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 179 of 196
Found at i:52268774 original size:25 final size:25
Alignment explanation
Indices: 52268739--52268827 Score: 83
Period size: 25 Copynumber: 3.6 Consensus size: 25
52268729 ACACACCACA
*
52268739 GCTCTCTTGAGCTTCCCGATACTTG
1 GCTCTCATGAGCTTCCCGATACTTG
*
52268764 GCTCTCATGAGCTTCCCGATA-TACG
1 GCTCTCATGAGCTTCCCGATACT-TG
* * *
52268789 GCTCGT-ATGAGTTTCCCGTTACTTA
1 GCTC-TCATGAGCTTCCCGATACTTG
* *
52268814 GCTCACACGAGCTT
1 GCTCTCATGAGCTT
52268828 TCCGTTATTC
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
24 1 0.02
25 48 0.94
26 2 0.04
ACGTcount: A:0.17, C:0.30, G:0.20, T:0.33
Consensus pattern (25 bp):
GCTCTCATGAGCTTCCCGATACTTG
Found at i:52268843 original size:50 final size:50
Alignment explanation
Indices: 52268746--52268854 Score: 119
Period size: 50 Copynumber: 2.2 Consensus size: 50
52268736 ACAGCTCTCT
* * * *
52268746 TGAGCTTCCCGATACTTGGCTCTCATGAGCTTCCCGATATACGGCTCGTA
1 TGAGCTTCCCGATACTTAGCTCACACGAGCTTCCCGATATACAGCTCGTA
* * * * * *
52268796 TGAGTTTCCCGTTACTTAGCTCACACGAGCTTTCCGTTATTCAGCTCGAA
1 TGAGCTTCCCGATACTTAGCTCACACGAGCTTCCCGATATACAGCTCGTA
*
52268846 AGAGCTTCC
1 TGAGCTTCC
52268855 TGTTTACATG
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.19, C:0.29, G:0.20, T:0.31
Consensus pattern (50 bp):
TGAGCTTCCCGATACTTAGCTCACACGAGCTTCCCGATATACAGCTCGTA
Found at i:52272078 original size:56 final size:57
Alignment explanation
Indices: 52271971--52272079 Score: 143
Period size: 56 Copynumber: 1.9 Consensus size: 57
52271961 AAAATGATTT
* * *
52271971 TTTTTTTAATTTTTAGAGTTAAAACTAAATTGATATATATTTTAAATATTGAGGCCAA
1 TTTTTTT-ATTTTTAGAATTAAAACTAAAATGATATATATTTTAAACATTGAGGCCAA
52272029 TTTTTTT-TTTTTAGAATTAAAACTAAAATGAT-TA-ATTTTGTAAACATTGAG
1 TTTTTTTATTTTTAGAATTAAAACTAAAATGATATATA-TTT-TAAACATTGAG
52272080 AGCTAAATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
54 1 0.02
55 5 0.11
56 33 0.72
58 7 0.15
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.48
Consensus pattern (57 bp):
TTTTTTTATTTTTAGAATTAAAACTAAAATGATATATATTTTAAACATTGAGGCCAA
Found at i:52282837 original size:14 final size:14
Alignment explanation
Indices: 52282818--52282853 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
52282808 TGGTTCAAGA
52282818 GCTGAAAGGCAGCG
1 GCTGAAAGGCAGCG
*
52282832 GCTGAAA-GCAGTG
1 GCTGAAAGGCAGCG
52282845 GCTGAAAGG
1 GCTGAAAGG
52282854 GAGAAGGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.31, C:0.17, G:0.42, T:0.11
Consensus pattern (14 bp):
GCTGAAAGGCAGCG
Found at i:52294720 original size:17 final size:15
Alignment explanation
Indices: 52294678--52294725 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
52294668 AGATCTGACA
*
52294678 CCTTCTCTTCTTTTT
1 CCTTCTTTTCTTTTT
52294693 CCTTCTTTTCTTTTT
1 CCTTCTTTTCTTTTT
*
52294708 CTCTCTTTTTTCTTTTT
1 C-CT-TCTTTTCTTTTT
52294725 C
1 C
52294726 ATGTTTAGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 15 0.52
16 2 0.07
17 12 0.41
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (15 bp):
CCTTCTTTTCTTTTT
Found at i:52298256 original size:23 final size:22
Alignment explanation
Indices: 52298230--52298288 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 22
52298220 TTCTTTCAGG
52298230 TGGTGTGTCTTTTATAGTTATTC
1 TGGTGTGTCTTTTATA-TTATTC
* *
52298253 TGGTGT-TC-TTAATATTGTTC
1 TGGTGTGTCTTTTATATTATTC
*
52298273 TGGGGTGTTCTTTTAT
1 TGGTGTG-TCTTTTAT
52298289 GAGGTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
20 10 0.34
21 5 0.17
22 4 0.14
23 10 0.34
ACGTcount: A:0.12, C:0.08, G:0.24, T:0.56
Consensus pattern (22 bp):
TGGTGTGTCTTTTATATTATTC
Found at i:52314601 original size:19 final size:21
Alignment explanation
Indices: 52314570--52314609 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
52314560 CACTAAATAA
52314570 TCAATATCATTGATA-TGTAT
1 TCAATATCATTGATAGTGTAT
52314590 TCAATA-CATTGATAGTGTAT
1 TCAATATCATTGATAGTGTAT
52314610 AAATTTATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (21 bp):
TCAATATCATTGATAGTGTAT
Found at i:52316556 original size:18 final size:19
Alignment explanation
Indices: 52316533--52316575 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
52316523 TATATTTTAT
*
52316533 TTTTTTA-TTTTAAAATAC
1 TTTTTTATTTTTAAAATAA
52316551 TTTTTTATTTTTAAAATAA
1 TTTTTTATTTTTAAAATAA
52316570 TTTTTT
1 TTTTTT
52316576 GGTGTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTTATTTTTAAAATAA
Found at i:52317069 original size:29 final size:29
Alignment explanation
Indices: 52317036--52317124 Score: 76
Period size: 29 Copynumber: 3.2 Consensus size: 29
52317026 TGTGAAAATC
52317036 TATTTATGTAGCAAGTATGAGAATTGAGA
1 TATTTATGTAGCAAGTATGAGAATTGAGA
* * ** * * * **
52317065 TATTTGTGAAATAAAT-TGTGAA--AATC
1 TATTTATGTAGCAAGTATGAGAATTGAGA
52317091 TATTTATGTAGCAAGTATGAGAATTGAGA
1 TATTTATGTAGCAAGTATGAGAATTGAGA
52317120 TATTT
1 TATTT
52317125 GTGCAAATAT
Statistics
Matches: 39, Mismatches: 18, Indels: 6
0.62 0.29 0.10
Matches are distributed among these distances:
26 12 0.31
27 5 0.13
28 5 0.13
29 17 0.44
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.38
Consensus pattern (29 bp):
TATTTATGTAGCAAGTATGAGAATTGAGA
Found at i:52317086 original size:55 final size:55
Alignment explanation
Indices: 52317014--52317133 Score: 231
Period size: 55 Copynumber: 2.2 Consensus size: 55
52317004 TATAATGAAA
52317014 TGTGAAATAAATTGTGAAAATCTATTTATGTAGCAAGTATGAGAATTGAGATATT
1 TGTGAAATAAATTGTGAAAATCTATTTATGTAGCAAGTATGAGAATTGAGATATT
52317069 TGTGAAATAAATTGTGAAAATCTATTTATGTAGCAAGTATGAGAATTGAGATATT
1 TGTGAAATAAATTGTGAAAATCTATTTATGTAGCAAGTATGAGAATTGAGATATT
52317124 TGTGCAAATA
1 TGTG-AAATA
52317134 TCTCAATTCT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 59 0.92
56 5 0.08
ACGTcount: A:0.40, C:0.04, G:0.20, T:0.36
Consensus pattern (55 bp):
TGTGAAATAAATTGTGAAAATCTATTTATGTAGCAAGTATGAGAATTGAGATATT
Found at i:52317453 original size:40 final size:40
Alignment explanation
Indices: 52317409--52317541 Score: 137
Period size: 40 Copynumber: 3.4 Consensus size: 40
52317399 CCAGTTTGGT
* *
52317409 ACCCAGTACCTCATCGGATAATTCGAAATAATAAGTTGAC
1 ACCCAGTGCCTCATCGGATAATTCGAAGTAATAAGTTGAC
* * **
52317449 ACCCAGTGTCTCATCGGCTAAACCGAAGT-A-AA-TTGAC
1 ACCCAGTGCCTCATCGGATAATTCGAAGTAATAAGTTGAC
** *
52317486 ACCCAGTGCCTCATCAAATTAATTCGAAGTAATAGGTTGAC
1 ACCCAGTGCCTCATCGGA-TAATTCGAAGTAATAAGTTGAC
* *
52317527 ATCCAGTGTCTCATC
1 ACCCAGTGCCTCATC
52317542 AACTTGAAGT
Statistics
Matches: 74, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
37 19 0.26
38 11 0.15
39 2 0.03
40 24 0.32
41 18 0.24
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.26
Consensus pattern (40 bp):
ACCCAGTGCCTCATCGGATAATTCGAAGTAATAAGTTGAC
Found at i:52317746 original size:24 final size:24
Alignment explanation
Indices: 52317701--52317747 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
52317691 TATATATACC
52317701 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
52317725 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
52317748 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:52335015 original size:21 final size:21
Alignment explanation
Indices: 52334991--52335052 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
52334981 CTTGTGGTAT
*
52334991 GAGGCAGAGGAAACTGAGGAG
1 GAGGTAGAGGAAACTGAGGAG
52335012 GAGGTAGAGGAAACTGAGGAG
1 GAGGTAGAGGAAACTGAGGAG
* *
52335033 GTGGTAGAGGAAATTGAGGA
1 GAGGTAGAGGAAACTGAGGA
52335053 TACACTTCCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.37, C:0.05, G:0.47, T:0.11
Consensus pattern (21 bp):
GAGGTAGAGGAAACTGAGGAG
Found at i:52336486 original size:30 final size:30
Alignment explanation
Indices: 52336450--52336510 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
52336440 TTTTTAACTT
* *
52336450 TATATAT-ATATTTAGAATTTTTTAAAAATA
1 TATATATAAAATTT-GAAATTTTTAAAAATA
*
52336480 TATATATAAAATTTGAAATTTTTATAAATA
1 TATATATAAAATTTGAAATTTTTAAAAATA
52336510 T
1 T
52336511 TTTGAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (30 bp):
TATATATAAAATTTGAAATTTTTAAAAATA
Found at i:52336514 original size:20 final size:21
Alignment explanation
Indices: 52336491--52336543 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 21
52336481 ATATATAAAA
52336491 TTTGAAATTTTTATAAA-TAT
1 TTTGAAATTTTTATAAACTAT
*
52336511 TTTG-AATTTTGA-AAACTAT
1 TTTGAAATTTTTATAAACTAT
52336530 TTT-ATAATTTTTAT
1 TTTGA-AATTTTTAT
52336544 TGAGAGAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
18 3 0.11
19 13 0.48
20 11 0.41
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.57
Consensus pattern (21 bp):
TTTGAAATTTTTATAAACTAT
Found at i:52338200 original size:17 final size:17
Alignment explanation
Indices: 52338178--52338238 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
52338168 AACTAAAGTC
52338178 TTATGTAATGTTTTTAA
1 TTATGTAATGTTTTTAA
* ***
52338195 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
52338214 CTTATGTAATGTTTTTAA
1 -TTATGTAATGTTTTTAA
52338232 TTATGTA
1 TTATGTA
52338239 GTAATTCAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 16 0.48
18 4 0.12
19 4 0.12
20 9 0.27
ACGTcount: A:0.31, C:0.03, G:0.15, T:0.51
Consensus pattern (17 bp):
TTATGTAATGTTTTTAA
Found at i:52338227 original size:37 final size:37
Alignment explanation
Indices: 52338172--52338247 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
52338162 AACTAAAACT
* *
52338172 AAAGTCTTATGTAATGTTTTTAATTATGTAGTGATTC
1 AAAGACTTATGTAATGTTTTTAATTATGTAGTAATTC
52338209 AAAGACTTATGTAATGTTTTTAATTATGTAGTAATTC
1 AAAGACTTATGTAATGTTTTTAATTATGTAGTAATTC
52338246 AA
1 AA
52338248 TTCGGTTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.46
Consensus pattern (37 bp):
AAAGACTTATGTAATGTTTTTAATTATGTAGTAATTC
Found at i:52338429 original size:3 final size:3
Alignment explanation
Indices: 52338421--52338460 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
52338411 TTATGATGGT
52338421 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
52338461 ATGTAATGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:52339565 original size:21 final size:21
Alignment explanation
Indices: 52339539--52339594 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
52339529 AATAGCGGTG
* *
52339539 GCGGTGAGATTAGTTATTGTA
