Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 178 of 211
Found at i:55291337 original size:11 final size:11
Alignment explanation
Indices: 55291316--55291348 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
55291306 AAGGGATGAC
55291316 AAAAAAA-AAA
1 AAAAAAACAAA
*
55291326 ACAAAAACAAA
1 AAAAAAACAAA
55291337 AAAAAAACAAA
1 AAAAAAACAAA
55291348 A
1 A
55291349 TCTACCAGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:55293161 original size:44 final size:44
Alignment explanation
Indices: 55293112--55293432 Score: 130
Period size: 44 Copynumber: 7.3 Consensus size: 44
55293102 CCCTGGACAA
*
55293112 TAGTGGAATAGATTGAAGATTTCAGATATTATCTCCCTAAGCAG
1 TAGTGGAGTAGATTGAAGATTTCAGATATTATCTCCCTAAGCAG
* * * * * * **
55293156 TAGTGGAGCAGATCGAAGATTGCGGATTTTACCTCCCT--GTGG
1 TAGTGGAGTAGATTGAAGATTTCAGATATTATCTCCCTAAGCAG
* * * * *
55293198 TTACAGTGGAGTACATTGAAG---CCA-ATAATTCTACTTCCCTGAGCAA
1 -T--AGTGGAGTAGATTGAAGATTTCAGAT-ATTAT-C-TCCCTAAGCAG
* * *
55293244 CAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAG
1 TAGTGGAGTAGATTGAAGATTTCAGATATTATCTCCCTAAGCAG
* * ** * * * **
55293288 TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCT--GTGG
1 TAGTGGAGTAGATTGAAGATTTCAGATATTATCTCCCTAAGCAG
* * *
55293330 TTACAGTGGAGTACATTGAAG---CCAG-TAATTATACTTCCCTGAA-CAA
1 -T--AGTGGAGTAGATTGAAGATTTCAGAT-ATTAT-C-TCCCT-AAGCAG
* *
55293376 CAGTGGAATAGATTGAAGATTTCAGATCA-TATCTCCCTAAGCAG
1 TAGTGGAGTAGATTGAAGATTTCAGAT-ATTATCTCCCTAAGCAG
*
55293420 TAGTGGAGCAGAT
1 TAGTGGAGTAGAT
55293433 CGAAAATGGC
Statistics
Matches: 193, Mismatches: 58, Indels: 52
0.64 0.19 0.17
Matches are distributed among these distances:
41 3 0.02
42 12 0.06
43 36 0.19
44 96 0.50
45 30 0.16
46 12 0.06
47 4 0.02
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (44 bp):
TAGTGGAGTAGATTGAAGATTTCAGATATTATCTCCCTAAGCAG
Found at i:55293204 original size:132 final size:132
Alignment explanation
Indices: 55293030--55293793 Score: 1210
Period size: 132 Copynumber: 5.8 Consensus size: 132
55293020 TTGACAGCGA
* *
55293030 AGCAGATCAAAGATGGCGGATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
55293095 TCTACTTCCCTGGACAATAGTGGAATAGATTGAAGATTTCAGATATTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
55293160 GG
131 GG
* *
55293162 AGCAGATCGAAGATTGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAATAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
55293227 TCTACTTCCCT-GAGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAG
66 TCTACTTCCCTGGA-CAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAG
55293291 TGG
130 TGG
55293294 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * *
55293359 TATACTTCCCTGAACAACAGTGGAATAGATTGAAGATTTCAGATCATATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
55293424 GG
131 GG
* * * *
55293426 AGCAGATCGAAAATGGCGGATTTTACCTCTCTGTGATTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * * * * * *
55293491 TTTACTTTCATAGACAACAGTGGAATAGATTGAAGATTTCAGGTCTTATCTCCTTAAGTAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
55293556 GG
131 GG
* * *
55293558 AGCAGATCGAAGATGGAGGATTTTACCTCCTTGTGGTTACATTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
55293623 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGGTCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
55293688 GG
131 GG
* * *
55293690 AACAGATCGAAGATGACGGATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA-
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * *
55293754 TCATA-TCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTT
66 TC-TACT-TCCCTGGACAACAGTGGAATAGATTGAAGATTT
55293794 TAAGTCCTAT
Statistics
Matches: 584, Mismatches: 44, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
131 5 0.01
132 578 0.99
133 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (132 bp):
AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
GG
Found at i:55294144 original size:19 final size:19
Alignment explanation
Indices: 55294117--55294209 Score: 132
Period size: 19 Copynumber: 4.9 Consensus size: 19
55294107 AATCTTTAGG
55294117 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
55294136 GATACGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
55294155 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
55294174 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
55294193 GATATGCAATCTTAGAT
1 GATATGCAATCTTAGAT
55294210 GATATGATTT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 66 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:55294565 original size:21 final size:21
Alignment explanation
Indices: 55294521--55294565 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
55294511 AGTTGTTTTT
*
55294521 TTTTATTTTTTTAATTTACCA
1 TTTTATTTTTTTAATTTACAA
*
55294542 TTTTATTTATTTTTATTT-CAA
1 TTTTATTT-TTTTAATTTACAA
55294563 TTT
1 TTT
55294566 GGTCTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTATTTTTTTAATTTACAA
Found at i:55298256 original size:132 final size:132
Alignment explanation
Indices: 55298013--55299698 Score: 2773
Period size: 132 Copynumber: 12.8 Consensus size: 132
55298003 TCCATTCCGC
* *
55298013 TTGGGAAGACAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGCAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* * * * *
55298078 TATTCAACCTGCTCCACTACTGCTTAGGGAGATAGGACTAACGGCTTAAATCAT-CTTCTCCACT
66 TCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATC-TGCTTCTCCACT
*
55298142 ATA
130 GTA
* *
55298145 TTGGGAAGATAAGATTCACCATATTCGATTTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* * * * * * *
55298210 TCTTCGACCTAATCCACTACTGCTTAGGGAGATTGGACAAATGGCTTAAATCTGCTTCTCCATTG
66 TCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
55298275 TA
131 TA
* *
55298277 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTATTGCTTAGGGTGACAGAATCTACAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* * **
55298342 TCTTCAACCTATTCTACTACTGTTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
66 TCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
55298407 TA
131 TA
* *
55298409 TTGGGAAGATAAGATTCACCATCTTCGATCTACTCCACTACTGCTTAGGGTGAAAGAATCTGCAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* * * * * *
55298474 TCTTCGAGCTACTCCACTACTGCTTAGGGAGATTGGACAAAATGGCTTAAATCTGCTTCTCCACT
66 TCTTCAACCTACTCCACTACTACTTAGGGTGATAGGAC-TAATGGCTTAAATCTGCTTCTCCACT
55298539 GTA
130 GTA
55298542 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* * * * *
55298607 ACTTCGACCTATTCCACTACTATTTAGAGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
66 TCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
55298672 TA
131 TA
* *
55298674 TTGGGAAGATAAGATTCACCATCTTCAATCTGCTCCACTACTGCTTAGGGTAACAGAATCTGCAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* *
55298739 TCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATGACTTAAATCTGCTTCTTCACTG
66 TCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
55298804 TA
131 TA
*
55298806 TTGGGAAGATAAGATTCACCATCTTCAATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* * * *
55298871 TCTTCAACCGACTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGTTTCACCACTA
66 TCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
55298936 TA
131 TA
*
55298938 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTACAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
55299003 TCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
66 TCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
55299068 TA
131 TA
*
55299070 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAGGGTGACAGAATCTGCAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* *
55299135 TCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATGACTTAAATCTGCTTCTCTACTG
66 TCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
55299200 TA
131 TA
*
55299202 TTGGGAAGATAAGATTCACCATCTTCAATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* *
55299267 TCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGTTTCACCACTG
66 TCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
55299332 TA
131 TA
*
55299334 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATTTGCAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* *
55299399 TCTTCAACCTAATCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATATGCTTCTCCACTG
66 TCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
55299464 TA
131 TA
*
55299466 TTGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* *
55299531 TCTTCAACCTACTCTACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCACCACTG
66 TCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
55299596 TA
131 TA
*
55299598 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAAAATCTGCAA
1 TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
* * *
55299663 TCTTCGACCTATTCCACTACT-GTCTAGGGTGATAGG
66 TCTTCAACCTACTCCACTACTACT-TAGGGTGATAGG
55299699 TTTGTGTCTT
Statistics
Matches: 1453, Mismatches: 98, Indels: 6
0.93 0.06 0.00
Matches are distributed among these distances:
131 2 0.00
132 1330 0.92
133 121 0.08
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (132 bp):
TTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAA
TCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTG
TA
Found at i:55299797 original size:43 final size:43
Alignment explanation
Indices: 55299748--55299885 Score: 136
Period size: 44 Copynumber: 3.2 Consensus size: 43
55299738 CAAGATCTGT
55299748 TGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTG
1 TGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTG
* * * * * * * * *
55299791 TGTCTTCGATCTGCTTCGCTATTAA-GGCAG-GAAGGCAAGATCTG
1 TGTCTTCAACCAGCTCCACTA-CAACCG-AGAG-AGGCAAGGTTTG
*
55299835 CTGTCTTCAACCAGCTCCACTACAACCGAGAGAGACAAGGTTTG
1 -TGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTG
55299879 TGTCTTC
1 TGTCTTC
55299886 GATCTGCTTC
Statistics
Matches: 70, Mismatches: 19, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
43 25 0.36
44 27 0.39
45 18 0.26
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (43 bp):
TGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTG
Found at i:55299801 original size:88 final size:88
Alignment explanation
Indices: 55299696--55299931 Score: 418
Period size: 88 Copynumber: 2.7 Consensus size: 88
55299686 CTAGGGTGAT
* * *
55299696 AGGTTTGTGTCTTCGATCTGCTTCACTGTCAAGGTAGGAAGGCAAGATCTGTTGTCTTCAACCAG
1 AGGTTTGTGTCTTCGATCTGCTTCGCTGTTAAGGCAGGAAGGCAAGATCTGTTGTCTTCAACCAG
*
55299761 CTCCACTACAACCGAGAGAGGCA
66 CTCCACTACAACCGAGAGAGACA
* *
55299784 AGGTTTGTGTCTTCGATCTGCTTCGCTATTAAGGCAGGAAGGCAAGATCTGCTGTCTTCAACCAG
1 AGGTTTGTGTCTTCGATCTGCTTCGCTGTTAAGGCAGGAAGGCAAGATCTGTTGTCTTCAACCAG
55299849 CTCCACTACAACCGAGAGAGACA
66 CTCCACTACAACCGAGAGAGACA
55299872 AGGTTTGTGTCTTCGATCTGCTTCGCTGTTAAGGCAGGAAGGCAAGATCTGTTGTCTTCA
1 AGGTTTGTGTCTTCGATCTGCTTCGCTGTTAAGGCAGGAAGGCAAGATCTGTTGTCTTCA
55299932 CTGATCTGTT
Statistics
Matches: 140, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 140 1.00
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (88 bp):
AGGTTTGTGTCTTCGATCTGCTTCGCTGTTAAGGCAGGAAGGCAAGATCTGTTGTCTTCAACCAG
CTCCACTACAACCGAGAGAGACA
Found at i:55302044 original size:8 final size:8
Alignment explanation
Indices: 55302033--55302069 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
55302023 TTTGACTTTG
