Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 42 of 208
Found at i:11550684 original size:4 final size:4
Alignment explanation
Indices: 11550675--11550701 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
11550665 TGATTTTAGT
11550675 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
11550702 TCTTTTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:11551343 original size:3 final size:3
Alignment explanation
Indices: 11551335--11551404 Score: 63
Period size: 3 Copynumber: 23.3 Consensus size: 3
11551325 TTGTTTTTAC
* * *
11551335 TAT TAT TAT TAT T-T AATT TAT TAT TAT TGT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
11551380 TAT TAT TGT TA- TAGG TAT TAT TAT T
1 TAT TAT TAT TAT TA-T TAT TAT TAT T
11551405 GTATTAGTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
2 3 0.06
3 47 0.87
4 4 0.07
ACGTcount: A:0.30, C:0.01, G:0.06, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:11551367 original size:12 final size:12
Alignment explanation
Indices: 11551325--11551391 Score: 64
Period size: 12 Copynumber: 5.6 Consensus size: 12
11551315 AAAATTGTCC
* *
11551325 TTGTTTTTACTA
1 TTGTTATTATTA
*
11551337 TTATTATTATTTA
1 TTGTTATTA-TTA
*
11551350 AT-TTATTATTA
1 TTGTTATTATTA
*
11551361 TTGTTATTACTA
1 TTGTTATTATTA
*
11551373 TTATTATTATTA
1 TTGTTATTATTA
11551385 TTGTTAT
1 TTGTTAT
11551392 AGGTATTATT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
11 4 0.09
12 37 0.84
13 3 0.07
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.66
Consensus pattern (12 bp):
TTGTTATTATTA
Found at i:11551398 original size:24 final size:24
Alignment explanation
Indices: 11551352--11551404 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
11551342 ATTATTTAAT
11551352 TTATTATTATTGTTATTACTATTA
1 TTATTATTATTGTTATTACTATTA
*
11551376 TTATTATTATTGTTA-TAGGTATTA
1 TTATTATTATTGTTATTA-CTATTA
11551400 TTATT
1 TTATT
11551405 GTATTAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 2 0.07
24 25 0.93
ACGTcount: A:0.28, C:0.02, G:0.08, T:0.62
Consensus pattern (24 bp):
TTATTATTATTGTTATTACTATTA
Found at i:11551761 original size:2 final size:2
Alignment explanation
Indices: 11551754--11551784 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
11551744 TTTCAACATT
*
11551754 TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11551785 TATTTGTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:11554579 original size:38 final size:38
Alignment explanation
Indices: 11554528--11554605 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
11554518 ATTTGTTGGC
11554528 ATTTGTGACTTATTTTTATCTTGGATTCATTTTACCAA
1 ATTTGTGACTTATTTTTATCTTGGATTCATTTTACCAA
11554566 ATTTGTGACTTATTTTTATCTTGGATTCATTTTACCAA
1 ATTTGTGACTTATTTTTATCTTGGATTCATTTTACCAA
11554604 AT
1 AT
11554606 GATCTCAAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.24, C:0.13, G:0.10, T:0.53
Consensus pattern (38 bp):
ATTTGTGACTTATTTTTATCTTGGATTCATTTTACCAA
Found at i:11558006 original size:148 final size:148
Alignment explanation
Indices: 11557712--11558062 Score: 361
Period size: 148 Copynumber: 2.3 Consensus size: 148
11557702 AAATAGGCAT
* * * *
11557712 TAAATATGGAATTTAACCATTCTT-TATAATCTCAAAAAATTAGAGGGATTAGAATTGATATTTG
1 TAAATATGAAATTTAACCATTCTTATATAATCTCAAAAAAGTAGAGGGACTAAAATTGATATTTG
** ** * * * * *
11557776 GCCATTAGCTTCTCATATTAAAGAAAGCAATTAACATTGGACAAGTATCATGTAAAAAGTAGAGG
66 AACATTAGCTTCTCATAAAAAAAAAAACAACTAACATTGGACAAGTATCATGTAAAAAGCAGAGA
*
11557841 GGTTAAAAAAGTAG-AAAA
131 GATT-AAAAAGTAGAAAAA
11557859 TAAATATGAAATTTAACCATTCTTATATAATCTCAAAAAAGTAGAGGGACTAAAATTGATATTTG
1 TAAATATGAAATTTAACCATTCTTATATAATCTCAAAAAAGTAGAGGGACTAAAATTGATATTTG
*** *
11557924 AACATTAGCTTCTCATGTAAGAAAAAAAAAACAACTAACATTGGATTGGTGTCATGTAAAAA-CA
66 AACATTAGCTTCTCA--T-A-AAAAAAAAAACAACTAACATTGGACAAGTATCATGTAAAAAGCA
** * *
11557988 GAGAGATTAGAATTGAAAAATAGGAA
127 GAGAGATTA-AAAAGTAGAA-A--AA
*
11558014 TTAAATATTG-AATTTAACTATTCTTATATAATCTC-AAAAAGTAGAGGGA
1 -TAAATA-TGAAATTTAACCATTCTTATATAATCTCAAAAAAGTAGAGGGA
11558063 TTGAACCCCA
Statistics
Matches: 169, Mismatches: 23, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
147 23 0.14
148 50 0.30
150 2 0.01
151 12 0.07
152 33 0.20
153 1 0.01
155 16 0.09
156 30 0.18
157 2 0.01
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.30
Consensus pattern (148 bp):
TAAATATGAAATTTAACCATTCTTATATAATCTCAAAAAAGTAGAGGGACTAAAATTGATATTTG
AACATTAGCTTCTCATAAAAAAAAAAACAACTAACATTGGACAAGTATCATGTAAAAAGCAGAGA
GATTAAAAAGTAGAAAAA
Found at i:11563589 original size:17 final size:18