1 GCGGTGAGATTAGATACTGTA
*
52339560 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
52339581 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
52339595 AAAAACGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.07, G:0.38, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:52339828 original size:15 final size:15
Alignment explanation
Indices: 52339808--52339863 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
52339798 ATTTACTAAA
*
52339808 ATTATAATATATAAT
1 ATTATAAAATATAAT
52339823 ATTATAAAATAT-A-
1 ATTATAAAATATAAT
*
52339836 ATT-TAAAATA-ATT
1 ATTATAAAATATAAT
*
52339849 ATTATTAAATATAAT
1 ATTATAAAATATAAT
52339864 TTAACAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
12 7 0.21
13 6 0.18
14 7 0.21
15 13 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTATAAAATATAAT
Found at i:52339858 original size:26 final size:25
Alignment explanation
Indices: 52339818--52339876 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
52339808 ATTATAATAT
52339818 ATAATATTATAAAATATAATTTAAA
1 ATAATATTATAAAATATAATTTAAA
*
52339843 ATAATTATTATTAAATATAATTTAACA
1 ATAA-TATTATAAAATATAATTTAA-A
*
52339870 AAAATAT
1 ATAATAT
52339877 ATACTTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 4 0.13
26 22 0.73
27 4 0.13
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
ATAATATTATAAAATATAATTTAAA
Found at i:52339876 original size:59 final size:59
Alignment explanation
Indices: 52339813--52340011 Score: 192
Period size: 59 Copynumber: 3.3 Consensus size: 59
52339803 CTAAAATTAT
52339813 AATATATAATATT-ATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAACAAA
1 AATATATAAT-TTAATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAACAAA
* * * * * * * ** *
52339872 AATATATACTTTAATAAAATTCTTAGTATT-AAAT-ATTCTTATATGAATTTACTAAAATC-AT
1 AATATATAATTTAATAAAA-T-ATAAT-TTAAAATAATTATTAT-TAAATATAATTTAA-CAAA
* *
52339933 AATATATAATACT-ATAAAATATAATTTAAAATAATTATGATTAAATATAATTTAACAAA
1 AATATATAAT-TTAATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAACAAA
52339992 AATATATAATTTAATAAAAT
1 AATATATAATTTAATAAAAT
52340012 TCTTAGTATT
Statistics
Matches: 106, Mismatches: 23, Indels: 22
0.70 0.15 0.15
Matches are distributed among these distances:
58 6 0.06
59 49 0.46
60 15 0.14
61 32 0.30
62 4 0.04
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (59 bp):
AATATATAATTTAATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAACAAA
Found at i:52339923 original size:120 final size:120
Alignment explanation
Indices: 52339791--52340030 Score: 444
Period size: 120 Copynumber: 2.0 Consensus size: 120
52339781 TTTAATAGAA
* * *
52339791 TATATGAATTTACTAAAATTATAATATATAATATTATAAAATATAATTTAAAATAATTATTATTA
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATGATTA
*
52339856 AATATAATTTAACAAAAATATATACTTTAATAAAATTCTTAGTATTAAATATTCT
66 AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
52339911 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATGATTA
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATGATTA
52339976 AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
66 AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
52340031 AATGATTGTA
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 116 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (120 bp):
TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATGATTA
AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
Found at i:52344938 original size:5 final size:5
Alignment explanation
Indices: 52344928--52344954 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
52344918 TTTGAGACCT
52344928 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
52344955 CCTATCTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:52347068 original size:15 final size:16
Alignment explanation
Indices: 52347043--52347076 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
52347033 TTACTAGATC
52347043 TGCAGATAGCTTTCCT
1 TGCAGATAGCTTTCCT
52347059 TGCA-ATAGCTTTCCT
1 TGCAGATAGCTTTCCT
52347074 TGC
1 TGC
52347077 TCCTGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (16 bp):
TGCAGATAGCTTTCCT
Found at i:52353090 original size:15 final size:15
Alignment explanation
Indices: 52353065--52353097 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
52353055 AATTGTTTCA
52353065 ATTTTATTTTAT-TT
1 ATTTTATTTTATATT
52353079 ATTTTAATTTTATATT
1 ATTTT-ATTTTATATT
52353095 ATT
1 ATT
52353098 CTATAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 7 0.41
16 5 0.29
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTTTATTTTATATT
Found at i:52354635 original size:40 final size:40
Alignment explanation
Indices: 52354588--52354693 Score: 158
Period size: 40 Copynumber: 2.6 Consensus size: 40
52354578 GCTCTCCCAT
* *
52354588 CCCTCTCCCTCTTCCCCACCATCCCTCCCCCCTACTCCGA
1 CCCTCTCCCTCTCCCCCACCGTCCCTCCCCCCTACTCCGA
** * *
52354628 TTCTCTCCCTCTCCCCCACCGTCCCTGCCCCCTACTCTGA
1 CCCTCTCCCTCTCCCCCACCGTCCCTCCCCCCTACTCCGA
52354668 CCCTCTCCCTCTCCCCCACCGTCCCT
1 CCCTCTCCCTCTCCCCCACCGTCCCT
52354694 TTCCCTCTGC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.08, C:0.63, G:0.05, T:0.25
Consensus pattern (40 bp):
CCCTCTCCCTCTCCCCCACCGTCCCTCCCCCCTACTCCGA
Found at i:52358748 original size:39 final size:40
Alignment explanation
Indices: 52358673--52358751 Score: 101
Period size: 39 Copynumber: 2.0 Consensus size: 40
52358663 TTATTAAAAA
52358673 TTTTAGAATATATATTTTTATATTTTTTAATGATTTTTAAT
1 TTTTAGAATATATATTTTTATATTTTTT-ATGATTTTTAAT
*
52358714 TTTTAGAA-ATA-GTTTTTATAATTTTTT-TGAATTTTTAA
1 TTTTAGAATATATATTTTTAT-ATTTTTTATG-ATTTTTAA
52358752 AATTTTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
38 2 0.06
39 15 0.43
40 10 0.29
41 8 0.23
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (40 bp):
TTTTAGAATATATATTTTTATATTTTTTATGATTTTTAAT
Found at i:52358756 original size:41 final size:43
Alignment explanation
Indices: 52358660--52358757 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 43
52358650 ATATTTAATT
*
52358660 AATTTATTAAAAATTTTAGAATATATATTTTTATATTTTTTAATG
1 AATTT-TTAAAATTTTTAGAATATATATTTTTATATTTTTT-ATG
*
52358705 -ATTTTT--AATTTTTAGAA-ATA-GTTTTTATAATTTTTT-TG
1 AATTTTTAAAATTTTTAGAATATATATTTTTAT-ATTTTTTATG
52358743 AATTTTTAAAATTTT
1 AATTTTTAAAATTTT
52358758 AAAAAATTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
38 2 0.04
39 13 0.28
40 10 0.21
41 16 0.34
43 2 0.04
44 4 0.09
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (43 bp):
AATTTTTAAAATTTTTAGAATATATATTTTTATATTTTTTATG
Found at i:52358758 original size:40 final size:42
Alignment explanation
Indices: 52358660--52358758 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 42
52358650 ATATTTAATT
52358660 AATTTATTAAAAATTTTAGAATATATATTTTTATATTTTTTAATG
1 AATTT-TT-AAAATTTTAGAATATATATTTTTATATTTTTT-ATG
* *
52358705 -ATTTTT-AATTTTTAGAA-ATA-GTTTTTATAATTTTTT-TG
1 AATTTTTAAAATTTTAGAATATATATTTTTAT-ATTTTTTATG
52358743 AATTTTTAAAATTTTA
1 AATTTTTAAAATTTTA
52358759 AAAAATTAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
38 2 0.04
39 13 0.27
40 17 0.35
41 10 0.21
43 2 0.04
44 4 0.08
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (42 bp):
AATTTTTAAAATTTTAGAATATATATTTTTATATTTTTTATG
Found at i:52364813 original size:20 final size:20
Alignment explanation
Indices: 52364779--52364820 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
52364769 AACTATTTAA
** *
52364779 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
52364799 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
52364819 AT
1 AT
52364821 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:52365291 original size:16 final size:18
Alignment explanation
Indices: 52365256--52365293 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
52365246 ATCTTTATTT
*
52365256 AAATAAAATACAGTAGTA
1 AAATAAAATACAGAAGTA
52365274 AAATAAAATA-A-AAGTA
1 AAATAAAATACAGAAGTA
52365290 AAAT
1 AAAT
52365294 CCCTATAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 1 0.05
18 10 0.53
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.21
Consensus pattern (18 bp):
AAATAAAATACAGAAGTA
Found at i:52366548 original size:21 final size:21
Alignment explanation
Indices: 52366524--52366563 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
52366514 AATTTCACCG
* *
52366524 CTACAGTATCCAATCTCACTA
1 CTACAATAACCAATCTCACTA
*
52366545 CTACAATAACTAATCTCAC
1 CTACAATAACCAATCTCAC
52366564 CGCCACTACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.33, G:0.03, T:0.28
Consensus pattern (21 bp):
CTACAATAACCAATCTCACTA
Found at i:52366700 original size:21 final size:21
Alignment explanation
Indices: 52366674--52366728 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
52366664 ATAGCGGTGG
* *
52366674 CGGTGAGATTAGTTATTGTAA
1 CGGTGAGATTAGATACTGTAA
* *
52366695 CGGTGAGATTGGATACTGTAG
1 CGGTGAGATTAGATACTGTAA
52366716 CGGTGAGATTAGA
1 CGGTGAGATTAGA
52366729 AACAACGGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.07, G:0.35, T:0.31
Consensus pattern (21 bp):
CGGTGAGATTAGATACTGTAA
Found at i:52366914 original size:18 final size:18
Alignment explanation
Indices: 52366891--52367024 Score: 72
Period size: 18 Copynumber: 7.9 Consensus size: 18
52366881 TTATTATTAA
52366891 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
*
52366909 ATATAATTTAAT-AGAAT
1 ATATAATTTAATAAAAAT
* *
52366926 ATATGAATTTACT-ACAAT
1 ATAT-AATTTAATAAAAAT
* * *
52366944 -TATAATAT-ATAATATT
1 ATATAATTTAATAAAAAT
* * *
52366960 ATAAAATATAATTTAAAAT
1 ATATAATTTAA-TAAAAAT
* *
52366979 A-ATTA-TT-AT--TAA-
1 ATATAATTTAATAAAAAT
*
52366991 ATATAATTTAACAAAAAT
1 ATATAATTTAATAAAAAT
52367009 ATATAATTTAATAAAA
1 ATATAATTTAATAAAA
52367025 TTCTTAGTAT
Statistics
Matches: 86, Mismatches: 19, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
12 1 0.01
13 5 0.06
14 2 0.02
15 3 0.03
16 8 0.09
17 21 0.24
18 41 0.48
19 5 0.06
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:52366962 original size:15 final size:15
Alignment explanation
Indices: 52366942--52366997 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
52366932 ATTTACTACA
*
52366942 ATTATAATATATAAT
1 ATTATAAAATATAAT
52366957 ATTATAAAATAT-A-
1 ATTATAAAATATAAT
*
52366970 ATT-TAAAATA-ATT
1 ATTATAAAATATAAT
*
