATATGAGATAAAAAATTGTGATAGT-AAGTTTG
1 AGAATTTAGTAACAGAAAAAGTCATGAAATTTATACAAAACAAAAAATTGTGATAATCAA-TTTG
*
661967 TGACGAAATTTAATTTTCAAAT
65 TGACAAAATTTAATTTT-AAAT
661989 AGAATTTAGTAA
1 AGAATTTAGTAA
662001 TGAGAATCAT
Statistics
Matches: 82, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
83 1 0.01
84 9 0.11
85 57 0.70
86 15 0.18
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (85 bp):
AGAATTTAGTAACAGAAAAAGTCATGAAATTTATACAAAACAAAAAATTGTGATAATCAATTTGT
GACAAAATTTAATTTTAAAT
Found at i:662704 original size:79 final size:79
Alignment explanation
Indices: 662590--662737 Score: 217
Period size: 79 Copynumber: 1.9 Consensus size: 79
662580 TGCGAATCAC
* * *
662590 AAAACAACCCTATTGACTATGTATTGATATTAAAATG-CGAACATGATCCTAAAAACTCAGATTT
1 AAAACAACCCTAATGACCATGTATTGATATGAAAATGTC-AACATGATCCTAAAAACTCAGATTT
662654 ATCATTAGAATTATT
65 ATCATTAGAATTATT
* * * *
662669 AAAACAACTCTAATGACCATTTATTGATATGAAAATGTCAACATGATCCTAAAGACTTAGATTTA
1 AAAACAACCCTAATGACCATGTATTGATATGAAAATGTCAACATGATCCTAAAAACTCAGATTTA
662734 TCAT
66 TCAT
662738 GAAAAGTCAA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
79 60 0.98
80 1 0.02
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (79 bp):
AAAACAACCCTAATGACCATGTATTGATATGAAAATGTCAACATGATCCTAAAAACTCAGATTTA
TCATTAGAATTATT
Found at i:662749 original size:38 final size:39
Alignment explanation
Indices: 662697--662781 Score: 136
Period size: 38 Copynumber: 2.2 Consensus size: 39
662687 ATTTATTGAT
662697 ATGAAAATGTCAACATGATCCTAAAGACTTAGATTTATC
1 ATGAAAATGTCAACATGATCCTAAAGACTTAGATTTATC
* *
662736 ATGAAAA-GTCAACATTATCCTAAAGACTTGGATTTATC
1 ATGAAAATGTCAACATGATCCTAAAGACTTAGATTTATC
*
662774 ATGGAAAT
1 ATGAAAAT
662782 TATCACAATG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
38 35 0.83
39 7 0.17
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (39 bp):
ATGAAAATGTCAACATGATCCTAAAGACTTAGATTTATC
Found at i:663067 original size:58 final size:58
Alignment explanation
Indices: 662956--663067 Score: 145
Period size: 57 Copynumber: 1.9 Consensus size: 58
662946 TAAATGGCTT
* * * * * *
662956 TAAAATGATGAAAATTGCTAAAATGGCCCTAGATTATGTTAAATAATTTAAATAGCCC
1 TAAAATGATAAAAATTGCTAAAATGACACTAGATTATATTAAATAACTCAAATAGCCC
*
663014 TAAAATGATAAAAATTGC-AAAATGACACTGGATTATATTAAATAACCTCAAATA
1 TAAAATGATAAAAATTGCTAAAATGACACTAGATTATATTAAATAA-CTCAAATA
663068 ATGGAATTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
57 23 0.50
58 23 0.50
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (58 bp):
TAAAATGATAAAAATTGCTAAAATGACACTAGATTATATTAAATAACTCAAATAGCCC
Found at i:663208 original size:57 final size:57
Alignment explanation
Indices: 663102--663209 Score: 155
Period size: 57 Copynumber: 1.9 Consensus size: 57
663092 TATTATGTTA
*
663102 AATAACCTAAATGGCTCCAAAATGATGGAAATTGCTAAACTAACCCTAGATCATGTG
1 AATAACCTAAATGGCTCCAAAATGATGGAAATTGCTAAAATAACCCTAGATCATGTG
* * * *
663159 AATAACTTAAATGGC-CCTAAAATGGTGGAAATTGCTAAAATGACTCTAGAT
1 AATAACCTAAATGGCTCC-AAAATGATGGAAATTGCTAAAATAACCCTAGAT
663210 TATCTAAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
56 2 0.04
57 43 0.96
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.26
Consensus pattern (57 bp):
AATAACCTAAATGGCTCCAAAATGATGGAAATTGCTAAAATAACCCTAGATCATGTG
Found at i:663277 original size:28 final size:29
