Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 118 of 196
Found at i:35650815 original size:68 final size:69
Alignment explanation
Indices: 35650684--35650818 Score: 173
Period size: 68 Copynumber: 2.0 Consensus size: 69
35650674 TGATTAAACT
* * * *
35650684 TAATCACTTTAATATTAAATTAGCATAATAGTTATCAAGATAAATTTTAAATTAAAATTAATATT
1 TAATCACTTTAATATTAAATTAACAAAATAGCTATCAAGATAAATATTAAATTAAAATTAATATT
35650749 AAGA
66 AAGA
* * * * * *
35650753 TAATCAGTTTAATATTAAATTAATAAAATA-CTATTAAGATAAGTATTAAATTTAATTTAATATT
1 TAATCACTTTAATATTAAATTAACAAAATAGCTATCAAGATAAATATTAAATTAAAATTAATATT
35650817 AA
66 AA
35650819 ACTATTAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
68 30 0.54
69 26 0.46
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (69 bp):
TAATCACTTTAATATTAAATTAACAAAATAGCTATCAAGATAAATATTAAATTAAAATTAATATT
AAGA
Found at i:35655476 original size:21 final size:21
Alignment explanation
Indices: 35655452--35655521 Score: 97
Period size: 21 Copynumber: 3.3 Consensus size: 21
35655442 GTGTTTTATT
*
35655452 TTCTGTTCAACTCTTATGAGT
1 TTCTGTTCAACTCTTATGAGC
*
35655473 TTCTGTTCAACTCTTACGAGC
1 TTCTGTTCAACTCTTATGAGC
*
35655494 TTCTGTTCAGCTCTT-TCGAGC
1 TTCTGTTCAACTCTTAT-GAGC
35655515 TTCTGTT
1 TTCTGTT
35655522 TAGCTTTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.14, C:0.24, G:0.16, T:0.46
Consensus pattern (21 bp):
TTCTGTTCAACTCTTATGAGC
Found at i:35655526 original size:21 final size:21
Alignment explanation
Indices: 35655452--35655535 Score: 93
Period size: 21 Copynumber: 4.1 Consensus size: 21
35655442 GTGTTTTATT
* *
35655452 TTCTGTTCAACTCTTAT-GAGT
1 TTCTGTTCAGCTCTT-TCGAGC
* *
35655473 TTCTGTTCAACTCTTACGAGC
1 TTCTGTTCAGCTCTTTCGAGC
35655494 TTCTGTTCAGCTCTTTCGAGC
1 TTCTGTTCAGCTCTTTCGAGC
*
35655515 TTCTGTTTAGCT-TTT-GAGC
1 TTCTGTTCAGCTCTTTCGAGC
35655534 TT
1 TT
35655536 TTGATTGGAG
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
19 6 0.11
20 3 0.05
21 48 0.84
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTTCGAGC
Found at i:35657451 original size:21 final size:21
Alignment explanation
Indices: 35657427--35657466 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
35657417 AAACTGCCTG
*
35657427 CTATGTCGCGACACGCCCCTA
1 CTATGTCGCAACACGCCCCTA
*
35657448 CTATGTCGCAACAGGCCCC
1 CTATGTCGCAACACGCCCC
35657467 CTTATGGTAG
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:0.20, C:0.42, G:0.20, T:0.17
Consensus pattern (21 bp):
CTATGTCGCAACACGCCCCTA
Found at i:35657706 original size:17 final size:19
Alignment explanation
Indices: 35657674--35657708 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
35657664 GAGACAAATT
35657674 ATTCTTAGGTTTTTATTTC
1 ATTCTTAGGTTTTTATTTC
35657693 ATTCTTA-G-TTTTATTT
1 ATTCTTAGGTTTTTATTT
35657709 TGTTTACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.17, C:0.09, G:0.09, T:0.66
Consensus pattern (19 bp):
ATTCTTAGGTTTTTATTTC
Found at i:35659217 original size:30 final size:30
Alignment explanation
Indices: 35659183--35659329 Score: 142
Period size: 30 Copynumber: 4.9 Consensus size: 30
35659173 TTTTATTTGT
35659183 TTAGGGTTTAAG-GTTTTAGAAAAAAATAAA
1 TTAGGGTTTAAGTGTTTTA-AAAAAAATAAA
35659213 TTAGGGTTTAGAG-GTTTT--AAAAAATAAA
1 TTAGGGTTTA-AGTGTTTTAAAAAAAATAAA
* * * *
35659241 TTAGGGTTTATGTTTTTTAAATAAATTAAA
1 TTAGGGTTTAAGTGTTTTAAAAAAAATAAA
* * * *
35659271 TTAGGGTTTATGTTTTTTAAAGAAATTAAA
1 TTAGGGTTTAAGTGTTTTAAAAAAAATAAA
35659301 TTAGGGTTTAAAGAT-TTTTAAAAATAAAT
1 TTAGGGTTT-AAG-TGTTTTAAAAA-AAAT
35659330 TTTTGTTTAG
Statistics
Matches: 102, Mismatches: 8, Indels: 12
0.84 0.07 0.10
Matches are distributed among these distances:
27 1 0.01
28 24 0.24
30 56 0.55
31 17 0.17
32 4 0.04
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (30 bp):
TTAGGGTTTAAGTGTTTTAAAAAAAATAAA
Found at i:35659247 original size:58 final size:60
Alignment explanation
Indices: 35659183--35659329 Score: 160
Period size: 58 Copynumber: 2.5 Consensus size: 60
35659173 TTTTATTTGT
35659183 TTAGGGTTTAAG-GTTTTAGAAAAAAATAAATTAGGGTTTA-GAGGTTTTAAA-AAA-TAAA
1 TTAGGGTTTAAGTGTTTTA-AAAAAAATAAATTAGGGTTTATG-GGTTTTAAAGAAATTAAA
* * * * **
35659241 TTAGGGTTTATGTTTTTTAAATAAATTAAATTAGGGTTTATGTTTTTTAAAGAAATTAAA
1 TTAGGGTTTAAGTGTTTTAAAAAAAATAAATTAGGGTTTATGGGTTTTAAAGAAATTAAA
35659301 TTAGGGTTTAAAGAT-TTTTAAAAATAAAT
1 TTAGGGTTT-AAG-TGTTTTAAAAA-AAAT
35659330 TTTTGTTTAG
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
58 37 0.51
59 9 0.12
60 13 0.18
61 10 0.14
62 4 0.05
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (60 bp):
TTAGGGTTTAAGTGTTTTAAAAAAAATAAATTAGGGTTTATGGGTTTTAAAGAAATTAAA
Found at i:35659563 original size:126 final size:125
Alignment explanation
Indices: 35659426--35660097 Score: 890
Period size: 125 Copynumber: 5.4 Consensus size: 125
35659416 TTTTTCAGTG
* *
35659426 AGCAAAAGTACTAAAAAGAGCTCCCAGCTGGACGCTATTTTTCTACAGTAGTTTCTAAAAAAATA
1 AGCAAAAGTACTAAAAA-AGCTCCCACCTGGACGCTCTTTTTCTACAGTAGTTTCTAAAAAAATA
* * ** * *
35659491 ATTTTGAGAAGATGATTCTGAAAAAATAAGGTAAAAAACATTTCAAGAAAGATGCACTGTC
65 ATTTTGAGAAGATGGTTCTGAAAAAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTGTC
* * * *
35659552 AGCAAAAGTACTGAAAAAAGCT--CACTTGGATGCTC-TTTTCTATAGTAGTTTCTGAAAAAATA
1 AGCAAAAGTACT-AAAAAAGCTCCCACCTGGACGCTCTTTTTCTACAGTAGTTTCTAAAAAAATA
* * * *
35659614 ATTTTGGGAAGATAGTTTTGAAAAAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTTTC
65 ATTTTGAGAAGATGGTTCTGAAAAAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTGTC
* * * *
35659675 AGCAAAAGTATCGAAAAAAGCTCCCACCTGGACACTCTTTTTCTACAATAATTTCTGAAAAAAAT
1 AGCAAAAGTA-CTAAAAAAGCTCCCACCTGGACGCTCTTTTTCTACAGTAGTTTCT-AAAAAAAT
* *
35659740 AA--TTGAGAAGATGGTTCTGAAAAAATAGGGTAAAAAATGCTTCAAGCAGGATGCACTGTT
64 AATTTTGAGAAGATGGTTCTGAAAAAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTGTC
*
35659800 AGCAAAAGTACTGAAAAAAGCTCCCACCTGGACGCTCTTTTTCTACAGTAGTTTCT-GAAAAATA
1 AGCAAAAGTACT-AAAAAAGCTCCCACCTGGACGCTCTTTTTCTACAGTAGTTTCTAAAAAAATA
* * *
35659864 ATTTTGAGAAGATGGTTCTGAAAAAATAGGGTAAAAAAAGCTTCAAGCAGGATGCACTTTT
65 ATTTTGAGAAGATGGTTCTGAAAAAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTGTC
* * * * *
35659925 AGCAAAAGTACTAAAAAAAGCTCCCACCTAGATGCTCTTTTTCTATAGTAGTTTTTGAAAAAATA
1 AGCAAAAGTACT-AAAAAAGCTCCCACCTGGACGCTCTTTTTCTACAGTAGTTTCTAAAAAAATA
* * *
35659990 ATTTTGAGAAGATGGTTCT-AAATAAATAGGGTCAAAAACGCTTCAAGCGGGATGCATTGTC
65 ATTTTGAGAAGATGGTTCTGAAA-AAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTGTC
* * *
35660051 AGCAAAAGTACTAAAAAAAGCTCCCACCTAGAAGCTTTTTTTCTACA
1 AGCAAAAGTACT-AAAAAAGCTCCCACCTGGACGCTCTTTTTCTACA
35660098 ATACATCCTA
Statistics
Matches: 483, Mismatches: 52, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
123 103 0.21
124 11 0.02
125 222 0.46
126 133 0.28
127 14 0.03
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (125 bp):
AGCAAAAGTACTAAAAAAGCTCCCACCTGGACGCTCTTTTTCTACAGTAGTTTCTAAAAAAATAA
TTTTGAGAAGATGGTTCTGAAAAAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTGTC
Found at i:35660196 original size:25 final size:25
Alignment explanation
Indices: 35660167--35660237 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
35660157 TTACAGCAAG
*
35660167 AGAAATT-AGAGAAGTTTAGAAGAAT
1 AGAAATTGA-AGAAGTTCAGAAGAAT
* *
35660192 AGAAATTGAAAAAGTTCAGAAGAGT
1 AGAAATTGAAGAAGTTCAGAAGAAT
* *
35660217 ATAAATTGAAGAAGTTGAGAA
1 AGAAATTGAAGAAGTTCAGAA
35660238 TGTATAAGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
25 38 0.97
26 1 0.03
ACGTcount: A:0.52, C:0.01, G:0.24, T:0.23
Consensus pattern (25 bp):
AGAAATTGAAGAAGTTCAGAAGAAT
Found at i:35662258 original size:17 final size:18
Alignment explanation
Indices: 35662238--35662271 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35662228 TAATCACCAC
*
35662238 TAATATT-ATTTTGTTTG
1 TAATATTCAATTTGTTTG
35662255 TAATATTCAATTTGTTT
1 TAATATTCAATTTGTTT
35662272 TTGAATGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.26, C:0.03, G:0.09, T:0.62
Consensus pattern (18 bp):
TAATATTCAATTTGTTTG
Found at i:35664303 original size:27 final size:27
Alignment explanation
Indices: 35664273--35664417 Score: 166
Period size: 27 Copynumber: 5.4 Consensus size: 27
35664263 GGGTATAATA
* * *
35664273 GTCATTTTACCCCATGAGAGTTTTTCG
1 GTCATTTTACCCAATGAGGGTATTTCG
*
35664300 GTCATTTTACCCAATGGGGGTATTTCG
1 GTCATTTTACCCAATGAGGGTATTTCG
* * *
35664327 GTTATTCTACCCAATGGGGGTATTTCG
1 GTCATTTTACCCAATGAGGGTATTTCG
* *
35664354 GTTATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCAATGAGGGTATTTCG
* * *
35664381 GTCATTTTACTCTATGA-GGTATTTTG
1 GTCATTTTACCCAATGAGGGTATTTCG
*
35664407 GTTATTTTACC
1 GTCATTTTACC
35664418 TATTTTGAGG
Statistics
Matches: 104, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
26 17 0.16
27 87 0.84
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCAATGAGGGTATTTCG
Found at i:35677577 original size:16 final size:17
Alignment explanation
Indices: 35677553--35677584 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
35677543 AAATTTTCTT
35677553 TTTATTTATTTTTTTCA
1 TTTATTTATTTTTTTCA
35677570 TTTA-TTATTTTTTTC
1 TTTATTTATTTTTTTC
35677585 TTTCAATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTATTTATTTTTTTCA
Found at i:35677579 original size:20 final size:18
Alignment explanation
Indices: 35677546--35677589 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 18
35677536 GCAAAAAAAA
35677546 TTTTC-TTTTTATTTATTT
1 TTTTCATTTTTATTT-TTT
35677564 TTTTCATTTATTATTTTTT
1 TTTTCATTT-TTATTTTTT
35677583 TCTTTCA
1 T-TTTCA
35677590 ATCTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.22
19 7 0.30
20 11 0.48
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTCATTTTTATTTTTT
Found at i:35678577 original size:12 final size:12
Alignment explanation