52366983 ATTATTAAATATAAT
1 ATTATAAAATATAAT
52366998 TTAACAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
12 7 0.21
13 6 0.18
14 7 0.21
15 13 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTATAAAATATAAT
Found at i:52366987 original size:26 final size:25
Alignment explanation
Indices: 52366952--52367134 Score: 86
Period size: 26 Copynumber: 7.5 Consensus size: 25
52366942 ATTATAATAT
52366952 ATAATATTATAAAATATAATTTAAA
1 ATAATATTATAAAATATAATTTAAA
*
52366977 ATAATTATTATTAAATATAATTTAACA
1 ATAA-TATTATAAAATATAATTTAA-A
* *
52367004 A-AA-A-TATATAATTTAA--TAAA
1 ATAATATTATAAAATATAATTTAAA
** * * *
52367024 ATTCTTAGTATTAAATAT--TCTT-AT
1 A-TAATATTATAAAATATAAT-TTAAA
*
52367048 ATGAAT-TTACTAAAATCATAA--T-AT
1 AT-AATATTA-TAAAAT-ATAATTTAAA
*
52367072 ATAATACTATAAAATATAATTTAAA
1 ATAATATTATAAAATATAATTTAAA
* *
52367097 ATAATTATGATTAAATATAATTTAAA
1 ATAA-TATTATAAAATATAATTTAAA
52367123 A-AATATATATAA
1 ATAATAT-TATAA
52367135 TTTAATAAAA
Statistics
Matches: 117, Mismatches: 21, Indels: 40
0.66 0.12 0.22
Matches are distributed among these distances:
20 2 0.02
21 3 0.03
22 4 0.03
23 22 0.19
24 27 0.23
25 17 0.15
26 40 0.34
27 2 0.02
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (25 bp):
ATAATATTATAAAATATAATTTAAA
Found at i:52367010 original size:59 final size:59
Alignment explanation
Indices: 52366947--52367145 Score: 185
Period size: 59 Copynumber: 3.3 Consensus size: 59
52366937 CTACAATTAT
52366947 AATATATAATATT-ATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAACAAA
1 AATATATAAT-TTAATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAACAAA
* * * * * * ** *
52367006 AATATATAATTTAATAAAATTCTTAGTATT-AAAT-ATTCTTATATGAATTTACTAAAATC-AT
1 AATATATAATTTAATAAAA-T-ATAAT-TTAAAATAATTATTAT-TAAATATAATTTAA-CAAA
* *
52367067 AATATATAATACT-ATAAAATATAATTTAAAATAATTATGATTAAATATAATTTAA-AAA
1 AATATATAAT-TTAATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAACAAA
52367125 ATATATATAATTTAATAAAAT
1 A-ATATATAATTTAATAAAAT
52367146 TCTTAGTATT
Statistics
Matches: 107, Mismatches: 21, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
58 7 0.07
59 48 0.45
60 15 0.14
61 33 0.31
62 4 0.04
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (59 bp):
AATATATAATTTAATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAACAAA
Found at i:52367058 original size:120 final size:120
Alignment explanation
Indices: 52366925--52367164 Score: 428
Period size: 120 Copynumber: 2.0 Consensus size: 120
52366915 TTTAATAGAA
* * * *
52366925 TATATGAATTTACTACAATTATAATATATAATATTATAAAATATAATTTAAAATAATTATTATTA
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATGATTA
52366990 AATATAATTTAACAAAA-ATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
66 AATATAATTTAA-AAAATATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
52367045 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATGATTA
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATGATTA
52367110 AATATAATTTAAAAAATATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
66 AATATAATTTAAAAAATATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
52367165 AATGATTGTA
Statistics
Matches: 115, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
119 4 0.03
120 111 0.97
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (120 bp):
TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATGATTA
AATATAATTTAAAAAATATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
Found at i:52367074 original size:61 final size:57
Alignment explanation
Indices: 52366990--52367164 Score: 153
Period size: 61 Copynumber: 3.0 Consensus size: 57
52366980 ATTATTATTA
*
52366990 AATATAATTTAACAAA-AATATATAATTTAATAAAATTCTTAGTATTAAATATTCTT
1 AATATAATTTAAAAAATAATATATAATTTAATAAAATTCTTAGTATTAAATATTCTT
* * * * * **
52367046 -ATATGAATTTACTAAAATCATAATATATAATACT-ATAAAATATAATTTA-AAATAATTATGAT
1 AATAT-AATTTA--AAAA--ATAATATATAAT-TTAATAAAAT-T--CTTAGTATTAAATATTCT
52367108 T
57 T
52367109 AAATATAATTTAAAAAAT-ATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
1 -AATATAATTTAAAAAATAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
52367165 AATGATTGTA
Statistics
Matches: 90, Mismatches: 15, Indels: 27
0.68 0.11 0.20
Matches are distributed among these distances:
55 4 0.04
56 9 0.10
57 8 0.09
58 5 0.06
59 16 0.18
60 3 0.03
61 17 0.19
62 6 0.07
63 9 0.10
64 9 0.10
65 4 0.04
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (57 bp):
AATATAATTTAAAAAATAATATATAATTTAATAAAATTCTTAGTATTAAATATTCTT
Found at i:52367141 original size:28 final size:26
Alignment explanation
Indices: 52367083--52367146 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
52367073 TAATACTATA
* *
52367083 AAATATAATTTAAAATAATTATGATT
1 AAATATAATTTAAAAAAATTATAATT
52367109 AAATATAATTTAAAAAATATATATAATT
1 AAATATAATTTAAAAAA-AT-TATAATT
* *
52367137 TAATAAAATT
1 AAATATAATT
52367147 CTTAGTATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 16 0.50
27 2 0.06
28 14 0.44
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
AAATATAATTTAAAAAAATTATAATT
Found at i:52385956 original size:62 final size:63
Alignment explanation
Indices: 52385841--52385967 Score: 238
Period size: 62 Copynumber: 2.0 Consensus size: 63
52385831 GAGTATCTAA
*
52385841 AATGATTTACTCTTGTCACAACAAAAGGGGTATGCTAAAGCTTTAATTTAAACAGGTTGCTTG
1 AATGATTTACTCTTGTCACAACAAAAGAGGTATGCTAAAGCTTTAATTTAAACAGGTTGCTTG
52385904 AATGATTTACTCTTGTCACAACAAAA-AGGTATGCTAAAGCTTTAATTTAAACAGGTTGCTTG
1 AATGATTTACTCTTGTCACAACAAAAGAGGTATGCTAAAGCTTTAATTTAAACAGGTTGCTTG
52385966 AA
1 AA
52385968 GGAGATCAAT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
62 37 0.59
63 26 0.41
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Consensus pattern (63 bp):
AATGATTTACTCTTGTCACAACAAAAGAGGTATGCTAAAGCTTTAATTTAAACAGGTTGCTTG
Found at i:52389166 original size:16 final size:18
Alignment explanation
Indices: 52389127--52389160 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52389117 TAAGTTTATA
52389127 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
52389144 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
52389161 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:52390037 original size:21 final size:21
Alignment explanation
Indices: 52390011--52390051 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
52390001 CAACGTGGCA
52390011 AGTTAACTGGCCACACCAGCT
1 AGTTAACTGGCCACACCAGCT
* *
52390032 AGTTAACTTGCCACATCAGC
1 AGTTAACTGGCCACACCAGC
52390052 GGTCCCGTTA
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:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (21 bp):
AGTTAACTGGCCACACCAGCT
Found at i:52390139 original size:30 final size:31
Alignment explanation
Indices: 52390086--52390154 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 31
52390076 ACTGTTAATC
*
52390086 AGTGACTGTTTTGTCACTTTTTTATAACGTT-
1 AGTGACTGTTTTGTCACTTTTTTA-AAAGTTG
*
52390117 AGTGACTGTTTTGTTA-TTTTTTAAAAGTTG
1 AGTGACTGTTTTGTCACTTTTTTAAAAGTTG
52390147 AGTGACTG
1 AGTGACTG
52390155 AAATGAAACC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
29 5 0.14
30 15 0.43
31 15 0.43
ACGTcount: A:0.22, C:0.09, G:0.20, T:0.49
Consensus pattern (31 bp):
AGTGACTGTTTTGTCACTTTTTTAAAAGTTG
Found at i:52391269 original size:30 final size:30
Alignment explanation
Indices: 52391235--52391297 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
52391225 ACTTAACAAT
52391235 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
*
52391265 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
52391295 CAA
1 CAA
52391298 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.16, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:52392481 original size:2 final size:2
Alignment explanation
Indices: 52392474--52392508 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
52392464 ATAAATATTA
52392474 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52392509 TTTAGATCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52393184 original size:6 final size:6
Alignment explanation
Indices: 52393173--52393200 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
52393163 CCATCAACAT
52393173 TGCTCA TGCTCA TGCTCA TGCTCA TGCT
1 TGCTCA TGCTCA TGCTCA TGCTCA TGCT
52393201 GTCGCTCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.32, G:0.18, T:0.36
Consensus pattern (6 bp):
TGCTCA
Found at i:52395809 original size:24 final size:24
Alignment explanation
Indices: 52395759--52395810 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
52395749 AATCAAAGTC
* **
52395759 AAATATATCATGCTAATAAATGTT
1 AAATATATCATACTAATAAATACT
* *
52395783 AAATATATTATACTCATAAATACT
1 AAATATATCATACTAATAAATACT
52395807 AAAT
1 AAAT
52395811 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATCATACTAATAAATACT
Found at i:52400018 original size:29 final size:27
Alignment explanation
Indices: 52399967--52400026 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
52399957 TACTAGCAGG
* *
52399967 CCTAAACCCACCCAAGCCCAAACTAAA
1 CCTAAACCCACCAAACCCCAAACTAAA
*
52399994 CCTAATACCCACCTAAACCCCAAACTAAC
1 CCTAA-ACCCACC-AAACCCCAAACTAAA
52400023 CCTA
1 CCTA
52400027 GCCCAGCAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 5 0.18
28 7 0.25
29 16 0.57
ACGTcount: A:0.42, C:0.45, G:0.02, T:0.12
Consensus pattern (27 bp):
CCTAAACCCACCAAACCCCAAACTAAA
Found at i:52400386 original size:7 final size:7
Alignment explanation
Indices: 52400374--52400404 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
52400364 AGTGATTGTC
52400374 TTTTATT
1 TTTTATT
52400381 TTTTATT
1 TTTTATT
52400388 TTTTA-T
1 TTTTATT
52400394 TTTTATT
1 TTTTATT
52400401 TTTT
1 TTTT
52400405 TTTGCCTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTATT
Found at i:52400405 original size:14 final size:14
Alignment explanation
Indices: 52400374--52400404 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
52400364 AGTGATTGTC
52400374 TTTTATTTTTTATT
1 TTTTATTTTTTATT
52400388 TTTTA-TTTTTATT
1 TTTTATTTTTTATT
52400401 TTTT
1 TTTT
52400405 TTTGCCTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTATTTTTTATT
Found at i:52401215 original size:16 final size:17
Alignment explanation
Indices: 52401196--52401229 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
52401186 TTTTTAAAAC