55302033 ATTTTTTT
1 ATTTTTTT
55302041 A-TTTTTT
1 ATTTTTTT
55302048 ATTTTTTT
1 ATTTTTTT
55302056 GA-TTTTTT
1 -ATTTTTTT
55302064 ATTTTT
1 ATTTTT
55302070 GATTTTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
7 8 0.31
8 17 0.65
9 1 0.04
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.84
Consensus pattern (8 bp):
ATTTTTTT
Found at i:55302047 original size:7 final size:7
Alignment explanation
Indices: 55302035--55302075 Score: 55
Period size: 7 Copynumber: 5.6 Consensus size: 7
55302025 TGACTTTGAT
55302035 TTTTTTA
1 TTTTTTA
55302042 TTTTTTA
1 TTTTTTA
55302049 TTTTTTTGA
1 -TTTTTT-A
55302058 TTTTTTA
1 TTTTTTA
*
55302065 TTTTTGA
1 TTTTTTA
55302072 TTTT
1 TTTT
55302076 GTTTTGTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
7 18 0.58
8 12 0.39
9 1 0.03
ACGTcount: A:0.12, C:0.00, G:0.05, T:0.83
Consensus pattern (7 bp):
TTTTTTA
Found at i:55302055 original size:30 final size:27
Alignment explanation
Indices: 55302043--55302100 Score: 53
Period size: 30 Copynumber: 2.0 Consensus size: 27
55302033 ATTTTTTTAT
* *
55302043 TTTTTATTTTTTTGATTTTTTATTTTTGA
1 TTTTTTTTTTTTTGATTTGTT-TTTTT-A
*
55302072 TTTTGTTTTGTTTTGATTTTGTTTTTTTA
1 TTTT-TTTTTTTTTGA-TTTGTTTTTTTA
55302101 GTCTGAACTC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
29 5 0.21
30 14 0.58
31 5 0.21
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.79
Consensus pattern (27 bp):
TTTTTTTTTTTTTGATTTGTTTTTTTA
Found at i:55302074 original size:23 final size:24
Alignment explanation
Indices: 55302029--55302075 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
55302019 TATTTTTGAC
*
55302029 TTTGATTTTTTTATTTTTTATTTT
1 TTTGATTTTTTTATTTTTGATTTT
55302053 TTTGA-TTTTTTATTTTTGATTTT
1 TTTGATTTTTTTATTTTTGATTTT
55302076 GTTTTGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.13, C:0.00, G:0.06, T:0.81
Consensus pattern (24 bp):
TTTGATTTTTTTATTTTTGATTTT
Found at i:55302085 original size:23 final size:22
Alignment explanation
Indices: 55302009--55302091 Score: 64
Period size: 23 Copynumber: 3.7 Consensus size: 22
55301999 TCTTCTTTCT
*
55302009 TTTTTTTTTCTATTTTTGACTTTG
1 TTTTGTTTT-TATTTTTGA-TTTG
* *
55302033 -ATT-TTTTTATTTTTTATTT-
1 TTTTGTTTTTATTTTTGATTTG
55302052 TTTTGATTTTTTATTTTTGATTTTG
1 TTTTG--TTTTTATTTTTGA-TTTG
*
55302077 TTTTGTTTTGATTTT
1 TTTTGTTTTTATTTT
55302092 GTTTTTTTAG
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
20 5 0.10
21 8 0.17
22 4 0.08
23 23 0.48
24 3 0.06
25 5 0.10
ACGTcount: A:0.11, C:0.02, G:0.08, T:0.78
Consensus pattern (22 bp):
TTTTGTTTTTATTTTTGATTTG
Found at i:55302092 original size:16 final size:15
Alignment explanation
Indices: 55302021--55302099 Score: 90
Period size: 16 Copynumber: 5.3 Consensus size: 15
55302011 TTTTTTTCTA
* *
55302021 TTTTTGACTTTGATT
1 TTTTTGATTTTGTTT
*
55302036 TTTTT-ATTTTTTATT
1 TTTTTGATTTTGT-TT
*
55302051 TTTTTGATTTT-TTA
1 TTTTTGATTTTGTTT
55302065 TTTTTGATTTTGTTT
1 TTTTTGATTTTGTTT
55302080 TGTTTTGATTTTGTTT
1 T-TTTTGATTTTGTTT
55302096 TTTT
1 TTTT
55302100 AGTCTGAACT
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
14 16 0.29
15 19 0.35
16 20 0.36
ACGTcount: A:0.10, C:0.01, G:0.10, T:0.78
Consensus pattern (15 bp):
TTTTTGATTTTGTTT
Found at i:55302097 original size:44 final size:45
Alignment explanation
Indices: 55302013--55302099 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 45
55302003 CTTTCTTTTT
*
55302013 TTTTTCTATTTTTGACTTTGATTTTTTTATTTTTTATTTTTTTGA
1 TTTTTCTATTTTTGACTTTGATTTTTTTATATTTTATTTTTTTGA
* *
55302058 TTTTT-TATTTTTGATTTTG-TTTTGTTT-TGATTTTGTTTTTTT
1 TTTTTCTATTTTTGACTTTGATTTT-TTTAT-ATTTTATTTTTTT
55302100 AGTCTGAACT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
43 5 0.14
44 27 0.73
45 5 0.14
ACGTcount: A:0.10, C:0.02, G:0.09, T:0.78
Consensus pattern (45 bp):
TTTTTCTATTTTTGACTTTGATTTTTTTATATTTTATTTTTTTGA
Found at i:55304148 original size:19 final size:17
Alignment explanation
Indices: 55304126--55304168 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 17
55304116 GTGAAATTTG
55304126 ATGCATGCAATGAAATGCA
1 ATGCATGC-ATGAAATG-A
55304145 ATGCAGATGCATGAAATGA
1 ATGC--ATGCATGAAATGA
55304164 ATGCA
1 ATGCA
55304169 AAAAAGAGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 1 0.05
19 9 0.41
20 8 0.36
21 4 0.18
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (17 bp):
ATGCATGCATGAAATGA
Found at i:55313905 original size:18 final size:18
Alignment explanation
Indices: 55313884--55313921 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
55313874 CTTCTACCCT
55313884 TTCCCCTTTCCCTTCCCC
1 TTCCCCTTTCCCTTCCCC
*
55313902 TTCCCTTTTCCCTTCCCC
1 TTCCCCTTTCCCTTCCCC
55313920 TT
1 TT
55313922 GGATTGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (18 bp):
TTCCCCTTTCCCTTCCCC
Found at i:55314015 original size:25 final size:25
Alignment explanation
Indices: 55313981--55314030 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
55313971 CAGGTAAGGC
*
55313981 TCCTTCTTCTTCTTCCGTTTTTCAT
1 TCCTTCTTCTTCTTCCGTTCTTCAT
* *
55314006 TCCTTTTTCTTCTTCTGTTCTTCAT
1 TCCTTCTTCTTCTTCCGTTCTTCAT
55314031 CTTCTCTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.04, C:0.30, G:0.04, T:0.62
Consensus pattern (25 bp):
TCCTTCTTCTTCTTCCGTTCTTCAT
Found at i:55317402 original size:15 final size:15
Alignment explanation
Indices: 55317363--55317415 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 15
55317353 GAACATTTGG
55317363 AATTTAATTAGATAAAA
1 AATTT-ATTA-ATAAAA
55317380 AACTTTTATTAATAAAA
1 AA--TTTATTAATAAAA
*
55317397 AATTTATTTATAAATA
1 AATTTATTAATAAA-A
55317413 AAT
1 AAT
55317416 CATTGCAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
15 11 0.34
16 4 0.12
17 10 0.31
18 4 0.12
19 3 0.09
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (15 bp):
AATTTATTAATAAAA
Found at i:55317489 original size:22 final size:20
Alignment explanation
Indices: 55317446--55317484 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
55317436 TAATTTAAAA
55317446 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
55317466 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
55317485 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:55317608 original size:20 final size:20
Alignment explanation
Indices: 55317583--55317622 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
55317573 AATATTTTCC
*
55317583 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
55317603 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
55317623 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:55317628 original size:34 final size:35
Alignment explanation
Indices: 55317571--55317637 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
55317561 CAAACACTAG
*
55317571 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
55317606 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
55317638 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:55317629 original size:14 final size:14
Alignment explanation
Indices: 55317606--55317645 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
55317596 ACAGAAAAGT
*
55317606 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
55317620 AAATCATTTTACGG
1 AAAACATTTTACAG
55317634 AAAACATTTTAC
1 AAAACATTTTAC
55317646 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:55317749 original size:13 final size:14
Alignment explanation
Indices: 55317725--55317753 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
55317715 AGGTTGTTAG
55317725 TATCAGTTAGCAGT
1 TATCAGTTAGCAGT
55317739 TATCA-TTAGCAGT
1 TATCAGTTAGCAGT
55317752 TA
1 TA
55317754 ATAAACCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (14 bp):
TATCAGTTAGCAGT
Found at i:55319446 original size:31 final size:31
Alignment explanation
Indices: 55319411--55319478 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
55319401 TAATAATATG
*
55319411 GTGACTTAAATAAAAAAATTTGAATAGTTTA
1 GTGACTTAAATAAAAAAATTTGAATAGTTCA
* **
55319442 GTGACTTAAATGAAAATTTTTGAATAGTTCA
1 GTGACTTAAATAAAAAAATTTGAATAGTTCA
55319473 GTGACT
1 GTGACT
55319479 ATTTTTAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (31 bp):
GTGACTTAAATAAAAAAATTTGAATAGTTCA
Found at i:55322794 original size:34 final size:34
Alignment explanation
Indices: 55322746--55322849 Score: 97
Period size: 34 Copynumber: 3.0 Consensus size: 34
55322736 ATACTAACAA
**
55322746 AATAATAACGAATAAAT-ATAACGAAAATAA-AACT
1 AATAATAATTAATAAATAATAAC-AAAATAATAA-T
55322780 AATAATAATTAAT-AATAATAACAATAATAATAAT
1 AATAATAATTAATAAATAATAACAA-AATAATAAT
* *
55322814 AATGATAATAATAATAAATGATGAACAAAATAATAA
1 AATAATAAT--TAATAAATAAT-AACAAAATAATAA
55322850 AATTGCTAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
33 5 0.08
34 30 0.51
35 2 0.03
36 4 0.07
37 13 0.22
38 5 0.08
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (34 bp):
AATAATAATTAATAAATAATAACAAAATAATAAT
Found at i:55322849 original size:3 final size:3
Alignment explanation
Indices: 55322779--55322830 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
55322769 AAAATAAAAC
* *
55322779 TAA TAA TAA TTAA TAA TAA TAA CAA TAA TAA TAA TAA TGA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55322825 TAA TAA
1 TAA TAA
55322831 ATGATGAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:55326172 original size:89 final size:89
Alignment explanation
Indices: 55325643--55326155 Score: 600
Period size: 89 Copynumber: 5.8 Consensus size: 89
55325633 GCTACTGCTT
* * * * * * *
55325643 AGGGAGATAAGGCTAGTG-CTTTCGATCTGCCTCACTGCCAGTACAGGAAGACAAGATCTACTAT
1 AGGGAGATCAGGCTTGTGTC-TTCGATCTGCTTCGCTGCCGGTATAGGAAGACAAGATCT-GT-T
*
55325707 -C-TTCAGTCTGCTCCGCTGCAAACTC
63 GCTTTTAGTCTGCTCCGCTGCAAACTC
* * * * * * * * *
55325732 AGGGAGGTCAGACTTGTGTCTTCAATCTGTTTCACTGCCAGTACATGAAGACAAGATCTGTTACT
1 AGGGAGATCAGGCTTGTGTCTTCGATCTGCTTCGCTGCCGGTATAGGAAGACAAGATCTGTTGCT
*
55325797 TTTAGTCTGCTCCGCTGCAAACTT
66 TTTAGTCTGCTCCGCTGCAAACTC
* * * *
55325821 AGGAAAATCAGGCTTGTGTCTTCGATTTGCTTCGCTGCCGGTATAGGAAGACTAGATCTGTTGCT
1 AGGGAGATCAGGCTTGTGTCTTCGATCTGCTTCGCTGCCGGTATAGGAAGACAAGATCTGTTGCT
* *
55325886 TTTAGTCTGCTTCACTGCAAACTC
66 TTTAGTCTGCTCCGCTGCAAACTC
* * ** * *
55325910 AAGGAGATCAGGCTTGTGTCTTCGATCTACTTCGCTATCGGTATAGGAAGACCAGATCTGCTGCT
1 AGGGAGATCAGGCTTGTGTCTTCGATCTGCTTCGCTGCCGGTATAGGAAGACAAGATCTGTTGCT
*
55325975 TTTAGTCTGCTCCGCTGCAAACCC
66 TTTAGTCTGCTCCGCTGCAAACTC
* * * * * *
55325999 AGAGAGGTCAGGCTTGTTTCTTCGATCTGCTTCGTTGCCGGTATAGGAAGACAATATCTGTTACT
1 AGGGAGATCAGGCTTGTGTCTTCGATCTGCTTCGCTGCCGGTATAGGAAGACAAGATCTGTTGCT
*
55326064 TTTAGTCTGCTCAGCTGCAAACTC
66 TTTAGTCTGCTCCGCTGCAAACTC
* * * *
55326088 AGGGAGATCAGACTTGTGTCTTTGATCTGCTTCGCTGCCCGTATAGGAAGACCAGATCTGTTGCT
1 AGGGAGATCAGGCTTGTGTCTTCGATCTGCTTCGCTGCCGGTATAGGAAGACAAGATCTGTTGCT
55326153 TTT
66 TTT
55326156 TTTCTATTCC
Statistics
Matches: 358, Mismatches: 63, Indels: 6
0.84 0.15 0.01
Matches are distributed among these distances:
87 1 0.00
88 2 0.01
89 354 0.99
90 1 0.00
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.31
Consensus pattern (89 bp):
AGGGAGATCAGGCTTGTGTCTTCGATCTGCTTCGCTGCCGGTATAGGAAGACAAGATCTGTTGCT
TTTAGTCTGCTCCGCTGCAAACTC
Found at i:55326381 original size:16 final size:16
Alignment explanation
Indices: 55326360--55326391 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
55326350 TAGGTGTGTA