Indices: 35678560--35678595 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
35678550 AATAAGTCTG
35678560 AAAAATAAAATA
1 AAAAATAAAATA
35678572 AAAAATAACAAT-
1 AAAAATAA-AATA
35678584 AAAAATAAAATA
1 AAAAATAAAATA
35678596 TAGTTCGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.14
12 16 0.73
13 3 0.14
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAAATAAAATA
Found at i:35689978 original size:42 final size:43
Alignment explanation
Indices: 35689877--35690002 Score: 114
Period size: 42 Copynumber: 2.9 Consensus size: 43
35689867 ATGCTAACGC
* * *
35689877 CCCAGACATGGTCTTACATGAAATTGAATATTGATGCCACTAT
1 CCCAGACATGGTCTTACATGAAATTCAATATCGATGCCAATAT
* * * *
35689920 CCCAGATAGGGTCTTACATGAAA-TC-ATATACGATGTCAATGT
1 CCCAGACATGGTCTTACATGAAATTCAATAT-CGATGCCAATAT
* * *
35689962 CCCAGACATGATCTTACACGAAAATCTCAA-ATCAATGCCAA
1 CCCAGACATGGTCTTACATG-AAAT-TCAATATCGATGCCAA
35690003 CGTCCTAGAC
Statistics
Matches: 65, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
41 4 0.06
42 25 0.38
43 24 0.37
44 7 0.11
45 4 0.06
46 1 0.02
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (43 bp):
CCCAGACATGGTCTTACATGAAATTCAATATCGATGCCAATAT
Found at i:35697360 original size:23 final size:23
Alignment explanation
Indices: 35697325--35697446 Score: 156
Period size: 23 Copynumber: 5.3 Consensus size: 23
35697315 ATAAGTGCCA
*
35697325 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGTCGAAGCTAC
* *
35697348 CCCTGATACGTAGTC-ATAGCTAC
1 CACTGATATGTAGTCGA-AGCTAC
*
35697371 CACTGAAATGTAGTCGAAGCTAC
1 CACTGATATGTAGTCGAAGCTAC
* * *
35697394 CACTGATAGGTAGCCGTAGCTAC
1 CACTGATATGTAGTCGAAGCTAC
*
35697417 CACTGAAATGTAGTCGAAGCTAC
1 CACTGATATGTAGTCGAAGCTAC
35697440 CACTGAT
1 CACTGAT
35697447 CAATAACACT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
22 1 0.01
23 80 0.98
24 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGTCGAAGCTAC
Found at i:35697392 original size:46 final size:46
Alignment explanation
Indices: 35697325--35697446 Score: 190
Period size: 46 Copynumber: 2.7 Consensus size: 46
35697315 ATAAGTGCCA
* * * *
35697325 CACTGATATGTAGCCGAAGCTACCCCTGATACGTAGTCATAGCTAC
1 CACTGAAATGTAGTCGAAGCTACCACTGATACGTAGCCATAGCTAC
* *
35697371 CACTGAAATGTAGTCGAAGCTACCACTGATAGGTAGCCGTAGCTAC
1 CACTGAAATGTAGTCGAAGCTACCACTGATACGTAGCCATAGCTAC
35697417 CACTGAAATGTAGTCGAAGCTACCACTGAT
1 CACTGAAATGTAGTCGAAGCTACCACTGAT
35697447 CAATAACACT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 70 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.23
Consensus pattern (46 bp):
CACTGAAATGTAGTCGAAGCTACCACTGATACGTAGCCATAGCTAC
Found at i:35700576 original size:18 final size:19
Alignment explanation
Indices: 35700535--35700578 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
35700525 TTCCCTTAAA
*
35700535 AGGAATTGGTAGGGTTAGC
1 AGGAGTTGGTAGGGTTAGC
35700554 A-GAGTTGGTAGGGTTAG-
1 AGGAGTTGGTAGGGTTAGC
35700571 AGGAGTTG
1 AGGAGTTG
35700579 AGAGTAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 21 0.91
19 1 0.04
ACGTcount: A:0.25, C:0.02, G:0.45, T:0.27
Consensus pattern (19 bp):
AGGAGTTGGTAGGGTTAGC
Found at i:35710800 original size:3 final size:3
Alignment explanation
Indices: 35710792--35710829 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
35710782 TAAAAAGAGG
35710792 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
35710830 CCTTAAGAAT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:35730527 original size:28 final size:27
Alignment explanation
Indices: 35730496--35730553 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
35730486 ATTCGCTACG
*
35730496 AAGGCTGTTCTTTTCAAGATTCACCACA
1 AAGG-TGTTCATTTCAAGATTCACCACA
* * *
35730524 AAGGTTTTCATTTCATGATTTACCACA
1 AAGGTGTTCATTTCAAGATTCACCACA
35730551 AAG
1 AAG
35730554 AATTTTCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (27 bp):
AAGGTGTTCATTTCAAGATTCACCACA
Found at i:35730543 original size:27 final size:27
Alignment explanation
Indices: 35730462--35730553 Score: 76
Period size: 28 Copynumber: 3.3 Consensus size: 27
35730452 TCATAATCCG
* * *
35730462 CCACAAAAGGTATTTCCTTTCATAATTCG
1 CCAC-AAAGGT-TTTCATTTCATGATTCA
* * * * *
35730491 CTACGAAGGCTGTTCTTTTCAAGATTCA
1 CCACAAAGG-TTTTCATTTCATGATTCA
*
35730519 CCACAAAGGTTTTCATTTCATGATTTA
1 CCACAAAGGTTTTCATTTCATGATTCA
35730546 CCACAAAG
1 CCACAAAG
35730554 AATTTTCTTT
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
27 22 0.45
28 23 0.47
29 4 0.08
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (27 bp):
CCACAAAGGTTTTCATTTCATGATTCA
Found at i:35730564 original size:27 final size:27
Alignment explanation
Indices: 35730507--35730564 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
35730497 AGGCTGTTCT
*
35730507 TTTCAAGATTCACCACAAAGGTTTTCA
1 TTTCAAGATTCACCACAAAGATTTTCA
* *
35730534 TTTCATGATTTACCACAAAGAATTTTC-
1 TTTCAAGATTCACCACAAAG-ATTTTCA
35730561 TTTC
1 TTTC
35730565 TTGACATGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.40
Consensus pattern (27 bp):
TTTCAAGATTCACCACAAAGATTTTCA
Found at i:35733430 original size:36 final size:36
Alignment explanation
Indices: 35733383--35733455 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
35733373 ATTCGAACCC
35733383 ATGCTTTTACTTACATCAAAGTGTATAATCACACAT
1 ATGCTTTTACTTACATCAAAGTGTATAATCACACAT
*
35733419 ATGCTTTTACTTACATCAAAGTGTATGATCACACAT
1 ATGCTTTTACTTACATCAAAGTGTATAATCACACAT
35733455 A
1 A
35733456 CATAGTCTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (36 bp):
ATGCTTTTACTTACATCAAAGTGTATAATCACACAT
Found at i:35734870 original size:21 final size:21
Alignment explanation
Indices: 35734844--35734926 Score: 121
Period size: 21 Copynumber: 4.0 Consensus size: 21
35734834 TGGACATGGT
35734844 CGTGTGGTTACTCCACACGCC
1 CGTGTGGTTACTCCACACGCC
* *
35734865 CGTGTGGTTACTCCACACTCT
1 CGTGTGGTTACTCCACACGCC
*
35734886 CATGTGGTTACTCCACACGCC
1 CGTGTGGTTACTCCACACGCC
* *
35734907 TGTGTGGTTACTCCATACGC
1 CGTGTGGTTACTCCACACGC
35734927 TCGTATGCAC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.16, C:0.34, G:0.22, T:0.29
Consensus pattern (21 bp):
CGTGTGGTTACTCCACACGCC
Found at i:35737785 original size:42 final size:43
Alignment explanation
Indices: 35737705--35737785 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
35737695 AAATATAATC
*
35737705 ATAAAATTAAATATAAAATATTTAAAAAATAATATTAAAAGAA
1 ATAAAATGAAATATAAAATATTTAAAAAATAATATTAAAAGAA
* *
35737748 ATAAAATGAAATATAAAGA-A-TTAAAAATTTATATTAAA
1 ATAAAATGAAATATAAA-ATATTTAAAAAATAATATTAAA
35737786 TAATAAGTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
42 16 0.47
43 17 0.50
44 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (43 bp):
ATAAAATGAAATATAAAATATTTAAAAAATAATATTAAAAGAA
Found at i:35744319 original size:3 final size:3
Alignment explanation
Indices: 35744311--35744336 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
35744301 GCTTTAGTTT
35744311 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
35744337 TTTTTTTTTT
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:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:35747463 original size:41 final size:41
Alignment explanation
Indices: 35747401--35747603 Score: 226
Period size: 41 Copynumber: 4.6 Consensus size: 41
35747391 GACTATACGT
35747401 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
35747442 CTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
35747483 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAAGTTCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCC-G-G---TG-----A--TCTGAATCAGGTTATAAAC
* * * *
35747536 CTAGTAGGCTAAGTGCCGGTGATCTGAACCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
35747577 CTTGCAGGCTAAGCGCCGGTGAATCTG
1 CTAGCAGGCTAAGTGCCGGTG-ATCTG
35747604 TTAAATTAAG
Statistics
Matches: 140, Mismatches: 9, Indels: 25
0.80 0.05 0.14
Matches are distributed among these distances:
41 90 0.64
42 6 0.04
43 2 0.01
46 2 0.01
48 2 0.01
51 2 0.01
52 1 0.01
53 35 0.25
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:35747584 original size:94 final size:95
Alignment explanation
Indices: 35747423--35747603 Score: 292
Period size: 94 Copynumber: 1.9 Consensus size: 95
35747413 GTGCCGGTGA
* * *
35747423 TCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGTTATAAACCTAGC
1 TCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGCTATAAACCTAGC
*
35747488 AGGCTAAGTGCCGGTG-ATCTGAATCAAGT
66 AGGCTAAGCGCCGGTGAATCTGAATCAAGT
* * *
35747517 TCTGAATCAGGTTATAAACCTAGTAGGCTAAGTGCCGGTGATCTGAACCAGGCTATAAGCCTTGC
1 TCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGCTATAAACCTAGC
35747582 AGGCTAAGCGCCGGTGAATCTG
66 AGGCTAAGCGCCGGTGAATCTG
35747604 TTAAATTAAG
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
94 74 0.94
95 5 0.06
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (95 bp):
TCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGCTATAAACCTAGC
AGGCTAAGCGCCGGTGAATCTGAATCAAGT
Found at i:35748374 original size:11 final size:11
Alignment explanation
Indices: 35748360--35748425 Score: 63
Period size: 11 Copynumber: 6.4 Consensus size: 11
35748350 TTATTTTTAA
35748360 TTTTAAAATAT
1 TTTTAAAATAT
35748371 TTTTAAAATACT
1 TTTTAAAATA-T
35748383 TTTT-AAAT-T
1 TTTTAAAATAT
*
35748392 TTTT----TAA
1 TTTTAAAATAT
35748399 TTTTAAAATAT
1 TTTTAAAATAT
35748410 TTTTAAAATACT
1 TTTTAAAATA-T
35748422 TTTT
1 TTTT
35748426 TTAATTTTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
6 1 0.02
7 4 0.09
9 5 0.11
11 26 0.57
12 10 0.22
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:35748377 original size:40 final size:40
Alignment explanation
Indices: 35748320--35748436 Score: 179
Period size: 39 Copynumber: 3.0 Consensus size: 40
35748310 AAATATATTT
*