52401196 TTTTATATATTT-TATA
1 TTTTATATATTTATATA
52401212 TTTTATATATTTATATA
1 TTTTATATATTTATATA
52401229 T
1 T
52401230 ACTCAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTATATATTTATATA
Found at i:52401400 original size:14 final size:14
Alignment explanation
Indices: 52401374--52401421 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
52401364 GTGTGTCTGA
52401374 TATATATTATATTTG
1 TATATA-TATATTTG
52401389 TATATATATATTTG
1 TATATATATATTTG
* * * *
52401403 CAAATATTTATTCG
1 TATATATATATTTG
52401417 TATAT
1 TATAT
52401422 GCTGTAAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
14 21 0.78
15 6 0.22
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.54
Consensus pattern (14 bp):
TATATATATATTTG
Found at i:52402334 original size:24 final size:24
Alignment explanation
Indices: 52402302--52402353 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
52402292 TCACTATGTC
* *
52402302 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
52402326 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
52402350 AAAT
1 AAAT
52402354 TTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:52410557 original size:30 final size:30
Alignment explanation
Indices: 52410522--52410578 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
52410512 ATCAGTTCCC
*
52410522 CCTCCCCACCTCATCAT-GCATATCATCCAA
1 CCTCCCCACCTCACCATAGC-TATCATCCAA
*
52410552 CCTCCCCTCCTCACCATAGCTATCATC
1 CCTCCCCACCTCACCATAGCTATCATC
52410579 AGCCCACCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.23, C:0.49, G:0.04, T:0.25
Consensus pattern (30 bp):
CCTCCCCACCTCACCATAGCTATCATCCAA
Found at i:52418933 original size:6 final size:6
Alignment explanation
Indices: 52418915--52418947 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
52418905 TCACGCATGG
*
52418915 GCCGCT GCTGCT GCCGCT GCCGCT GCCGCT GCC
1 GCCGCT GCCGCT GCCGCT GCCGCT GCCGCT GCC
52418948 ACCTCTCTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.33, T:0.18
Consensus pattern (6 bp):
GCCGCT
Found at i:52426202 original size:29 final size:29
Alignment explanation
Indices: 52426148--52426203 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
52426138 TTTGAAGGAT
* ***
52426148 AAACTATTAAACAATTAGGTTGCTTAAGA
1 AAACTATTAAACAAGTAGGCAACTTAAGA
52426177 AAACTATTAAACAAGTAGGCAACTTAA
1 AAACTATTAAACAAGTAGGCAACTTAA
52426204 TAAAGATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (29 bp):
AAACTATTAAACAAGTAGGCAACTTAAGA
Found at i:52428592 original size:24 final size:24
Alignment explanation
Indices: 52428548--52428626 Score: 88
Period size: 24 Copynumber: 3.2 Consensus size: 24
52428538 CCGGGCTTAA
*
52428548 TAACAGGAAGCTCACAAAGAGC-CT
1 TAACAGGAAGCTC-CGAAGAGCACT
* * *
52428572 ATATCGGGTAGCTCCGAAGAGCACT
1 -TAACAGGAAGCTCCGAAGAGCACT
52428597 TAACAGGAAGCTCCGAAGAGCACTT
1 TAACAGGAAGCTCCGAAGAGCAC-T
52428622 TAACA
1 TAACA
52428627 TAGAGCACCG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
24 27 0.60
25 18 0.40
ACGTcount: A:0.37, C:0.24, G:0.23, T:0.16
Consensus pattern (24 bp):
TAACAGGAAGCTCCGAAGAGCACT
Found at i:52428971 original size:18 final size:19
Alignment explanation
Indices: 52428942--52428981 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
52428932 ATCGAGTTTC
* *
52428942 ATTCATTTTATCGGGACTT
1 ATTCATTTTATCAGGAATT
52428961 ATTCA-TTTATCAGGAATT
1 ATTCATTTTATCAGGAATT
52428979 ATT
1 ATT
52428982 AGATATGAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (19 bp):
ATTCATTTTATCAGGAATT
Found at i:52429220 original size:33 final size:33
Alignment explanation
Indices: 52429177--52429243 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
52429167 CTGAATCTAT
*
52429177 ATGAGTAAATTTAACATCAATTCTATCCAAGTC
1 ATGAGCAAATTTAACATCAATTCTATCCAAGTC
52429210 ATGAGCAAATTTAACATCAATTCTATCCAAGTC
1 ATGAGCAAATTTAACATCAATTCTATCCAAGTC
52429243 A
1 A
52429244 CATCTTAGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.31
Consensus pattern (33 bp):
ATGAGCAAATTTAACATCAATTCTATCCAAGTC
Found at i:52432750 original size:46 final size:46
Alignment explanation
Indices: 52432678--52432911 Score: 355
Period size: 46 Copynumber: 5.1 Consensus size: 46
52432668 ACAATGCTAT
* *
52432678 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTTTTCATTGAAATACCATACCTACTTTTCAC
* *
52432724 AACTCAGTATGGTTTTTTTCATTGAAACACCATACCTATTTTTCAC
1 AACTCAGTATGGTTTTTTTCATTGAAATACCATACCTACTTTTCAC
*
52432770 AACTCAGTATGGTTTTCTTT-ATTGAAATACCATATCTACTTTTCAC
1 AACTCAGTATGGTTTT-TTTCATTGAAATACCATACCTACTTTTCAC
*
52432816 AAGTCAGTATGGTTTTCTTT-ATTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTT-TTTCATTGAAATACCATACCTACTTTTCAC
* * *
52432862 AACTCTGTATGGTTTTCTTCATTGAAAAACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTTTTCATTGAAATACCATACCTACTTTTCAC
52432908 AACT
1 AACT
52432912 TTGCCATGGA
Statistics
Matches: 173, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
45 2 0.01
46 168 0.97
47 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (46 bp):
AACTCAGTATGGTTTTTTTCATTGAAATACCATACCTACTTTTCAC
Found at i:52436433 original size:15 final size:15
Alignment explanation
Indices: 52436413--52436442 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
52436403 ATGCAATTTC
52436413 TTATGAAATGACTTA
1 TTATGAAATGACTTA
52436428 TTATGAAATGACTTA
1 TTATGAAATGACTTA
52436443 ACATGTGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (15 bp):
TTATGAAATGACTTA
Found at i:52437791 original size:18 final size:21
Alignment explanation
Indices: 52437755--52437793 Score: 57
Period size: 18 Copynumber: 2.0 Consensus size: 21
52437745 TGAGCTTTTC
52437755 ATTTTTAATATATATTTAAAT
1 ATTTTTAATATATATTTAAAT
52437776 ATTTTT-ATAT-TA-TTAAAT
1 ATTTTTAATATATATTTAAAT
52437794 TATATTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 2 0.11
20 4 0.22
21 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTTTTAATATATATTTAAAT
Found at i:52442195 original size:14 final size:14
Alignment explanation
Indices: 52442176--52442214 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
52442166 AAAGATAAAT
*
52442176 AAAAAATAAAACGA
1 AAAAAATAAAAAGA
*
52442190 AAAAAAGAAAAAGA
1 AAAAAATAAAAAGA
52442204 AAAAGAATAAA
1 AAAA-AATAAA
52442215 CTTAAAGGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.82, C:0.03, G:0.10, T:0.05
Consensus pattern (14 bp):
AAAAAATAAAAAGA
Found at i:52442266 original size:18 final size:17
Alignment explanation
Indices: 52442243--52442284 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
52442233 AATAATAGTA
52442243 AAAAATA-CTAAAAATAAT
1 AAAAATAGC-AAAAA-AAT
52442261 AAAAATAGCAAAAAAAT
1 AAAAATAGCAAAAAAAT
*
52442278 TAAAATA
1 AAAAATA
52442285 AATTTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 12 0.55
19 1 0.05
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (17 bp):
AAAAATAGCAAAAAAAT
Found at i:52442344 original size:5 final size:5
Alignment explanation
Indices: 52442336--52442385 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
52442326 AAAAATTAGG
*
52442336 AAAAT AAAA- ATAAAT AATAT AAAA- AAAAT AATAAAT AAAAT AAAAT
1 AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT -A-AAAT AAAAT AAAAT
52442382 AAAA
1 AAAA
52442386 GGGGTAGCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 5 0.13
5 26 0.68
6 3 0.08
7 4 0.11
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:52442360 original size:21 final size:21
Alignment explanation
Indices: 52442306--52442385 Score: 71
Period size: 21 Copynumber: 3.9 Consensus size: 21
52442296 TAAGTATAAG
52442306 AATAATA-AATAAATAAA-ATA
1 AATAATATAA-AAATAAAAATA
*
52442326 AAAAAT-TAGGAAAATAAAAATA
1 AATAATATA--AAAATAAAAATA
52442348 AATAATATAAAAA-AAATAATA
1 AATAATATAAAAATAAA-AATA
*
52442369 AATAAAAT-AAAATAAAA
1 AATAATATAAAAATAAAA
52442386 GGGGTAGCTT
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
20 14 0.28
21 25 0.50
22 9 0.18
23 2 0.04
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (21 bp):
AATAATATAAAAATAAAAATA
Found at i:52442372 original size:31 final size:30
Alignment explanation
Indices: 52442306--52442385 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 30
52442296 TAAGTATAAG
*
52442306 AATAATAAATAAATAAAATAAAAAATTAGGAA
1 AATAA-AAATAAATAAAATAAAAAAATA-GAA
*
52442338 AATAAAAATAAATAATATAAAAAAAATA-ATA
1 AATAAAAATAAATAAAAT-AAAAAAATAGA-A
52442369 AAT-AAAATAAAATAAAA
1 AATAAAAAT-AAATAAAA
52442386 GGGGTAGCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
30 6 0.14
31 23 0.55
32 13 0.31
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (30 bp):
AATAAAAATAAATAAAATAAAAAAATAGAA
Found at i:52442381 original size:35 final size:35
Alignment explanation
Indices: 52442309--52442384 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
52442299 GTATAAGAAT
* *
52442309 AATAAATAAATAAAATAAAAAATTAGGAAAATAAA
1 AATAAATAAATAAAATAAAAAATAAAGAAAATAAA
*
52442344 AATAAATAATATAAAA-AAAATAATAAATAAAAT-AA
1 AATAAATAA-ATAAAATAAAA-AATAAAGAAAATAAA
52442379 AATAAA
1 AATAAA
52442385 AGGGGTAGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 21 0.58
36 15 0.42
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (35 bp):
AATAAATAAATAAAATAAAAAATAAAGAAAATAAA
Found at i:52466082 original size:26 final size:26
Alignment explanation
Indices: 52466053--52466106 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
52466043 ATATATAGCC
* *
52466053 ATTCATAATAAATAATATATGAAATA
1 ATTCAAAATAAATAATATATAAAATA
* * *
52466079 ATTCAAAATACATCATATCTAAAATA
1 ATTCAAAATAAATAATATATAAAATA
52466105 AT
1 AT
52466107 ATAAAACAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (26 bp):
ATTCAAAATAAATAATATATAAAATA
Found at i:52466132 original size:24 final size:23
Alignment explanation
Indices: 52466100--52466186 Score: 79
Period size: 24 Copynumber: 3.6 Consensus size: 23
52466090 ATCATATCTA
*
52466100 AAATAATATA-AAACAGTTTAATAT
1 AAATAATATATAAA-AG-TTAAAAT
52466124 AAATAATATATAAAAGTTAAAAT
1 AAATAATATATAAAAGTTAAAAT
*
52466147 AAATAAAAATATAAAACTGTTAAAA-
1 AAAT-AATATATAAAA--GTTAAAAT
*
52466172 ATGATAATATATAAA
1 A-AATAATATATAAA
52466187 GGGAAAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
23 10 0.19
24 22 0.41
25 13 0.24
26 9 0.17
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (23 bp):
AAATAATATATAAAAGTTAAAAT