55326360 TGAATGATATTTGCAT
1 TGAATGATATTTGCAT
55326376 TGAATGATATTTGCAT
1 TGAATGATATTTGCAT
55326392 GAGTGTAGAA
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:0.06, G:0.19, T:0.44
Consensus pattern (16 bp):
TGAATGATATTTGCAT
Found at i:55327220 original size:93 final size:93
Alignment explanation
Indices: 55327061--55327347 Score: 430
Period size: 93 Copynumber: 3.0 Consensus size: 93
55327051 GAAAAATGCT
* *
55327061 TGAAAAAGATTATCACAATGGACAAAATGAAATTTTATTGAGGACAAATCTCAAAATGAATGAAT
1 TGAAAAAGATTATCACAATGGACAAAATGAAATTTTATTGAGAACAAAGCTCAAAATGAATGAAT
55327126 TATGATAGCAAATTTTGCTAAGATAAGA
66 TATGATAGCAAATTTTGCTAAGATAAGA
* * *
55327154 TGAAAAAGATTATCACAATGGACAAAAAGAAATTTTATTGAGAATAAAGCTCGAAATGAATGAAT
1 TGAAAAAGATTATCACAATGGACAAAATGAAATTTTATTGAGAACAAAGCTCAAAATGAATGAAT
*
55327219 TATGATAGCAAATTTTGGTAAGATAAGA
66 TATGATAGCAAATTTTGCTAAGATAAGA
* * * * * *
55327247 TGAAAAAGATTATTACAATGGATAAGATGAAATTTTATTAAGAACAAGGCTCAAAATGAATAAAT
1 TGAAAAAGATTATCACAATGGACAAAATGAAATTTTATTGAGAACAAAGCTCAAAATGAATGAAT
55327312 TAATCAAGATAGCAAATTTTGCTAAGATAAGA
66 T-AT---GATAGCAAATTTTGCTAAGATAAGA
55327344 TGAA
1 TGAA
55327348 TAAGTTGAAA
Statistics
Matches: 174, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
93 144 0.83
94 2 0.01
97 28 0.16
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (93 bp):
TGAAAAAGATTATCACAATGGACAAAATGAAATTTTATTGAGAACAAAGCTCAAAATGAATGAAT
TATGATAGCAAATTTTGCTAAGATAAGA
Found at i:55333082 original size:3 final size:3
Alignment explanation
Indices: 55332985--55333063 Score: 95
Period size: 3 Copynumber: 26.0 Consensus size: 3
55332975 AAAATAAAAC
* * * * *
55332985 TAA TAA TAA TTAA TAG TAG TAG TAG TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
55333031 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55333064 ATGATGAACA
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
3 68 0.96
4 3 0.04
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:55335825 original size:12 final size:13
Alignment explanation
Indices: 55335794--55335824 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
55335784 GCGTTTGAAC
55335794 AAAAAATGCCGCT
1 AAAAAATGCCGCT
55335807 AAAAAATGCCGCT
1 AAAAAATGCCGCT
55335820 AAAAA
1 AAAAA
55335825 TCGAGGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.55, C:0.19, G:0.13, T:0.13
Consensus pattern (13 bp):
AAAAAATGCCGCT
Found at i:55335964 original size:41 final size:41
Alignment explanation
Indices: 55335919--55336109 Score: 204
Period size: 41 Copynumber: 4.7 Consensus size: 41
55335909 GCGTTTTAAA
* * *
55335919 AAAAGCGTCGCTAATTCCCAGATCTTTAGCGGTGTTTTTGG
1 AAAAGCGCCGCTAATGCTCAGATCTTTAGCGGTGTTTTTGG
* * * * *
55335960 AAAAGCGCCGATAATGCTCAGATATTTAGCGGCGTTTCTGT
1 AAAAGCGCCGCTAATGCTCAGATCTTTAGCGGTGTTTTTGG
* * **
55336001 AGAAGCGCCGCTAATGCTCAGATCTTTATCGGTGTTTTTCC
1 AAAAGCGCCGCTAATGCTCAGATCTTTAGCGGTGTTTTTGG
* * * * * **
55336042 AAAATCGCCGC-GATGCTCAAATCTTTAGCGGCGTTTATAT
1 AAAAGCGCCGCTAATGCTCAGATCTTTAGCGGTGTTTTTGG
55336082 AAAAGCGCCGCTAATGCTCAGATCTTTA
1 AAAAGCGCCGCTAATGCTCAGATCTTTA
55336110 ATTATACTTC
Statistics
Matches: 121, Mismatches: 28, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
40 32 0.26
41 89 0.74
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (41 bp):
AAAAGCGCCGCTAATGCTCAGATCTTTAGCGGTGTTTTTGG
Found at i:55336095 original size:81 final size:81
Alignment explanation
Indices: 55335901--55336109 Score: 249
Period size: 82 Copynumber: 2.6 Consensus size: 81
55335891 ACTTTCGAGG
* * * * * **
55335901 ATTTAGTGGCGTTTTAAAAAAAGCGTCGCTAATTCCCAGATCTTTAGCGGTGTTTTTGGAAAAGC
1 ATTTAGCGGCGTTTT-ATAAAAGCGCCGCTAATGCTCAGATCTTTAGCGGTGTTTTTCCAAAAGC
* *
55335966 GCCGATAATGCTCAGAT
65 GCCGACAATGCTCAAAT
* * * *
55335983 ATTTAGCGGCGTTTCTGTAGAAGCGCCGCTAATGCTCAGATCTTTATCGGTGTTTTTCCAAAATC
1 ATTTAGCGGCGTTT-TATAAAAGCGCCGCTAATGCTCAGATCTTTAGCGGTGTTTTTCCAAAAGC
*
55336048 GCCG-CGATGCTCAAAT
65 GCCGACAATGCTCAAAT
*
55336064 CTTTAGCGGCGTTTATATAAAAGCGCCGCTAATGCTCAGATCTTTA
1 ATTTAGCGGCGTTT-TATAAAAGCGCCGCTAATGCTCAGATCTTTA
55336110 ATTATACTTC
Statistics
Matches: 108, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
81 51 0.47
82 56 0.52
83 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (81 bp):
ATTTAGCGGCGTTTTATAAAAGCGCCGCTAATGCTCAGATCTTTAGCGGTGTTTTTCCAAAAGCG
CCGACAATGCTCAAAT
Found at i:55336467 original size:43 final size:43
Alignment explanation
Indices: 55336420--55336580 Score: 166
Period size: 43 Copynumber: 3.7 Consensus size: 43
55336410 GATCAGGGTA
* ** * *
55336420 TTTAGCGGCGATTGTTGGAGTAGCGCCGCTAAAGGTCATTATC
1 TTTAGCGGCGTTTGTTGGAGTAGCGCCGCTAAAGACCATGACC
*
55336463 TTTAGCGGCGTTTGTTTG-GTAAGCGCCGCTAAAGACCATGACC
1 TTTAGCGGCGTTTGTTGGAGT-AGCGCCGCTAAAGACCATGACC
** * *
55336506 TTTAGCGGCGTTTG-TGGTAAAAGCGCCGCTAATGACCATGACT
1 TTTAGCGGCGTTTGTTGG-AGTAGCGCCGCTAAAGACCATGACC
* *
55336549 TTTAGCGGCGTTTG-TGGTGAAAGCGCCGCTAA
1 TTTAGCGGCGTTTGTTGGAG-TAGCGCCGCTAA
55336581 CGTTAGCGAC
Statistics
Matches: 101, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
42 4 0.04
43 97 0.96
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTTGGAGTAGCGCCGCTAAAGACCATGACC
Found at i:55336510 original size:86 final size:85
Alignment explanation
Indices: 55336420--55336580 Score: 193
Period size: 86 Copynumber: 1.9 Consensus size: 85
55336410 GATCAGGGTA
** ** *
55336420 TTTAGCGGCGATTGTTGG-AGTAGCGCCGCTAAAGGTCATTA-TCTTTAGCGGCGTTTGTTTGGT
1 TTTAGCGGCGATTG-TGGTAAAAGCGCCGCTAAAGACCATGACT-TTTAGCGGCGTTTG--TGGT
55336483 -AAGCGCCGCTAAAGACCATGACC
62 AAAGCGCCGCTAAAGACCATGACC
* *
55336506 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAATGACCATGACTTTTAGCGGCGTTTGTGGTGAAA
1 TTTAGCGGCGATTGTGGTAAAAGCGCCGCTAAAGACCATGACTTTTAGCGGCGTTTGTGGT-AAA
55336571 GCGCCGCTAA
65 GCGCCGCTAA
55336581 CGTTAGCGAC
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
84 4 0.06
85 3 0.05
86 56 0.88
87 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (85 bp):
TTTAGCGGCGATTGTGGTAAAAGCGCCGCTAAAGACCATGACTTTTAGCGGCGTTTGTGGTAAAG
CGCCGCTAAAGACCATGACC
Found at i:55348082 original size:25 final size:25
Alignment explanation
Indices: 55348047--55348097 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
55348037 GGGGAGGGTT
55348047 ATTATTATTATTTAAAATTAATATA
1 ATTATTATTATTTAAAATTAATATA
* *
55348072 ATTATTTTTATTTAATATTAATATA
1 ATTATTATTATTTAAAATTAATATA
55348097 A
1 A
55348098 AATTTAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATTATTATTATTTAAAATTAATATA
Found at i:55350411 original size:16 final size:16
Alignment explanation
Indices: 55350379--55350421 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
55350369 TTAAAAATTC
55350379 AATATTATCTT-TATAT
1 AATATTAT-TTATATAT
*
55350395 AATATTATTTATTTAT
1 AATATTATTTATATAT
*
55350411 ATTATTATTTA
1 AATATTATTTA
55350422 AATTTTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 2 0.08
16 22 0.92
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
AATATTATTTATATAT
Found at i:55355260 original size:22 final size:21
Alignment explanation
Indices: 55355217--55355269 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
55355207 ATAAAGGCAA
*
55355217 AAAAAAATAAAACAAGCCAAT
1 AAAAAAATAAAACAAGCAAAT
* *
55355238 AAAAAAATAATAATAAGTAAAT
1 AAAAAAATAA-AACAAGCAAAT
*
55355260 AAATAAATAA
1 AAAAAAATAA
55355270 GATATTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.74, C:0.06, G:0.04, T:0.17
Consensus pattern (21 bp):
AAAAAAATAAAACAAGCAAAT
Found at i:55357595 original size:13 final size:13
Alignment explanation
Indices: 55357577--55357605 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
55357567 TCTCAGAGGA
55357577 TGTTGGGGTAATT
1 TGTTGGGGTAATT
55357590 TGTTGGGGTAATT
1 TGTTGGGGTAATT
55357603 TGT
1 TGT
55357606 CCGGGTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.38, T:0.48
Consensus pattern (13 bp):
TGTTGGGGTAATT
Found at i:55362425 original size:13 final size:14
Alignment explanation
Indices: 55362407--55362440 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
55362397 ATGAGGGTAG
55362407 GATTCTGTATATCT
1 GATTCTGTATATCT
*
55362421 G-TTCTGTTTATCT
1 GATTCTGTATATCT
55362434 GATTCTG
1 GATTCTG
55362441 CTATCTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.53
Consensus pattern (14 bp):
GATTCTGTATATCT
Found at i:55367032 original size:21 final size:21
Alignment explanation
Indices: 55366987--55367064 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 21
55366977 ATCTTCAAGG
55366987 ATATGCAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
55367006 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
55367027 ATATGCAATCTTAGAAGATATGAT
1 ATATGCAATCTT---AGATATGAT
*
55367051 -TATGTAATCTTAGA
1 ATATGCAATCTTAGA
55367065 GATTTAATTT
Statistics
Matches: 53, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
19 19 0.36
20 3 0.06
21 12 0.23
23 10 0.19
24 9 0.17
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:55367308 original size:23 final size:23
Alignment explanation
Indices: 55367267--55367311 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
55367257 TCTTATTTTG
*
55367267 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTTATTTA
**
55367290 TTGATTTGTATATTTTTTATTT
1 TTGATTTGTATATAATTTATTT
55367312 CAAGTCTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (23 bp):
TTGATTTGTATATAATTTATTTA
Found at i:55368622 original size:7 final size:7
Alignment explanation
Indices: 55368610--55368641 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
55368600 AGAGATGGAG
55368610 AGAATAA
1 AGAATAA
55368617 AGAATAA
1 AGAATAA
55368624 AGAATAA
1 AGAATAA
55368631 AGAATAA
1 AGAATAA
55368638 AGAA
1 AGAA
55368642 AATATGAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (7 bp):
AGAATAA
Found at i:55371552 original size:12 final size:12
Alignment explanation
Indices: 55371537--55371562 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
55371527 ATCAATATTG
55371537 CATTTTCTTAAT
1 CATTTTCTTAAT
55371549 CATTTTCTTAAT
1 CATTTTCTTAAT
55371561 CA
1 CA
55371563 ATACTCTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.19, G:0.00, T:0.54
Consensus pattern (12 bp):
CATTTTCTTAAT
Found at i:55376558 original size:18 final size:18
Alignment explanation
Indices: 55376513--55376560 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
55376503 AGATATAGGT
* *
55376513 AATATATATATAGGTTTG
1 AATATATATATAAGTATG
55376531 AATGAT-TATATAAGTATG
1 AAT-ATATATATAAGTATG
*
55376549 TATATATATATA
1 AATATATATATA
55376561 TAAAGTCGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 2 0.08
18 21 0.84
19 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (18 bp):
AATATATATATAAGTATG
Found at i:55376943 original size:41 final size:41
Alignment explanation
Indices: 55376886--55377123 Score: 433
Period size: 41 Copynumber: 5.8 Consensus size: 41
55376876 GAATGTAATA
* *
55376886 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
55376927 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
*
55376968 CAGACTATATGTCTAGCAGGCTTAATGTCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
55377009 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
55377050 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
55377091 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG
1 CAGACTATATGTCTAGCAGGCTTAA-TGCCGGTG
55377124 TACTGAATCA
Statistics