35748320 ATTTTTAAA-ATTTTTAAAATACTTTTTTTATTATTTTTA
1 ATTTTAAAATATTTTTAAAATACTTTTTTTATTATTTTTA
**
35748359 ATTTTAAAATATTTTTAAAATACTTTTTAAATT-TTTTTA
1 ATTTTAAAATATTTTTAAAATACTTTTTTTATTATTTTTA
35748398 ATTTTAAAATATTTTTAAAATACTTTTTTTA--ATTTTTA
1 ATTTTAAAATATTTTTAAAATACTTTTTTTATTATTTTTA
35748436 A
1 A
35748437 AATAAATATT
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
38 7 0.10
39 43 0.61
40 21 0.30
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (40 bp):
ATTTTAAAATATTTTTAAAATACTTTTTTTATTATTTTTA
Found at i:35748385 original size:29 final size:30
Alignment explanation
Indices: 35748319--35748393 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
35748309 TAAATATATT
** *
35748319 TATTTTTAAAATTTTTAAAATACTTTTTTTAT
1 TATTTTT-AAA-TTTTAAAATACTTTTTAAAA
35748351 TATTTTT-AATTTTAAAATA-TTTTTAAAA
1 TATTTTTAAATTTTAAAATACTTTTTAAAA
35748379 TACTTTTTAAATTTT
1 TA-TTTTTAAATTTT
35748394 TTTAATTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
28 8 0.21
29 15 0.39
30 8 0.21
32 7 0.18
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (30 bp):
TATTTTTAAATTTTAAAATACTTTTTAAAA
Found at i:35751314 original size:22 final size:23
Alignment explanation
Indices: 35751296--35751339 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
35751286 AGGATTAAAT
*
35751296 TAGAATTTAAAATAAATTAAAGG
1 TAGAATTTAAAAAAAATTAAAGG
* *
35751319 TCGAATTTAAAAAAAAATAAA
1 TAGAATTTAAAAAAAATTAAA
35751340 AAAACCTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.61, C:0.02, G:0.09, T:0.27
Consensus pattern (23 bp):
TAGAATTTAAAAAAAATTAAAGG
Found at i:35752714 original size:132 final size:132
Alignment explanation
Indices: 35752507--35752934 Score: 617
Period size: 132 Copynumber: 3.2 Consensus size: 132
35752497 TAGTGTTTTA
* * * * * *
35752507 ATCTACTCCTCTGCAACTTTAGGGAGATAAGA-CT-TGTAGCTTCAACCTTCTCCACTGCTGCTT
1 ATCTGCTCCACTGCAAC-TTAGGGAGATAAGATCTAT-AATCTTCAACCTTCTCCGCTGCTGCTC
* * *
35752570 AGGGAGACAAGGCTTGGTGGCTTTAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTC
64 AGGGAGATAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTC
35752635 TTCG
129 TTCG
* * *
35752639 ATCTGCTCCACTGCAACTTAGGAAGATAAGATCTATAATCTTCATCCTTCTCTGCTGCTGCTCAG
1 ATCTGCTCCACTGCAACTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCGCTGCTGCTCAG
* * *
35752704 GAAGATAAGGCTTGGTGGCTTAAATCTGCTTCTCACTATCTTGGAAAGATAAGATTCACCGTCTT
66 GGAGATAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTT
35752769 CG
131 CG
* ** *
35752771 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCGCTACTGCTCAG
1 ATCTGCTCCACTGCAACTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCGCTGCTGCTCAG
*
35752836 GGAGATAAGGCTTGGTGTCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTT
66 GGAGATAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTT
35752901 CG
131 CG
* *
35752903 ATCTGCTCTACTGTAACTTCAGGGAGATAAGA
1 ATCTGCTCCACTGCAACTT-AGGGAGATAAGA
35752935 CTACTGGTTA
Statistics
Matches: 262, Mismatches: 31, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
131 13 0.05
132 236 0.90
133 13 0.05
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (132 bp):
ATCTGCTCCACTGCAACTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCGCTGCTGCTCAG
GGAGATAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTT
CG
Found at i:35764431 original size:98 final size:98
Alignment explanation
Indices: 35764262--35764458 Score: 385
Period size: 98 Copynumber: 2.0 Consensus size: 98
35764252 GTGCAATAAA
35764262 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
35764327 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
35764360 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
*
35764425 CCTCTAAAATCTCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
35764458 A
1 A
35764459 TTATTTTTAG
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:35765055 original size:27 final size:27
Alignment explanation
Indices: 35765025--35765082 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
35765015 ATATTTATAT
35765025 ATAT-AAATAATAATAATTTTAAAAAAA
1 ATATCAAA-AATAATAATTTTAAAAAAA
* * * *
35765052 ATATCAGAAATACTGATTTTAAGAAAA
1 ATATCAAAAATAATAATTTTAAAAAAA
35765079 ATAT
1 ATAT
35765083 GGAAAAAAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (27 bp):
ATATCAAAAATAATAATTTTAAAAAAA
Found at i:35765260 original size:22 final size:23
Alignment explanation
Indices: 35765242--35765285 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
35765232 AGGATTAAAT
*
35765242 TAGAATTTAAAATAAATTAAAGG
1 TAGAATTTAAAAAAAATTAAAGG
* *
35765265 TCGAATTTAAAAAAAAATAAA
1 TAGAATTTAAAAAAAATTAAA
35765286 AAAAAAACCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.61, C:0.02, G:0.09, T:0.27
Consensus pattern (23 bp):
TAGAATTTAAAAAAAATTAAAGG
Found at i:35770715 original size:81 final size:81
Alignment explanation
Indices: 35770580--35770819 Score: 453
Period size: 81 Copynumber: 3.0 Consensus size: 81
35770570 ATCCCTTTCT
35770580 CTCAATCTAAATATTTCTGTTATGTTAAACCTAAAGTAACTAAGGCCTATTATAAGCTGAAATTC
1 CTCAATCTAAATATTTCTGTTATGTTAAACCTAAAGTAACTAAGGCCTATTATAAGCTGAAATTC
35770645 CTTGAAGTGCACATCG
66 CTTGAAGTGCACATCG
*
35770661 CTCAATCTAAATATTTCTGTTATGTTAAACCTAAACTAACTAAGGCCTATTATAAGCTGAAATTC
1 CTCAATCTAAATATTTCTGTTATGTTAAACCTAAAGTAACTAAGGCCTATTATAAGCTGAAATTC
35770726 CTTGAAGTGCACATCG
66 CTTGAAGTGCACATCG
35770742 CTCAATCTAAATATTTCTGTTATGTTAAACCTAAAGTAACTAAGGCCTATTTATAAGCTGAAATT
1 CTCAATCTAAATATTTCTGTTATGTTAAACCTAAAGTAACTAAGGCCTA-TTATAAGCTGAAATT
*
35770807 CTTTGAAGTGCAC
65 CCTTGAAGTGCAC
35770820 GTCGTCATGC
Statistics
Matches: 155, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
81 128 0.83
82 27 0.17
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (81 bp):
CTCAATCTAAATATTTCTGTTATGTTAAACCTAAAGTAACTAAGGCCTATTATAAGCTGAAATTC
CTTGAAGTGCACATCG
Found at i:35775544 original size:3 final size:3
Alignment explanation
Indices: 35775536--35775569 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
35775526 TGTCTTGAAT
35775536 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
35775570 AGTATCAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:35779913 original size:14 final size:14
Alignment explanation
Indices: 35779881--35779918 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
35779871 ACCTTTTGTC
*
35779881 CTTTTTTTG-TTTT
1 CTTTATTTGTTTTT
35779894 -TTTATTTGTTTTT
1 CTTTATTTGTTTTT
35779907 CTTTATTTGTTT
1 CTTTATTTGTTT
35779919 ATTATTTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 11 0.50
ACGTcount: A:0.05, C:0.05, G:0.08, T:0.82
Consensus pattern (14 bp):
CTTTATTTGTTTTT
Found at i:35779929 original size:25 final size:25
Alignment explanation
Indices: 35779881--35779954 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 25
35779871 ACCTTTTGTC
* *
35779881 CTTTTTTTGTTTTTTTATTTGTTTTT
1 CTTTATTTG-TTTATTATTTGTTTTT
35779907 CTTTATTTGTTTATTATTTGTTTTT
1 CTTTATTTGTTTATTATTTGTTTTT
** *
35779932 -TAAAATTGTTTATTATTTGTTTT
1 CTTTATTTGTTTATTATTTGTTTT
35779955 ATAATATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
24 20 0.47
25 15 0.35
26 8 0.19
ACGTcount: A:0.14, C:0.03, G:0.08, T:0.76
Consensus pattern (25 bp):
CTTTATTTGTTTATTATTTGTTTTT
Found at i:35779933 original size:14 final size:12
Alignment explanation
Indices: 35779882--35779954 Score: 62
Period size: 12 Copynumber: 6.1 Consensus size: 12
35779872 CCTTTTGTCC
35779882 TTTT-TTTGTTT
1 TTTTATTTGTTT
35779893 TTTTATTTGTTTT
1 TTTTATTTG-TTT
35779906 TCTTTATTTG-TT
1 T-TTTATTTGTTT
*
35779918 TATTATTTGTTT
1 TTTTATTTGTTT
* *
35779930 TTTAAAATTG-TT
1 TTT-TATTTGTTT
*
35779942 TATTATTTGTTT
1 TTTTATTTGTTT
35779954 T
1 T
35779955 ATAATATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
11 15 0.31
12 18 0.37
13 8 0.16
14 8 0.16
ACGTcount: A:0.14, C:0.01, G:0.08, T:0.77
Consensus pattern (12 bp):
TTTTATTTGTTT
Found at i:35780077 original size:10 final size:10
Alignment explanation
Indices: 35780049--35780078 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
35780039 TTATTATTTG
35780049 TTTTATAATA
1 TTTTATAATA
35780059 TTTTA-AATA
1 TTTTATAATA
35780068 TTTTATAATA
1 TTTTATAATA
35780078 T
1 T
35780079 AATTTTCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTTATAATA
Found at i:35780661 original size:363 final size:361
Alignment explanation
Indices: 35780083--35781092 Score: 1431
Period size: 363 Copynumber: 2.8 Consensus size: 361
35780073 TAATATAATT
* * * * * *
35780083 TTCCTTTTTCTGGTGGAGCTAAATAATTTGCCGCCACCAAATTTCAAC-CC-CT-CT----GTTA
1 TTCCTTTTTCTAGTGGAGCCAAATAATTTGGCGCCACCAAATTCCAACACCTCTGCTACCATTTG
* * *
35780141 TC-TTTTGTC--TTTTTT-TCTGTTTTTCTTTATTTGTTTATTATTTGTTTTATAATGTTTTATG
66 TCATTTT-TCTATTTTTTATTTGTTTTTCTTTATTTCTTTATTATTTGTTTTATAATATTTTATG
* * * *
35780202 TATACTTTTTAGGTGGAGCCATTCTAAATGACGTCACCAATACGTTTTTTTAAATTTATTTTTTA
130 TATATTTTTTTGGTGGAGCCATTCTAAATGGCATCACCAATA--TTTTTTT-AATTTATTTTTTA
*
35780267 TATTTAAAATTTTTAAAAAATAATATTTTATTTGGTAGAGCCATTTTATTTGGCGTGACCAAATT
192 TATTTAAAATTTTT-AAAAATAATATTTTATTTGGTAGAGCCATTCTATTTGGCGTGACCAAATT
35780332 TATATATATAAGCCTCTCAATGACACATGAATCTAAGTTGAAAGAAAAAAATTACTTATACTTTG
256 TATATATATAAGCCTCTCAATGACACATGAATCTAAGTTG-AA-AAAAAAA-TACTTATACTTTG
*
35780397 TTAGAGGATGAAT-GTGATG-AAAAGGGGGGGCTTTAAACAAATA
318 TTAGAGGATGAATAG-GATGAAAAAGGGGGAGCTTTAAACAAATA
* * *
35780440 TTCCTTTTTCTGGTGGAGCCAAATACTTTGGCGCCACCAGATTCCAACACCTCTGCTA-CATTTG
1 TTCCTTTTTCTAGTGGAGCCAAATAATTTGGCGCCACCAAATTCCAACACCTCTGCTACCATTTG
* * *
35780504 TCCTTTTTCTGTTTTTTATTTGTTTTTCTTTATTTCTTTATTACTTGTTTTATAATATTTTATGT
66 TCATTTTTCTATTTTTTATTTGTTTTTCTTTATTTCTTTATTATTTGTTTTATAATATTTTATGT
*
35780569 AT-TTTTTTTTGTGGAGCCATTCTAAATGGCATCACCAATATATTTTTTAATTTATTTTTTATAT