Alignment explanation
Indices: 11563558--11563592 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
11563548 AAAAGCCTCA
*
11563558 TTTTATTTATTTATTTAC
1 TTTTATTTATATATTTAC
11563576 TTTT-TTTATATATTTAC
1 TTTTATTTATATATTTAC
11563593 ATCGCAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTATTTATATATTTAC
Found at i:11564010 original size:30 final size:30
Alignment explanation
Indices: 11563971--11564063 Score: 125
Period size: 30 Copynumber: 3.1 Consensus size: 30
11563961 TCAGGCATTA
* *
11563971 ACATTAGCATCGACTACTGCATGGGCATCT
1 ACATCAGCATCGACTACTACATGGGCATCT
11564001 ACATCAGCATCGACTACTACATGGGCATCT
1 ACATCAGCATCGACTACTACATGGGCATCT
* * *
11564031 ACATC-GACATCGATTGCTATATGGGCATCT
1 ACATCAG-CATCGACTACTACATGGGCATCT
11564061 ACA
1 ACA
11564064 CCTATATCGT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 1 0.02
30 56 0.98
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (30 bp):
ACATCAGCATCGACTACTACATGGGCATCT
Found at i:11567530 original size:19 final size:18
Alignment explanation
Indices: 11567503--11567541 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
11567493 ATTTTTTATA
*
11567503 TATTCTTTATATTGTTTTT
1 TATTCTTTATAAT-TTTTT
*
11567522 TATTTTTTATAATTTTTT
1 TATTCTTTATAATTTTTT
11567540 TA
1 TA
11567542 AAAATATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (18 bp):
TATTCTTTATAATTTTTT
Found at i:11567601 original size:19 final size:19
Alignment explanation
Indices: 11567546--11567601 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 19
11567536 TTTTTAAAAA
**
11567546 TATAAATT-TTTAAATTTT
1 TATAAATTATTTTGATTTT
*
11567564 TATAAA-TATTTTGAATTT
1 TATAAATTATTTTGATTTT
11567582 TATAAATTATTTTGATTTT
1 TATAAATTATTTTGATTTT
11567601 T
1 T
11567602 TTTGTATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 1 0.03
18 19 0.59
19 12 0.38
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (19 bp):
TATAAATTATTTTGATTTT
Found at i:11576050 original size:39 final size:38
Alignment explanation
Indices: 11575996--11576138 Score: 151
Period size: 39 Copynumber: 3.7 Consensus size: 38
11575986 TGATTATTCA
* *
11575996 GGCTATGTGGCTAGCAGGCTGTGTGCTGGTAATTACTTG
1 GGCTATGTGCCTAGCAGGCTGTGTGCCGGTAATTA-TTG
* * * **
11576035 GGCTATGTGCCTAGCAAGCTGGGTGCCGGTTATTATCCA
1 GGCTATGTGCCTAGCAGGCTGTGTGCCGGTAATTAT-TG
* * * *
11576074 GGTTATGTGTCTAGTAGGCTGTGTGCCGGTGATTATTCG
1 GGCTATGTGCCTAGCAGGCTGTGTGCCGGTAATTATT-G
*
11576113 GGCTATGTGCCTAGCAGGCTATGTGC
1 GGCTATGTGCCTAGCAGGCTGTGTGC
11576139 TGGTGTATTA
Statistics
Matches: 83, Mismatches: 19, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
38 1 0.01
39 82 0.99
ACGTcount: A:0.15, C:0.18, G:0.34, T:0.32
Consensus pattern (38 bp):
GGCTATGTGCCTAGCAGGCTGTGTGCCGGTAATTATTG
Found at i:11578543 original size:140 final size:138
Alignment explanation
Indices: 11578191--11578572 Score: 432
Period size: 139 Copynumber: 2.7 Consensus size: 138
11578181 TAATTAGAAA
*
11578191 AGTTAAAAGCTCCCAACTGTCATTCTAAGGCTCGCAGTTCTAATA-C-TATGGCCTCCAAACAGT
1 AGTTAAAAGCTCCCAACTGTCATTCTAAGGCTCGCAGTT-TAATATCGCA--GCCTCCAAACAGT
* * * ** *
11578254 TAGCGAGAGTTAGAATCTCTCAGCTATCATTTTAAGGCTTGCAAGTTTAATACTGCGACCTCTAT
63 TAGCGAGAGTTAAAAGCTCCCAGCTATCATTTTAAGGCTCACAAGTTTAATACCGCGACCTCTAT
* *
11578319 AAATTAGTGAG
128 AAATTAGCGAC
* * * * *
11578330 AGTTAAAAGCTCCCAGCTATCATTCTAAGGTTCGCATGTTCAATATCGC-GACCTCTAAACAGTT
1 AGTTAAAAGCTCCCAACTGTCATTCTAAGGCTCGCA-GTTTAATATCGCAG-CCTCCAAACAGTT
* *
11578394 AGCGAGAGTTAAAAGCTCCCAGCTTTCATTTTAAGGCTCACAGGTTTAATACCGC-AGCCTCTA-
64 AGCGAGAGTTAAAAGCTCCCAGCTATCATTTTAAGGCTCACAAGTTTAATACCGCGA-CCTCTAT
11578457 AATAGTTAGCGAC
128 AA-A-TTAGCGAC
* * * *
11578470 AGTTAAAAGCTCCTAACTGTCATTCTAAGGGTCACAGGTTTAATATCGCAGCCTCCAAACTGTTA
1 AGTTAAAAGCTCCCAACTGTCATTCTAAGGCTCGCA-GTTTAATATCGCAGCCTCCAAACAGTTA
* * * *
11578535 GCAAGAGTTAAAAGTTCCCAACTATCATTCTAAGGCTC
65 GCGAGAGTTAAAAGCTCCCAGCTATCATTTTAAGGCTC
11578573 GTAGGTTCGA
Statistics
Matches: 205, Mismatches: 30, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
138 4 0.02
139 103 0.50
140 97 0.47
141 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.29
Consensus pattern (138 bp):
AGTTAAAAGCTCCCAACTGTCATTCTAAGGCTCGCAGTTTAATATCGCAGCCTCCAAACAGTTAG
CGAGAGTTAAAAGCTCCCAGCTATCATTTTAAGGCTCACAAGTTTAATACCGCGACCTCTATAAA
TTAGCGAC
Found at i:11578579 original size:70 final size:69
Alignment explanation
Indices: 11578191--11578579 Score: 376
Period size: 70 Copynumber: 5.6 Consensus size: 69
11578181 TAATTAGAAA
* * *