Matches: 192, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
40 3 0.02
41 189 0.98
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (41 bp):
CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
Found at i:55377148 original size:123 final size:123
Alignment explanation
Indices: 55376886--55377165 Score: 440
Period size: 123 Copynumber: 2.3 Consensus size: 123
55376876 GAATGTAATA
55376886 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTA
* *
55376951 ATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGTCGGTGATACATTT
66 ATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATAT
* *
55377009 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTA
55377074 ATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG-TAC-TGAAT
66 ATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTAA-TGCCGGTGATACAT--AT
* * **
55377132 CAGGCTTTAAGCCTAGCAGGCAAAATGCCGGTGA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
55377166 ATCTGTTTAA
Statistics
Matches: 144, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
121 1 0.01
122 6 0.04
123 137 0.95
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.30
Consensus pattern (123 bp):
CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTA
ATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATAT
Found at i:55384606 original size:41 final size:41
Alignment explanation
Indices: 55384549--55384786 Score: 442
Period size: 41 Copynumber: 5.8 Consensus size: 41
55384539 GAATGTAATA
* *
55384549 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
55384590 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
55384631 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
55384672 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
55384713 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
55384754 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG
1 CAGACTATATGTCTAGCAGGCTTAA-TGCCGGTG
55384787 TACTGAATCA
Statistics
Matches: 194, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
40 3 0.02
41 191 0.98
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (41 bp):
CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
Found at i:55384811 original size:123 final size:123
Alignment explanation
Indices: 55384549--55384828 Score: 449
Period size: 123 Copynumber: 2.3 Consensus size: 123
55384539 GAATGTAATA
55384549 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTA
*
55384614 ATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
66 ATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATAT
* *
55384672 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTA
55384737 ATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG-TAC-TGAAT
66 ATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTAA-TGCCGGTGATACAT--AT
* * **
55384795 CAGGCTTTAAGCCTAGCAGGCAAAATGCCGGTGA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
55384829 ATCTGTTTAA
Statistics
Matches: 145, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
121 1 0.01
122 6 0.04
123 138 0.95
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (123 bp):
CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTA
ATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATAT
Found at i:55391817 original size:42 final size:42
Alignment explanation
Indices: 55391767--55392066 Score: 242
Period size: 42 Copynumber: 7.3 Consensus size: 42
55391757 CTATAACTTC
* *
55391767 AGGGAGATATGATTTTTTTTTCTGTCTGCTCCACTACTGCTT
1 AGGGAGATAAGATTTTTGTTTCTGTCTGCTCCACTACTGCTT
* * * * *
55391809 AGGAAGATAAGATCTGTGGTTT-TGTCTGGTCTACTACTGCTT
1 AGGGAGATAAGAT-TTTTGTTTCTGTCTGCTCCACTACTGCTT
* * *
55391851 AGGGAGATAAGA--CTTGATGC-GATCTGCTCCACTACTGCTT
1 AGGGAGATAAGATTTTTGTTTCTG-TCTGCTCCACTACTGCTT
* * *
55391891 AGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTT
1 AGGGAGATAAGATTTTTGTTTCTGTCTGCTCCACTACTGCTT
* * *** *
55391933 AGGTAGATAAGA--CTTGAGGC-GATTTGCTCCACTACTGCTT
1 AGGGAGATAAGATTTTTGTTTCTG-TCTGCTCCACTACTGCTT
* ** *
55391973 AGGGAGATAAGACTTAAG--GC-GATCTGCTCCACTACTGCTT
1 AGGGAGATAAGATTTTTGTTTCTG-TCTGCTCCACTACTGCTT
* * * *
55392013 AGTGAGATAAGATATGTGGTTCTGTCTGCTCCACTACTGCTT
1 AGGGAGATAAGATTTTTGTTTCTGTCTGCTCCACTACTGCTT
*
55392055 AGGGAGTTAAGA
1 AGGGAGATAAGA
55392067 CTTGAGGCGA
Statistics
Matches: 208, Mismatches: 38, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
39 5 0.02
40 93 0.45
42 103 0.50
43 7 0.03
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (42 bp):
AGGGAGATAAGATTTTTGTTTCTGTCTGCTCCACTACTGCTT
Found at i:55391886 original size:82 final size:82
Alignment explanation
Indices: 55391791--55392104 Score: 353
Period size: 82 Copynumber: 3.9 Consensus size: 82
55391781 TTTTTTTCTG
* * * *
55391791 TCTGCTCCACTACTGCTTAGGAAGATAAGATCTGTGGTTTTGTCTGGTCTACTACTGCTTAGGGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTTAGGGA
*
55391856 GATAAGACTTGATGCGA
66 GATAAGACTTGAGGCGA
*
55391873 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTTAGGTA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTTAGGGA
55391938 GATAAGACTTGAGGCGA
66 GATAAGACTTGAGGCGA
*
55391955 TTTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TAAGG--C-GATCTGCTCCACTACTGCTTAG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT--GGTTCTG-TCTGCTCCACTACTGCTTAG
* *
55392015 TGAGATAAGA-TATGTGGTTCTG-
63 GGAGATAAGACT-TGAGG--C-GA
* * *
55392037 TCTGCTCCACTACTGCTTAGGGAGTTAAGA-CT-TGAG-GC-GATCTGCTCTACTACTGCTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTG-GTTCTG-TCTGCTCCACTACTGCTTAGG
*
55392098 AAGATAA
64 GAGATAA
55392105 AATCTGTGGT
Statistics
Matches: 208, Mismatches: 15, Indels: 18
0.86 0.06 0.07
Matches are distributed among these distances:
79 2 0.01
80 35 0.17
81 3 0.01
82 167 0.80
83 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (82 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTTAGGGA
GATAAGACTTGAGGCGA
Found at i:55391895 original size:40 final size:40
Alignment explanation
Indices: 55391791--55392104 Score: 337
Period size: 40 Copynumber: 7.7 Consensus size: 40
55391781 TTTTTTTCTG
* * **
55391791 TCTGCTCCACTACTGCTTAGGAAGATAAGATCTGTGGTTTTG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-T-GATGCGA
* *
55391833 TCTGGTCTACTACTGCTTAGGGAGATAAGACTTGATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
* *
55391873 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGATGC-GA
* *
55391915 TCTGCTCCACTACTGCTTAGGTAGATAAGACTTGAGGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
* * *
55391955 TTTGCTCCACTACTGCTTAGGGAGATAAGACTTAAGGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
* * * *
55391995 TCTGCTCCACTACTGCTTAGTGAGATAAGATATGTGGTTCTG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGATGC-GA
* *
55392037 TCTGCTCCACTACTGCTTAGGGAGTTAAGACTTGAGGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
* *
55392077 TCTGCTCTACTACTGCTTAGGAAGATAA
1 TCTGCTCCACTACTGCTTAGGGAGATAA
55392105 AATCTGTGGT
Statistics
Matches: 230, Mismatches: 33, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
39 5 0.02
40 125 0.54
41 8 0.03
42 90 0.39
43 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (40 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
Found at i:55392008 original size:122 final size:122
Alignment explanation
Indices: 55391786--55392104 Score: 469
Period size: 122 Copynumber: 2.6 Consensus size: 122
55391776 TGATTTTTTT
* *** *
55391786 TTCTGTCTGCTCCACTACTGCTTAGGAAGATAAGA-TCTGTGGTTTTGTCTGGTCTACTACTGCT
1 TTCTGTCTGCTCCACTACTGCTTAGGAAGATAAGACT-TGAGGCGAT-T-TGCTCTACTACTGCT
* * *
55391850 TAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGG
63 TAGGGAGATAAGACTTAAGGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATATGTGG
* *
55391910 TTCTGTCTGCTCCACTACTGCTTAGGTAGATAAGACTTGAGGCGATTTGCTCCACTACTGCTTAG
1 TTCTGTCTGCTCCACTACTGCTTAGGAAGATAAGACTTGAGGCGATTTGCTCTACTACTGCTTAG
*
55391975 GGAGATAAGACTTAAGGCGATCTGCTCCACTACTGCTTAGTGAGATAAGATATGTGG
66 GGAGATAAGACTTAAGGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATATGTGG
* * *
55392032 TTCTGTCTGCTCCACTACTGCTTAGGGAGTTAAGACTTGAGGCGATCTGCTCTACTACTGCTTAG
1 TTCTGTCTGCTCCACTACTGCTTAGGAAGATAAGACTTGAGGCGATTTGCTCTACTACTGCTTAG
*
55392097 GAAGATAA
66 GGAGATAA
55392105 AATCTGTGGT
Statistics
Matches: 178, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
122 137 0.77
123 1 0.01
124 39 0.22
125 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (122 bp):
TTCTGTCTGCTCCACTACTGCTTAGGAAGATAAGACTTGAGGCGATTTGCTCTACTACTGCTTAG
GGAGATAAGACTTAAGGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATATGTGG
Found at i:55392297 original size:100 final size:99
Alignment explanation
Indices: 55392193--55392409 Score: 308
Period size: 99 Copynumber: 2.2 Consensus size: 99
55392183 ACCACCGAGG
* * *
55392193 AAGTAAGATTCGCCGTTGCGACTTTAATCTTTTAAATTGCAATATCGGGGAAGCAAGATTCGCCA
1 AAGTAAGATTCACCGTTGCGACTTCAATCTTTTAAATTGAAATATCGGGGAA-CAAGATTCGCCA
* * *
55392258 TCGTAGCTTTAATCTGTTCCATTGTATCGCCAGGA
65 TCGTAGCTTTAATCTGATCCACTGCATCGCCAGGA
* * *
55392293 AAGTAAGATTCACCGTTGCGACTTCAATCTTTTTAATTGAAATGTCGGGGAACAAGATTCGCCGT
1 AAGTAAGATTCACCGTTGCGACTTCAATCTTTTAAATTGAAATATCGGGGAACAAGATTCGCCAT
* * *
55392358 TGTAGCTTTAATCTGATCCACTGCATCGTCAGGG
66 CGTAGCTTTAATCTGATCCACTGCATCGCCAGGA
*
55392392 AAGTAAGATTCATCGTTG
1 AAGTAAGATTCACCGTTG
55392410 TAGCTTTAAT
Statistics
Matches: 104, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
99 57 0.55
100 47 0.45
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (99 bp):
AAGTAAGATTCACCGTTGCGACTTCAATCTTTTAAATTGAAATATCGGGGAACAAGATTCGCCAT
CGTAGCTTTAATCTGATCCACTGCATCGCCAGGA
Found at i:55392403 original size:99 final size:100
Alignment explanation
Indices: 55392133--55392409 Score: 342
Period size: 100 Copynumber: 2.8 Consensus size: 100
55392123 GATTAACTGT
* * * ** * *
55392133 AATGTCGGGGAAGTAAGATTCGCTGTTGTAGCTTTAATCAGTTCTGCTGCA-CCACCGAGGAAGT
1 AATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGTTCCACTGCATCGACAG-GGAAGT
* * *
55392197 AAGATTCGCCGTTGCGACTTTAATCTTTTAAATTGC
65 AAGATTCACCGTTGCGACTTCAATCTTTTAAATTGA
* * * * * * *
55392233 AATATCGGGGAAGCAAGATTCGCCATCGTAGCTTTAATCTGTTCCATTGTATCGCCAGGAAAGTA
1 AATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGTTCCACTGCATCGACAGGGAAGTA
*
55392298 AGATTCACCGTTGCGACTTCAATCTTTTTAATTGA
66 AGATTCACCGTTGCGACTTCAATCTTTTAAATTGA
* *
55392333 AATGTCGGGGAA-CAAGATTCGCCGTTGTAGCTTTAATCTGATCCACTGCATCGTCAGGGAAGTA
1 AATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGTTCCACTGCATCGACAGGGAAGTA
*
55392397 AGATTCATCGTTG
66 AGATTCACCGTTG
55392410 TAGCTTTAAT
Statistics
Matches: 149, Mismatches: 27, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
99 57 0.38
100 89 0.60
101 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (100 bp):
AATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGTTCCACTGCATCGACAGGGAAGTA
AGATTCACCGTTGCGACTTCAATCTTTTAAATTGA
Found at i:55392494 original size:50 final size:50
Alignment explanation
Indices: 55392133--55392513 Score: 184
Period size: 50 Copynumber: 7.6 Consensus size: 50
55392123 GATTAACTGT
* * ** ***
55392133 AATGTCGGGGAAGTAAGATTCGCTGTTGTAGCTTTAATCAGTTCTGCTGC
1 AATGTCAGGGAAGTAAGATTCGCCGTTGTAGCTTTAATCTTTTCAATTGC
*** * * *
55392183 -ACCACCGAGGAAGTAAGATTCGCCGTTG-CGACTTTAATCTTTTAAATTGC