Alignment explanation
Indices: 663214--663287 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 29
663204 CTAGATTATC
*
663214 TAAAATAATCTAA-ATGATCCTAAATTGA
1 TAAAATAACCTAAGATGATCCTAAATTGA
663242 TAGAAATAA-CTAAGATGATCCTAGAATATG-
1 TA-AAATAACCTAAGATGATCCTA-AAT-TGA
663272 T-AAATAACCT-AGATGA
1 TAAAATAACCTAAGATGA
663288 CCTTAGGAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
28 18 0.44
29 17 0.41
30 4 0.10
31 2 0.05
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28
Consensus pattern (29 bp):
TAAAATAACCTAAGATGATCCTAAATTGA
Found at i:663799 original size:14 final size:14
Alignment explanation
Indices: 663777--663844 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
663767 GAACAATGTT
*
663777 TTCTCTTTTCTTTC
1 TTCTTTTTTCTTTC
663791 TTCTTTTTTCTTTC
1 TTCTTTTTTCTTTC
663805 TT-TTCTCTTTCTTTTC
1 TTCTT-T-TTTC-TTTC
*
663821 CTCTTTTTT-TTT-
1 TTCTTTTTTCTTTC
*
663833 TCCTTTTTTCTT
1 TTCTTTTTTCTT
663845 GATGAAAGTG
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
12 7 0.16
13 7 0.16
14 16 0.36
15 7 0.16
16 6 0.13
17 2 0.04
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TTCTTTTTTCTTTC
Found at i:663809 original size:30 final size:32
Alignment explanation
Indices: 663775--663844 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 32
663765 TAGAACAATG
*
663775 TTTTCTCTTTTC-TTTCTTCTTTTTTCTTT-C
1 TTTTCTCTTTTCTTTTCCTCTTTTTTCTTTCC
*
663805 TTTTCTC-TTTCTTTTCCTCTTTTTTTTTTCC
1 TTTTCTCTTTTCTTTTCCTCTTTTTTCTTTCC
*
663836 TTTTTTCTT
1 TTTTCTCTT
663845 GATGAAAGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 4 0.12
30 22 0.65
31 7 0.21
32 1 0.03
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (32 bp):
TTTTCTCTTTTCTTTTCCTCTTTTTTCTTTCC
Found at i:663831 original size:12 final size:11
Alignment explanation
Indices: 663780--663830 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
663770 CAATGTTTTC
*
663780 TCTTTTCTTTCT
1 TCTTTTCTCT-T
*
663792 TCTTTTTTCTT
1 TCTTTTCTCTT
663803 TCTTTTCTCTT
1 TCTTTTCTCTT
663814 TCTTTTCCTCTT
1 TCTTTT-CTCTT
663826 T-TTTT
1 TCTTTT
663831 TTTCCTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
11 21 0.60
12 14 0.40
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TCTTTTCTCTT
Found at i:666903 original size:19 final size:19
Alignment explanation
Indices: 666868--666904 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
666858 TTTAAGTTTT
**
666868 GAATTAAAAATTTAAAAAA
1 GAATTAAAAATAAAAAAAA
666887 GAATTAAAAATAAAAAAA
1 GAATTAAAAATAAAAAAA
666905 TATAAATGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (19 bp):
GAATTAAAAATAAAAAAAA
Found at i:669092 original size:21 final size:20
Alignment explanation
Indices: 669068--669107 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
669058 AAAGGTCAAA
*
669068 ACCTAAAATGTATCGATACAC
1 ACCT-AAATGTATCAATACAC
*
669089 ACCTAGATGTATCAATACA
1 ACCTAAATGTATCAATACA
669108 TATTGCTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (20 bp):
ACCTAAATGTATCAATACAC
Found at i:669158 original size:32 final size:33
Alignment explanation
Indices: 669096--669159 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
669086 CACACCTAGA
669096 TGTATCAATACATATTGCTTAGTATCGATACAT
1 TGTATCAATACATATTGCTTAGTATCGATACAT
* *
669129 TGTATCAATACATGTT-CTTTGTATCGATACA