11578191 AGTTAAAAGCTCCCAACTGTCATTCTAAGGCTCGCA-GTTCTAATAC-TATGGCCTCCAAACAGT
1 AGTTAAAAGCTCCCAACTATCATTCTAAGGCTCGCAGGTT-TAATACGCA--GCCTCTAAACAGT
11578254 TAGCGAG
63 TAGCGAG
* * * * * * *
11578261 AGTTAGAATCTCTCAGCTATCATTTTAAGGCTTGCAAGTTTAATACTGC-GACCTCTATAA-A-T
1 AGTTAAAAGCTCCCAACTATCATTCTAAGGCTCGCAGGTTTAATAC-GCAG-CCTCTA-AACAGT
*
11578323 TAGTGAG
63 TAGCGAG
* * * *
11578330 AGTTAAAAGCTCCCAGCTATCATTCTAAGGTTCGCATGTTCAATATCGC-GACCTCTAAACAGTT
1 AGTTAAAAGCTCCCAACTATCATTCTAAGGCTCGCAGGTTTAATA-CGCAG-CCTCTAAACAGTT
11578394 AGCGAG
64 AGCGAG
* * * * *
11578400 AGTTAAAAGCTCCCAGCTTTCATTTTAAGGCTCACAGGTTTAATACCGCAGCCTCTAAATAGTTA
1 AGTTAAAAGCTCCCAACTATCATTCTAAGGCTCGCAGGTTTAATA-CGCAGCCTCTAAACAGTTA
*
11578465 GCGAC
65 GCGAG
* * * * * *
11578470 AGTTAAAAGCTCCTAACTGTCATTCTAAGGGTCACAGGTTTAATATCGCAGCCTCCAAACTGTTA
1 AGTTAAAAGCTCCCAACTATCATTCTAAGGCTCGCAGGTTTAATA-CGCAGCCTCTAAACAGTTA
*
11578535 GCAAG
65 GCGAG
* *
11578540 AGTTAAAAGTTCCCAACTATCATTCTAAGGCTCGTAGGTT
1 AGTTAAAAGCTCCCAACTATCATTCTAAGGCTCGCAGGTT
11578580 CGATACCATA
Statistics
Matches: 265, Mismatches: 45, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
68 2 0.01
69 56 0.21
70 201 0.76
71 6 0.02
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (69 bp):
AGTTAAAAGCTCCCAACTATCATTCTAAGGCTCGCAGGTTTAATACGCAGCCTCTAAACAGTTAG
CGAG
Found at i:11578890 original size:16 final size:16
Alignment explanation
Indices: 11578869--11578899 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
11578859 GAGATAGAAT
11578869 ATCATGATATTGACAC
1 ATCATGATATTGACAC
11578885 ATCATGATATTGACA
1 ATCATGATATTGACA
11578900 ATCGAACTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (16 bp):
ATCATGATATTGACAC
Found at i:11581769 original size:20 final size:20
Alignment explanation
Indices: 11581744--11581786 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
11581734 TCATAGGAGT
11581744 AGTGGGGTCAAGTCATGAAC
1 AGTGGGGTCAAGTCATGAAC
* * *
11581764 AGTGGGGTTATGTCGTGAAC
1 AGTGGGGTCAAGTCATGAAC
11581784 AGT
1 AGT
11581787 AATAGTATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.12, G:0.37, T:0.26
Consensus pattern (20 bp):
AGTGGGGTCAAGTCATGAAC
Found at i:11583049 original size:16 final size:16
Alignment explanation
Indices: 11583028--11583059 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11583018 CATACCTTAT
11583028 ATCCAAGTTGATCTAA
1 ATCCAAGTTGATCTAA
11583044 ATCCAAGTTGATCTAA
1 ATCCAAGTTGATCTAA
11583060 CAGTCAATGT
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:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (16 bp):
ATCCAAGTTGATCTAA
Found at i:11591992 original size:18 final size:18
Alignment explanation
Indices: 11591969--11592006 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
11591959 TACCAGATGC
*
11591969 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
11591987 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
11592005 GT
1 GT
11592007 TTTCTTTTCC
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:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:11596324 original size:16 final size:16
Alignment explanation
Indices: 11596300--11596353 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
11596290 TTTGGTTCGC
* *
11596300 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
11596316 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
11596332 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
11596348 TGTAAT
1 TGTAAT
11596354 AGCAAATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:11596437 original size:39 final size:43
Alignment explanation
Indices: 11596332--11596441 Score: 120
Period size: 45 Copynumber: 2.6 Consensus size: 43
11596322 GGAATAGAGG
11596332 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * * ***
11596377 TGTAATGGCATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
11596417 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
11596442 TAAAGGAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
39 19 0.35
40 2 0.04
43 1 0.02
44 11 0.20
45 22 0.40
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:11596575 original size:25 final size:25
Alignment explanation
Indices: 11596547--11596595 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
11596537 AATATCAGTA
11596547 ATAAATAAT-TTAATCATATTTTAAC
1 ATAAATAATATTAAT-ATATTTTAAC
* *
11596572 ATAATTATTATTAATATATTTTAA
1 ATAAATAATATTAATATATTTTAA
11596596 TTAAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (25 bp):
ATAAATAATATTAATATATTTTAAC
Found at i:11599545 original size:43 final size:43