Found at i:52466134 original size:26 final size:26
Alignment explanation
Indices: 52466105--52466186 Score: 82
Period size: 25 Copynumber: 3.3 Consensus size: 26
52466095 ATCTAAAATA
*
52466105 ATATAAAACAGTTTAATATAAATAAT
1 ATATAAAACAGTTTAAAATAAATAAT
*
52466131 ATAT-AAA-AG-TTAAAATAAATAAAA
1 ATATAAAACAGTTTAAAATAAAT-AAT
* * *
52466155 ATATAAAACTGTTAAAAAT-GATAAT
1 ATATAAAACAGTTTAAAATAAATAAT
52466180 ATATAAA
1 ATATAAA
52466187 GGGAAAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
23 10 0.22
24 8 0.17
25 15 0.33
26 7 0.15
27 6 0.13
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.30
Consensus pattern (26 bp):
ATATAAAACAGTTTAAAATAAATAAT
Found at i:52469809 original size:42 final size:42
Alignment explanation
Indices: 52469747--52469829 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
52469737 GTGCTTGATA
*
52469747 ATGTAAAGGAGGAAGACGAGTACTATGAAAAGCCAATATCTG
1 ATGTAAAGAAGGAAGACGAGTACTATGAAAAGCCAATATCTG
* * * *
52469789 ATGTAAAGAAGGAAGGCGAGTACTGTGATAAGCTAATATCT
1 ATGTAAAGAAGGAAGACGAGTACTATGAAAAGCCAATATCT
52469830 TGCCTAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.41, C:0.11, G:0.27, T:0.22
Consensus pattern (42 bp):
ATGTAAAGAAGGAAGACGAGTACTATGAAAAGCCAATATCTG
Found at i:52472439 original size:50 final size:50
Alignment explanation
Indices: 52472324--52472481 Score: 235
Period size: 50 Copynumber: 3.1 Consensus size: 50
52472314 AATAATAACA
** *
52472324 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTCGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * **
52472375 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
52472425 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
52472475 TGCCAAA
1 TGCCAAA
52472482 TATAGCCCAA
Statistics
Matches: 95, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
50 62 0.65
51 33 0.35
ACGTcount: A:0.20, C:0.31, G:0.24, T:0.25
Consensus pattern (50 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:52474967 original size:19 final size:19
Alignment explanation
Indices: 52474943--52475007 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
52474933 TAACTTTTAT
*
52474943 TTTTTAAAATTATTTATAA
1 TTTTTAAAATTTTTTATAA
* *
52474962 TTTTTAAATTTCTTTTATTA
1 TTTTTAAAATT-TTTTATAA
*
52474982 TTTTTAATTATTTTTTATAA
1 TTTTTAA-AATTTTTTATAA
52475002 TATTTT
1 T-TTTT
52475008 GAACTATGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
19 10 0.27
20 21 0.57
21 6 0.16
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTAAAATTTTTTATAA
Found at i:52475178 original size:20 final size:19
Alignment explanation
Indices: 52475126--52475183 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
52475116 TTTTTTAGGA
*
52475126 TTTTT-TAATATTTTATAA-
1 TTTTTATAATATTCTA-AAC
52475144 TTTTTAATAAT-TTCTACAAC
1 TTTTT-ATAATATTCTA-AAC
52475164 TTTTTATAATATTCTAAAC
1 TTTTTATAATATTCTAAAC
52475183 T
1 T
52475184 ACGTCCAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 5 0.15
19 15 0.44
20 14 0.41
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTTATAATATTCTAAAC
Found at i:52484481 original size:28 final size:26
Alignment explanation
Indices: 52484446--52484503 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
52484436 CCATACTGAA
52484446 TTAATATTAATCGAATT-AATTAATTTT
1 TTAATATTAATCGAATTGAATT--TTTT
*
52484473 TTAATTATTAATTGAATTGAATTTTTT
1 TTAA-TATTAATCGAATTGAATTTTTT
52484500 TTAA
1 TTAA
52484504 AAAAAATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 12 0.43
28 12 0.43
29 4 0.14
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (26 bp):
TTAATATTAATCGAATTGAATTTTTT
Found at i:52487400 original size:2 final size:2
Alignment explanation
Indices: 52487393--52487424 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
52487383 CTGAATATTC
52487393 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52487425 TCCTCATCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52491592 original size:12 final size:13
Alignment explanation
Indices: 52491569--52491608 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 13
52491559 ACCATTGACT
*
52491569 TTATATTTTTTTG
1 TTATCTTTTTTTG
52491582 TTATCTTTTTTGCTG
1 TTATCTTTTTT--TG
52491597 TTATCTTTTTTT
1 TTATCTTTTTTT
52491609 AAACTTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 11 0.46
15 13 0.54
ACGTcount: A:0.10, C:0.07, G:0.07, T:0.75
Consensus pattern (13 bp):
TTATCTTTTTTTG
Found at i:52494253 original size:12 final size:13
Alignment explanation
Indices: 52494216--52494258 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
52494206 AACATTACAA
*
52494216 TATAATCTAATAT
1 TATAATCTTATAT
*
52494229 TAT-ATCTTTTAT
1 TATAATCTTATAT
52494241 TATAAT-TTATAT
1 TATAATCTTATAT
52494253 TATAAT
1 TATAAT
52494259 AATAGTGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 21 0.81
13 5 0.19
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (13 bp):
TATAATCTTATAT
Found at i:52494790 original size:22 final size:22
Alignment explanation
Indices: 52494764--52494820 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
52494754 CTCGCAAGCA
52494764 CCGCACATCGCGCCCGTCGCTC
1 CCGCACATCGCGCCCGTCGCTC
* **
52494786 CCGCACATCACGCTTGTCGCTC
1 CCGCACATCGCGCCCGTCGCTC
* *
52494808 CCACGCATCGCGC
1 CCGCACATCGCGC
52494821 GCACTCAACA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.12, C:0.51, G:0.21, T:0.16
Consensus pattern (22 bp):
CCGCACATCGCGCCCGTCGCTC
Found at i:52495714 original size:3 final size:3
Alignment explanation
Indices: 52495706--52495754 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
52495696 TATTACTTGT
* * *
52495706 TTA TTA TTA CTA TTA TTG TCTA TTA TTA TTA TTA ATA TTA TTCA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TT-A TTA
52495753 TT
1 TT
52495755 TTCATGTACA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
3 33 0.87
4 5 0.13
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:52495724 original size:19 final size:20
Alignment explanation
Indices: 52495693--52495739 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
52495683 TATTTTATGG
*
52495693 TACTATTACTTGTTTATTAT
1 TACTATTACTTGTCTATTAT
52495713 TACTATTA-TTGTCTATTAT
1 TACTATTACTTGTCTATTAT
*
52495732 TATTATTA
1 TACTATTA
52495740 ATATTATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.60
Consensus pattern (20 bp):
TACTATTACTTGTCTATTAT
Found at i:52496030 original size:33 final size:32
Alignment explanation
Indices: 52495955--52496030 Score: 77
Period size: 33 Copynumber: 2.4 Consensus size: 32
52495945 CTTTTATATA
* **
52495955 CTTTATATTTT-ATATATATATTTATACATTT
1 CTTTATATTTTAATATATACATAAATACATTT
52495986 CTATTAT-TTTTAAATATATACATAAATACATATT
1 CT-TTATATTTT-AATATATACATAAATACAT-TT
52496020 -TTTATATTTTA
1 CTTTATATTTTA
52496031 TTTTACAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
31 6 0.16
32 9 0.24
33 20 0.54
34 2 0.05
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (32 bp):
CTTTATATTTTAATATATACATAAATACATTT
Found at i:52499410 original size:45 final size:45
Alignment explanation
Indices: 52499335--52499449 Score: 198
Period size: 45 Copynumber: 2.6 Consensus size: 45
52499325 TATGTATGAT
* *
52499335 CACTTATCAC-TTGTC-CCTAATCAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
52499378 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
52499423 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
52499450 AGTACTCAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
43 10 0.15
44 5 0.07
45 53 0.78
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (45 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
Found at i:52499889 original size:28 final size:29
Alignment explanation
Indices: 52499858--52499935 Score: 70
Period size: 28 Copynumber: 2.7 Consensus size: 29
52499848 TATTATTATT
*
52499858 TATATAAATATATAAATTA-ATTATAAAG
1 TATATAAATAAATAAATTACATTATAAAG
* * *
52499886 TATATTATTAAATTAATTACATTATAAA-
1 TATATAAATAAATAAATTACATTATAAAG
*
52499914 TATTATATTAAGAAATAAATTA
1 TA-TATA--AATAAATAAATTA
52499936 AATAAAGACA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
28 17 0.45
29 11 0.29
31 10 0.26
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (29 bp):
TATATAAATAAATAAATTACATTATAAAG
Found at i:52499935 original size:31 final size:28
Alignment explanation
Indices: 52499869--52499936 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
52499859 ATATAAATAT
**
52499869 ATAAATTAATTATAAAGTATATTATTAA
1 ATAAATTAATTATAAAGTATATTAAGAA
* *
52499897 ATTAATTACATTATAAATATTATATTAAGAA
1 ATAAATTA-ATTAT-AA-AGTATATTAAGAA
52499928 ATAAATTAA
1 ATAAATTAA
52499937 ATAAAGACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.22
29 5 0.16
30 3 0.09
31 17 0.53
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (28 bp):
ATAAATTAATTATAAAGTATATTAAGAA
Found at i:52500834 original size:18 final size:18
Alignment explanation
Indices: 52500811--52500859 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
52500801 ATGTGAGGTA
*
52500811 AGTATTAATATTAGTATT
1 AGTATTATTATTAGTATT
52500829 AGTATTATTATTAGTATT
1 AGTATTATTATTAGTATT
*
52500847 ATTATTATTATTA
1 AGTATTATTATTA
52500860 TTAGTGGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (18 bp):
AGTATTATTATTAGTATT
Found at i:52500839 original size:3 final size:3
Alignment explanation
Indices: 52500813--52500862 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
52500803 GTGAGGTAAG
* * * *
52500813 TAT TAA TAT TAG TAT TAG TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
52500861 TA
1 TA
52500863 GTGGGAATTA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:52500860 original size:12 final size:12
Alignment explanation
Indices: 52500813--52500862 Score: 73
Period size: 12 Copynumber: 4.2 Consensus size: 12
52500803 GTGAGGTAAG
* *
52500813 TATTAATATTAG
1 TATTAGTATTAT
52500825 TATTAGTATTAT
1 TATTAGTATTAT
52500837 TATTAGTATTAT
1 TATTAGTATTAT
*
52500849 TATTATTATTAT
1 TATTAGTATTAT
52500861 TA
1 TA
52500863 GTGGGAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (12 bp):
TATTAGTATTAT
Found at i:52501055 original size:24 final size:24
Alignment explanation
Indices: 52501001--52501072 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 24
52500991 TGTGTGAAGT
*
52501001 TGTGAAATAATTATTG-ATTG-AAA
1 TGTGAAA-AATGATTGAATTGAAAA
*
52501024 GGTGGAAAAATGATTGAATTGAAAA