1 TGTATCAATACATATTGCTTAGTATCGATACA
669160 CCATAAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (33 bp):
TGTATCAATACATATTGCTTAGTATCGATACAT
Found at i:669293 original size:52 final size:52
Alignment explanation
Indices: 669207--669309 Score: 125
Period size: 52 Copynumber: 2.0 Consensus size: 52
669197 ACCCTAAGTG
* * *
669207 AATTGTATCGATACATGGCAAATTGCATCGATACATTAAGCCCACTGGCTAT
1 AATTGTATCGATACATGACAAATTGCATCAATACATTAAGCCCAATGGCTAT
* ** * * *
669259 AATTGTATCGATACATTATGAATTGTATCAATACATTGAGTCCAATGGCTA
1 AATTGTATCGATACATGACAAATTGCATCAATACATTAAGCCCAATGGCTA
669310 GTAGAGTTTC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (52 bp):
AATTGTATCGATACATGACAAATTGCATCAATACATTAAGCCCAATGGCTAT
Found at i:670904 original size:12 final size:12
Alignment explanation
Indices: 670889--670913 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
670879 TCAACCATCA
670889 ATGATGATGAAG
1 ATGATGATGAAG
670901 ATGATGATGAAG
1 ATGATGATGAAG
670913 A
1 A
670914 GGTTGACTCG
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:0.44, C:0.00, G:0.32, T:0.24
Consensus pattern (12 bp):
ATGATGATGAAG
Found at i:675388 original size:19 final size:19
Alignment explanation
Indices: 675366--675408 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
675356 AGATATATTG
675366 ATACAAAAAAATTATATCA
1 ATACAAAAAAATTATATCA
** * *
675385 ATACATTAAAATTGTATCG
1 ATACAAAAAAATTATATCA
675404 ATACA
1 ATACA
675409 TTTGGACTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (19 bp):
ATACAAAAAAATTATATCA
Found at i:675409 original size:19 final size:19
Alignment explanation
Indices: 675373--675410 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
675363 TTGATACAAA
675373 AAAATTATATCAATACATT
1 AAAATTATATCAATACATT
* *
675392 AAAATTGTATCGATACATT
1 AAAATTATATCAATACATT
675411 TGGACTCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (19 bp):
AAAATTATATCAATACATT
Found at i:677160 original size:16 final size:16
Alignment explanation
Indices: 677139--677180 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 16
677129 ATGTTTTATG
677139 TGTTTTATGAATGTGT
1 TGTTTTATGAATGTGT
677155 TGTTTTATATGAATGTGT
1 TG-TTT-TATGAATGTGT
677173 TGTTTTAT
1 TGTTTTAT
677181 CACATACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.21
17 6 0.25
18 13 0.54
ACGTcount: A:0.19, C:0.00, G:0.21, T:0.60
Consensus pattern (16 bp):
TGTTTTATGAATGTGT
Found at i:677167 original size:18 final size:18
Alignment explanation
Indices: 677144--677180 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
677134 TTATGTGTTT
677144 TATGAATGTGTTGTTTTA
1 TATGAATGTGTTGTTTTA
677162 TATGAATGTGTTGTTTTA
1 TATGAATGTGTTGTTTTA
677180 T
1 T
677181 CACATACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.57
Consensus pattern (18 bp):
TATGAATGTGTTGTTTTA
Found at i:679158 original size:21 final size:21
Alignment explanation
Indices: 679126--679182 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
679116 GGCTTAAACT
*
679126 ATCATCTAAGCTTAAGCTTGGG
1 ATCAT-TAAGCTCAAGCTTGGG
*
679148 GTCATTAAGCTCAAGCTTGGG
1 ATCATTAAGCTCAAGCTTGGG
679169 ATCATTAAGCTCAA
1 ATCATTAAGCTCAA
679183 AATATAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 28 0.88
22 4 0.12
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (21 bp):