Alignment explanation
Indices: 11599478--11599707 Score: 311
Period size: 43 Copynumber: 5.4 Consensus size: 43
11599468 ATATTTTTTT
* * * * * *
11599478 TAAAGGTTAT-GTTTTTAGCAGCGTTTTTGTGCAAAGCGCCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
*
11599520 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGTCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* *
11599563 TAAAGGTCATGGTCTTTAGCGGCGTTTTTGGG-AAAGCGCCAC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* * *
11599605 TGAAGGTCTTGGTCATTAGCGGCGTTTGTGGGAAAAGCGCCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* *
11599648 TGAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
*
11599691 TAAAGGTCTTGGTCTTT
1 TAAAGGTCATGGTCTTT
11599708 TCGAATTCAC
Statistics
Matches: 169, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
42 45 0.27
43 124 0.73
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (43 bp):
TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
Found at i:11599624 original size:85 final size:85
Alignment explanation
Indices: 11599478--11599704 Score: 321
Period size: 85 Copynumber: 2.7 Consensus size: 85
11599468 ATATTTTTTT
* * * * * *
11599478 TAAAGGTTAT-GTTTTTAGCAGCGTTTTTGTGCAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGG
1 TAAAGGTCATGGTCTTTAGCGGCGTTTTTG-GGAAAGCGCCGCTAAAGGTCTTGGTCATTAGCGG
*
11599542 CGTTTGTGGGAAAAGCGTCGC
65 CGTTTGTGGGAAAAGCGCCGC
* *
11599563 TAAAGGTCATGGTCTTTAGCGGCGTTTTTGGGAAAGCGCCACTGAAGGTCTTGGTCATTAGCGGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAAAGGTCTTGGTCATTAGCGGC
11599628 GTTTGTGGGAAAAGCGCCGC
66 GTTTGTGGGAAAAGCGCCGC
* * *
11599648 TGAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTTTGGG-AAAGCGCCGCTAAAGGTCTTGGTC
11599705 TTTTCGAATT
Statistics
Matches: 126, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
85 87 0.69
86 39 0.31
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.30
Consensus pattern (85 bp):
TAAAGGTCATGGTCTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAAAGGTCTTGGTCATTAGCGGC
GTTTGTGGGAAAAGCGCCGC
Found at i:11600797 original size:13 final size:13
Alignment explanation
Indices: 11600779--11600805 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11600769 GTAAACGATA
11600779 AAAATTTTCACAC
1 AAAATTTTCACAC
11600792 AAAATTTTCACAC
1 AAAATTTTCACAC
11600805 A
1 A
11600806 TATAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:11601542 original size:125 final size:126
Alignment explanation
Indices: 11601266--11601659 Score: 499
Period size: 125 Copynumber: 3.1 Consensus size: 126
11601256 GTCAAGCAAA
** *
11601266 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAAATTTTTTCAGTAATTTTGCTGACAGTGCAGCC
1 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCC
* * *
11601331 TGTTTGAAGTGTTTTTTACACTATTTTTTTCAAAACCGTC-TTCTAAAATTTATTTTTTCAAG
66 TGTTTGAAGCGTTTTTTACACTA-TTTTTTCAGAACCGTCTTTTTAAAA-TTATTTTTTCAAG
* * * *
11601393 AACTACTGCAGAAAAAGATG-GTCCACGTGGGAGCTTTTTTCAATAATTCTGTTGACAGTGCATC
1 AACTACTGTAGAAAAAGA-GCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
* ** * * *
11601457 CTGCTTGAAG-AATTTTGAAACTATTTTTTCAGAATCGTCTTTTTAAAATTATTTTTTCAAG
65 CTGTTTGAAGCGTTTTTTACACTATTTTTTCAGAACCGTCTTTTTAAAATTATTTTTTCAAG
* * * *
11601518 AACTACTATAGAAAAAGAGCGTCCACATGGGAGCTTTTTTTAGTAATTTTGCTAACAGTGCATCC
1 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCC
* * * * *
11601583 TGTTTGAAGCGTTTTTTACATTATTTTTTCAGAACCATCTTCTCAAAATTAATTTTTCTAA-
66 TGTTTGAAGCGTTTTTTACACTATTTTTTCAGAACCGTCTTTTTAAAATTATTTTTTC-AAG
11601644 AACTACTGTAGAAAAA
1 AACTACTGTAGAAAAA
11601660 AACAAAATCC
Statistics
Matches: 227, Mismatches: 35, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
124 1 0.00
125 90 0.40
126 69 0.30
127 66 0.29
128 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.38
Consensus pattern (126 bp):
AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCC
TGTTTGAAGCGTTTTTTACACTATTTTTTCAGAACCGTCTTTTTAAAATTATTTTTTCAAG
Found at i:11601841 original size:33 final size:33
Alignment explanation
Indices: 11601715--11601840 Score: 150
Period size: 34 Copynumber: 3.8 Consensus size: 33
11601705 CTAAACACAA
11601715 AATTATTTTTTTAAAAA--CTAAACCCTAATTT
1 AATTATTTTTTTAAAAACTCTAAACCCTAATTT
*
11601746 AATTAATTTTCTTAAAAACTCTAAACCCTAATTTT
1 AATT-ATTTTTTTAAAAACTCTAAACCCTAA-TTT
* * * *
11601781 ATTTATTTATTT-AAAACCCTTAAAACCTAATTT
1 AATTATTTTTTTAAAAACTC-TAAACCCTAATTT
11601814 AATTATTTTTTTAAAAAACTCTAAACC
1 AATTATTTTTTT-AAAAACTCTAAACC
11601841 TTGATTTATT
Statistics