1 AATGTCAG-GGAAGTAAGATTCGCCGTTGTAG-CTTTAATCTTTTCAATTGC
* * * * * * *
55392233 AATATCGGGGAAGCAAGATTCGCCATCGTAGCTTTAATCTGTTCCATTG-
1 AATGTCAGGGAAGTAAGATTCGCCGTTGTAGCTTTAATCTTTTCAATTGC
* * * * * * * *
55392282 TATCGCCAGGAAAGTAAGATTCACCGTTG-CGACTTCAATCTTTTTAATTGA
1 AAT-GTCAGGGAAGTAAGATTCGCCGTTGTAG-CTTTAATCTTTTCAATTGC
* * ** * *
55392333 AATGTCGGGGAA-CAAGATTCGCCGTTGTAGCTTTAATCTGATCCACTGC
1 AATGTCAGGGAAGTAAGATTCGCCGTTGTAGCTTTAATCTTTTCAATTGC
** * ***
55392382 -ATCGTCAGGGAAGTAAGATTCATCGTTGTAGCTTTAAT-TTGATCCGCTGC
1 AAT-GTCAGGGAAGTAAGATTCGCCGTTGTAGCTTTAATCTT-TTCAATTGC
**** * * *
55392432 ACCACCAAGGAAGTAAGATTCGCCGTTG-AGGCTTCAATCTTTTAAATTGC
1 AATGTCAGGGAAGTAAGATTCGCCGTTGTA-GCTTTAATCTTTTCAATTGC
* * * *
55392482 AATGTCGGGGAAGCAAGATTTGCCGTCGTAGC
1 AATGTCAGGGAAGTAAGATTCGCCGTTGTAGC
55392514 AAGATTTGCC
Statistics
Matches: 237, Mismatches: 79, Indels: 30
0.68 0.23 0.09
Matches are distributed among these distances:
48 2 0.01
49 42 0.18
50 184 0.78
51 9 0.04
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.30
Consensus pattern (50 bp):
AATGTCAGGGAAGTAAGATTCGCCGTTGTAGCTTTAATCTTTTCAATTGC
Found at i:55392516 original size:18 final size:18
Alignment explanation
Indices: 55392493--55392531 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
55392483 ATGTCGGGGA
55392493 AGCAAGATTTGCCGTCGT
1 AGCAAGATTTGCCGTCGT
55392511 AGCAAGATTTGCCGTCGT
1 AGCAAGATTTGCCGTCGT
55392529 AGC
1 AGC
55392532 TTTAATCTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (18 bp):
AGCAAGATTTGCCGTCGT
Found at i:55392618 original size:50 final size:50
Alignment explanation
Indices: 55392559--55392739 Score: 139
Period size: 50 Copynumber: 3.6 Consensus size: 50
55392549 TATCGCCATA
* * * *
55392559 GAAGTAAGATTCGCCGTTGCGGCATCAATCTTTTTAATTGCAATGTCGGG
1 GAAGCAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATATCGGG
* ** * ***** * * **
55392609 GAAGCAAGATTCGTCGTTGTAGCTTTAATCTACCCCACTGC-ATCTCCAAG
1 GAAGCAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATAT-CGGG
* * * *
55392659 GAAGTAAGATTCACTGATGCGGCTTCAATCTTTTAAATTGCAATATCGGG
1 GAAGCAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATATCGGG
**
55392709 GAAGCAAGATTCGCCGTTGTAGCTTCAATCT
1 GAAGCAAGATTCGCCGTTGCGGCTTCAATCT
55392740 ATTCCACTGC
Statistics
Matches: 91, Mismatches: 38, Indels: 4
0.68 0.29 0.03
Matches are distributed among these distances:
49 3 0.03
50 85 0.93
51 3 0.03
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (50 bp):
GAAGCAAGATTCGCCGTTGCGGCTTCAATCTTTTAAATTGCAATATCGGG
Found at i:55392648 original size:100 final size:100
Alignment explanation
Indices: 55392511--55392754 Score: 337
Period size: 100 Copynumber: 2.4 Consensus size: 100
55392501 TTGCCGTCGT
* * * * *
55392511 AGCAAGATTTGCCGTCGTAGCTTTAATCTGCTCCACTGTATCGCCATA-GAAGTAAGATTCGCCG
1 AGCAAGATTCGCCGTTGTAGCTTTAATCTACTCCACTGCATCGCCA-AGGAAGTAAGATTCACCG
* * *
55392575 TTGCGGCATCAATCTTTTTAATTGCAATGTCGGGGA
65 ATGCGGCATCAATCTTTTAAATTGCAATATCGGGGA
* * * *
55392611 AGCAAGATTCGTCGTTGTAGCTTTAATCTACCCCACTGCATCTCCAAGGAAGTAAGATTCACTGA
1 AGCAAGATTCGCCGTTGTAGCTTTAATCTACTCCACTGCATCGCCAAGGAAGTAAGATTCACCGA
*
55392676 TGCGGCTTCAATCTTTTAAATTGCAATATCGGGGA
66 TGCGGCATCAATCTTTTAAATTGCAATATCGGGGA
* *
55392711 AGCAAGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCATCGC
1 AGCAAGATTCGCCGTTGTAGCTTTAATCTACTCCACTGCATCGC
55392755 GAGAGAGATA
Statistics
Matches: 125, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
99 1 0.01
100 124 0.99
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.30
Consensus pattern (100 bp):
AGCAAGATTCGCCGTTGTAGCTTTAATCTACTCCACTGCATCGCCAAGGAAGTAAGATTCACCGA
TGCGGCATCAATCTTTTAAATTGCAATATCGGGGA
Found at i:55399403 original size:99 final size:101
Alignment explanation
Indices: 55399189--55399380 Score: 273
Period size: 101 Copynumber: 1.9 Consensus size: 101
55399179 CAACCCCTTT
* * * * *
55399189 AAATTTTGTAAAATTACTTTTGAATGCCTTTTAAGTTTTATTTTTTTTATTTTTATATTATAATT
1 AAATTTTGTAAAATTACTTTTGAAGGCCTCTTAAGTTTTATATTTTTTAATTTGATATTATAATT
*
55399254 AGTGCTTAAAAAAAGGAAAAATTTGTGTTCTGCCCT
66 AGTGCTTAAAAAAAGGAAAAATTTGTGTTCTGCCCC
*
55399290 AAATTTTGTAAAATTATTTTTGAAGGCC-CTTAAGTTTTA-ATTTTTTAATTTGATATTATAATT
1 AAATTTTGTAAAATTACTTTTGAAGGCCTCTTAAGTTTTATATTTTTTAATTTGATATTATAATT
** *
55399353 AGTG-TTTGAAAAAGGATAAATTTGTGTT
66 AGTGCTTAAAAAAAGGAAAAATTTGTGTT
55399381 TGAGCCCCCA
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
98 21 0.26
99 25 0.30
100 10 0.12
101 26 0.32
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.49
Consensus pattern (101 bp):
AAATTTTGTAAAATTACTTTTGAAGGCCTCTTAAGTTTTATATTTTTTAATTTGATATTATAATT
AGTGCTTAAAAAAAGGAAAAATTTGTGTTCTGCCCC
Found at i:55402281 original size:26 final size:26
Alignment explanation
Indices: 55402232--55402281 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
55402222 TTTTTATAAA
**
55402232 AATTATGAAAATTTTATATTTTTTTG
1 AATTATGAAAATTTTATAAATTTTTG
* *
55402258 AATTTTGAATATTTTATAAATTTT
1 AATTATGAAAATTTTATAAATTTT
55402282 AAATTGTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (26 bp):
AATTATGAAAATTTTATAAATTTTTG
Found at i:55402291 original size:18 final size:17
Alignment explanation
Indices: 55402240--55402292 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
55402230 AAAATTATGA
* *
55402240 AAATTTTATATTTTTTT
1 AAATTTTAAATTTTTAT
* *
55402257 GAATTTTGAATATTTTAT
1 AAATTTTAAAT-TTTTAT
55402275 AAATTTTAAATTGTTTAT
1 AAATTTTAAATT-TTTAT
55402293 TGACGTGACG
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 9 0.32
18 19 0.68
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (17 bp):
AAATTTTAAATTTTTAT
Found at i:55402556 original size:6 final size:6
Alignment explanation
Indices: 55402545--55402570 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
55402535 TATATTTTAT
55402545 TTTAAA TTTAAA TTTAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TT
55402571 CATTATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:55407771 original size:21 final size:21
Alignment explanation
Indices: 55407725--55407772 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
55407715 AAACTATCCA
* *
55407725 AAATAACATAAAATATTATAT
1 AAATAACATAAAATATAAAAT
*
55407746 TAATAACATTAAAA-ATAAAAT
1 AAATAACA-TAAAATATAAAAT
55407767 AAATAA
1 AAATAA
55407773 TCTTTTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATAACATAAAATATAAAAT
Found at i:55409011 original size:20 final size:20
Alignment explanation
Indices: 55408951--55409012 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
55408941 TATAGAGAAT
**
55408951 AAATTGTGTATATTAAAATTA
1 AAATTGT-TATAAAAAAATTA
55408972 AAA-TG-TATAAAAATATATTA
1 AAATTGTTATAAAAA-A-ATTA
*
55408992 AAATTGTTATAGAAAAATTA
1 AAATTGTTATAAAAAAATTA
55409012 A
1 A
55409013 TAAAAAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
18 6 0.18
19 1 0.03
20 14 0.41
21 6 0.18
22 7 0.21
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (20 bp):
AAATTGTTATAAAAAAATTA
Found at i:55416685 original size:302 final size:302
Alignment explanation
Indices: 55416134--55416694 Score: 827
Period size: 302 Copynumber: 1.9 Consensus size: 302
55416124 AGTATTAAGA
* * * * *
55416134 TTTTGAGGAAGAGCCGATTCAGATTTTGGATCGAGATATTAAGGTTATGAGTAGGAAGTCTATTC
1 TTTTGAGGAAGAGCCAATTCAAATTTTAGATCGAGATATTAAGGTTATGAGGAGGAAGTCCATTC
* * *
55416199 AATTAATTAAGGTTCTCTGGCAGAATCATGGCACTGAGGAAGCCACGTGGGAACCTTAGGACTCG
66 AATTAATTAAGGTTCTCTGGCAGAATCATGACACTGAGGAAGCCACGTGGGAACCTGAGAACTCG
*
55416264 ATGTGTCAGTAGTATCCTCATCTGTTTAGATCAGGTAAATTTCGAGTCTGAAATTTCTTTTAGGG
131 ATGCGTCAGTAGTATCCTCATCTGTTTAGATCAGGTAAATTTCGAGTCTGAAATTTCTTTTAGGG
* * * * * * *
55416329 GGTAGAGTTGTAAGGTCCTGAGTAATTTAAGTCTGTTTTTATGAAGTATGATATAAATATGTATT
196 GGTAGAGTTGTAACGCCCTGAATAATTTAAGTCTATGTGTATGAAATATGATATAAATATGTATT
55416394 TGTTGAGGAGATCGAGGAGATCGAAGTTAGACCGGACTTAAC
261 TGTTGAGGAGATCGAGGAGATCGAAGTTAGACCGGACTTAAC
* * * * *
55416436 TTTTGAGGAGGATCCAATTCAAATTTTAGATCGAGCTATTAAGGTTTTGCGGAGGAAGTCCATTC
1 TTTTGAGGAAGAGCCAATTCAAATTTTAGATCGAGATATTAAGGTTATGAGGAGGAAGTCCATTC
* * * *
55416501 AATTAGTTAAGGTTCTGTGGCATAATCATGACACTGAGGAAGCCACGTGGGAACCTGAGAACTTG
66 AATTAATTAAGGTTCTCTGGCAGAATCATGACACTGAGGAAGCCACGTGGGAACCTGAGAACTCG
* * **
55416566 ATGCGTTAGTAGTATCCTCATCTGTTTGGATCAGGTAAATTTCGAAG-CTGGGATTTCTTTTAGG
131 ATGCGTCAGTAGTATCCTCATCTGTTTAGATCAGGTAAATTTCG-AGTCTGAAATTTCTTTTAGG
* *
55416630 GGGTAGAGTTGTAACGCCCTGAATAATTTAAGTCTATGTGTGTGAAATCTGATATAAATATGTAT
195 GGGTAGAGTTGTAACGCCCTGAATAATTTAAGTCTATGTGTATGAAATATGATATAAATATGTAT
55416695 CTGCTTCAGT
Statistics
Matches: 227, Mismatches: 31, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
302 225 0.99
303 2 0.01
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.33
Consensus pattern (302 bp):
TTTTGAGGAAGAGCCAATTCAAATTTTAGATCGAGATATTAAGGTTATGAGGAGGAAGTCCATTC
AATTAATTAAGGTTCTCTGGCAGAATCATGACACTGAGGAAGCCACGTGGGAACCTGAGAACTCG
ATGCGTCAGTAGTATCCTCATCTGTTTAGATCAGGTAAATTTCGAGTCTGAAATTTCTTTTAGGG
GGTAGAGTTGTAACGCCCTGAATAATTTAAGTCTATGTGTATGAAATATGATATAAATATGTATT
TGTTGAGGAGATCGAGGAGATCGAAGTTAGACCGGACTTAAC
Found at i:55418244 original size:13 final size:14
Alignment explanation
Indices: 55418226--55418263 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
55418216 ATTCAAGTAG
*
55418226 GATTCTGTTTATCT
1 GATTCTGTATATCT
55418240 G-TTCTGTATATCT
1 GATTCTGTATATCT
55418253 GATTCTG-ATAT
1 GATTCTGTATAT
55418264 TTGTTTCAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.18, C:0.13, G:0.16, T:0.53
Consensus pattern (14 bp):
GATTCTGTATATCT
Found at i:55437033 original size:17 final size:16
Alignment explanation
Indices: 55437007--55437045 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
55436997 TGTGAAAATG
55437007 TTTTTATTTT-ATTTT
1 TTTTTATTTTCATTTT
55437022 ATTTTCTATTTTCATTTT
1 -TTTT-TATTTTCATTTT
55437040 TTTTTA
1 TTTTTA
55437046 AAAAAACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 6 0.29
17 10 0.48
18 5 0.24
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTATTTTCATTTT
Found at i:55437865 original size:16 final size:16
Alignment explanation
Indices: 55437830--55437874 Score: 63
Period size: 16 Copynumber: 2.7 Consensus size: 16
55437820 TTTTGGACAT
*
55437830 AATTATTTTCAAATAAC
1 AATTATTTT-AAACAAC
55437847 AATTATTTTAAACAAC
1 AATTATTTTAAACAAC
55437863 AATTATTCTTAA
1 AATTATT-TTAA
55437875 CTAGAGTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTATTTTAAACAAC
Found at i:55440230 original size:28 final size:29
Alignment explanation
Indices: 55440198--55440252 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
55440188 TTTTAATGTG
55440198 CAATTGTATACATG-AATTTTGATTTGTA
1 CAATTGTATACATGAAATTTTGATTTGTA
*
55440226 CAATTTTATACATGAAATTTTGATTTG
1 CAATTGTATACATGAAATTTTGATTTG
55440253 ATCCAATTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (29 bp):
CAATTGTATACATGAAATTTTGATTTGTA
Found at i:55440470 original size:29 final size:30
Alignment explanation
Indices: 55440395--55440479 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 30
55440385 GATTAAATCA
* *
55440395 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAGTTTCATGTATACAATTGAACC
* * * *
55440425 ACAATTAGAGTTTCATGTGTATAATTGCACC
1 A-AATTAAAGTTTCATGTATACAATTGAACC
55440456 AAATTAAAG-TTCATGTATACAATT
1 AAATTAAAGTTTCATGTATACAATT
55440480 TTACATTAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 13 0.29