1 TGT-GAAAAATGATTGAATTGAAAA
52501049 TGTGAAAAATTGTAATTGAATTGA
1 TGTGAAAAA-TG--ATTGAATTGA
52501073 GAATATATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 9 0.22
24 14 0.35
25 7 0.17
27 10 0.25
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (24 bp):
TGTGAAAAATGATTGAATTGAAAA
Found at i:52501275 original size:37 final size:39
Alignment explanation
Indices: 52501216--52501311 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
52501206 CGGATAGATT
* * * *
52501216 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
52501253 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
52501292 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
52501312 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:52512235 original size:32 final size:32
Alignment explanation
Indices: 52512194--52512284 Score: 164
Period size: 32 Copynumber: 2.8 Consensus size: 32
52512184 TTTATCAAAA
52512194 GATTTTCGCTGTTAGTAAGACTGGTCATTTAG
1 GATTTTCGCTGTTAGTAAGACTGGTCATTTAG
52512226 GATTTTCGCTGTTAGTAAGACTGGTCATTTAG
1 GATTTTCGCTGTTAGTAAGACTGGTCATTTAG
**
52512258 GATTTTCATTGTTAGTAAGACTGGTCA
1 GATTTTCGCTGTTAGTAAGACTGGTCA
52512285 ACTGAAGTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.23, C:0.12, G:0.24, T:0.41
Consensus pattern (32 bp):
GATTTTCGCTGTTAGTAAGACTGGTCATTTAG
Found at i:52526785 original size:14 final size:14
Alignment explanation
Indices: 52526759--52526799 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
52526749 TATAGGGTTT
52526759 TTGAA-TATTGGGC
1 TTGAAGTATTGGGC
*
52526772 TAT-AAGTTTTGGGC
1 T-TGAAGTATTGGGC
52526786 TTGAAGTATTGGGC
1 TTGAAGTATTGGGC
52526800 CTGGTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.22, C:0.07, G:0.32, T:0.39
Consensus pattern (14 bp):
TTGAAGTATTGGGC
Found at i:52527387 original size:50 final size:50
Alignment explanation
Indices: 52527306--52528094 Score: 564
Period size: 50 Copynumber: 15.7 Consensus size: 50
52527296 CAATCTGTTC
* * *
52527306 GTCGGGGAAGTAAGATTCACTGTTGTGGCTTCAATCTTTTTAACTGCATT
1 GTCGGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTTTTTAACTGCAAT
* * ** * * * ** * **
52527356 GTCGGGGAAGCAAGATTCGCTATTATAGCTTCAACCTGTTCCACTACACC
1 GTCGGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTTTTTAACTGCAAT
* * * * * *
52527406 G-CTAGGGAAGTAAGATTCGCTGTTGTGGCTTCAATCTTTTTAATTGTAAT
1 GTC-GGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTTTTTAACTGCAAT
* * * ** * **
52527456 GTCGGGGAAGCAAGATTCGCCATTGTAGCTTCAATAAGTTCT-ACTGCACC
1 GTCGGGGAAGTAAGATTCACCGTTGTAGCTTCAAT-CTTTTTAACTGCAAT
* * * *
52527506 GCCAGGGAAGTAAGATTCACCGTTG-AGGCTTCAATCTTTTTAATTTCAAT
1 GTCGGGGAAGTAAGATTCACCGTTGTA-GCTTCAATCTTTTTAACTGCAAT
* * * ** **
52527556 GTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACC
1 GTCGGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTTTTTAACTGCAAT
* * * *
52527606 GCCAGTGAAGTAAGATTCACCGTTGTAGCTTCAATCTTTTTAAATGCAAT
1 GTCGGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTTTTTAACTGCAAT
* * * * ** *
52527656 GTTGGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCAC
1 GTCGGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTTTTTAACTGCA--AT
* * * * * *
52527708 CT-AGGGAAGTATGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAAT
1 GTCGGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTTTTTAACTGCAAT
* * * * ** * **
52527757 GTCGTGGAAGCAAGATTCACCGTTGTAGCTTTAATCTGTTCCATTGCACC
1 GTCGGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTTTTTAACTGCAAT
* * * * *
52527807 GCCAGGGAAGTAAGATTCACCATTGTGGCTTCAATCTTTTTAATTGCAAT
1 GTCGGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTTTTTAACTGCAAT
* * * * **
52527857 ATCGGGGAAGCAAGATTCACCGTTGTAGCATCAATCTGTTCCACTGCACCAT
1 GTCGGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTTTTTAACTGCA--AT
* * *
52527909 CT-GGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTTTTCAACTGCAAT
1 GTCGGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTTTTTAACTGCAAT
* * * * ** **
52527958 GTCGAGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACC
1 GTCGGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTTTTTAACTGCAAT
* * * * * * *
52528008 GCCTGGGAAAGTGAGATTCGCTGTTGTAGCTTCAAT-ATTTTAATTGCAAT
1 GTC-GGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTTTTTAACTGCAAT
* * * * *
52528058 ATCGGGGAAGCAAGATTTACCGTTGCAGCTTTAATCT
1 GTCGGGGAAGTAAGATTCACCGTTGTAGCTTCAATCT
52528095 GTTCCACTGC
Statistics
Matches: 561, Mismatches: 164, Indels: 28
0.75 0.22 0.04
Matches are distributed among these distances:
49 34 0.06
50 413 0.74
51 109 0.19
52 5 0.01
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (50 bp):
GTCGGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTTTTTAACTGCAAT
Found at i:52527485 original size:100 final size:100
Alignment explanation
Indices: 52527310--52528125 Score: 1076
Period size: 100 Copynumber: 8.1 Consensus size: 100
52527300 CTGTTCGTCG
* * *
52527310 GGGAAGTAAGATTCACTGTTGTGGCTTCAATCTTTTTAACTGCATTGTCGGGGAAGCAAGATTCG
1 GGGAAGTAAGATTCACTGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
** * * * *
52527375 CTATTATAGCTTCAACCTGTTCCACTACACCGCTA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
* * *
52527410 GGGAAGTAAGATTCGCTGTTGTGGCTTCAATCTTTTTAATTGTAATGTCGGGGAAGCAAGATTCG
1 GGGAAGTAAGATTCACTGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
* ** *
52527475 CCATTGTAGCTTCAATAAGTTCTACTGCACCGCCA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
* * * *
52527510 GGGAAGTAAGATTCACCGTTGAGGCTTCAATCTTTTTAATTTCAATGTCAGGGAAGCAAGATTCA
1 GGGAAGTAAGATTCACTGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
52527575 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
* * * * * * * *
52527610 GTGAAGTAAGATTCACCGTTGTAGCTTCAATCTTTTTAAATGCAATGTTGGGAAAGTAAGATTCG
1 GGGAAGTAAGATTCACTGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
*
52527675 CCGTTGTAGCTTCAATCTGTTCCACTGCACCACCTA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCC-A
* * * *
52527711 GGGAAGTATGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGTGGAAGCAAGATTCA
1 GGGAAGTAAGATTCACTGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
* *
52527776 CCGTTGTAGCTTTAATCTGTTCCATTGCACCGCCA
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
** *
52527811 GGGAAGTAAGATTCACCATTGTGGCTTCAATCTTTTTAATTGCAATATCGGGGAAGCAAGATTCA
1 GGGAAGTAAGATTCACTGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
* * **
52527876 CCGTTGTAGCATCAATCTGTTCCACTGCACCATCTG
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACC-GCCA
* * * * *
52527912 GGGAAGTAAGATTCACTGTTGTAGCTTCAATCTTTTCAACTGCAATGTCGAGGAAGCAAGATTCG
1 GGGAAGTAAGATTCACTGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
*
52527977 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCT
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
* * * * * *
52528012 GGGAAAGTGAGATTCGCTGTTGTAGCTTCAAT-ATTTTAATTGCAATATCGGGGAAGCAAGATTT
1 GGG-AAGTAAGATTCACTGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTC
* *
52528076 ACCGTTGCAGCTTTAATCTGTTCCACTGCACCGCCA
65 ACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
* *
52528112 GTGAAATAAGATTC
1 GGGAAGTAAGATTC
52528126 GCTGCCTTCG
Statistics
Matches: 628, Mismatches: 85, Indels: 7
0.87 0.12 0.01
Matches are distributed among these distances:
99 9 0.01
100 418 0.67
101 201 0.32
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (100 bp):
GGGAAGTAAGATTCACTGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCA
CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
Found at i:52527796 original size:201 final size:200
Alignment explanation
Indices: 52527310--52528125 Score: 1071
Period size: 201 Copynumber: 4.1 Consensus size: 200
52527300 CTGTTCGTCG
* * *
52527310 GGGAAGTAAGATTCACTGTTGTGGCTTCAATCTTTTTAACTGCATTGTCGGGGAAGCAAGATTCG
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAACTGCAATGTC-GGGAAGCAAGATTCA
** * * * * * * *
52527375 CTATTATAGCTTCAACCTGTTCCACTACACCGCTAGGGAAGTAAGATTCGCTGTTGTGGCTTCAA
65 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTAGCTTCAA
* * * * ** *
52527440 TCTTTTTAATTGTAATGTCGGGGAAGCAAGATTCGCCATTGTAGCTTCAATAAGTTCTACTGCAC
130 TCTTTTTAATTGCAATATCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCAC
*
52527505 CGCC-A
195 CACCTA
* * *
52527510 GGGAAGTAAGATTCACCGTTGAGGCTTCAATCTTTTTAATTTCAATGTCAGGGAAGCAAGATTCA
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAACTGCAATGTC-GGGAAGCAAGATTCA
*
52527575 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGTGAAGTAAGATTCACCGTTGTAGCTTCAA
65 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTAGCTTCAA
* * * * * *
52527640 TCTTTTTAAATGCAATGTTGGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCAC
130 TCTTTTTAATTGCAATATCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCAC
52527705 CACCTA
195 CACCTA
* * *
52527711 GGGAAGTATGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGTGGAAGCAAGATTCA
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAACTGCAATGTCG-GGAAGCAAGATTCA
* * * *
52527776 CCGTTGTAGCTTTAATCTGTTCCATTGCACCGCCAGGGAAGTAAGATTCACCATTGTGGCTTCAA
65 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTAGCTTCAA
*
52527841 TCTTTTTAATTGCAATATCGGGGAAGCAAGATTCACCGTTGTAGCATCAATCTGTTCCACTGCAC
130 TCTTTTTAATTGCAATATCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCAC
* *
52527906 CATCTG
195 CACCTA
* * * *
52527912 GGGAAGTAAGATTCACTGTTGTAGCTTCAATCTTTTCAACTGCAATGTCGAGGAAGCAAGATTCG
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAACTGCAATGTCG-GGAAGCAAGATTCA
* * * *
52527977 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAAGTGAGATTCGCTGTTGTAGCTTCA
65 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGG-AAGTAAGATTCACCGTTGTAGCTTCA
* * * *
52528042 AT-ATTTTAATTGCAATATCGGGGAAGCAAGATTTACCGTTGCAGCTTTAATCTGTTCCACTGCA
129 ATCTTTTTAATTGCAATATCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCA
*
52528106 CCGCC-A
194 CCACCTA
* *
52528112 GTGAAATAAGATTC
1 GGGAAGTAAGATTC
52528126 GCTGCCTTCG
Statistics
Matches: 542, Mismatches: 71, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
200 185 0.34
201 334 0.62
202 23 0.04
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (200 bp):
GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAACTGCAATGTCGGGAAGCAAGATTCAC
CGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTAGCTTCAAT
CTTTTTAATTGCAATATCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACC
ACCTA
Found at i:52528189 original size:44 final size:44
Alignment explanation
Indices: 52528131--52528337 Score: 115
Period size: 44 Copynumber: 4.7 Consensus size: 44
52528121 GATTCGCTGC
* *
52528131 CTTCGATCTGCTCCACTACTACTTAGGGAGACATGATTTACAAT
1 CTTCGACCTACTCCACTACTACTTAGGGAGACATGATTTACAAT
* * *
52528175 CTTCGACCTACTCCACTACTGCTTAGTGAGATAGAACTGGTGGTTTA-AAT
1 CTTCGACCTACTCCACTACTACTTAG-G-G--AG-AC--ATGATTTACAAT
* * * * * * **
52528225 C-T-G--CT--TCC-CTACTATATTTGGAAGATAAGATTCACCGT
1 CTTCGACCTACTCCACTACTA-CTTAGGGAGACATGATTTACAAT
* * * * *
52528263 TTTTGATCTGCTCCACTACTACTTAGGGAGACAGGATTTACAAT
1 CTTCGACCTACTCCACTACTACTTAGGGAGACATGATTTACAAT
*
52528307 CTTCGACCTACTCCACTACTGCTTAGGGAGA
1 CTTCGACCTACTCCACTACTACTTAGGGAGA
52528338 TAGGACTAGT
Statistics
Matches: 117, Mismatches: 30, Indels: 32
0.65 0.17 0.18
Matches are distributed among these distances:
37 4 0.03
38 1 0.01
39 2 0.02
40 3 0.03
42 2 0.02
43 6 0.05
44 73 0.62
45 7 0.06
46 3 0.03
48 3 0.03
49 3 0.03
50 4 0.03
51 6 0.05
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (44 bp):
CTTCGACCTACTCCACTACTACTTAGGGAGACATGATTTACAAT
Found at i:52528327 original size:132 final size:132
Alignment explanation
Indices: 52528132--52528484 Score: 564
Period size: 132 Copynumber: 2.7 Consensus size: 132
52528122 ATTCGCTGCC
*
52528132 TTCGATCTGCTCCACTACTACTTAGGGAGACATGATTTACAATCTTCGACCTACTCCACTACTGC
1 TTCGATCTGCTCCACTACTACTTAGGGAGACAGGATTTACAATCTTCGACCTACTCCACTACTGC
* * *
52528197 TTAGTGAGATAGAACTGGTGGTTTAAATCTGCTTCCCTACTATATTTG-GAAGATAAGATTCACC
66 TTAGGGAGATAGGACTGGTGGTTTAAATCTGCTTCCCTACTACA-TTGAGAAGATAAGATTCACC
* *
52528261 GTT
130 ATA
*
52528264 TTTGATCTGCTCCACTACTACTTAGGGAGACAGGATTTACAATCTTCGACCTACTCCACTACTGC
1 TTCGATCTGCTCCACTACTACTTAGGGAGACAGGATTTACAATCTTCGACCTACTCCACTACTGC
*
52528329 TTAGGGAGATAGGACTAGTGGTTTAAATCTGCTTCCCTACTACATTGAGAAGATAAGATTCACCA
66 TTAGGGAGATAGGACTGGTGGTTTAAATCTGCTTCCCTACTACATTGAGAAGATAAGATTCACCA
52528394 TA
131 TA
* * * * *
52528396 TTCGATTTTCTCCACTACTACTTAGGGAGACAGGATCTAAAATCTTTGACCTACTCCACTACTGC
1 TTCGATCTGCTCCACTACTACTTAGGGAGACAGGATTTACAATCTTCGACCTACTCCACTACTGC
*
52528461 TCAGGGAGATAGGACTGGTGGTTT
66 TTAGGGAGATAGGACTGGTGGTTT
52528485 CACCGATCTG
Statistics
Matches: 204, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
131 3 0.01
132 201 0.99
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.32
Consensus pattern (132 bp):
TTCGATCTGCTCCACTACTACTTAGGGAGACAGGATTTACAATCTTCGACCTACTCCACTACTGC
TTAGGGAGATAGGACTGGTGGTTTAAATCTGCTTCCCTACTACATTGAGAAGATAAGATTCACCA
TA
Found at i:52529737 original size:25 final size:22
Alignment explanation
Indices: 52529706--52529757 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
52529696 TGGCCTCTCA
*
52529706 TTTTTC-T-TTTTCTTATGTTCT
1 TTTTTCTTCTTTTCTT-TATTCT
52529727 TTCTTTCTTCTTTTCTTTATTCT
1 TT-TTTCTTCTTTTCTTTATTCT
52529750 TTTTTCTT
1 TTTTTCTT
52529758 TAAATATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 2 0.07
22 10 0.37
23 8 0.30
24 7 0.26
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTTCTTCTTTTCTTTATTCT
Found at i:52532438 original size:12 final size:12
Alignment explanation
Indices: 52532407--52532440 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
52532397 CTTTTCTAGT
52532407 TGTTCTTGCATC
1 TGTTCTTGCATC
**
52532419 TGGGCTTGCATC
1 TGTTCTTGCATC
52532431 TGTTCTTGCA
1 TGTTCTTGCA
52532441 ATTGCTCTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.09, C:0.24, G:0.24, T:0.44
Consensus pattern (12 bp):
TGTTCTTGCATC
Found at i:52557942 original size:23 final size:20
Alignment explanation
Indices: 52557916--52557962 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
52557906 TAATTTTTCC
*
52557916 ATTAATCTTTTAAAAATAATTTA
1 ATTAAT-TTTAAAAAAT-A-TTA
52557939 ATT-ATTTTAAAAAATATTA
1 ATTAATTTTAAAAAATATTA
52557958 ATTAA
1 ATTAA
52557963 AACATTGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 6 0.27
20 2 0.09
21 9 0.41
22 2 0.09
23 3 0.14
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTAATTTTAAAAAATATTA
Found at i:52557950 original size:19 final size:20
Alignment explanation
Indices: 52557923--52557961 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
52557913 TCCATTAATC
52557923 TTTTAAAAATAAT-TTAATTA
1 TTTTAAAAA-AATATTAATTA
52557943 TTTT-AAAAAATATTAATTA
1 TTTTAAAAAAATATTAATTA
52557962 AAACATTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 11 0.61
20 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTTAAAAAAATATTAATTA
Found at i:52561218 original size:4 final size:4
Alignment explanation
Indices: 52561209--52561234 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
52561199 CATTACACTA
52561209 TCAT TCAT TCAT TCAT TCAT TCAT TC
1 TCAT TCAT TCAT TCAT TCAT TCAT TC
52561235 CCTGTCCACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (4 bp):
TCAT
Found at i:52573197 original size:9 final size:9
Alignment explanation
Indices: 52573171--52573238 Score: 63
Period size: 9 Copynumber: 7.7 Consensus size: 9
52573161 TTTTCATTCA
52573171 CTTTTATTCT
1 CTTTT-TTCT
52573181 -TTTATTTCT
1 CTTT-TTTCT
52573190 CTTTTTTCT
1 CTTTTTTCT
52573199 -TTTTTT-T
1 CTTTTTTCT
52573206 CTTTTTT-T
1 CTTTTTTCT
52573214 CTTTTCTTCT
1 CTTTT-TTCT
* *
52573224 TTTTTTTTT
1 CTTTTTTCT
52573233 CTTTTT
1 CTTTTT
52573239 GAGAAGGCGG
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
7 1 0.02
8 18 0.36
9 22 0.44
10 9 0.18
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (9 bp):
CTTTTTTCT
Found at i:52573238 original size:8 final size:8
Alignment explanation
Indices: 52573171--52573229 Score: 73
Period size: 8 Copynumber: 7.0 Consensus size: 8
52573161 TTTTCATTCA
*
52573171 CTTTTATT
1 CTTTTTTT
52573179 CTTTTATTT
1 CTTTT-TTT
52573188 CTCTTTTTT
1 CT-TTTTTT
52573197 CTTTTTTTT
1 C-TTTTTTT
52573206 CTTTTTTT
1 CTTTTTTT
*
52573214 CTTTTCTT
1 CTTTTTTT
52573222 CTTTTTTT
1 CTTTTTTT
52573230 TTTCTTTTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
8 26 0.58
9 15 0.33
10 4 0.09
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.81
Consensus pattern (8 bp):
CTTTTTTT
Found at i:52574671 original size:31 final size:32
Alignment explanation
Indices: 52574633--52574692 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
52574623 ATGATTAAAA
*
52574633 TATCATTATA-TT-AATTTGTTAAAATATTGTT
1 TATCATTATATTTAAAATT-TTAAAATATTGTT
52574664 TATCATTATATTTAAAATTTTAAAATATT
1 TATCATTATATTTAAAATTTTAAAATATT
52574693 TTGTTTATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 10 0.38
32 12 0.46
33 4 0.15
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (32 bp):
TATCATTATATTTAAAATTTTAAAATATTGTT
Found at i:52575855 original size:27 final size:30
Alignment explanation
Indices: 52575779--52575857 Score: 85
Period size: 27 Copynumber: 2.8 Consensus size: 30
52575769 ACAATTGGAC
** *
52575779 CTAAATTTTTAAATTTAAAAAGTAGAAGGA
1 CTAAATTCCTAAATATAAAAAGTAGAAGGA
* *
52575809 TTAAATTCCTAAAAAT-AAAAGTAG-A-GA
1 CTAAATTCCTAAATATAAAAAGTAGAAGGA
52575836 CTAAATTCC-AAATATAAAAAGT
1 CTAAATTCCTAAATATAAAAAGT
52575858 GTATAGAGAT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
26 5 0.12
27 16 0.39
28 1 0.02
29 8 0.20
30 11 0.27
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (30 bp):
CTAAATTCCTAAATATAAAAAGTAGAAGGA
Found at i:52576169 original size:5 final size:5
Alignment explanation
Indices: 52576161--52576190 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
52576151 AATAAAATTC
52576161 GATTT GATTT GATTT GATTT GATTT GATTT
1 GATTT GATTT GATTT GATTT GATTT GATTT
52576191 AAACAATAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
GATTT
Found at i:52576920 original size:111 final size:108
Alignment explanation
Indices: 52576802--52577722 Score: 991
Period size: 111 Copynumber: 8.5 Consensus size: 108
52576792 AAGAAAAACG
*
52576802 AAAAAAAAAA-TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTTTAAAAAAATT
1 AAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAA-TTTAAAAAAAATT
* *
52576866 CTTTTTTTTTCGTGTCAGAATCATATATAAATATACGGAAAAAAAAAAG
65 C-TTTTTTTTCGTGTCAGAATCAGATATAAATATAC-G---AAAAAAAT
* * *
52576915 AAAAAAAAATTATTTTGGGTGTTGGCCTGTTAATGGCCGGCACCCAATACAAATTCTAGAAAAAA
1 AAAAAAAAA--ATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATT-T--AAAAAA
*
52576980 AATTTCTTTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAATAT
61 AA-TTC-TTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAAT
* * * *
52577030 -AAAAAAATATTTTGGGTGCTAGCCTATCAATGGCCGGCACCTAGTACAAA-TTAAAAAAAA---
1 AAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAAAATTC
***
52577090 --AAATTTCGTGTCAGAATCAGATATAAATATACGAAAAAAAT
66 TTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAAT
** * * *
52577131 AAAAAAATTTATTTTAGGTGCTGGTCTGTCAATGGCCGGCACCTAGTACAAATTTAAAAAAAATT
1 AAAAAAA-AAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAAAATT
*
52577196 CTTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAATTTT
65 CTTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAA--AT
* * *
52577242 AAAAAAATAATTTTTGGGTGCTGGCCTGTCAATAGCCGGTACCCAGTACAAATTTAAAAAAAATT
1 AAAAAAA-AAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAAAATT
*
52577307 CTTTTTTTTCGTGTCAGAATCAAATATAAATATACGAAAAAAATT
65 CTTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAA-T
52577352 AAAAAATATATATATTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAA
1 AAAAAA-A-A-A-A--TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAA
*
52577417 AAATGTTTTTCTTTTTTTTTCGTGTCAGAATTAGATATAAATATACGAAAAAAATTTT
60 AAA-----TTC-TTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAA---T
* * * *
52577475 AAAAAAAAACTTTTTTGGGTGCTGGACTGTCAATGACCGGCACCCAGTACAAATTTTAAAAAAA-
1 AAAAAAAAA--ATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAAAAT
* *
52577539 --------TTCATGTCAAAATCAGATATAAATATACGAAAAAAAT
64 TCTTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAAT
*
52577576 AAATAAAAAAATTTT-GGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTAAAAAAAA--
1 AAA-AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAAAATT
*
52577638 -----ATTT-GTGTCAGAATCAGATATAAATATACGAAAAAAAT