Matches: 78, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
31 4 0.05
32 12 0.15
33 19 0.24
34 31 0.40
35 12 0.15
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (33 bp):
AATTATTTTTTTAAAAACTCTAAACCCTAATTT
Found at i:11603669 original size:21 final size:21
Alignment explanation
Indices: 11603631--11603670 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
11603621 GTCAAGGATG
* *
11603631 CTCAATTTCATGATACCTAGT
1 CTCAATGTCATGACACCTAGT
*
11603652 CTCAATGTCGTGACACCTA
1 CTCAATGTCATGACACCTA
11603671 CATCAAATGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.33
Consensus pattern (21 bp):
CTCAATGTCATGACACCTAGT
Found at i:11611825 original size:13 final size:13
Alignment explanation
Indices: 11611794--11611869 Score: 62
Period size: 13 Copynumber: 5.8 Consensus size: 13
11611784 TTCTTTATTA
*
11611794 CTTTTTAGAAGTG
1 CTTTTGAGAAGTG
* *
11611807 TTTTTTGGGAAGTG
1 -CTTTTGAGAAGTG
* *
11611821 CTTTTCAGAACTG
1 CTTTTGAGAAGTG
11611834 CTTTTGAGAAGTG
1 CTTTTGAGAAGTG
* * *
11611847 ATTTGGAGGAGTG
1 CTTTTGAGAAGTG
*
11611860 CTTTTAAGAA
1 CTTTTGAGAA
11611870 ATTTGAGTGT
Statistics
Matches: 46, Mismatches: 16, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
13 36 0.78
14 10 0.22
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.41
Consensus pattern (13 bp):
CTTTTGAGAAGTG
Found at i:11612477 original size:22 final size:21
Alignment explanation
Indices: 11612452--11612495 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
11612442 AAGCATATGA
*
11612452 AAATGATTTGGTTATATTCAAT
1 AAATGATTTGGTTA-ATACAAT
11612474 AAATGATTTGGTTAATACAAT
1 AAATGATTTGGTTAATACAAT
11612495 A
1 A
11612496 CTTATATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (21 bp):
AAATGATTTGGTTAATACAAT
Found at i:11620486 original size:21 final size:21
Alignment explanation
Indices: 11620461--11620502 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
11620451 ATTATCAGTG
11620461 CAAAAGCAACCAA-AACACCAA
1 CAAAAGCAACCAAGAA-ACCAA
*
11620482 CAAAAGCACCCAAGAAACCAA
1 CAAAAGCAACCAAGAAACCAA
11620503 ATACCAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.60, C:0.33, G:0.07, T:0.00
Consensus pattern (21 bp):
CAAAAGCAACCAAGAAACCAA
Found at i:11626565 original size:197 final size:190
Alignment explanation
Indices: 11626217--11626569 Score: 481
Period size: 197 Copynumber: 1.8 Consensus size: 190
11626207 ATCCTATCAC
** * *
11626217 AAATTTAAAACACAAATGTCTGTTTAAAATAACATATAATAAATAATAAAACATATGATTTGAAA
1 AAATTTAAAACACAAATGTCCATTTAAAATAACATAAAACAAATAATAAAACATATGATTTGAAA
* * *
11626282 CTAATTAATAATAATACATGAAATATGTATGTTATTCAAATAAAAAATTAGATTAAATTGTTTAT
66 CTAATTAATAATAACACATGAAATATGTATGTTATTAAAAGAAAAAATTAGATTAAATTGTTTAT
* *
11626347 CATGGTGTTGTCATTAATCTTAAGTCAGTCCTATCATACGTATATGCGTGTGGAGACCTT
131 CATGATGTTGTCATCAATCTTAAGTCAGTCCTATCATACGTATATGCGTGTGGAGACCTT
* * * * * * *
11626407 AAATTTAGAACACAAATTTCCATTTAAAAATAGCATAAAACAAATACTGAAACTTATGGTTTGAA
1 AAATTTAAAACACAAATGTCCATTT-AAAATAACATAAAACAAATAATAAAACATATGATTTGAA
11626472 ACTAATTTAATAATAACACATGAAGTATATATGTATGTTATTAAAAAGAAAAAATTAGATTAAAT
65 ACTAA-TTAATAATAACACATG-A--A-ATATGTATGTTATT-AAAAGAAAAAATTAGATTAAAT
* *
11626537 TGTTTATTATGATGTTGTTATCAATCTTAAGTC
124 TGTTTATCATGATGTTGTCATCAATCTTAAGTC
11626570 GGTGTCGAAT
Statistics
Matches: 138, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
190 21 0.15
191 37 0.27
192 15 0.11
193 1 0.01
195 1 0.01
196 14 0.10
197 49 0.36
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (190 bp):
AAATTTAAAACACAAATGTCCATTTAAAATAACATAAAACAAATAATAAAACATATGATTTGAAA
CTAATTAATAATAACACATGAAATATGTATGTTATTAAAAGAAAAAATTAGATTAAATTGTTTAT
CATGATGTTGTCATCAATCTTAAGTCAGTCCTATCATACGTATATGCGTGTGGAGACCTT
Found at i:11626678 original size:18 final size:19
Alignment explanation
Indices: 11626639--11626682 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
11626629 ATGGATGTAA
11626639 TAAAATGTGCATAATAAAAT
1 TAAAATGT-CATAATAAAAT
11626659 TAAAATGT-ATAA-AAATAT
1 TAAAATGTCATAATAAA-AT
11626677 TAAAAT
1 TAAAAT
11626683 AAAACTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.13
18 12 0.52
20 8 0.35
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (19 bp):
TAAAATGTCATAATAAAAT
Found at i:11629171 original size:31 final size:31
Alignment explanation
Indices: 11629136--11629238 Score: 111
Period size: 31 Copynumber: 3.4 Consensus size: 31
11629126 TAATTACATT
*
11629136 AATATTAAATTAATAAAATATTATCTAGATA
1 AATATTAAATTAATAAAATAATATCTAGATA
** * *
11629167 AATATTAAATT-A-AATTTAATATCTCATATT
1 AATATTAAATTAATAAAATAATATCT-AGATA