30 8 0.18
31 24 0.53
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (30 bp):
AAATTAAAGTTTCATGTATACAATTGAACC
Found at i:55450207 original size:5 final size:5
Alignment explanation
Indices: 55450197--55450224 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
55450187 CTCCATTATA
55450197 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
55450225 TAACCTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:55452378 original size:7 final size:7
Alignment explanation
Indices: 55452344--55452378 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
55452334 ATCTTCCTTC
55452344 TTAAAAA
1 TTAAAAA
*
55452351 TTTAAAA
1 TTAAAAA
*
55452358 TTCAAAA
1 TTAAAAA
55452365 TTAAAAA
1 TTAAAAA
55452372 TTAAAAA
1 TTAAAAA
55452379 ATGAATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (7 bp):
TTAAAAA
Found at i:55459823 original size:19 final size:17
Alignment explanation
Indices: 55459792--55459838 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
55459782 ATAAACTGAT
55459792 AAATAAT-AAAATAAAGTA
1 AAATAATAAAAAT-AA-TA
55459810 AAATAATAAAAATAATA
1 AAATAATAAAAATAATA
55459827 AAA-AATAAAAAT
1 AAATAATAAAAAT
55459839 TGGGTTGCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.32
17 5 0.18
18 9 0.32
19 5 0.18
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (17 bp):
AAATAATAAAAATAATA
Found at i:55470268 original size:24 final size:24
Alignment explanation
Indices: 55470241--55470287 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
55470231 TCCTATATCC
55470241 AGTAGCTCCAAAGAGCAATTAACA
1 AGTAGCTCCAAAGAGCAATTAACA
55470265 AGTAGCTCCAAAGAGCAATTAAC
1 AGTAGCTCCAAAGAGCAATTAAC
55470288 GGGAAGCACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.45, C:0.21, G:0.17, T:0.17
Consensus pattern (24 bp):
AGTAGCTCCAAAGAGCAATTAACA
Found at i:55482727 original size:23 final size:26
Alignment explanation
Indices: 55482693--55482748 Score: 82
Period size: 23 Copynumber: 2.3 Consensus size: 26
55482683 GGCCCGGCCA
*
55482693 TTTTTAATTAAAATTAAAA-TTATT-
1 TTTTTAATTAAAATTAAAACTAATTG
55482717 TTTTTAA-TAAAATTAAAACTAATTG
1 TTTTTAATTAAAATTAAAACTAATTG
55482742 TTTTTAA
1 TTTTTAA
55482749 AATTAGTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 11 0.38
24 11 0.38
25 7 0.24
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
TTTTTAATTAAAATTAAAACTAATTG
Found at i:55484683 original size:22 final size:23
Alignment explanation
Indices: 55484635--55484681 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
55484625 AAGTAAAGTA
55484635 TTAAAATAAAAAACTATTATATT
1 TTAAAATAAAAAACTATTATATT
55484658 TTAAAATAAAAAA-TATATATATT
1 TTAAAATAAAAAACTAT-TATATT
55484681 T
1 T
55484682 AATATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
TTAAAATAAAAAACTATTATATT
Found at i:55492124 original size:22 final size:22
Alignment explanation
Indices: 55492080--55492135 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
55492070 TATGGATTAT
55492080 GGTTTA-ATGGTT-GGGATTTAA
1 GGTTTAGA-GGTTAGGGATTTAA
*
55492101 GGTTTAGAGGTTAGGGGTTTAA
1 GGTTTAGAGGTTAGGGATTTAA
* *
55492123 GGGTTAGATGTTA
1 GGTTTAGAGGTTA
55492136 TAGGATTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 10 0.33
22 20 0.67
ACGTcount: A:0.23, C:0.00, G:0.38, T:0.39
Consensus pattern (22 bp):
GGTTTAGAGGTTAGGGATTTAA
Found at i:55492314 original size:14 final size:14
Alignment explanation
Indices: 55492292--55492343 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
55492282 TTAATTATGA
*
55492292 TTATAGTTTAGGGT
1 TTATGGTTTAGGGT
55492306 TTATGGTTTAGGGT
1 TTATGGTTTAGGGT
* * *
55492320 ATATGGTGTAAGGT
1 TTATGGTTTAGGGT
*
55492334 TTAAGGTTTA
1 TTATGGTTTA
55492344 AGAGTTACTA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (14 bp):
TTATGGTTTAGGGT
Found at i:55492345 original size:14 final size:14
Alignment explanation
Indices: 55492292--55492401 Score: 55
Period size: 14 Copynumber: 7.7 Consensus size: 14
55492282 TTAATTATGA
* *
55492292 TTATAGTTTAGGGT
1 TTATGGTTTAAGGT
*
55492306 TTATGGTTTAGGGT
1 TTATGGTTTAAGGT
* *
55492320 ATATGGTGTAAGGT
1 TTATGGTTTAAGGT
*
55492334 TTAAGGTTTAAGAGT
1 TTATGGTTTAAG-GT
*
55492349 TACTAT--TTTAAAGT
1 T--TATGGTTTAAGGT
* *
55492363 TTATGGATTATGAGT
1 TTATGGTTTAAG-GT
* *
55492378 TTA-GAGATTACGGT
1 TTATG-GTTTAAGGT
55492392 TTATGGTTTA
1 TTATGGTTTA
55492402 TTGTTTAAGG
Statistics
Matches: 74, Mismatches: 14, Indels: 16
0.71 0.13 0.15
Matches are distributed among these distances:
12 3 0.04
14 49 0.66
15 20 0.27
17 2 0.03
ACGTcount: A:0.26, C:0.02, G:0.26, T:0.45
Consensus pattern (14 bp):
TTATGGTTTAAGGT
Found at i:55493950 original size:12 final size:13
Alignment explanation
Indices: 55493919--55493952 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
55493909 GTTTTTTTTT
55493919 CTTTGATTATTTA
1 CTTTGATTATTTA
*
55493932 TTTTGATTA-TTA
1 CTTTGATTATTTA
55493944 CTTTGATTA
1 CTTTGATTA
55493953 ATGTCACCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.24, C:0.06, G:0.09, T:0.62
Consensus pattern (13 bp):
CTTTGATTATTTA
Found at i:55494520 original size:23 final size:23
Alignment explanation
Indices: 55494452--55494521 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
55494442 GTCTTGAAAT
55494452 GATCCTTGTATGGCAGTGTCTTA
1 GATCCTTGTATGGCAGTGTCTTA
* ***
55494475 GATTCTTGTGATTATAGTGTCTTA
1 GATCCTTGT-ATGGCAGTGTCTTA
55494499 GATCCTTGTATGGCAGTGTCTTA
1 GATCCTTGTATGGCAGTGTCTTA
55494522 AATTGAAACT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
23 19 0.50
24 19 0.50
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.43
Consensus pattern (23 bp):
GATCCTTGTATGGCAGTGTCTTA
Found at i:55494608 original size:14 final size:14
Alignment explanation
Indices: 55494589--55494631 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
55494579 TCATTGTTTA
55494589 TGATTTATACATAT
1 TGATTTATACATAT
55494603 TGATTTATACATA-
1 TGATTTATACATAT
*
55494616 -G-TGTATACATAT
1 TGATTTATACATAT
55494628 TGAT
1 TGAT
55494632 CAAATCAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
11 9 0.36
12 1 0.04
13 1 0.04
14 14 0.56
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.47
Consensus pattern (14 bp):
TGATTTATACATAT
Found at i:55498547 original size:43 final size:43
Alignment explanation
Indices: 55498500--55498655 Score: 215
Period size: 43 Copynumber: 3.6 Consensus size: 43
55498490 AGAATGTATC
*
55498500 TTTTAGCGGCGTTTGT-GATAAAAGCGTCGCTAAAGATCATGTT
1 TTTTAGCGGCGTTTGTGGAT-AAAGCGTCGTTAAAGATCATGTT
* *
55498543 TTTTAGCGGTGTTTGTGGATAAAGTGTCGTTAAAGATCATGTT
1 TTTTAGCGGCGTTTGTGGATAAAGCGTCGTTAAAGATCATGTT
* * * *
55498586 CTTTACCGGCGTTTGTGGGTAAAGTGTCGTTAAAGATCATGTT
1 TTTTAGCGGCGTTTGTGGATAAAGCGTCGTTAAAGATCATGTT
* *
55498629 TTTTAGCGGCGCTTGTTGATAAAGCGT
1 TTTTAGCGGCGTTTGTGGATAAAGCGT
55498656 AGGGAAAGCG
Statistics
Matches: 99, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
43 96 0.97
44 3 0.03
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (43 bp):
TTTTAGCGGCGTTTGTGGATAAAGCGTCGTTAAAGATCATGTT
Found at i:55498598 original size:86 final size:86
Alignment explanation
Indices: 55498476--55498652 Score: 227
Period size: 86 Copynumber: 2.1 Consensus size: 86
55498466 GCGTTTTCCC
* *
55498476 ATAAA-TGTTGTTAAAGAATGTATCTTTTAGCGGCGTTTGT-GATAAAAGCGTCGCTAAAGATCA
1 ATAAAGTGTCGTTAAAGAATGTATCTTTTACCGGCGTTTGTGGAT-AAAGCGTCGCTAAAGATCA
* *
55498539 TGTTTTTTAGCGGTGTTTGTGG
65 TGTTTTTTAGCGGCGCTTGTGG
* * *
55498561 ATAAAGTGTCGTTAAAGATCATGT-TC-TTTACCGGCGTTTGTGGGTAAAGTGTCGTTAAAGATC
1 ATAAAGTGTCGTTAAAGA--ATGTATCTTTTACCGGCGTTTGTGGATAAAGCGTCGCTAAAGATC
*
55498624 ATGTTTTTTAGCGGCGCTTGTTG
64 ATGTTTTTTAGCGGCGCTTGTGG
55498647 ATAAAG
1 ATAAAG
55498653 CGTAGGGAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
85 5 0.06
86 67 0.84
87 4 0.05
88 4 0.05
ACGTcount: A:0.25, C:0.11, G:0.26, T:0.38
Consensus pattern (86 bp):
ATAAAGTGTCGTTAAAGAATGTATCTTTTACCGGCGTTTGTGGATAAAGCGTCGCTAAAGATCAT
GTTTTTTAGCGGCGCTTGTGG
Found at i:55501556 original size:19 final size:19
Alignment explanation
Indices: 55501526--55501570 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
55501516 GAGGCGTGAC
*
55501526 AAATATTATATATAATAATA
1 AAATA-TATATACAATAATA
* *
55501546 AAATATATATACAATTATT
1 AAATATATATACAATAATA
55501565 AAATAT
1 AAATAT
55501571 TAAATAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATATATATACAATAATA
Found at i:55504433 original size:17 final size:18
Alignment explanation
Indices: 55504402--55504435 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55504392 TATTATATTT
*
55504402 ATCTATATATGCATATGC
1 ATCTATATATACATATGC
55504420 ATCT-TATATACATATG
1 ATCTATATATACATATG
55504436 TTACATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (18 bp):
ATCTATATATACATATGC
Found at i:55506835 original size:21 final size:21
Alignment explanation
Indices: 55506809--55506848 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
55506799 AGTAACATGG
*
55506809 ATTTATTATTTATT-ATGTTTT
1 ATTTA-TATCTATTCATGTTTT
55506830 ATTTATATCTATTCATGTT
1 ATTTATATCTATTCATGTT
55506849 AAATTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (21 bp):
ATTTATATCTATTCATGTTTT
Found at i:55511560 original size:28 final size:28
Alignment explanation
Indices: 55511528--55511625 Score: 160
Period size: 28 Copynumber: 3.5 Consensus size: 28
55511518 TGACTTTTGA
55511528 CACTAAGTGTGCGAGTTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
55511556 CACTAAGTGTGCGAGTTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* * **
55511584 CACTAAGTGTGCGAGTTTGATTATTGAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
55511612 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
55511626 ACTTATTAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.32
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATTGTAAAG
Found at i:55512488 original size:70 final size:70
Alignment explanation
Indices: 55512361--55513043 Score: 1048
Period size: 70 Copynumber: 9.7 Consensus size: 70
55512351 TTTGCTTAAA
* *
55512361 TGCTGCCAATTTGTTTTATATAAGCTGTCCAATTTTTGGTGTAAAAATGTTGCTCAATTTGTTGT
1 TGCTGCCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTTGT
* *
55512426 GTAAT
66 ATATT
* * * *
55512431 TGCTGTCCAATTTGTTGTGTATAAGCTGTCCAA-TTTTGGTGCAAAAATGCTGTTCAATTCGTTG
1 TGCTG-CCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTTG
55512495 TATATT
65 TATATT
*
55512501 TGCTGCCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTATTGT
1 TGCTGCCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTTGT
55512566 ATATT
66 ATATT
*
55512571 TGCTGCCAATTTGTTTTATATAAGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTTGT
1 TGCTGCCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTTGT
* *
55512636 GTAAT
66 ATATT
* * *
55512641 TGCTGTCCAATTTGTTGTGTATAAGCTGTCCAA-TTTTGGTGCAAAAATGCTGCTCAATTCGTTG
1 TGCTG-CCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTTG
55512705 TATATT
65 TATATT
55512711 TGCTGCCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTTGT
1 TGCTGCCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTTGT
55512776 ATATT
66 ATATT
55512781 TGCTGCCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTTGT
1 TGCTGCCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTTGT
55512846 ATATT
66 ATATT
*
55512851 TGCTGCCAATTTGTTTTATATAAGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTTGT
1 TGCTGCCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTTGT
* *
55512916 GTAAT
66 ATATT
* * * * *
55512921 TGCTATCCAATTTGTTGTGTATAAGCTGT-CAAATTTTGGTGCAAAAATGCTGCTCAATATGTTG
1 TGCT-GCCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTTG
*
55512985 TATATA
65 TATATT
* * * * *
55512991 TGCTGCCTAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTGAAATTGCTG
1 TGCTGCC-AATTTGTTGTATATAAGCTGTCCAATTTTTGGTGTAAAAATGCTG
55513044 TTTAGTTTGG
Statistics
Matches: 561, Mismatches: 45, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
69 54 0.10
70 416 0.74
71 91 0.16
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.43
Consensus pattern (70 bp):
TGCTGCCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTTGT
ATATT
Found at i:55515676 original size:50 final size:50
Alignment explanation
Indices: 55515552--55515800 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
55515542 GATAATAACA
* * ** * *
55515552 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
55515603 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
55515653 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
55515703 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
55515758 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
55515801 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:55515730 original size:100 final size:104
Alignment explanation
Indices: 55515551--55515800 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
55515541 TGATAATAAC
**
55515551 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
55515616 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
55515653 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
55515716 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
55515758 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
55515801 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:55515916 original size:13 final size:13
Alignment explanation
Indices: 55515895--55515926 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
55515885 GCTTGGATCA
*
55515895 TCATCAAATAAAT
1 TCATAAAATAAAT
55515908 TCATAAAATAAAT
1 TCATAAAATAAAT
55515921 TCATAA
1 TCATAA
55515927 TTGCTGGAAA
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:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:55516173 original size:30 final size:30
Alignment explanation
Indices: 55516138--55516195 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
55516128 CCTCGACTCT
*
55516138 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
55516168 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
55516196 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:55523275 original size:50 final size:50
Alignment explanation
Indices: 55523151--55523399 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
55523141 GATAATAACA
* * ** * *
55523151 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
55523202 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
55523252 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
55523302 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
55523357 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
55523400 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:55523329 original size:100 final size:104
Alignment explanation
Indices: 55523150--55523399 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
55523140 TGATAATAAC
**
55523150 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
55523215 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
55523252 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
55523315 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
55523357 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
55523400 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:55523515 original size:13 final size:13
Alignment explanation
Indices: 55523494--55523525 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
55523484 GCTTGGATCA
*
55523494 TCATCAAATAAAT
1 TCATAAAATAAAT
55523507 TCATAAAATAAAT
1 TCATAAAATAAAT
55523520 TCATAA
1 TCATAA
55523526 TTGCTGGAAA
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:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:55523772 original size:30 final size:30
Alignment explanation
Indices: 55523737--55523794 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
55523727 CCTCGACTCT
*
55523737 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
55523767 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
55523795 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:55524899 original size:22 final size:24
Alignment explanation
Indices: 55524871--55524914 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
55524861 GATGAGAGAT
55524871 ATCATTT-TT-TTCACCCAAAACC
1 ATCATTTCTTCTTCACCCAAAACC
*
55524893 ATCATTTCTTCTTCCCCCAAAA
1 ATCATTTCTTCTTCACCCAAAA
55524915 TTTCCATCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 2 0.11
24 10 0.53
ACGTcount: A:0.30, C:0.34, G:0.00, T:0.36
Consensus pattern (24 bp):
ATCATTTCTTCTTCACCCAAAACC
Found at i:55538730 original size:13 final size:13
Alignment explanation
Indices: 55538712--55538736 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55538702 ATTAAAATTA
55538712 ATAAAATATTAAT
1 ATAAAATATTAAT
55538725 ATAAAATATTAA
1 ATAAAATATTAA
55538737 AATTTTTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAAAATATTAAT
Found at i:55538730 original size:22 final size:22
Alignment explanation
Indices: 55538704--55538748 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
55538694 TAAAAAAAAT
55538704 TAAAATTAATAAAA-TATTAATA
1 TAAAA-TAATAAAATTATTAATA
* *
55538726 TAAAATATTAAAATTTTTAATA
1 TAAAATAATAAAATTATTAATA
55538748 T
1 T
55538749 TATTAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAAATAATAAAATTATTAATA
Found at i:55538925 original size:15 final size:15
Alignment explanation
Indices: 55538846--55538928 Score: 60
Period size: 13 Copynumber: 6.2 Consensus size: 15
55538836 CAATTTTATC
55538846 TTAATAAT-AA-ATT
1 TTAATAATAAATATT
55538859 TTAA-AA-AAATATT
1 TTAATAATAAATATT
*
55538872 TTTA-AAT-AATATT
1 TTAATAATAAATATT
*
55538885 TT-AGAA-AAATA-T
1 TTAATAATAAATATT
* *
55538897 TCAAT-ATTAATATT
1 TTAATAATAAATATT
55538911 TTAATAATAAATATT
1 TTAATAATAAATATT
55538926 TTA
1 TTA
55538929 TAGTATAATG
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
12 8 0.15
13 31 0.56
14 5 0.09
15 11 0.20
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (15 bp):
TTAATAATAAATATT
Found at i:55539689 original size:21 final size:21
Alignment explanation
Indices: 55539663--55539704 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
55539653 TCTCAAATGT
55539663 ATGTTTGTTTTATTACACACA
1 ATGTTTGTTTTATTACACACA
55539684 ATGTTTGTTTTATTACACACA
1 ATGTTTGTTTTATTACACACA
55539705 CATCAATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.48
Consensus pattern (21 bp):
ATGTTTGTTTTATTACACACA
Found at i:55541005 original size:42 final size:41
Alignment explanation
Indices: 55540922--55541087 Score: 162
Period size: 42 Copynumber: 4.1 Consensus size: 41
55540912 AAAAACACTG
* * * * *
55540922 CAAAAGGTAAAG-CAATAGCGACGTTTTCTCATAAACACCA
1 CAAAAGGTTAAGACTATAGCGGCATTTTCTCATAAACGCCA
* *
55540962 CAAAAGGTTATGACTATAGCGGCATTTTTCTCATAAATGCCA
1 CAAAAGGTTAAGACTATAGCGGCA-TTTTCTCATAAACGCCA
* * *
55541004 CAAAAAGGTTAAAACTATAGCGGCGTTTTCTCACAAACGCCGA
1 C-AAAAGGTTAAGACTATAGCGGCATTTTCTCATAAACGCC-A
* *
55541047 -AAAAGG-TAAG-CAATAGCGGCATTTT-TCATAAATGCCA
1 CAAAAGGTTAAGACTATAGCGGCATTTTCTCATAAACGCCA
55541084 CAAA
1 CAAA
55541088 TATTTATTAA
Statistics
Matches: 104, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
37 1 0.01
38 12 0.12
39 13 0.12
40 13 0.12
41 14 0.13
42 30 0.29
43 21 0.20
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.23
Consensus pattern (41 bp):
CAAAAGGTTAAGACTATAGCGGCATTTTCTCATAAACGCCA
Found at i:55541034 original size:84 final size:79
Alignment explanation
Indices: 55540923--55541087 Score: 206
Period size: 84 Copynumber: 2.0 Consensus size: 79
55540913 AAAACACTGC
* * * *
55540923 AAAAGGTAAAGCAATAGCGACGTTTTCTCATAAACACC-ACAAAAGGTTATGACTATAGCGGCAT
1 AAAAGGTAAAACAATAGCGACGTTTTCTCACAAACACCGA-AAAAGG-TAAG-CAATAGCGGCA-
55540987 TTTTCTCATAAATGCCACA
62 TTTT-TCATAAATGCCACA
* * *
55541006 AAAAGGTTAAAACTATAGCGGCGTTTTCTCACAAACGCCGAAAAAGGTAAGCAATAGCGGCATTT
1 AAAAGG-TAAAACAATAGCGACGTTTTCTCACAAACACCGAAAAAGGTAAGCAATAGCGGCATTT
55541071 TTCATAAATGCCACA
65 TTCATAAATGCCACA
55541086 AA
1 AA
55541088 TATTTATTAA
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
80 16 0.22
81 4 0.05
82 10 0.14
83 9 0.12
84 33 0.45
85 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (79 bp):
AAAAGGTAAAACAATAGCGACGTTTTCTCACAAACACCGAAAAAGGTAAGCAATAGCGGCATTTT
TCATAAATGCCACA
Found at i:55545327 original size:3 final size:3
Alignment explanation
Indices: 55545321--55545430 Score: 96
Period size: 3 Copynumber: 36.7 Consensus size: 3
55545311 TATTTAGCTA
** * * * *
55545321 ATT ATT ATT AAC ATT ATT ATT TTT AAT ATT TTT ACT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
55545369 ATT ATT ATT ATT ATC ATCT -TT ACT ATT ATT ATT AAT ATT AAT GTT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
55545414 ATT ATT ATT ATC ATT AT
1 ATT ATT ATT ATT ATT AT
55545431 ATTTCTATTT
Statistics
Matches: 81, Mismatches: 24, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
2 1 0.01
3 80 0.99
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:55545351 original size:36 final size:34
Alignment explanation
Indices: 55545305--55545408 Score: 109
Period size: 36 Copynumber: 2.9 Consensus size: 34
55545295 TTTTAGCATC
* *
55545305 TTTTATTATTTAGCTAATTATTATTAACATTATTAT
1 TTTTAATATTTA-CT-ATTATTATTAATATTATTAT
*
55545341 TTTTAATATTTTTACTATTATTATTATTATTATTAT
1 TTTTAATA--TTTACTATTATTATTAATATTATTAT
* *
55545377 TATTATCATCTTTACTATTATTATTAATATTA
1 T-TT-TAATATTTACTATTATTATTAATATTA
55545409 ATGTTATTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
36 47 0.81
37 4 0.07
38 7 0.12
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.61
Consensus pattern (34 bp):
TTTTAATATTTACTATTATTATTAATATTATTAT
Found at i:55546303 original size:110 final size:109
Alignment explanation
Indices: 55546090--55546408 Score: 412
Period size: 110 Copynumber: 2.9 Consensus size: 109
55546080 AAATTTTTCT
* * *
55546090 AAATGAGGCAATATTTAGCATTTGGAAATATGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATT
1 AAATAAGGCAATGTTTTGCATTTGGAAAT-TGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATT
* * *
55546155 TTTCTCGTTCAACCAAATGGCTTAATATCCTTTAAAAAAAATTCA
65 TTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAAAATTCA
* * * *
55546200 AAATATGGTAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATT
1 AAATAAGGCAATGTTTTGCATTTGGAAATT-GAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATT
*
55546265 TTTCTCATTCAACCAAATGGCTAAATATCCTTTT-AAAAATTTCA
65 TTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAAAATTCA
* * *
55546309 AAATAAGGCAATGTTTTGCATTTGGAAATTTGAG-GAACGTACCCTAAGGTGCTGGGTTTCGA--
1 AAATAAGGCAATGTTTTGCATTTGGAAA-TTGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATT
* * * *
55546371 TTTCTCATTTAACCAAATTGCCAAAATATCCTCTTAAA
65 TTTCTCATTCAACCAAA-TGGCTAAATATCCTTTTAAA