131 ATATTTTTTTGGTGGAGCCATTCTAAATGGCATCACCAATAT-TTTTTTAATTTATTTTTTATAT
*
35780633 TTAAAATTTTTAAAATATAATATTTTATTTGGTAGAGCCATTCTATTTGGCATGACCAAATTTAT
195 TTAAAATTTTTAAAA-ATAATATTTTATTTGGTAGAGCCATTCTATTTGGCGTGACCAAATTTAT
*
35780698 ATATATAAGCCTCTCAATGACACATGAATCTGAGTTGAAAAAAAAATACTTATACTTTGTTAGAG
259 ATATATAAGCCTCTCAATGACACATGAATCTAAGTTGAAAAAAAAATACTTATACTTTGTTAGAG
* *
35780763 GATGAATAGGATGAAAAAATGGGGAGTTTTAAACAAATA
324 GATGAATAGGATG-AAAAAGGGGGAGCTTTAAACAAATA
** *
35780802 TTCCTTTTTCTAGTGGAGCCAAATAATTTGGCGCCACCAAATTCCAATGCCTCTGCTACCTTTTG
1 TTCCTTTTTCTAGTGGAGCCAAATAATTTGGCGCCACCAAATTCCAACACCTCTGCTACCATTTG
* *
35780867 TCATTTTTCTATTTTTTATTTGTTTTTATTTATTTTTTTATTATTTGTTTTATAATATTTTATGT
66 TCATTTTTCTATTTTTTATTTGTTTTTCTTTATTTCTTTATTATTTGTTTTATAATATTTTATGT
* *
35780932 ATATTTTTTTGGTGGAGCCATTTTAAATGGCGA-CACCAATGCGTTCTTTTTTAATTTATTTTTT
131 ATATTTTTTTGGTGGAGCCATTCTAAATGGC-ATCACCAAT---AT-TTTTTTAATTTATTTTTT
*
35780996 ATATTTAAAATTTTTAAAAATAATATTTTATTTGGTGGAGCCATTCTATTTGGCGTGACCAAATT
191 ATATTTAAAATTTTTAAAAATAATATTTTATTTGGTAGAGCCATTCTATTTGGCGTGACCAAATT
* *
35781061 TGTATATATAAGTCTCTCAATGACACATGAAT
256 TATATATATAAGCCTCTCAATGACACATGAAT
35781093 TGAGTCGAAA
Statistics
Matches: 591, Mismatches: 41, Indels: 33
0.89 0.06 0.05
Matches are distributed among these distances:
357 43 0.07
358 2 0.00
359 2 0.00
360 32 0.05
361 8 0.01
362 80 0.14
363 184 0.31
364 43 0.07
365 40 0.07
366 119 0.20
367 38 0.06
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (361 bp):
TTCCTTTTTCTAGTGGAGCCAAATAATTTGGCGCCACCAAATTCCAACACCTCTGCTACCATTTG
TCATTTTTCTATTTTTTATTTGTTTTTCTTTATTTCTTTATTATTTGTTTTATAATATTTTATGT
ATATTTTTTTGGTGGAGCCATTCTAAATGGCATCACCAATATTTTTTTAATTTATTTTTTATATT
TAAAATTTTTAAAAATAATATTTTATTTGGTAGAGCCATTCTATTTGGCGTGACCAAATTTATAT
ATATAAGCCTCTCAATGACACATGAATCTAAGTTGAAAAAAAAATACTTATACTTTGTTAGAGGA
TGAATAGGATGAAAAAGGGGGAGCTTTAAACAAATA
Found at i:35780910 original size:11 final size:11
Alignment explanation
Indices: 35780878--35780941 Score: 51
Period size: 11 Copynumber: 5.5 Consensus size: 11
35780868 CATTTTTCTA
35780878 TTTTTTATT-T
1 TTTTTTATTAT
*
35780888 GTTTTTATTTAT
1 TTTTTTA-TTAT
35780900 TTTTTTATTAT
1 TTTTTTATTAT
35780911 TTGTTTTATAATAT
1 TT-TTTTAT--TAT
*
35780925 TTTATGTA-TAT
1 TTT-TTTATTAT
35780936 TTTTTT
1 TTTTTT
35780942 GGTGGAGCCA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 8 0.18
11 14 0.32
12 13 0.30
13 1 0.02
14 8 0.18
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (11 bp):
TTTTTTATTAT
Found at i:35780925 original size:25 final size:24
Alignment explanation
Indices: 35780878--35780927 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
35780868 CATTTTTCTA
*
35780878 TTTTTTATTTGTTTTTATTTATTT
1 TTTTTTATTTGTTTTTATATATTT
35780902 TTTTATTATTTG-TTTTATAATATTT
1 TTTT-TTATTTGTTTTTAT-ATATTT
35780927 T
1 T
35780928 ATGTATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (24 bp):
TTTTTTATTTGTTTTTATATATTT
Found at i:35780927 original size:22 final size:24
Alignment explanation
Indices: 35780876--35780929 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
35780866 GTCATTTTTC
*
35780876 TATTTT-TTATTTGTTTTTATTTAT
1 TATTTTATTATTTGTTTTTA-TTAA
*
35780900 TTTTTTATTATTTG-TTTTA-TAA
1 TATTTTATTATTTGTTTTTATTAA
35780922 TATTTTAT
1 TATTTTAT
35780930 GTATATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 9 0.35
24 10 0.38
25 7 0.27
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (24 bp):
TATTTTATTATTTGTTTTTATTAA
Found at i:35780936 original size:25 final size:25
Alignment explanation
Indices: 35780882--35780941 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
35780872 TTTCTATTTT
* *
35780882 TTATTTGTTTTTATTTATTTTTTTA
1 TTATTTGTTTTTATATATTTTTGTA
35780907 TTATTTG-TTTTATAATATTTTATGTA
1 TTATTTGTTTTTAT-ATATTTT-TGTA
35780933 -TATTT-TTTT
1 TTATTTGTTTT
35780942 GGTGGAGCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 6 0.20
25 21 0.70
26 3 0.10
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (25 bp):
TTATTTGTTTTTATATATTTTTGTA
Found at i:35789516 original size:13 final size:13
Alignment explanation
Indices: 35789498--35789523 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35789488 ATATTATAAA
35789498 ACATTTAAAATAT
1 ACATTTAAAATAT
35789511 ACATTTAAAATAT
1 ACATTTAAAATAT
35789524 TATAAAACAA
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:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATTTAAAATAT
Found at i:35792676 original size:20 final size:20
Alignment explanation
Indices: 35792651--35792691 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
35792641 TCCAATATTG
35792651 ACACGGCAATACTCGTGAAT
1 ACACGGCAATACTCGTGAAT
35792671 ACACGGCAATACTCGTGAAT
1 ACACGGCAATACTCGTGAAT
35792691 A
1 A
35792692 ACTCACAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ACACGGCAATACTCGTGAAT
Found at i:35795199 original size:20 final size:20
Alignment explanation
Indices: 35795165--35795206 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
35795155 AACTATTTAA
** *
35795165 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
35795185 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
35795205 AT
1 AT
35795207 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:35806296 original size:50 final size:50
Alignment explanation
Indices: 35806154--35806395 Score: 227
Period size: 50 Copynumber: 4.7 Consensus size: 50
35806144 GATAATAACA
* ** * *
35806154 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATATTTCTTATAC--
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* ** *
35806203 TGCCAATGTCATATCCCAGACATGGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * ** *
35806253 TGCCCATGTCATGTCCCAGACATGGTTTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
35806303 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
* * *
35806359 TGCCAATGCCATGTTCCAAACATGGTCTTACATGGGA
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGA
35806396 TCTCATCACC
Statistics
Matches: 158, Mismatches: 27, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
49 41 0.26
50 80 0.51
53 2 0.01
56 35 0.22
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (50 bp):
TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:35820936 original size:22 final size:23
Alignment explanation
Indices: 35820911--35820967 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
35820901 TGCACTAATG
35820911 AACAGAGAGCACTA-AAGTGCTA
1 AACAGAGAGCACTATAAGTGCTA
*
35820933 AACAGAGAGCAC-ATATGTGCTA
1 AACAGAGAGCACTATAAGTGCTA
* *
35820955 AACGGAGAACACT
1 AACAGAGAGCACT
35820968 TCCTGCTAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.03
22 29 0.97
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (23 bp):
AACAGAGAGCACTATAAGTGCTA
Found at i:35822016 original size:24 final size:24
Alignment explanation
Indices: 35821989--35822035 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
35821979 ATAAGTAAAT
35821989 TATACATATTATTACAAATGTATG
1 TATACATATTATTACAAATGTATG
* * *
35822013 TATATATTTTATTACACATGTAT
1 TATACATATTATTACAAATGTAT
35822036 TTTATTATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (24 bp):
TATACATATTATTACAAATGTATG
Found at i:35822595 original size:16 final size:16
Alignment explanation
Indices: 35822574--35822605 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
35822564 TTTGTTGAGT
35822574 ATGACTCATATTTCAG
1 ATGACTCATATTTCAG
35822590 ATGACTCATATTTCAG
1 ATGACTCATATTTCAG
35822606 TTAAATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (16 bp):
ATGACTCATATTTCAG
Found at i:35824981 original size:2 final size:2
Alignment explanation
Indices: 35824974--35825012 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
35824964 TCCGTCATCC
35824974 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
35825013 GACTTCCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:35827327 original size:27 final size:27
Alignment explanation
Indices: 35827297--35827384 Score: 149
Period size: 27 Copynumber: 3.3 Consensus size: 27
35827287 CCTAAACCCC
* *
35827297 AATGTAAAAACTTTATGATTTCATTAA
1 AATGTAAAAACCTTATGGTTTCATTAA
*
35827324 AATGTAAAAACCCTATGGTTTCATTAA
1 AATGTAAAAACCTTATGGTTTCATTAA
35827351 AATGTAAAAACCTTATGGTTTCATTAA
1 AATGTAAAAACCTTATGGTTTCATTAA
35827378 AATGTAA
1 AATGTAA
35827385 CACCTACTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (27 bp):
AATGTAAAAACCTTATGGTTTCATTAA
Found at i:35828597 original size:154 final size:154
Alignment explanation
Indices: 35828314--35828601 Score: 391
Period size: 156 Copynumber: 1.9 Consensus size: 154
35828304 AAAACACTAC
* * *
35828314 TTTTCTTAAAATTCAAAACTTTATTTCGAAATTGTTGAAAAAGATGAAAACTTTATTTTAAAAAA
1 TTTTCTTAAAATTCAAAACTTTATTTCGAAATAGTTGAAAAAAATCAAAACTTTATTTTAAAAAA
**
35828379 TTTAATTTTTCCTTTAAAATAACTAAAAAACAGATTTTTATTTTAAAAATCTAAACTTTCTCTTT
66 TTTAAACTTTCCTTTAAAATAACTAAAAAACAGATTTTTATTTTAAAAATCTAAACTTTCTCTTT
35828444 TTAAAAGAGAAAAACACACTATTT
131 TTAAAAGAGAAAAACACACTATTT
** * *
35828468 TTTTCTTAAAGA-TCAATGCTTTATTTTGAAATAGTTGAAAAAAAAATCAAAACTTTGTTTT-AA
1 TTTTCTTAAA-ATTCAAAACTTTATTTCGAAATAGTTG--AAAAAAATCAAAACTTTATTTTAAA
* * * * *
35828531 AATTTTAAACTTTCCTTTAAAATGACTAAAAAAACATATTTTTGTTTTTAAAATCTAAACTTTCT
63 AAATTTAAACTTTCCTTTAAAATAACT-AAAAAACAGATTTTTATTTTAAAAATCTAAACTTTCT
*
35828596 TTTTTT
127 CTTTTT
35828602 TTTAAATCAA
Statistics
Matches: 115, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
154 31 0.27
155 26 0.23
156 58 0.50
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (154 bp):
TTTTCTTAAAATTCAAAACTTTATTTCGAAATAGTTGAAAAAAATCAAAACTTTATTTTAAAAAA
TTTAAACTTTCCTTTAAAATAACTAAAAAACAGATTTTTATTTTAAAAATCTAAACTTTCTCTTT
TTAAAAGAGAAAAACACACTATTT
Found at i:35828758 original size:20 final size:21
Alignment explanation