ATCATTAAGCTCAAGCTTGGG
Found at i:679382 original size:20 final size:20
Alignment explanation
Indices: 679353--679390 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
679343 GTTCTCCCTT
679353 TTTCTTTTTCTT-TTTTTTC
1 TTTCTTTTTCTTGTTTTTTC
679372 TTTCTTTTTTCTTGTTTTT
1 TTTC-TTTTTCTTGTTTTT
679391 AAAGTTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 8 0.47
21 5 0.29
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (20 bp):
TTTCTTTTTCTTGTTTTTTC
Found at i:679915 original size:28 final size:28
Alignment explanation
Indices: 679880--680076 Score: 162
Period size: 28 Copynumber: 7.0 Consensus size: 28
679870 ACCAAAGGTT
*
679880 TAATTAAAAATTCTATATACAAAAAGTA
1 TAATTAAAAATTCTATATATAAAAAGTA
* *
679908 TAATTAAAAATTCTATATATAACAAGTT
1 TAATTAAAAATTCTATATATAAAAAGTA
* *
679936 TAATTAAAAATTCTATATATAAAAGGTT
1 TAATTAAAAATTCTATATATAAAAAGTA
* * * * * *
679964 TAGTTAGAAAGTCTATAAATAAAAATTT
1 TAATTAAAAATTCTATATATAAAAAGTA
* * * * *
679992 TAATTGAAATTTTTTTA-AGTAAAAAGTT
1 TAATTAAAAATTCTATATA-TAAAAAGTA
* * * **
680020 TAGTTAAAACTTTTATGCATAAAAAGTA
1 TAATTAAAAATTCTATATATAAAAAGTA
*
680048 TAATTAAAAGTTTCATATATATAAAAAGT
1 TAATTAAAA-ATTC-TATATATAAAAAGT
680077 GATGACAAGT
Statistics
Matches: 135, Mismatches: 30, Indels: 6
0.79 0.18 0.04
Matches are distributed among these distances:
27 1 0.01
28 119 0.88
29 3 0.02
30 12 0.09
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.38
Consensus pattern (28 bp):
TAATTAAAAATTCTATATATAAAAAGTA
Found at i:680998 original size:15 final size:15
Alignment explanation
Indices: 680965--681012 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
680955 ATCGAATTTA
*
680965 TTAATTAATTTTTCATT
1 TTAA-TAATTTTT-TTT
*
680982 TTGATAATTTTTTTT
1 TTAATAATTTTTTTT
680997 TTAATAATTTTTTTT
1 TTAATAATTTTTTTT
681012 T
1 T
681013 AAGTTTAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 17 0.61
16 8 0.29
17 3 0.11
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (15 bp):
TTAATAATTTTTTTT
Found at i:681228 original size:15 final size:14
Alignment explanation
Indices: 681208--681238 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
681198 ACTAGTTACA
681208 TTTTTTTTATAGAAT
1 TTTTTTTTA-AGAAT
681223 TTTTTTTTAAGAAT
1 TTTTTTTTAAGAAT
681237 TT
1 TT
681239 AACTTTTGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (14 bp):
TTTTTTTTAAGAAT
Found at i:681379 original size:15 final size:15
Alignment explanation
Indices: 681359--681400 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 15
681349 CACCAATGAA
681359 TTTTCTCATTCATTT
1 TTTTCTCATTCATTT
681374 TTTTCTCTAATATCATTT
1 TTTTCTC--AT-TCATTT
681392 TTTT-TCATT
1 TTTTCTCATT
681401 TAGTTTACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 1 0.04
15 9 0.38
17 4 0.17
18 10 0.42
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTCTCATTCATTT
Found at i:686065 original size:255 final size:257
Alignment explanation
Indices: 685543--686083 Score: 582
Period size: 255 Copynumber: 2.1 Consensus size: 257
685533 ATATATGAAA
* * *
685543 GCATGTAACCTTAATACTTTAAATATTTAGACGCATTGGCATTTAATATTGGTGCGCATTTTTCA
1 GCATGTATCCTTAATACCTTAAATATTTAGACGCATTGGCATTTAATATTGGTGCACATTTTTCA
** *
685608 TAAAGTTTAGGGAAAAGACATGCCTCCTAACACCATCTAAACGTGCCTAAATGCTTTATAGAACT