* *
11629197 AATATTAAATTAATAAAGTAATAACTAGATA
1 AATATTAAATTAATAAAATAATATCTAGATA
*
11629228 AATATTTAATT
1 AATATTAAATT
11629239 TAATTTAATA
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
29 9 0.16
30 15 0.26
31 25 0.43
32 9 0.16
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (31 bp):
AATATTAAATTAATAAAATAATATCTAGATA
Found at i:11629228 original size:61 final size:61
Alignment explanation
Indices: 11629133--11629248 Score: 187
Period size: 61 Copynumber: 1.9 Consensus size: 61
11629123 AATTAATTAC
* *
11629133 ATTAATATTAAATTAATAAAATATTATCTAGATAAATATTAAATTAAATTTAATATCTCAT
1 ATTAATATTAAATTAATAAAATAATAACTAGATAAATATTAAATTAAATTTAATATCTCAT
* * *
11629194 ATTAATATTAAATTAATAAAGTAATAACTAGATAAATATTTAATTTAATTTAATA
1 ATTAATATTAAATTAATAAAATAATAACTAGATAAATATTAAATTAAATTTAATA
11629249 ATAAATTCAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 50 1.00
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (61 bp):
ATTAATATTAAATTAATAAAATAATAACTAGATAAATATTAAATTAAATTTAATATCTCAT
Found at i:11632486 original size:25 final size:25
Alignment explanation
Indices: 11632449--11632542 Score: 125
Period size: 25 Copynumber: 3.8 Consensus size: 25
11632439 CGGGCACACC
* **
11632449 ACAGCTCGTATGAGCTTCCTATTAT
1 ACAGCTCGCATGAGCTTCCCGTTAT
11632474 ACAGCTCGCATGAGCTTCCCGTTAT
1 ACAGCTCGCATGAGCTTCCCGTTAT
*
11632499 TCAGCTCGCATGAGCTTCCCGTTAT
1 ACAGCTCGCATGAGCTTCCCGTTAT
* * *
11632524 TCAGCTCGGAGGAGCTTCC
1 ACAGCTCGCATGAGCTTCC
11632543 TGTTTATAGA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 63 1.00
ACGTcount: A:0.19, C:0.30, G:0.21, T:0.30
Consensus pattern (25 bp):
ACAGCTCGCATGAGCTTCCCGTTAT
Found at i:11639936 original size:25 final size:25
Alignment explanation
Indices: 11639904--11639962 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
11639894 AGCATTAGAT
*
11639904 TTCT-GTTATACAACTCGCATGAGC
1 TTCTCGTTATACAACTCGCACGAGC
** *
11639928 TTCTCGTTATTTAGCTCGCACGAGC
1 TTCTCGTTATACAACTCGCACGAGC
*
11639953 TTCCCGTTAT
1 TTCTCGTTAT
11639963 TTAGCTCGGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 4 0.14
25 25 0.86
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (25 bp):
TTCTCGTTATACAACTCGCACGAGC
Found at i:11639963 original size:25 final size:25
Alignment explanation
Indices: 11639917--11639985 Score: 102
Period size: 25 Copynumber: 2.8 Consensus size: 25
11639907 TGTTATACAA
* *
11639917 CTCGCATGAGCTTCTCGTTATTTAG
1 CTCGCACGAGCTTCCCGTTATTTAG
11639942 CTCGCACGAGCTTCCCGTTATTTAG
1 CTCGCACGAGCTTCCCGTTATTTAG
* *
11639967 CTCGGAGGAGCTTCCCGTT
1 CTCGCACGAGCTTCCCGTT
11639986 TATAGATCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.14, C:0.29, G:0.23, T:0.33
Consensus pattern (25 bp):
CTCGCACGAGCTTCCCGTTATTTAG
Found at i:11655654 original size:5 final size:5
Alignment explanation
Indices: 11655644--11655688 Score: 63
Period size: 5 Copynumber: 8.8 Consensus size: 5
11655634 TGAATAGGGA
* *
11655644 CTTTT CTTTT CTTTT CTTTT CTTTT CTCTT CTCTTT CTCTT CTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CT-TTT CTTTT CTTT
11655689 GTTTTGGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 31 0.89
6 4 0.11
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (5 bp):
CTTTT
Found at i:11662636 original size:14 final size:13
Alignment explanation
Indices: 11662618--11662678 Score: 55
Period size: 13 Copynumber: 5.1 Consensus size: 13
11662608 AAATATAAAC
11662618 AAAAATATATATT
1 AAAAATATATATT
11662631 ACAAAAT-T-TA-T
1 A-AAAATATATATT
11662642 --AAATATATATT
1 AAAAATATATATT
11662653 AAAAATATAT-TAT
1 AAAAATATATAT-T
11662666 AAAAAT-TATATT
1 AAAAATATATATT
11662678 A
1 A
11662679 TTGTGGCTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 17
0.70 0.00 0.30
Matches are distributed among these distances:
8 4 0.10
9 1 0.03
10 2 0.05
11 2 0.05
12 8 0.20
13 18 0.45
14 5 0.12
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (13 bp):
AAAAATATATATT
Found at i:11662679 original size:14 final size:13
Alignment explanation
Indices: 11662618--11662679 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 13
11662608 AAATATAAAC
11662618 AAAAATATA-TATT
1 AAAAATATATTA-T
*
11662631 ACAAA-AT-TTAT
1 AAAAATATATTAT
*
11662642 AAATATATA-T-T
1 AAAAATATATTAT
11662653 AAAAATATATTAT
1 AAAAATATATTAT
11662666 AAAAATTATATTAT
1 AAAAA-TATATTAT
11662680 TGTGGCTTAC
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
11 13 0.33
12 8 0.21
13 10 0.26
14 8 0.21
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAAATATATTAT
Found at i:11662729 original size:22 final size:23
Alignment explanation
Indices: 11662704--11662763 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
11662694 AACATATATT
11662704 ATTA-AAATTTATATTATAAAAA
1 ATTATAAATTTATATTATAAAAA
11662726 ATTATGAAA-TTATATTATAAAAA
1 ATTAT-AAATTTATATTATAAAAA
*
11662749 A-TATAAATATATATT
1 ATTATAAATTTATATT
11662764 TTTATAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
21 3 0.09
22 13 0.38
23 15 0.44
24 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
ATTATAAATTTATATTATAAAAA
Found at i:11669076 original size:12 final size:12
Alignment explanation
Indices: 11669061--11669089 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
11669051 AATATTAGAT
11669061 TAAATTTAATAC
1 TAAATTTAATAC
11669073 TAAATTTAATAC
1 TAAATTTAATAC
11669085 TAAAT
1 TAAAT
11669090 CTTATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAATTTAATAC
Found at i:11670856 original size:16 final size:16
Alignment explanation
Indices: 11670835--11670865 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11670825 CTATGCATGC
*
11670835 AAAATATAAAAGACAG
1 AAAATACAAAAGACAG
11670851 AAAATACAAAAGACA
1 AAAATACAAAAGACA
11670866 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAG
Found at i:11675879 original size:17 final size:17
Alignment explanation
Indices: 11675857--11675905 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
11675847 AAGGCCAATC
11675857 TGGGCATGTGGGCCACA
1 TGGGCATGTGGGCCACA
*
11675874 TGGGCATGTTGGCCCACA
1 TGGGCATG-TGGGCCACA
*
11675892 CGGGCATGTGGGCC
1 TGGGCATGTGGGCC
11675906 CAAACTTCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.14, C:0.27, G:0.41, T:0.18
Consensus pattern (17 bp):
TGGGCATGTGGGCCACA
Found at i:11682561 original size:15 final size:15
Alignment explanation
Indices: 11682543--11682575 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
11682533 ATATCACAAT
11682543 TATAAA-ATTATATAA
1 TATAAATATTATA-AA
11682558 TATAAATATTATAAA
1 TATAAATATTATAAA
11682573 TAT
1 TAT
11682576 TATAAAACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TATAAATATTATAAA
Found at i:11682572 original size:9 final size:9
Alignment explanation
Indices: 11682541--11682581 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
11682531 ATATATCACA
11682541 ATTATAAA-
1 ATTATAAAT
11682549 ATTAT--AT
1 ATTATAAAT
*
11682556 AATATAAAT
1 ATTATAAAT
11682565 ATTATAAAT
1 ATTATAAAT
11682574 ATTATAAA
1 ATTATAAA
11682582 ACAGATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
6 1 0.04
7 4 0.14
8 5 0.18
9 18 0.64
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
ATTATAAAT
Found at i:11685863 original size:18 final size:17
Alignment explanation
Indices: 11685837--11685884 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
11685827 AATAAAAATA
11685837 AACGTTTTGAAATTGAAT
1 AACGTTTTGAAA-TGAAT
*
11685855 AACGATTTGTAAATGAAT
1 AACGTTTTG-AAATGAAT
*
11685873 AATGTTTTGAAA
1 AACGTTTTGAAA
11685885 ACGAACGACA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.12
18 20 0.77
19 3 0.12
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.38
Consensus pattern (17 bp):
AACGTTTTGAAATGAAT
Found at i:11686344 original size:20 final size:18
Alignment explanation
Indices: 11686244--11686345 Score: 72
Period size: 20 Copynumber: 5.7 Consensus size: 18
11686234 TTCAACTATA
11686244 ATTAAACTTAATCACTTTAAT
1 ATTAAA-TTAAT-A-TTTAAT
11686265 ATTAAATTAATA--TAAT
1 ATTAAATTAATATTTAAT
* * *
11686281 ATT-TATTAAGA-TAAAT
1 ATTAAATTAATATTTAAT
*
11686297 ATTAGATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
11686314 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
11686334 ATTAAATTAATA
1 ATTAAATTAATA
11686346 AAATACTATT
Statistics
Matches: 67, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
15 6 0.09
16 14 0.21
17 16 0.24
18 1 0.01
19 4 0.06
20 20 0.30
21 6 0.09
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:11686378 original size:68 final size:69
Alignment explanation
Indices: 11686252--11686386 Score: 227
Period size: 68 Copynumber: 2.0 Consensus size: 69
11686242 TAATTAAACT
* * *
11686252 TAATCACTTTAATATTAAATTAATATAATATTTATTAAGATAAATATTAGATTAAATTTAATATT
1 TAATCACTTTAATATTAAATTAATAAAATATCTATTAAGATAAATATTAAATTAAATTTAATATT
11686317 AAGA
66 AAGA
*
11686321 TAATCACTTTAATATTAAATTAATAAAATA-CTATTAAGATAAGTATTAAATTAAATTTAATATT
1 TAATCACTTTAATATTAAATTAATAAAATATCTATTAAGATAAATATTAAATTAAATTTAATATT
11686385 AA
66 AA
11686387 ACTATTAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
68 33 0.53
69 29 0.47