55546409 TTTTAATCCA
Statistics
Matches: 183, Mismatches: 22, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
106 16 0.09
107 14 0.08
108 26 0.14
109 38 0.21
110 89 0.49
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (109 bp):
AAATAAGGCAATGTTTTGCATTTGGAAATTGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTT
TTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAAAATTCA
Found at i:55548472 original size:50 final size:50
Alignment explanation
Indices: 55548355--55548640 Score: 401
Period size: 50 Copynumber: 5.7 Consensus size: 50
55548345 ACATGCCACA
* ** * *
55548355 GCCATGTCCCAGACGTGGTCTTACATGGGATGTACTCATGTCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCT-CTCATCTCGGTGCCAAT
** *
55548406 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
* * * * *
55548456 GCTATGTCTCAAACATGGTCTTATATGGGACCTCTCATCTCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
* * * *
55548506 GCCATGTCCCAGACATGGTCGTACAGGGGACCTATGATCTCGGTGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
*
55548556 GCCATGTCCCAGACATGGTCTTACATGGGACCTCACATCTCGGTGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
55548606 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
55548641 TTACCCAAAT
Statistics
Matches: 204, Mismatches: 31, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
50 176 0.86
51 28 0.14
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
Found at i:55549016 original size:30 final size:30
Alignment explanation
Indices: 55548981--55549038 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
55548971 CCTCGACTCT
55548981 AACTTTTTCAAAATTACGA-TTTTGCCCCTA
1 AACTTTTTCAAAATTAC-ATTTTTGCCCCTA
*
55549011 AACTTTTTCATAATTACATTTTTGCCCC
1 AACTTTTTCAAAATTACATTTTTGCCCC
55549039 AAGGCTCGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.28, C:0.24, G:0.05, T:0.43
Consensus pattern (30 bp):
AACTTTTTCAAAATTACATTTTTGCCCCTA
Found at i:55553903 original size:6 final size:6
Alignment explanation
Indices: 55553884--55553935 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
55553874 AAGAAAAAGA
* * * * * *
55553884 AAAATC AAAATC AAAGTC AAAATG AAAATG AAAATG AAAATG AAAATG
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
55553932 AAAA
1 AAAA
55553936 AAATCAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.67, C:0.06, G:0.12, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:55553952 original size:6 final size:6
Alignment explanation
Indices: 55553902--55553935 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
55553892 AATCAAAGTC
55553902 AAAATG AAAATG AAAATG AAAATG AAAATG AAAA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAA
55553936 AAATCAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:55554949 original size:7 final size:7
Alignment explanation
Indices: 55554937--55555009 Score: 125
Period size: 7 Copynumber: 10.9 Consensus size: 7
55554927 CTGAGTAAAA
55554937 AAAAATG
1 AAAAATG
55554944 AAAAATG
1 AAAAATG
55554951 -AAAATG
1 AAAAATG
55554957 AAAAATG
1 AAAAATG
55554964 AAAAATG
1 AAAAATG
55554971 -AAAATG
1 AAAAATG
55554977 -AAAATG
1 AAAAATG
55554983 AAAAATG
1 AAAAATG
55554990 AAAAATG
1 AAAAATG
55554997 AAAAATG
1 AAAAATG
55555004 AAAAAT
1 AAAAAT
55555010 AGAGAGGCTA
Statistics
Matches: 64, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
6 18 0.28
7 46 0.72
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.15
Consensus pattern (7 bp):
AAAAATG
Found at i:55554956 original size:13 final size:13
Alignment explanation
Indices: 55554938--55555007 Score: 115
Period size: 13 Copynumber: 5.3 Consensus size: 13
55554928 TGAGTAAAAA
55554938 AAAATGAAAAATG
1 AAAATGAAAAATG
55554951 AAAATGAAAAATG
1 AAAATGAAAAATG
55554964 AAAAATG-AAAATG
1 -AAAATGAAAAATG
55554977 AAAATGAAAAATG
1 AAAATGAAAAATG
55554990 AAAAATGAAAAATG
1 -AAAATGAAAAATG
55555004 AAAA
1 AAAA
55555008 ATAGAGAGGC
Statistics
Matches: 54, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.11
13 29 0.54
14 19 0.35
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:55554962 original size:20 final size:20
Alignment explanation
Indices: 55554937--55555009 Score: 130
Period size: 20 Copynumber: 3.6 Consensus size: 20
55554927 CTGAGTAAAA
55554937 AAAAATGAAAAATGAAAATG
1 AAAAATGAAAAATGAAAATG
55554957 AAAAATGAAAAATGAAAATG
1 AAAAATGAAAAATGAAAATG
55554977 -AAAATGAAAAATGAAAAATG
1 AAAAATGAAAAATG-AAAATG
55554997 AAAAATGAAAAAT
1 AAAAATGAAAAAT
55555010 AGAGAGGCTA
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
19 13 0.25
20 26 0.51
21 12 0.24
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.15
Consensus pattern (20 bp):
AAAAATGAAAAATGAAAATG
Found at i:55556456 original size:44 final size:44
Alignment explanation
Indices: 55556258--55556809 Score: 253
Period size: 44 Copynumber: 12.7 Consensus size: 44
55556248 GAAGAATTTC
* * * * *
55556258 AGATCTTATCTTCCTGAGGTTACAGTGGAGCAGATT-AAAATAA
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
* * ** * * * *
55556301 AGGATCATATCTCTCTGA-AGTTACAGCAGAGTAGATCGCA-TCAG
1 A-GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGACAG
* * ** *
55556345 -G-TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGA-ATTTC
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACA---G
* *
55556389 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
* *
55556433 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA-
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
** * * * * * *
55556476 CTATCCTATCTCCCTGA-AGTTATAGTGGAGCGGATT-AAAATAA
1 AGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGACAG
* * ** * * * *
55556519 ATGATATTATCTCTCTGA-AGTTACAGCAGAGTAGATCGCA-TCAG
1 A-GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGACAG
* ** ** * * *
55556563 -G-TCTTATCTCCCTGAGGTTACAGTGGAATAGA-CCAAAAAATTTC
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACA---G
* *
55556607 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
* * * *
55556651 AAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGATAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
* * * * *
55556695 TA-ATCCTATCTCCCTGAGATTACAGTGGAGCGGATT-AAAATAA
1 -AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
* ** * * * *
55556738 AGGATCTTATCTCTCTGA-AGTTACAGCAGAGTAGATCGCA-TCAG
1 A-GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGACAG
*
55556782 -G-TCTTATCTCCCTGAGGTTACAGTGGAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAG
55556810 TAGACCGAAG
Statistics
Matches: 380, Mismatches: 100, Indels: 60
0.70 0.19 0.11
Matches are distributed among these distances:
40 2 0.01
41 76 0.20
42 9 0.02
43 34 0.09
44 186 0.49
45 6 0.02
46 63 0.17
47 4 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAG
Found at i:55556659 original size:218 final size:219
Alignment explanation
Indices: 55556264--55556859 Score: 1000
Period size: 218 Copynumber: 2.7 Consensus size: 219
55556254 TTTCAGATCT
* * *
55556264 TATCTTCCTGAGGTTACAGTGGAGCAGATTAAAATAAAGGATCA-TATCTCTCTGAAGTTACAGC
1 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGAT-ATTATCTCTCTGAAGTTACAGC
55556328 AGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGAT
65 AGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGAT
* *
55556393 CTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAG
130 CTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAG
55556458 CGGAGCAGATCGAAGACACT-ATCC
195 CGGAGCAGATCGAAGACACTAATCC
* *
55556482 TATCTCCCTGAAGTTATAGTGGAGCGGATTAAAATAAATGATATTATCTCTCTGAAGTTACAGCA
1 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATATTATCTCTCTGAAGTTACAGCA
* * *
55556547 GAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAATAGACCAAAAAATTTCAGATC
66 GAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATC
55556612 TTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGC
131 TTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGC
* * *
55556677 GGAGCAGATTGAAGATAGTAATCC
196 GGAGCAGATCGAAGACACTAATCC
*
55556701 TATCTCCCTG-AGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGC
1 TATCTCCCTGAAG-TTACAGTGGAGCGGATTAAAATAAAGGATATTATCTCTCTGAAGTTACAGC
*
55556765 AGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCATAT
65 AGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGAT
* *
55556830 CTTATCTCCCTGAAGTTACAGTGGAACAGA
130 CTTATCTCCCTGAGGTTACAGTGGAGCAGA
55556860 CGAAAAATAC
Statistics
Matches: 353, Mismatches: 22, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
217 1 0.00
218 201 0.57
219 151 0.43
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (219 bp):
TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATATTATCTCTCTGAAGTTACAGCA
GAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATC
TTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGC
GGAGCAGATCGAAGACACTAATCC
Found at i:55556898 original size:175 final size:173
Alignment explanation
Indices: 55556611--55557083 Score: 398
Period size: 175 Copynumber: 2.7 Consensus size: 173
55556601 AATTTCAGAT
* * ** ** * *
55556611 CTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAAATCTTATCTCCCT-AAGATTACA
1 CTTATCTCCCTGAAGTCACAGTGGAGCAGACCGAAGATACAAGTCTTATCTCCCTGAAG-TTACA
* * *** * ** * * * *
55556675 GCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTG-AGATTACAGTGGAGCGGATTAAAATAAA
65 GTGGAACAGACAAAAAATACCAATCGTGTCTCCCTGAAG-TTACAGTGGAGTGGATAAAAATAAA
* * ***
55556739 GGATCTTAT-CTCTCTGAAGTTACAGCAGAGTAG-ATCGCATCAGGT
129 GAATCATATAC-CTCTGAAGTTACAGCAG-GTAGAATCGCATCAAAC
* * * *
55556784 CTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCATA-TCTTATCTCCCTGAAGTTA
1 CTTATCTCCCTGAAGTCACAGTGGAGCAGACCGAAG-A-TACA-AGTCTTATCTCCCTGAAGTTA
* * * **
55556848 CAGTGGAACAGACGAAAAATACCAATCGTGTCTCCCTGAAGTTGCAGTGGAGTGGATGAAAACGA
63 CAGTGGAACAGACAAAAAATACCAATCGTGTCTCCCTGAAGTTACAGTGGAGTGGATAAAAATAA
* * * * * *
55556913 TGAATCATATACCTCTGAAGTTGCAGTAGGTCGAATTGGATCAAAC
128 AGAATCATATACCTCTGAAGTTACAGCAGGTAGAATCGCATCAAAC
* *** * * *
55556959 CTTATCTCCCTGAAGTCGCAGTGGAGCAGGTTGATGATACAAGTCTTATCTCTCTGAAGTTGCAG
1 CTTATCTCCCTGAAGTCACAGTGGAGCAGACCGAAGATACAAGTCTTATCTCCCTGAAGTTACAG
* * *
55557024 TGGAGCAGACAAAAAATACCAATCGTGTCTCCCTAAATTTACAGTGGAGTGGATAAAAAT
66 TGGAACAGACAAAAAATACCAATCGTGTCTCCCTGAAGTTACAGTGGAGTGGATAAAAAT
55557084 CAATCCTATA
Statistics
Matches: 241, Mismatches: 51, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
172 1 0.00
173 109 0.45
174 4 0.02
175 120 0.50
176 7 0.03
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (173 bp):
CTTATCTCCCTGAAGTCACAGTGGAGCAGACCGAAGATACAAGTCTTATCTCCCTGAAGTTACAG
TGGAACAGACAAAAAATACCAATCGTGTCTCCCTGAAGTTACAGTGGAGTGGATAAAAATAAAGA
ATCATATACCTCTGAAGTTACAGCAGGTAGAATCGCATCAAAC
Found at i:55562700 original size:1 final size:1
Alignment explanation
Indices: 55562694--55562808 Score: 68
Period size: 1 Copynumber: 115.0 Consensus size: 1
55562684 AATTCAGTTC
* * * * * * * * * *
55562694 AAAAAAAAGAGAAAAAAAACAAAAAAACAAAAAAACAAAAAAACAAAAAATAGAAAAAAATAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * *
55562759 AAAAAAGAACAAAAAAGAACAAAAAACAAAAAACAAAAAGAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
55562809 CCTCTACCGG
Statistics
Matches: 78, Mismatches: 36, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 78 1.00
ACGTcount: A:0.84, C:0.08, G:0.06, T:0.02
Consensus pattern (1 bp):
A
Done.