Indices: 35828721--35828762 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
35828711 TCTATGGCAT
* *
35828721 AAAAAAAGAGATAGAAATAGA
1 AAAAAAAGAGAAAAAAATAGA
35828742 AAAAAAAGA-AAAAAAATAGA
1 AAAAAAAGAGAAAAAAATAGA
35828762 A
1 A
35828763 TGATTGTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (21 bp):
AAAAAAAGAGAAAAAAATAGA
Found at i:35842193 original size:17 final size:18
Alignment explanation
Indices: 35842161--35842195 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
35842151 TTACCCTTGC
*
35842161 TACAAATATTAATTTATT
1 TACAAATATGAATTTATT
35842179 TACAAAT-TGAATTTATT
1 TACAAATATGAATTTATT
35842196 GTTTTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (18 bp):
TACAAATATGAATTTATT
Found at i:35843631 original size:19 final size:19
Alignment explanation
Indices: 35843594--35843631 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
35843584 CTAATTAAGT
*
35843594 TTTAATTAGATGAATTTAG
1 TTTAATTAGATGAAATTAG
35843613 TTTAATTAAGA-GAAATTAG
1 TTTAATT-AGATGAAATTAG
35843632 GAAAAATGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (19 bp):
TTTAATTAGATGAAATTAG
Found at i:35843903 original size:13 final size:13
Alignment explanation
Indices: 35843887--35843918 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
35843877 TGTTTGAATG
35843887 AAATTTCACAGTT
1 AAATTTCACAGTT
*
35843900 AAATTTCATAGTT
1 AAATTTCACAGTT
35843913 AAATTT
1 AAATTT
35843919 GAGTTTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (13 bp):
AAATTTCACAGTT
Found at i:35844509 original size:23 final size:22
Alignment explanation
Indices: 35844482--35844546 Score: 89
Period size: 23 Copynumber: 3.0 Consensus size: 22
35844472 GCCTTGCCGA
35844482 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCAC-TTATGTGTCGTATT
*
35844505 TCAGGCACCTCATGTGTCG--TT
1 TCAGGCA-CTTATGTGTCGTATT
35844526 TCAGGCACTTATGTGTCGTAT
1 TCAGGCACTTATGTGTCGTAT
35844547 ACTGATCAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
20 10 0.27
21 9 0.24
22 1 0.03
23 16 0.43
24 1 0.03
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (22 bp):
TCAGGCACTTATGTGTCGTATT
Found at i:35844703 original size:9 final size:9
Alignment explanation
Indices: 35844689--35844716 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
35844679 GATTGATCGT
35844689 AATATTGAA
1 AATATTGAA
35844698 AATATTGAA
1 AATATTGAA
35844707 AATATTGAA
1 AATATTGAA
35844716 A
1 A
35844717 GAAATGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (9 bp):
AATATTGAA
Found at i:35849865 original size:23 final size:22
Alignment explanation
Indices: 35849813--35849877 Score: 80
Period size: 23 Copynumber: 3.0 Consensus size: 22
35849803 CCTGATCAAT
*
35849813 ATACAACACATAAGTGCCTG-A
1 ATACGACACATAAGTGCCTGAA
*
35849834 A-ACGACACATGAGGTGCCTGAA
1 ATACGACACAT-AAGTGCCTGAA
35849856 ATACGACACATAAAGTGCCTGA
1 ATACGACACAT-AAGTGCCTGA
35849878 TCGGTAAGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 8 0.22
21 9 0.24
22 2 0.05
23 18 0.49
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (22 bp):
ATACGACACATAAGTGCCTGAA
Found at i:35850832 original size:9 final size:9
Alignment explanation
Indices: 35850814--35850862 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
35850804 CTGCTGCTCT
*
35850814 TTTTGTTTC
1 TTTTCTTTC
35850823 TTTTAC-TTC
1 TTTT-CTTTC
35850832 TTTTCTTTC
1 TTTTCTTTC
35850841 TTTTCTTTC
1 TTTTCTTTC
**
35850850 TTTAGTTTC
1 TTTTCTTTC
35850859 TTTT
1 TTTT
35850863 TATTTACTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
8 1 0.03
9 33 0.97
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.76
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:35850835 original size:18 final size:18
Alignment explanation
Indices: 35850814--35850862 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
35850804 CTGCTGCTCT
35850814 TTTTGTTTCTTTTAC-TTC
1 TTTTGTTTCTTTT-CTTTC
*
35850832 TTTTCTTTCTTTTCTTTC
1 TTTTGTTTCTTTTCTTTC
*
35850850 TTTAGTTTCTTTT
1 TTTTGTTTCTTTT
35850863 TATTTACTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.76
Consensus pattern (18 bp):
TTTTGTTTCTTTTCTTTC
Found at i:35851118 original size:24 final size:24
Alignment explanation
Indices: 35851086--35851147 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
35851076 ATATCATCTA
* *
35851086 TACCATACACTTGTATTAAATCAT
1 TACCATACATTTGTATTAAACCAT
35851110 TACCATACATTTGTATTAAACCAT
1 TACCATACATTTGTATTAAACCAT
35851134 TACCATACATTTGT
1 TACCATACATTTGT
35851148 CTTTATTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (24 bp):
TACCATACATTTGTATTAAACCAT
Found at i:35853605 original size:46 final size:46
Alignment explanation
Indices: 35853538--35853770 Score: 378
Period size: 46 Copynumber: 5.1 Consensus size: 46
35853528 ACATTGCTAT
* *
35853538 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTAATTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
*
35853584 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
*
35853630 AACTCAGTATAGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
* *
35853676 AACTCAGTATGGTTTTCTTTACCGAAATACCATACTTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
* * *
35853722 AACTCAGTATGGTTTTCTTCACTGAAATACCATACATACGTTTCA-
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
35853767 AACT
1 AACT
35853771 TTTCCATGGA
Statistics
Matches: 176, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
45 4 0.02
46 172 0.98
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
Found at i:35855037 original size:17 final size:17
Alignment explanation
Indices: 35855017--35855063 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
35855007 ATTCTTTTTA
35855017 AAATTACAAAATTCAAT
1 AAATTACAAAATTCAAT
* *
35855034 AAATCACAAAATTCACT
1 AAATTACAAAATTCAAT
*
35855051 AATTTA-AAAATTC
1 AAATTACAAAATTC
35855064 TTCTAAATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATTACAAAATTCAAT
Found at i:35855657 original size:21 final size:21
Alignment explanation
Indices: 35855605--35855651 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
35855595 ATTTTCTTGT
* * *
35855605 TGCCTCTACTGCCCTTGCTGC
1 TGCCTCTGCTTCCCTCGCTGC
35855626 TGCCTCTGCTTCCCTCGCTGC
1 TGCCTCTGCTTCCCTCGCTGC
35855647 TGCCT
1 TGCCT
35855652 TCGCTTTAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.02, C:0.45, G:0.19, T:0.34
Consensus pattern (21 bp):
TGCCTCTGCTTCCCTCGCTGC
Found at i:35856777 original size:21 final size:21
Alignment explanation
Indices: 35856753--35856793 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
35856743 GCCTAAGATG
35856753 TGAATTGGATTGA-ATTGAGTA
1 TGAATTGGATT-ACATTGAGTA
*
35856774 TGAATTGTATTACATTGAGT
1 TGAATTGGATTACATTGAGT
35856794 TAAATTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.32, C:0.02, G:0.24, T:0.41
Consensus pattern (21 bp):
TGAATTGGATTACATTGAGTA
Found at i:35857209 original size:24 final size:25
Alignment explanation
Indices: 35857156--35857203 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
35857146 TTGGCCCTCT
* *
35857156 CGAGCTTCCCGTTATATGGTTCTTG
1 CGAGCTTCCCGTTATATAGCTCTTG
35857181 CGAGCTTCCCGTTA-ATAGCTCTT
1 CGAGCTTCCCGTTATATAGCTCTT
35857204 CGGAGCATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.15, C:0.27, G:0.21, T:0.38
Consensus pattern (25 bp):
CGAGCTTCCCGTTATATAGCTCTTG
Found at i:35857522 original size:25 final size:25
Alignment explanation
Indices: 35857456--35857515 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
35857446 TATGGCTCTT
**
35857456 ATGAGCTTCCCGTTATACAGCCCGG
1 ATGAGCTTCCCGTTATACAGCCCAC
* *
35857481 ATAAGCTTCCCGTTATACAGCTCAC
1 ATGAGCTTCCCGTTATACAGCCCAC
35857506 ATGAGCTTCC
1 ATGAGCTTCC
35857516 TATTATATGC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.27
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATACAGCCCAC
Found at i:35869289 original size:42 final size:42
Alignment explanation
Indices: 35869220--35869309 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
35869210 GTGTCCTCAC
* * *
35869220 CCGTGTAACTCACTGAGATGCCCCACACACCCGTGTGCCAGG
1 CCGTGTAACTCACTAAGATGCCACACACACCCATGTGCCAGG
** * *
35869262 CCGTGTAACTCTTTAAGTTGCCACACACGCCCATGTGCCAGG
1 CCGTGTAACTCACTAAGATGCCACACACACCCATGTGCCAGG
*
35869304 TCGTGT
1 CCGTGT
35869310 GTTGGGCCAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.20, C:0.34, G:0.23, T:0.22
Consensus pattern (42 bp):
CCGTGTAACTCACTAAGATGCCACACACACCCATGTGCCAGG
Found at i:35870462 original size:43 final size:43
Alignment explanation
Indices: 35870167--35870462 Score: 398
Period size: 43 Copynumber: 6.9 Consensus size: 43
35870157 TTTTAGAAAT
* * * *
35870167 AAACGTCGTTAAAGACCAAGACCTTTAGCGACGC-TTTCACCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTC-CCAC
* * * *
35870210 AAATGCCGCTAAAGATCAAGACCTTTAGCGGCGCTCTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* *
35870253 AAACGTCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* *
35870296 AAACGCCGCTAAAGACCATGACTTTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* * *
35870339 AAACGCCGCTAAAAGACCATGACCTCTAGCGGCGTTTTTCCAAC
1 AAACGCCGCT-AAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* *
35870383 -AACGCCGCTAAAGACCATGACCTTTAGCAGCACTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
*
35870425 AAACGCCGCTAAAAACCATGACCTTTAGCGGCGCTTTT
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTT
35870463 TTTAAAATCG
Statistics
Matches: 224, Mismatches: 26, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
42 28 0.12
43 163 0.73
44 33 0.15
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:35873436 original size:15 final size:15
Alignment explanation
Indices: 35873394--35873440 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
35873384 AACCCTTAAT
*
35873394 TAAA-CCATAACCCC
1 TAAATCCATAATCCC