66 TAAAGTTTAGGGAAAAGACATGCCTCCTAACACCATCTAAACACGCCTAAAAGCTTTATAGAACT
* *
685673 ATCTCCAAAATATATACATGAAATAGGTGCGCTAGTATGAAATTTAGGCGCATTATTTTACTAAA
131 ATCTCCAAAATAGATACATGAAATAGGTGCACTAGTATGAAATTTAGGCGCATTATTTTACTAAA
* * * **** * *
685738 GTTTAGAGAAAAGATTCTCTTTTTCAATCCATTTAAGTGTGCCTAAATGCTATACCGTGAAG
196 GTTTAAAAAAAAGATTCTCTTTTTCAATCCATATAAGCACACCTAAATGCTATACCATAAAG
* * * ** * *
685800 ACAAGTATCCTTAATGCCTTAAATATTTAGGTGCATTGGTATTTAAT-TTCGGTGCACCTATTTT
1 GCATGTATCCTTAATACCTTAAATATTTAGACGCATTGGCATTTAATATT-GGTGCACAT-TTTT
* * * * * *
685864 -GTAAAGTTTAGGG-AAAGGCAT-CCTCTTAATACCTTTTAAACACGCCTAAAAGCTTTATAGAA
64 CATAAAGTTTAGGGAAAAGACATGCCTCCTAACACCATCTAAACACGCCTAAAAGCTTTATAG-A
* * *
685926 ACTATCTCCAAAATAGATATATGAAATA-G-GCACATCGTTATGAAATTTA-G-GTATGT-TGTT
128 ACTATCTCCAAAATAGATACATGAAATAGGTGCAC-TAG-TATGAAATTTAGGCGCAT-TAT-TT
* * * *
685986 TATTAAAGTTCTAAAAAAAAG-TTGGT-TTTTTCAATCTATATAAGCACACCTAAATGGTATACC
189 TACTAAAGTT-TAAAAAAAAGATT-CTCTTTTTCAATCCATATAAGCACACCTAAATGCTATACC
686049 ATAAAG
252 ATAAAG
*
686055 GCATGTATCCTTAATATCTTAAATATTTA
1 GCATGTATCCTTAATACCTTAAATATTTA
686084 TACGTGCCAT
Statistics
Matches: 234, Mismatches: 41, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
254 7 0.03
255 109 0.47
256 56 0.24
257 58 0.25
258 4 0.02
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (257 bp):
GCATGTATCCTTAATACCTTAAATATTTAGACGCATTGGCATTTAATATTGGTGCACATTTTTCA
TAAAGTTTAGGGAAAAGACATGCCTCCTAACACCATCTAAACACGCCTAAAAGCTTTATAGAACT
ATCTCCAAAATAGATACATGAAATAGGTGCACTAGTATGAAATTTAGGCGCATTATTTTACTAAA
GTTTAAAAAAAAGATTCTCTTTTTCAATCCATATAAGCACACCTAAATGCTATACCATAAAG
Found at i:686679 original size:21 final size:21
Alignment explanation
Indices: 686653--686709 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
686643 AAAAAAATTA
686653 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
686674 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
686695 AATGTATCGATACAT
1 AATGTATCGATACAT
686710 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:686789 original size:19 final size:19
Alignment explanation
Indices: 686765--686832 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
686755 AATTCAACAA
686765 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
686784 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
686799 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
686816 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
686833 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:686804 original size:13 final size:13
Alignment explanation
Indices: 686786--686810 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
686776 ACATAAGTTT
686786 TGTATCGATACAA
1 TGTATCGATACAA
686799 TGTATCGATACA
1 TGTATCGATACA
686811 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:686808 original size:32 final size:32
Alignment explanation
Indices: 686767--686829 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
686757 TTCAACAATT
*
686767 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
686799 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
686830 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:686890 original size:13 final size:13
Alignment explanation
Indices: 686872--686897 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