65 CTTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAAT
* * *
52577676 --TAAAAAAA-TTTGGGTGATGGCCTGTCAATGGTCGGCACCCAGTACAA
1 AAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAA
52577723 TCATATATAT
Statistics
Matches: 713, Mismatches: 59, Indels: 88
0.83 0.07 0.10
Matches are distributed among these distances:
96 3 0.00
97 40 0.06
99 43 0.06
100 36 0.05
101 43 0.06
102 12 0.02
103 39 0.05
104 43 0.06
108 8 0.01
109 36 0.05
110 8 0.01
111 103 0.14
112 37 0.05
113 9 0.01
114 7 0.01
115 59 0.08
116 38 0.05
118 8 0.01
119 86 0.12
120 4 0.01
121 42 0.06
122 1 0.00
123 8 0.01
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (108 bp):
AAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAAAATTC
TTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAAAT
Found at i:52577635 original size:99 final size:99
Alignment explanation
Indices: 52577439--52577723 Score: 373
Period size: 97 Copynumber: 2.8 Consensus size: 99
52577429 TTTTTTTTCG
* * *
52577439 TGTCAGAATTAGATATAAATATACGAAAAAAATTTTAAA-AAAAAACTTTTTTGGGTGCTGGACT
1 TGTCAGAATCAGATATAAATATACGAAAAAAA---TAAATAAAAAA--ATTTT-GGTGCTGGCCT
*
52577503 GTCAATGACCGGCACCCAGTACAAATTTT-AAAAAAATTCA
60 GTCAATGGCCGGCACCCAGTAC-AATTTTAAAAAAAATTCA
*
52577543 TGTCAAAATCAGATATAAATATACGAAAAAAATAAATAAAAAAATTTTGGTGCTGGCCTGTCAAT
1 TGTCAGAATCAGATATAAATATACGAAAAAAATAAATAAAAAAATTTTGGTGCTGGCCTGTCAAT
**
52577608 GGCCGGCACCCAGTACAATTTTAAAAAAAAATTTG
66 GGCCGGCACCCAGTACAATTTT-AAAAAAAATTCA
* *
52577643 TGTCAGAATCAGATATAAATATACGAAAAAAAT---TAAAAAAATTTGGGTGATGGCCTGTCAAT
1 TGTCAGAATCAGATATAAATATACGAAAAAAATAAATAAAAAAATTTTGGTGCTGGCCTGTCAAT
*
52577705 GGTCGGCACCCAGTACAAT
66 GGCCGGCACCCAGTACAAT
52577724 CATATATATA
Statistics
Matches: 167, Mismatches: 11, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
97 45 0.27
98 6 0.04
99 31 0.19
100 45 0.27
101 4 0.02
102 6 0.04
104 30 0.18
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (99 bp):
TGTCAGAATCAGATATAAATATACGAAAAAAATAAATAAAAAAATTTTGGTGCTGGCCTGTCAAT
GGCCGGCACCCAGTACAATTTTAAAAAAAATTCA
Found at i:52582637 original size:108 final size:107
Alignment explanation
Indices: 52582413--52583223 Score: 789
Period size: 108 Copynumber: 7.9 Consensus size: 107
52582403 ATATGACTTT
* * * **
52582413 GTATATTTGTATATGATTCTGACACG-AAAAAAAA-A-----TTTAAATTTGTACTGGAAGCCGG
1 GTATATTTATATTTGATTCTGACACGAAAAAAAAAGATTTTTTTTTAATTTGTACTGGGTGCCGG
* * *
52582471 CCATT-ACCAAGCCTGCACTC-AAATTTTTTTTTATTTTTTTC
66 CCATTGA-CAGGCCAGCACCCAAAATTTTTTTTTATTTTTTTC
* * *
52582512 GTATATGTATATCTGATTTTGACACGAAAAAAATAAGATTTTTTTTTAATTTGTACTGGGTGCCG
1 GTATATTTATATTTGATTCTGACACGAAAAAAA-AAGATTTTTTTTTAATTTGTACTGGGTGCCG
* *
52582577 GCCATTGTCAGGTCAGCACCCAAAATTTTTTTTTATTTTTTTC
65 GCCATTGACAGGCCAGCACCCAAAATTTTTTTTTATTTTTTTC
* * *
52582620 GTATATTTATATCTGATTCTGACACGAAAAAAATA-ATTTTTTTTAAAAATTTGTACTGGGTGCC
1 GTATATTTATATTTGATTCTGACACGAAAAAAAAAGATTTTTTTT--TAATTTGTACTGGGTGCC
* * *
52582684 AGCCATTGATAGGCCTGCACCCAAAATTTTTTTTTATTTTTTTC
64 GGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTATTTTTTTC
* * * * *
52582728 GTATATTTATATATGATTCTG--AC-----AATAA-ATTTTTTTTAAATTCGTACTGGGTGCTGG
1 GTATATTTATATTTGATTCTGACACGAAAAAAAAAGATTTTTTTTTAATTTGTACTGGGTGCCGG
* *
52582785 CCATTGACAGGCTAACACCC--AA-----TTTT-TTTTTTTC
66 CCATTGACAGGCCAGCACCCAAAATTTTTTTTTATTTTTTTC
**
52582819 GTATATTTATATTTGATTCTGACACGAAAAAAAAAGAATTTTTTTTTAAATTTTGTACTAAGTGC
1 GTATATTTATATTTGATTCTGACACGAAAAAAAAAG-ATTTTTTTTT-AA-TTTGTACTGGGTGC
* *
52582884 CGACCATTGACAGACCAGCA-CCAAAA-------TT-TTTTTTTC
63 CGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTATTTTTTTC
* * * * * *
52582920 GTATATTTATATATGATTCTGACATGAAAAAAAAAGAATTTTTTTTAATTTCTACTGGTTGCTGG
1 GTATATTTATATTTGATTCTGACACGAAAAAAAAAGATTTTTTTTTAATTTGTACTGGGTGCCGG
* * *
52582985 CCATTGACAGGCAACCA-CCAAACTTTTTTTTTATTTTTTTC
66 CCATTGACAGGCCAGCACCCAAAATTTTTTTTTATTTTTTTC
* *
52583026 GTATATTTATATTTGATTCTGACACGAAAAAAAAATAATTTTTTTTTAAATTTGTACTGGGTTCC
1 GTATATTTATATTTGATTCTGACACGAAAAAAAAA-GATTTTTTTTT-AATTTGTACTGGGTGCC
* *
52583091 AGCCATTGACAGGACAGCA-CC--AA-------TT-TTTTTTTC
64 GGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTATTTTTTTC
* *
52583124 GTATATTTATATTTGATTTTGACACGAAAAAAAAGAAATTTTTTTTTAAATTTGTACTGGGTGCC
1 GTATATTTATATTTGATTCTGACACGAAAAAAAA-AGATTTTTTTTT-AATTTGTACTGGGTGCC
52583189 GGCCATTGACAGGCCAGCACCCAAAATTTTTTTTT
64 GGCCATTGACAGGCCAGCACCCAAAATTTTTTTTT
52583224 CGTTTTTCTT
Statistics
Matches: 594, Mismatches: 72, Indels: 83
0.79 0.10 0.11
Matches are distributed among these distances:
91 28 0.05
92 4 0.01
93 2 0.00
97 2 0.00
98 120 0.20
99 62 0.10
100 24 0.04
101 64 0.11
102 27 0.05
103 2 0.00
105 2 0.00
106 53 0.09
107 44 0.07
108 160 0.27
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (107 bp):
GTATATTTATATTTGATTCTGACACGAAAAAAAAAGATTTTTTTTTAATTTGTACTGGGTGCCGG
CCATTGACAGGCCAGCACCCAAAATTTTTTTTTATTTTTTTC
Found at i:52583012 original size:98 final size:100
Alignment explanation
Indices: 52582612--52583226 Score: 612
Period size: 98 Copynumber: 6.1 Consensus size: 100
52582602 TTTTTTTTTA
* * *
52582612 TTTTTTTCGTATATTTATATCTGATTCTGACACG--AAAAAAATAATTTTTTTTAAAAATTTGTA
1 TTTTTTTCGTATATTTATATTTGATTCTGACACGAAAAAAAAAGAATTTTTTTT-TAAATTTGTA
* * **
52582675 CTGGGTGCCAGCCATTGATAGGCCTGCACCCAAAATT
65 CTGGGTGCCGGCCATTGACAGGCAAGCA-CCAAAATT
** * * * ** * * *
52582712 TTTTTTTATTTTTTTCGTATATTT-ATATATGATTCTG---ACAATA-AA-TTTTTTTTAAATTC
1 TTTTTTTCGTATATT--TATATTTGAT-TCTGACAC-GAAAAAAAAAGAATTTTTTTTTAAATTT
* **
52582771 GTACTGGGTGCTGGCCATTGACAGGCTAA-CACCCAATTTT
62 GTACTGGGTGCCGGCCATTGACAGGC-AAGCA-CCAAAATT
52582811 TTTTTTTCGTATATTTATATTTGATTCTGACACGAAAAAAAAAGAATTTTTTTTTAAATTTTGTA
1 TTTTTTTCGTATATTTATATTTGATTCTGACACGAAAAAAAAAGAATTTTTTTTTAAA-TTTGTA
** * * *
52582876 CTAAGTGCCGACCATTGACAGACCAGCACCAAAATT
65 CTGGGTGCCGGCCATTGACAGGCAAGCACCAAAATT
* * *
52582912 TTTTTTTCGTATATTTATATATGATTCTGACATGAAAAAAAAAGAA-TTTTTTTT-AATTTCTAC
1 TTTTTTTCGTATATTTATATTTGATTCTGACACGAAAAAAAAAGAATTTTTTTTTAAATTTGTAC
* * * *
52582975 TGGTTGCTGGCCATTGACAGGCAACCACCAAACTTTTTTTTT
66 TGGGTGCCGGCCATTGACAGGCAAGCACCAAA-------ATT
*
52583017 ATTTTTTTCGTATATTTATATTTGATTCTGACACGAAAAAAAAATAATTTTTTTTTAAATTTGTA
1 -TTTTTTTCGTATATTTATATTTGATTCTGACACGAAAAAAAAAGAATTTTTTTTTAAATTTGTA
* *
52583082 CTGGGTTCCAGCCATTGACAGG-ACAGCACC--AATT
65 CTGGGTGCCGGCCATTGACAGGCA-AGCACCAAAATT
*
52583116 TTTTTTTCGTATATTTATATTTGATTTTGACACG-AAAAAAAAGAAATTTTTTTTTAAATTTGTA
1 TTTTTTTCGTATATTTATATTTGATTCTGACACGAAAAAAAAAG-AATTTTTTTTTAAATTTGTA
*
52583180 CTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATT
65 CTGGGTGCCGGCCATTGACAGGCAAGCA-CCAAAATT
52583217 TTTTTTTCGT
1 TTTTTTTCGT
52583227 TTTTCTTTTT
Statistics
Matches: 422, Mismatches: 64, Indels: 57
0.78 0.12 0.10
Matches are distributed among these distances:
96 1 0.00
97 20 0.05
98 109 0.26
99 58 0.14
100 28 0.07
101 80 0.19
102 40 0.09
103 1 0.00
105 2 0.00
106 44 0.10
107 9 0.02
108 30 0.07
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (100 bp):
TTTTTTTCGTATATTTATATTTGATTCTGACACGAAAAAAAAAGAATTTTTTTTTAAATTTGTAC
TGGGTGCCGGCCATTGACAGGCAAGCACCAAAATT
Found at i:52583248 original size:17 final size:16
Alignment explanation
Indices: 52583216--52583246 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
52583206 CACCCAAAAT
52583216 TTTTTTTTCGTTTTTC
1 TTTTTTTTCGTTTTTC
52583232 TTTTTTTTCGTTTTT
1 TTTTTTTTCGTTTTT
52583247 TCGTATATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (16 bp):
TTTTTTTTCGTTTTTC
Found at i:52584086 original size:21 final size:22
Alignment explanation
Indices: 52584062--52584102 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
52584052 TTGTTGTTGG
52584062 ATATCATAAATG-ATCACATCA
1 ATATCATAAATGCATCACATCA
*
52584083 ATATCCTAAATGCATCACAT
1 ATATCATAAATGCATCACAT
52584103 TTACCACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.44, C:0.22, G:0.05, T:0.29
Consensus pattern (22 bp):
ATATCATAAATGCATCACATCA
Found at i:52585897 original size:21 final size:21
Alignment explanation
Indices: 52585873--52585935 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
52585863 CGGGAACCCG
52585873 TAAGGGTTAAACAGAAGCTCA
1 TAAGGGTTAAACAGAAGCTCA
* * *
52585894 TAAGAGCTT-AACAGAAACCCA
1 TAAG-GGTTAAACAGAAGCTCA
*
52585915 TAAGGGTTAAACTGAAGCTCA
1 TAAGGGTTAAACAGAAGCTCA
52585936 AAAGTGCTGA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
20 3 0.09
21 27 0.82
22 3 0.09
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (21 bp):
TAAGGGTTAAACAGAAGCTCA
Found at i:52585913 original size:42 final size:42
Alignment explanation
Indices: 52585867--52585987 Score: 129
Period size: 42 Copynumber: 2.9 Consensus size: 42
52585857 GCTAAACGGG
*
52585867 AACCCGTAAGGGTTAAACAGAAGCTCATAAGAGCTTAACAGA
1 AACCCGTAAGGGTTAAACTGAAGCTCATAAGAGCTTAACAGA
* * * * **
52585909 AACCCATAAGGGTTAAACTGAAGCTCAAAAGTGCTGAATTGA
1 AACCCGTAAGGGTTAAACTGAAGCTCATAAGAGCTTAACAGA
* * *
52585951 AACCTAG-AAGGGTTAAACTGAAACTCATATGAG-TTAA
1 AACC-CGTAAGGGTTAAACTGAAGCTCATAAGAGCTTAA
52585988 TTGAAGCTCA
Statistics
Matches: 64, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
41 3 0.05
42 61 0.95
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.21
Consensus pattern (42 bp):
AACCCGTAAGGGTTAAACTGAAGCTCATAAGAGCTTAACAGA
Found at i:52590725 original size:13 final size:13
Alignment explanation
Indices: 52590701--52590734 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
52590691 TTTAAGCATG
52590701 ATATAA-AAAAAA
1 ATATAATAAAAAA
52590713 ATATAATAAAAAA
1 ATATAATAAAAAA
*
52590726 TTATAATAA
1 ATATAATAA
52590735 GATTAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
ATATAATAAAAAA
Found at i:52590731 original size:10 final size:12
Alignment explanation
Indices: 52590701--52590763 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
52590691 TTTAAGCATG
*
52590701 ATATAAAAAAAA
1 ATATAATAAAAA
52590713 ATATAATAAAAA
1 ATATAATAAAAA
*
52590725 AT-T-ATAATAAG
1 ATATAATAA-AAA
52590736 AT-TAATATTAAAA
1 ATATAATA--AAAA
*
52590749 ATATAATAATAA
1 ATATAATAAAAA
52590761 ATA
1 ATA
52590764 CAAATTGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 4 0.10
11 6 0.14
12 22 0.52
13 4 0.10
14 6 0.14
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (12 bp):
ATATAATAAAAA
Done.