*
35873408 T-AATCTATAATCCC
1 TAAATCCATAATCCC
*
35873422 TAAATCCATACTCCC
1 TAAATCCATAATCCC
35873437 TAAA
1 TAAA
35873441 CCTTAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 2 0.07
14 10 0.37
15 15 0.56
ACGTcount: A:0.40, C:0.34, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:35873879 original size:42 final size:43
Alignment explanation
Indices: 35873815--35874029 Score: 319
Period size: 42 Copynumber: 5.1 Consensus size: 43
35873805 CGCTGTTGCT
*
35873815 AACGCCGCTATAGATCAGGACCTTTAGCGGCGC-TTTCCCACA
1 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACA
35873857 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTT-CCACA
1 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACA
* * *
35873899 AACACCGCTATAGCTCAAGATCTTTAGCGGCGCTTTTCCCACA
1 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACA
* * *
35873942 AATGCCGCTATAGAGC-AGACCTTTAGCGACGCTTTTCCCACA
1 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACA
* * *
35873984 AACGCCGCTATAGATCAAGACTTTTAGCGGCACTTTTCACACA
1 AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACA
35874027 AAC
1 AAC
35874030 ACCACTAAAA
Statistics
Matches: 154, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
42 109 0.71
43 45 0.29
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (43 bp):
AACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACA
Found at i:35873992 original size:85 final size:84
Alignment explanation
Indices: 35873815--35874029 Score: 308
Period size: 85 Copynumber: 2.5 Consensus size: 84
35873805 CGCTGTTGCT
* *
35873815 AACGCCGCTATAGATCAGGACCTTTAGCGGCGC-TTTCCCACAAACGCCGCTATAGATCAAGACC
1 AACGCCGCTATAGATCAAGA-CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAGCAAGACC
*
35873879 TTTAGCGGCGCTTTTCCACA
65 TTTAGCGACGCTTTTCCACA
* * *
35873899 AACACCGCTATAGCTCAAGATCTTTAGCGGCGCTTTTCCCACAAATGCCGCTATAGAGC-AGACC
1 AACGCCGCTATAGATCAAGA-CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAGCAAGACC
35873963 TTTAGCGACGCTTTTCCCACA
65 TTTAGCGACGCTTTT-CCACA
* *
35873984 AACGCCGCTATAGATCAAGACTTTTAGCGGCACTTTTCACACAAAC
1 AACGCCGCTATAGATCAAGAC-TTTAGCGGCGCTTTTCCCACAAAC
35874030 ACCACTAAAA
Statistics
Matches: 116, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
84 49 0.42
85 67 0.58
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (84 bp):
AACGCCGCTATAGATCAAGACTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAGCAAGACCT
TTAGCGACGCTTTTCCACA
Found at i:35878356 original size:21 final size:21
Alignment explanation
Indices: 35878332--35878372 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
35878322 CATTCACACA
*
35878332 CAACCTCTAAACCTTAAACCC
1 CAACCTCTAAACCATAAACCC
*
35878353 CAACCTTTAAACCATAAACC
1 CAACCTCTAAACCATAAACC
35878373 ATAAACCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (21 bp):
CAACCTCTAAACCATAAACCC
Found at i:35878370 original size:7 final size:7
Alignment explanation
Indices: 35878360--35878413 Score: 63
Period size: 7 Copynumber: 7.6 Consensus size: 7
35878350 CCCCAACCTT
35878360 TAAACCA
1 TAAACCA
35878367 TAAACCA
1 TAAACCA
35878374 TAAACCA
1 TAAACCA
* *
35878381 TAATCCC
1 TAAACCA
35878388 TAAACCCA
1 TAAA-CCA
*
35878396 TAATCCA
1 TAAACCA
*
35878403 TAAACCT
1 TAAACCA
35878410 TAAA
1 TAAA
35878414 ATGGCAACAC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
7 34 0.87
8 5 0.13
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAACCA
Found at i:35878398 original size:15 final size:14
Alignment explanation
Indices: 35878360--35878408 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
35878350 CCCCAACCTT
*
35878360 TAAACCATAAACCA
1 TAAACCATAATCCA
*
35878374 TAAACCATAATCCC
1 TAAACCATAATCCA
35878388 TAAACCCATAATCCA
1 TAAA-CCATAATCCA
35878403 TAAACC
1 TAAACC
35878409 TTAAAATGGC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
14 18 0.58
15 13 0.42
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.18
Consensus pattern (14 bp):
TAAACCATAATCCA
Found at i:35878644 original size:66 final size:66
Alignment explanation
Indices: 35878538--35878671 Score: 259
Period size: 66 Copynumber: 2.0 Consensus size: 66
35878528 CCCTAAACTA
*
35878538 TAGTGATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTAT
1 TAGTGATAATTAATTCAATAGTTTAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTAT
35878603 T
66 T
35878604 TAGTGATAATTAATTCAATAGTTTAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTAT
1 TAGTGATAATTAATTCAATAGTTTAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTAT
35878669 T
66 T
35878670 TA
1 TA
35878672 ATATATAAAT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (66 bp):
TAGTGATAATTAATTCAATAGTTTAAAATTAATACTATCTCTTTTACGATTATATAAGAAATTAT
T
Found at i:35878846 original size:41 final size:41
Alignment explanation
Indices: 35878791--35879151 Score: 569
Period size: 41 Copynumber: 8.8 Consensus size: 41
35878781 CCACAGCATT
* * * *
35878791 ATTAGCGGCACTTTCCCAAAAACGCCGCTAAAGCCCTTGGC
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGGC
* *
35878832 ATTAGCGGCGCTTTCACAAAAACGACGCTAAAGGCCTGGAC
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGGC
*
35878873 ATTAGCGGCGTTTTCACAAAAACGCCGCTAAAGGCCTGGGC
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGGC
*
35878914 ATTAGCGGTGCTTTCACAAAAACGCCGCTAAAGGCCTGGGC
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGGC
*
35878955 ATTAGCGGTGCTTTCACAAAAACGCCGCTAAAGGCCTGGGC
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGGC
*
35878996 ATTAGCGGCGCTTTCACAAAACCGCCGCTAAAGGCCTGGGC
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGGC
* * *
35879037 ATTAGCGGCGCTTTCACAAAAAGGCTGCTAAAGGCCTAGGC
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGGC
*
35879078 ATTAGCGGCACTTTCACAAAAACGCCGCTAAAGGCCTAGGGC
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCT-GGGC
**
35879120 ATTAGCGGCGCTTTCTTAAAAACGCCGCTAAA
1 ATTAGCGGCGCTTTCACAAAAACGCCGCTAAA
35879152 TCCTCGAAAG
Statistics
Matches: 295, Mismatches: 24, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
41 263 0.89
42 32 0.11
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19
Consensus pattern (41 bp):
ATTAGCGGCGCTTTCACAAAAACGCCGCTAAAGGCCTGGGC
Found at i:35879277 original size:40 final size:40
Alignment explanation
Indices: 35879216--35879324 Score: 143
Period size: 40 Copynumber: 2.8 Consensus size: 40
35879206 ATTGAAAACG
* *
35879216 CCGCTAATGCT-TAT-TATTAGCGGCGTTTTCCATAAAGCA
1 CCGCTAATGCTCGATCT-TTAGCGGCGTTTTCCAAAAAGCA
* *
35879255 CCGTTAAAT-CTCGATCTTTAGCGGCATTTTCCAAAAAGCA
1 CCGCT-AATGCTCGATCTTTAGCGGCGTTTTCCAAAAAGCA
35879295 CCGCTAATGCTCGATCTTTAGCGGCGTTTT
1 CCGCTAATGCTCGATCTTTAGCGGCGTTTT
35879325 TTATCCAAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
39 9 0.15
40 50 0.83
41 1 0.02
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (40 bp):
CCGCTAATGCTCGATCTTTAGCGGCGTTTTCCAAAAAGCA
Found at i:35879906 original size:114 final size:114
Alignment explanation
Indices: 35879689--35880112 Score: 573
Period size: 116 Copynumber: 3.7 Consensus size: 114
35879679 ATATTTTGTA
* * *
35879689 CCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTTGTTGGGCTTAGGTTTTTTTTGCAGCGCTTTC
1 CCGCTAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGG-TTTTTTTGCGGCGCTTTC
* *
35879754 TCAAAAACGCCGCTAAAGCCTTGAGCATTAGCGACGCTTTCTAAAAAACG
65 TCAAAAACGCCGCTAAAGCCTTGAGCATTAGCGGCGCTTTCTTAAAAACG
* * * * *
35879804 CCGCTAAATCCACGAAAGCTCAGAAAGCCGCGTCATTGGGCTTAGGTTTTTTTGCGGCGCTTTCT
1 CCGCTAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCT
* * * * *
35879869 CAAAAACGCTGCGAAATCCCTGAGCATTAGCGGCGCTTTCTTAGAAACG
66 CAAAAACGCCGCTAAAGCCTTGAGCATTAGCGGCGCTTTCTTAAAAACG
* * *
35879918 CCGCTAAATCCCCAAAAGCTCACAAAACGGCATCGTTGGGCTTATGTTTTTTTTTGCGGCGCTTT
1 CCGCTAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTA-G-GTTTTTTTGCGGCGCTTT
* * *
35879983 ATCAAAAACGCCGCTAAAGCCTTGAGCATTAGCGGCGTTTTCTTAAAAACC
64 CTCAAAAACGCCGCTAAAGCCTTGAGCATTAGCGGCGCTTTCTTAAAAACG
* *
35880034 CCGCTAAATCCCCAAAAGCTC-GAAAAACGGCGTGGTTGGGCTTAGG-TTTTTTCCGGCGCTTTC
1 CCGCTAAATCCCCAAAAGCTCAG-AAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTC
**
35880097 TGGAAAACGCCGCTAA
65 TCAAAAACGCCGCTAA
35880113 TGCTTATTTT
Statistics
Matches: 269, Mismatches: 37, Indels: 8
0.86 0.12 0.03
Matches are distributed among these distances:
113 29 0.11
114 97 0.36
115 43 0.16
116 100 0.37
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (114 bp):
CCGCTAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCT
CAAAAACGCCGCTAAAGCCTTGAGCATTAGCGGCGCTTTCTTAAAAACG
Found at i:35884503 original size:22 final size:20
Alignment explanation
Indices: 35884467--35884525 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
35884457 GGCCCGGCCC
35884467 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
35884489 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAA-TAAAAA
**
35884510 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
35884526 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 7 0.21
23 8 0.24
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:35884539 original size:38 final size:37
Alignment explanation
Indices: 35884496--35884589 Score: 152
Period size: 38 Copynumber: 2.5 Consensus size: 37
35884486 AAAATTTATT
35884496 TTAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAATTAAAAAAA-TATTTTAAAAATATTTTAAAA
*
35884534 TTAAAAAATAAAAAAATATTTTAAAAATATTTTAAAA
1 TTAAAAATTAAAAAAATATTTTAAAAATATTTTAAAA
*
35884571 TTAAAAAATTTAAAAAATA
1 TT-AAAAATTAAAAAAATA
35884590 AATATATTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
37 23 0.44
38 29 0.56
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (37 bp):
TTAAAAATTAAAAAAATATTTTAAAAATATTTTAAAA