686862 CATTTTTCTG
686872 TGTATCGATACAT
1 TGTATCGATACAT
686885 TGTATCGATACAT
1 TGTATCGATACAT
686898 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:686894 original size:33 final size:33
Alignment explanation
Indices: 686852--686918 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
686842 GCCAAGGAAA
***
686852 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
686885 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
686918 T
1 T
686919 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:689381 original size:28 final size:27
Alignment explanation
Indices: 689314--689386 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
689304 CTTCACAATC
* *
689314 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
689341 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
689369 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
689387 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:689431 original size:51 final size:51
Alignment explanation
Indices: 689369--689539 Score: 180
Period size: 51 Copynumber: 3.3 Consensus size: 51
689359 TTATTTCTGA
* * *
689369 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * * *
689420 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCCATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * * *
689473 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAAATTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
689525 GAGGATACTCCAACC
1 GGGGATACTCCAACC
689540 TCGTTATTTC
Statistics
Matches: 95, Mismatches: 22, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
51 36 0.38
52 18 0.19
53 32 0.34
54 9 0.09
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:689558 original size:28 final size:28
Alignment explanation
Indices: 689522--689603 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
689512 AATTTTCACA
*
689522 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
689550 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
689578 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
689604 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:702016 original size:16 final size:16
Alignment explanation
Indices: 701995--702060 Score: 71
Period size: 16 Copynumber: 4.0 Consensus size: 16
701985 CACCTCTCTT
701995 CAAAAAAAAAAAAGAG
1 CAAAAAAAAAAAAGAG
702011 CAAAAAAAAAAAAG-G
1 CAAAAAAAAAAAAGAG
* * *
702026 GAAAAAAAAACAAAAAA
1 CAAAAAAAAA-AAAGAG
702043 CAAAACAAAGAAAAAGAG
1 CAAAA-AAA-AAAAAGAG
702061 AGAAAGAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
15 10 0.25
16 17 0.43
17 4 0.10
18 7 0.17
19 2 0.05
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (16 bp):
CAAAAAAAAAAAAGAG
Found at i:703416 original size:55 final size:53
Alignment explanation
Indices: 703208--703575 Score: 249
Period size: 55 Copynumber: 6.6 Consensus size: 53
703198 AAAAAAAAAA
*
703208 ACACCTTTCCAAAG-CCACACAAGTTGGTGGCA-TTCCAGTCCTCAAA-AG-AGG
1 ACACCTTT--AAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGG
* * *
703259 ACACCTTTTAAGCCCACACAAGTTGGTAGGCATTTTCCAGTCC-CTAAGGAGCAAGAGG
1 ACACCTTTAAAGCCCACACAAGTTGGT-GGCACTTT-CAGTCCTC-AAAGAGC---AGG
* * *
703317 ACAAACCTTTCAAAGCCCCCACAAGTTGGTGGCATTTTCCAGTCCTCAACGAGCAGG
1 AC--ACCTTT-AAAGCCCACACAAGTTGGTGGCACTTT-CAGTCCTCAAAGAGCAGG
* *
703374 ACACCTCTTAAAAG-CCACACAAGTTTGTGGCACCTTTCAGTCCCCAAAGAGCAGG
1 ACACCT-TT-AAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGG
*
703429 ACAACATCTTAAAGCCCACACAAG-TGGTGGCACCTTTTCAGT-CTCAAAGAGCAGG
1 AC-ACCT-TTAAAGCCCACACAAGTTGGTGGCA-C-TTTCAGTCCTCAAAGAGCAGG
* *
703484 ACACGCTATTCAAAG-CCACAC-A-TT-GTTG-AGTTTGCCAGTCCTCAAAGAGCCAGG
1 ACAC-CT-TT-AAAGCCCACACAAGTTGGTGGCACTTT--CAGTCCTCAAAGAG-CAGG
* *
703538 ACGCCTTTTCAAAGCGCCACAACGAGTTTGGTGGCACT
1 ACACC-TTT-AAAGC-CCAC-ACAAG-TTGGTGGCACT
703576 GTTTACTCCT
Statistics
Matches: 260, Mismatches: 22, Indels: 60
0.76 0.06 0.18
Matches are distributed among these distances:
49 3 0.01
50 17 0.07
51 12 0.05
52 8 0.03
53 28 0.11
54 14 0.05
55 78 0.30
56 37 0.14
57 6 0.02
58 5 0.02
59 2 0.01
60 30 0.12
61 20 0.08
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (53 bp):
ACACCTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGG
Found at i:703443 original size:111 final size:111
Alignment explanation
Indices: 703210--703505 Score: 301
Period size: 111 Copynumber: 2.6 Consensus size: 111
703200 AAAAAAAAAC
* *
703210 ACCTTTCCAAAG-CCACACAAGTTGGTGGCA--TTCCAGTCCTCAAAAG-AGGACACCTTTTAAG
1 ACCTTT-CAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAGAGCAGGACACCTTTAAAG
* * *
703271 CCCACACAAGTTGGTAGGCATTTTCCAGTCCCTAAGGAGCAAGAGGACAA
65 -CCACACAAGTTGGTAGGCACTTTCCAGTCCCCAAAGAGC-A-AGGACAA
*
703321 ACCTTTCAAAGCCCCCACAAGTTGGTGGCATTTTCCAGTCCTCAACGAGCAGGACACCTCTTAAA
1 ACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAA-GAGCAGGACACCT-TT-AA
*
703386 AGCCACACAAGTTTGT-GGCACCTTT-CAGTCCCCAAAGAGC-AGGAC-A
63 AGCCACACAAGTTGGTAGGCA-CTTTCCAGTCCCCAAAGAGCAAGGACAA
*
703432 ACATCTT-AAAGCCCACACAAG-TGGTGGCACCTTTT-CAGT-CTCAAAGAGCAGGACACGCTAT
1 ACCT-TTCAAAGCCCACACAAGTTGGTGGCA--TTTTCCAGTCCTC-AAGAGCAGGACAC-CT-T
703493 TCAAAGCCACACA
60 T-AAAGCCACACA
703506 TTGTTGAGTT
Statistics
Matches: 161, Mismatches: 11, Indels: 26
0.81 0.06 0.13
Matches are distributed among these distances:
110 27 0.17
111 61 0.38
112 11 0.07
113 13 0.08
114 2 0.01
115 26 0.16
116 18 0.11
117 3 0.02
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.20
Consensus pattern (111 bp):
ACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAGAGCAGGACACCTTTAAAGC
CACACAAGTTGGTAGGCACTTTCCAGTCCCCAAAGAGCAAGGACAA
Found at i:704286 original size:22 final size:23
Alignment explanation
Indices: 704258--704312 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 23
704248 TTTAAAATAG
704258 ATCGATACATTGTGTAGAAT-GT-
1 ATCGATACATT-TGTAGAATAGTA
*
704280 ATCGATACATTTGTGGAATAGTA
1 ATCGATACATTTGTAGAATAGTA
704303 ATCGATACAT
1 ATCGATACAT
704313 CCTACAAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 7 0.23
22 13 0.43
23 10 0.33
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (23 bp):
ATCGATACATTTGTAGAATAGTA
Found at i:704500 original size:12 final size:14
Alignment explanation
Indices: 704482--704513 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
704472 TTTTCTGTGG
704482 GGTATCGAT-ACAT
1 GGTATCGATAACAT
704495 -GTATCGATAACAT
1 GGTATCGATAACAT
704508 GGTATC
1 GGTATC
704514 TTAGGTCGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 8 0.47
13 4 0.24
14 5 0.29
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (14 bp):
GGTATCGATAACAT
Done.