Found at i:35884556 original size:37 final size:37
Alignment explanation
Indices: 35884496--35884589 Score: 152
Period size: 37 Copynumber: 2.5 Consensus size: 37
35884486 AAAATTTATT
*
35884496 TTAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAATAAAAAAA-TATTTTAAAAATATTTTAAAA
35884534 TTAAAAAATAAAAAAATATTTTAAAAATATTTTAAAA
1 TTAAAAAATAAAAAAATATTTTAAAAATATTTTAAAA
*
35884571 TTAAAAAATTTAAAAAATA
1 TTAAAAAA-TAAAAAAATA
35884590 AATATATTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
37 29 0.55
38 24 0.45
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (37 bp):
TTAAAAAATAAAAAAATATTTTAAAAATATTTTAAAA
Found at i:35884571 original size:10 final size:11
Alignment explanation
Indices: 35884545--35884570 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
35884535 TAAAAAATAA
35884545 AAAAATATTTT
1 AAAAATATTTT
35884556 AAAAATATTTT
1 AAAAATATTTT
35884567 AAAA
1 AAAA
35884571 TTAAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:35884599 original size:17 final size:16
Alignment explanation
Indices: 35884557--35884599 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
35884547 AAATATTTTA
* *
35884557 AAAATATTTTAAAATT
1 AAAATATTTAAAAAAT
*
35884573 AAAAAATTTAAAAAAT
1 AAAATATTTAAAAAAT
35884589 AAATATATTTA
1 AAA-ATATTTA
35884600 TTATATCGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATATTTAAAAAAT
Found at i:35885203 original size:270 final size:273
Alignment explanation
Indices: 35884670--35885208 Score: 1012
Period size: 270 Copynumber: 2.0 Consensus size: 273
35884660 GTTTTCTAAA
35884670 CGGGCCTCATTTTTTTGCCCAAGCCTATATTTCGGGCCTATATTTTTACGCAAACCCTCCCATAT
1 CGGGCCTCATTTTTTTGCCCAAGCCTATATTTCGGGCCTATATTTTTACGCAAACCCTCCCATAT
*
35884735 TTCGGGCGGGCCGTCAGGCCGGGCCAGGTCGGGCCGCCCGGCCCATGAGCACATCTACTCCGAAC
66 TTCGGGCGGGCCGTCAAGCCGGGCCAGGTCGGGCCGCCCGGCCCATGAGCACATCTACTCCGAAC
*
35884800 TATCGCCAATGTCTCTCACCAGACCCCTTGTTGCCCCTTTTGATCTTTCACTGTCCATGTTTGAT
131 TATCGCCAATGTCTCTCACCAGACCCCTCGTTGCCCCTTTTGATCTTTCACTGTCCATGTTTGAT
*
35884865 CTCTTTGAAGAACCCGAGTGGCATTATCGCTTGATGTTTTTAACCCCAGTGGTACATCAAACTTT
196 CTATTTGAAGAACCCGAGTGGCATTATCGCTTGATGTTTTTAACCCCAGTGGTACATCAAACTTT
35884930 CGATGCTATATTT
261 CGATGCTATATTT
35884943 CGGGCCTCATTTTTTTGCCCAAGCCTATATTTCGGGCCTATATTTTTACGCAAACCCTCCCATAT
1 CGGGCCTCATTTTTTTGCCCAAGCCTATATTTCGGGCCTATATTTTTACGCAAACCCTCCCATAT
35885008 TTCGGGCGGGCCGTCAAGCCGGGCCAGGTCGGGCCG-CCGG-CCATGAGCACATCTACTCCGAAC
66 TTCGGGCGGGCCGTCAAGCCGGGCCAGGTCGGGCCGCCCGGCCCATGAGCACATCTACTCCGAAC
*
35885071 TATCGCCAATGTCTCTCACCAGA-CCCTCGTTGCCCCTTTTGATCTTTCACTGTCTATGTTTGAT
131 TATCGCCAATGTCTCTCACCAGACCCCTCGTTGCCCCTTTTGATCTTTCACTGTCCATGTTTGAT
*
35885135 CTATTTGAAGAACCCGAGTGGCATTATCGCTTGATGTTTTTAACCCCAGTGGTACATCAAGCTTT
196 CTATTTGAAGAACCCGAGTGGCATTATCGCTTGATGTTTTTAACCCCAGTGGTACATCAAACTTT
35885200 CGATGCTAT
261 CGATGCTAT
35885209 TACCGACGTG
Statistics
Matches: 261, Mismatches: 5, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
270 111 0.43
271 46 0.18
272 4 0.02
273 100 0.38
ACGTcount: A:0.19, C:0.30, G:0.20, T:0.31
Consensus pattern (273 bp):
CGGGCCTCATTTTTTTGCCCAAGCCTATATTTCGGGCCTATATTTTTACGCAAACCCTCCCATAT
TTCGGGCGGGCCGTCAAGCCGGGCCAGGTCGGGCCGCCCGGCCCATGAGCACATCTACTCCGAAC
TATCGCCAATGTCTCTCACCAGACCCCTCGTTGCCCCTTTTGATCTTTCACTGTCCATGTTTGAT
CTATTTGAAGAACCCGAGTGGCATTATCGCTTGATGTTTTTAACCCCAGTGGTACATCAAACTTT
CGATGCTATATTT
Found at i:35888554 original size:23 final size:23
Alignment explanation
Indices: 35888528--35888626 Score: 171
Period size: 23 Copynumber: 4.3 Consensus size: 23
35888518 AGTGTTATTG
*
35888528 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
35888551 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
35888574 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
35888597 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
35888620 ATCAGTG
1 ATCAGTG
35888627 TGGCACTTAT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 72 1.00
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:35888581 original size:46 final size:46
Alignment explanation
Indices: 35888528--35888626 Score: 189
Period size: 46 Copynumber: 2.2 Consensus size: 46
35888518 AGTGTTATTG
*
35888528 ATCAGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCAGCTACAT
35888574 ATCAGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCAGCTACAT
35888620 ATCAGTG
1 ATCAGTG
35888627 TGGCACTTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACGTATCAGTGGTAGCTTCAGCTACAT
Found at i:35890248 original size:33 final size:30
Alignment explanation
Indices: 35890172--35890295 Score: 185
Period size: 30 Copynumber: 4.0 Consensus size: 30
35890162 TCCTCTTTAC
*
35890172 ATAACAAACAAACTTATTTTTATGACTCAT
1 ATAACAAACAAACTTACTTTTATGACTCAT
* *
35890202 ATAACAAATAAACTTACTTTTTTGACTCATACT
1 ATAACAAACAAACTTACTTTTATGACTC--A-T
35890235 ATAACAAACAAACTTACTTTTATGACTCAT
1 ATAACAAACAAACTTACTTTTATGACTCAT
*
35890265 ATAACAAACAAACTTACTTTTATAACTCAT
1 ATAACAAACAAACTTACTTTTATGACTCAT
35890295 A
1 A
35890296 CAAAATAATA
Statistics
Matches: 85, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
30 56 0.66
31 1 0.01
32 1 0.01
33 27 0.32
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (30 bp):
ATAACAAACAAACTTACTTTTATGACTCAT
Found at i:35890271 original size:63 final size:63
Alignment explanation
Indices: 35890172--35890296 Score: 214
Period size: 63 Copynumber: 2.0 Consensus size: 63
35890162 TCCTCTTTAC
* * * *
35890172 ATAACAAACAAACTTATTTTTATGACTCATATAACAAATAAACTTACTTTTTTGACTCATACT
1 ATAACAAACAAACTTACTTTTATGACTCATATAACAAACAAACTTACTTTTATAACTCATACT
35890235 ATAACAAACAAACTTACTTTTATGACTCATATAACAAACAAACTTACTTTTATAACTCATAC
1 ATAACAAACAAACTTACTTTTATGACTCATATAACAAACAAACTTACTTTTATAACTCATAC
35890297 AAAATAATAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.35
Consensus pattern (63 bp):
ATAACAAACAAACTTACTTTTATGACTCATATAACAAACAAACTTACTTTTATAACTCATACT
Found at i:35911656 original size:73 final size:73
Alignment explanation
Indices: 35911537--35911683 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
35911527 CAAAGTTTTC
35911537 AAAATTTCCCCAATTGATATCGATACCCCATGAAGGTACTGATACCAAAATTAACTTCGATGTTT
1 AAAATTTCCCCAATTGATATCGATACCCCATGAAGGTACTGATACCAAAATTAACTTCGATGTTT
35911602 CATAAAAT
66 CATAAAAT
35911610 AAAATTTCCCCAATTGATATCGATACCCCATGAAGGTACTGATACCAAAATTAACTTCGATGTTT
1 AAAATTTCCCCAATTGATATCGATACCCCATGAAGGTACTGATACCAAAATTAACTTCGATGTTT
35911675 CATAAAAT
66 CATAAAAT
35911683 A
1 A
35911684 CTTTCTTTTA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (73 bp):
AAAATTTCCCCAATTGATATCGATACCCCATGAAGGTACTGATACCAAAATTAACTTCGATGTTT
CATAAAAT
Found at i:35913970 original size:41 final size:40
Alignment explanation
Indices: 35913893--35913970 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 40
35913883 TGATTTAGTA
* * *
35913893 ACAATTACATGCTTTACATGCAATCATTATACAGTAACAG
1 ACAATGACATGCTTTACATGCAATCATAACACAGTAACAG
* *
35913933 ACAATGACATGCTTTTTCATGCAATCATAACATAGTAA
1 ACAATGACATGC-TTTACATGCAATCATAACACAGTAA
35913971 TAATCATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
40 11 0.34
41 21 0.66
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (40 bp):
ACAATGACATGCTTTACATGCAATCATAACACAGTAACAG
Found at i:35914693 original size:4 final size:4
Alignment explanation
Indices: 35914684--35914708 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
35914674 ATTTTTTGAA
35914684 TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT T
35914709 GAAGTTCGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:35922932 original size:15 final size:15
Alignment explanation
Indices: 35922909--35922939 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35922899 AACTGAATTC
*
35922909 AAAAGTTTAAATTTA
1 AAAAATTTAAATTTA
35922924 AAAAATTTAAATTTA
1 AAAAATTTAAATTTA
35922939 A
1 A
35922940 GCAGAGTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
AAAAATTTAAATTTA
Found at i:35924593 original size:34 final size:34
Alignment explanation
Indices: 35924550--35924617 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
35924540 CCATGTTGCA
35924550 GGATCAATATACTAGTCACCATACAGACCAATAT
1 GGATCAATATACTAGTCACCATACAGACCAATAT
*
35924584 GGATCAATATACTAGTCACTATACAGACCAATAT
1 GGATCAATATACTAGTCACCATACAGACCAATAT
35924618 AATTAGATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (34 bp):
GGATCAATATACTAGTCACCATACAGACCAATAT
Found at i:35927576 original size:14 final size:14
Alignment explanation
Indices: 35927557--35927584 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35927547 GATTGTGCAT
35927557 CTACCTGGTTTCAC
1 CTACCTGGTTTCAC
35927571 CTACCTGGTTTCAC
1 CTACCTGGTTTCAC
35927585 TTTATATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.36, G:0.14, T:0.36
Consensus pattern (14 bp):
CTACCTGGTTTCAC
Found at i:35930902 original size:39 final size:40
Alignment explanation
Indices: 35930853--35930930 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
35930843 AAAATGTTTA
*
35930853 AAATTTTTAT-AT-AAACTTTAAAAA-TACAAAAAAAAATTT
1 AAATTATTATAATAAAAC-TTAAAAACTA-AAAAAAAAATTT
35930892 AAATTATTATAATAAAACTTAAAAACTAAAAAAAAAATT
1 AAATTATTATAATAAAACTTAAAAACTAAAAAAAAAATT
35930931 GACGGTATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
39 9 0.26
40 20 0.57
41 6 0.17
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (40 bp):
AAATTATTATAATAAAACTTAAAAACTAAAAAAAAAATTT
Found at i:35931632 original size:17 final size:17
Alignment explanation
Indices: 35931597--35931632 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
35931587 TTAAGATAAG
**
35931597 TATTAAATTTAATTTAA
1 TATTAAATTTAATAAAA
35931614 TATTAAATTTAATAAAA
1 TATTAAATTTAATAAAA
35931631 TA
1 TA
35931633 ATAATATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTAAATTTAATAAAA
Found at i:35955504 original size:21 final size:22
Alignment explanation
Indices: 35955456--35955505 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
35955446 TTTATCAGTC
*
35955456 ATATCAA--TTTTTAATAGAAA
1 ATATCAATTTTTTTAATACAAA
*
35955476 AAAT-AATTTTTTTAA-ACAAA
1 ATATCAATTTTTTTAATACAAA
35955496 ATATCAATTT
1 ATATCAATTT
35955506 ATATAAAGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 2 0.08
20 10 0.42
21 12 0.50
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (22 bp):
ATATCAATTTTTTTAATACAAA
Found at i:35961391 original size:18 final size:21
Alignment explanation
Indices: 35961352--35961395 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
35961342 ACATGTATAA
35961352 GTATGTGTATTGATTAAAAAT
1 GTATGTGTATTGATTAAAAAT
35961373 GTATGTGTATT-A-T-AAAAT
1 GTATGTGTATTGATTAAAAAT
35961391 GTATG
1 GTATG
35961396 CATGTATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.43
19 1 0.04
20 1 0.04
21 11 0.48
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.43
Consensus pattern (21 bp):
GTATGTGTATTGATTAAAAAT
Found at i:35965572 original size:55 final size:55
Alignment explanation
Indices: 35965509--35965653 Score: 236
Period size: 55 Copynumber: 2.6 Consensus size: 55
35965499 TCTTCTTAAT
* *
35965509 TGTTGGAATACTGCTTCTTTTGAATTGATTTTTTATATGTTTAAATCGATTGTCA
1 TGTTGGAATACTGCTTCTTTTGAATCGATTTTTTATATGTTTAAATCGATTATCA
* * *
35965564 TGTTGGAATACTGCTTCTTTTAAATCGATTATTTATATGTTTAAATCGATTATTA
1 TGTTGGAATACTGCTTCTTTTGAATCGATTTTTTATATGTTTAAATCGATTATCA
35965619 TGTTGGAATACTGCTTCTTTTGAATCGATTATTTT
1 TGTTGGAATACTGCTTCTTTTGAATCGATT-TTTT
35965654 TACATAGCAC
Statistics
Matches: 82, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
55 79 0.96
56 3 0.04
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.50
Consensus pattern (55 bp):
TGTTGGAATACTGCTTCTTTTGAATCGATTTTTTATATGTTTAAATCGATTATCA
Found at i:35971779 original size:23 final size:22
Alignment explanation
Indices: 35971736--35971779 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
35971726 TGCTGCCAAG
*
35971736 ACTGACTTTGAAAACACAAAAA
1 ACTGACTTTGAAAAAACAAAAA
*
35971758 ACTGACTTTGAAAAAACTAAAA
1 ACTGACTTTGAAAAAACAAAAA
35971780 CATAAACAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.16, G:0.09, T:0.20
Consensus pattern (22 bp):
ACTGACTTTGAAAAAACAAAAA
Found at i:35974528 original size:98 final size:98
Alignment explanation
Indices: 35974349--35974545 Score: 315
Period size: 98 Copynumber: 2.0 Consensus size: 98
35974339 GTACAATAAA
*
35974349 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* *
35974414 CCTCTAGAATCTCAAACTCGGAATATTTTCTTT
66 CCTCTAGAATCCCAAACTCGGAATATTTCCTTT
* * *
35974447 ACTTTAAAGGGACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
35974512 CCTTTA-AATTCCCAAACTCGGAATATTTCCTTT
66 CCTCTAGAA-TCCCAAACTCGGAATATTTCCTTT
35974545 A
1 A
35974546 TTATTTTTAA
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
97 2 0.02
98 89 0.98
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAGAATCCCAAACTCGGAATATTTCCTTT
Found at i:35975208 original size:23 final size:23
Alignment explanation
Indices: 35975180--35975223 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
35975170 ATATATATAT
35975180 GAAAATATTCATTTAAAAAAAAG
1 GAAAATATTCATTTAAAAAAAAG
* *
35975203 GAAAATATTCGTTTTAAAAAA
1 GAAAATATTCATTTAAAAAAA
35975224 TATATATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.30
Consensus pattern (23 bp):
GAAAATATTCATTTAAAAAAAAG
Found at i:35975871 original size:19 final size:19
Alignment explanation
Indices: 35975847--35975978 Score: 210
Period size: 19 Copynumber: 6.8 Consensus size: 19
35975837 AATCATATAT
35975847 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
35975866 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
*
35975885 TCTAAGATTGAATATCATA
1 TCTAAGATTGCATATCATA
35975904 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
35975925 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
35975944 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
35975963 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
35975979 CTCAAAAATT
Statistics
Matches: 104, Mismatches: 7, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
19 85 0.82
21 19 0.18
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:35975931 original size:59 final size:59
Alignment explanation
Indices: 35975847--35975977 Score: 212
Period size: 59 Copynumber: 2.3 Consensus size: 59
35975837 AATCATATAT
*
35975847 TCTAAGATTGC--ATATCATATCTAAGATTATATATCATATCTAAGATTGAATATCATA
1 TCTAAGATTGCATATATCATATCTAAGATTACATATCATATCTAAGATTGAATATCATA
* * *
35975904 TCTAAGATTGCATATATCATATCTAAGATTGCATATCATATCTAGGATTGCATATCATA
1 TCTAAGATTGCATATATCATATCTAAGATTACATATCATATCTAAGATTGAATATCATA
35975963 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
35975978 CCTCAAAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
57 11 0.16
59 57 0.84
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (59 bp):
TCTAAGATTGCATATATCATATCTAAGATTACATATCATATCTAAGATTGAATATCATA
Found at i:35976173 original size:38 final size:37
Alignment explanation
Indices: 35976122--35976271 Score: 113
Period size: 38 Copynumber: 3.9 Consensus size: 37
35976112 TTACAAGTGC
* *
35976122 CATTTTGAAGGTTCACCTGATATTCATATCGCGGTTGT
1 CATTTTTACGGTTC-CCTGATATTCATATCGCGGTTGT
* * * ***
35976160 CATTTTTACGGTTCGCTTAGTATTCATATTGCAACCT-T
1 CATTTTTACGGTTCCCTGA-TATTCATATCGC-GGTTGT
* *
35976198 CAATGTTTTAACAGTTCGCTTGATATTCATATCGCGGTTGT
1 C-AT-TTTT-ACGGTTC-CCTGATATTCATATCGCGGTTGT
* *
35976239 CATTTTTACGGTTCGCTCAATATTCATATCGCG
1 CATTTTTACGGTTCCCT-GATATTCATATCGCG
35976272 ACCTTCGATA
Statistics
Matches: 84, Mismatches: 20, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
37 4 0.05
38 45 0.54
39 7 0.08
40 7 0.08
41 19 0.23
42 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.41
Consensus pattern (37 bp):
CATTTTTACGGTTCCCTGATATTCATATCGCGGTTGT
Found at i:35976276 original size:79 final size:79
Alignment explanation
Indices: 35976139--35976333 Score: 248
Period size: 79 Copynumber: 2.5 Consensus size: 79
35976129 AAGGTTCACC
* * * *
35976139 TGATATTCATATCGCGGTTGTCATTTTTACGGTTCGCTTAGTATTCATATTGCAACCTTCAATGT
1 TGATATTCATATCGCGGTTGTCATTTTTACGGTTCGCTCAATATTCATATCGCAACCTTCAATAT
* *
35976204 TTTAACAGTTCGCT
66 TCTAACAATTCGCT
* *
35976218 TGATATTCATATCGCGGTTGTCATTTTTACGGTTCGCTCAATATTCATATCGCGACCTTCGATAT
1 TGATATTCATATCGCGGTTGTCATTTTTACGGTTCGCTCAATATTCATATCGCAACCTTCAATAT
35976283 TCTAACAATTCGCT
66 TCTAACAATTCGCT
* * * *** *
35976297 CGAT-TTAAGATCGCAACTGTCATTTTCACGGTTCGCT
1 TGATATTCATATCGCGGTTGTCATTTTTACGGTTCGCT
35976334 GATTTTAACT
Statistics
Matches: 101, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
78 27 0.27
79 74 0.73
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (79 bp):
TGATATTCATATCGCGGTTGTCATTTTTACGGTTCGCTCAATATTCATATCGCAACCTTCAATAT
TCTAACAATTCGCT
Found at i:35977556 original size:6 final size:7
Alignment explanation
Indices: 35977537--35977564 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
35977527 TTAGATGTCG
35977537 TATTTTT
1 TATTTTT
35977544 TATTTTT
1 TATTTTT
35977551 TATTTTT
1 TATTTTT
35977558 TATTTTT
1 TATTTTT
35977565 CAATTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TATTTTT
Found at i:35987822 original size:24 final size:24
Alignment explanation
Indices: 35987795--35987840 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
35987785 TGTATTATGC
*
35987795 TTAAGTTAGCT-AAGTGTAAATGTT
1 TTAAATTAGCTCAAGTG-AAATGTT
*
35987819 TTAAATTGGCTCAAGTGAAATG
1 TTAAATTAGCTCAAGTGAAATG
35987841 GTTGCTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.37
Consensus pattern (24 bp):
TTAAATTAGCTCAAGTGAAATGTT
Found at i:35990918 original size:23 final size:23
Alignment explanation
Indices: 35990892--35990967 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
35990882 ATAAGTGCCA
35990892 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
35990915 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
35990938 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
35990961 CACTGAT
1 CACTGAT
35990968 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:35991066 original size:8 final size:8
Alignment explanation
Indices: 35991053--35991081 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
35991043 CCCCGGGACT
35991053 CACTGTAA
1 CACTGTAA
35991061 CACTGTAA
1 CACTGTAA
35991069 CACTGTAA
1 CACTGTAA
35991077 CACTG
1 CACTG
35991082 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:35991212 original size:18 final size:17
Alignment explanation
Indices: 35991186--35991224 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
35991176 ATTTTCCTTC
35991186 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
35991203 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
35991221 CACA
1 CACA
35991225 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:35998254 original size:23 final size:23
Alignment explanation
Indices: 35998228--35998303 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
35998218 ATAAGTGCCA
35998228 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
35998251 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
35998274 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
35998297 CACTGAT
1 CACTGAT
35998304 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:35998403 original size:8 final size:8
Alignment explanation
Indices: 35998390--35998418 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
35998380 ACCCGGGACT
35998390 CACTGTAA
1 CACTGTAA
35998398 CACTGTAA
1 CACTGTAA
35998406 CACTGTAA
1 CACTGTAA
35998414 CACTG
1 CACTG
35998419 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Done.