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (69 bp):
TAATCACTTTAATATTAAATTAATAAAATATCTATTAAGATAAATATTAAATTAAATTTAATATT
AAGA
Found at i:11687988 original size:29 final size:29
Alignment explanation
Indices: 11687952--11688011 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
11687942 CAGAAAATAC
11687952 AAAAGACATAATAGTGAAATGTGAAATTA
1 AAAAGACATAATAGTGAAATGTGAAATTA
11687981 AAAAGACATAATAGTGAAATGTGAAATTA
1 AAAAGACATAATAGTGAAATGTGAAATTA
11688010 AA
1 AA
11688012 TTTATTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.57, C:0.03, G:0.17, T:0.23
Consensus pattern (29 bp):
AAAAGACATAATAGTGAAATGTGAAATTA
Found at i:11688282 original size:18 final size:18
Alignment explanation
Indices: 11688259--11688296 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
11688249 ATAGGTGTCT
*
11688259 TTAATTTTGTCCCAAAAA
1 TTAATTTTGGCCCAAAAA
11688277 TTAATTTTGGCCCAAAAA
1 TTAATTTTGGCCCAAAAA
11688295 TT
1 TT
11688297 TTAGTGATTA
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:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (18 bp):
TTAATTTTGGCCCAAAAA
Found at i:11689496 original size:20 final size:20
Alignment explanation
Indices: 11689439--11689496 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
11689429 TTCGTACTCT
*
11689439 TATTAGCACTACGGTGCTCC
1 TATTAGCACTACGGTGCTCA
* **
11689459 TAATAGCAC-ATCCATGCTCA
1 TATTAGCACTA-CGGTGCTCA
*
11689479 TGTTAGCACTACGGTGCT
1 TATTAGCACTACGGTGCT
11689497 TTTGATGGCA
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (20 bp):
TATTAGCACTACGGTGCTCA
Found at i:11696572 original size:18 final size:17
Alignment explanation
Indices: 11696542--11696575 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
11696532 TGTTTAATGG
11696542 TAAAGAACGAAATGGAC
1 TAAAGAACGAAATGGAC
*
11696559 TAAATGAACTAAATGGA
1 TAAA-GAACGAAATGGA
11696576 AATGTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.53, C:0.09, G:0.21, T:0.18
Consensus pattern (17 bp):
TAAAGAACGAAATGGAC
Found at i:11698026 original size:28 final size:28
Alignment explanation
Indices: 11697986--11698049 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
11697976 TGCTATTTTA
11697986 TTAGTTTAAGAAACCCTAAAAGTATCTC
1 TTAGTTTAAGAAACCCTAAAAGTATCTC
11698014 TTAGTTTAAGAAACCCTAAAAGTATCTC
1 TTAGTTTAAGAAACCCTAAAAGTATCTC
*
11698042 TTATTTTA
1 TTAGTTTA
11698050 CTTTCCTGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (28 bp):
TTAGTTTAAGAAACCCTAAAAGTATCTC
Found at i:11698628 original size:13 final size:13
Alignment explanation
Indices: 11698610--11698723 Score: 52
Period size: 13 Copynumber: 8.7 Consensus size: 13
11698600 TAAATGTGTA
11698610 ATATGAAATGATT
1 ATATGAAATGATT
* * *
11698623 ATATGAGACGGTT
1 ATATGAAATGATT
* *
11698636 ATACG-AATGGTT
1 ATATGAAATGATT
* *
11698648 ATATAAAATGAAT
1 ATATGAAATGATT
*
11698661 ATATGAAAGGATT
1 ATATGAAATGATT
* * *
11698674 GTTTG-AATCAATT
1 ATATGAAAT-GATT
*
11698687 ATATGGAAATAATT
1 ATAT-GAAATGATT
* *
11698701 ATATAAAACTGTTT
1 ATATGAAA-TGATT
*
11698715 ATACGAAAT
1 ATATGAAAT
11698724 TTTTATATGG
Statistics
Matches: 72, Mismatches: 24, Indels: 10
0.68 0.23 0.09
Matches are distributed among these distances:
12 10 0.14
13 41 0.57
14 18 0.25
15 3 0.04
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (13 bp):
ATATGAAATGATT
Found at i:11705530 original size:125 final size:124
Alignment explanation
Indices: 11705289--11705520 Score: 376
Period size: 125 Copynumber: 1.9 Consensus size: 124
11705279 TGCTTCTACT
* * *
11705289 AGGATGCTATTTGAGAAGAAATTGTGAAATCGTGGCCTCGTGGACGCGATTTCGGTACAGTGGTC
1 AGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTGGTC
11705354 ATGTAAGAAATAAATTTTTTTGACGTTTTCTGAGCAAATAGTATAAAATCGCTGATACA
66 ATGTAAGAAATAAATTTTTTTGACGTTTTCTGAGCAAATAGTATAAAATCGCTGATACA
* *
11705413 AGGATGCTATATTGGGCAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGG
1 AGGATGCTAT-TTGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATTTCGCTACAG-TGG
* *
11705478 TCATGTAGGAAATAATTTTTTTTGACG-TTTCTGAGCAAATAGT
64 TCATGTAAGAAATAAATTTTTTTGACGTTTTCTGAGCAAATAGT
11705521 GTCATATCGC
Statistics
Matches: 99, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
124 10 0.10
125 61 0.62
126 28 0.28
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (124 bp):
AGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTGGTC
ATGTAAGAAATAAATTTTTTTGACGTTTTCTGAGCAAATAGTATAAAATCGCTGATACA
Found at i:11707488 original size:30 final size:31
Alignment explanation
Indices: 11707411--11707488 Score: 104
Period size: 35 Copynumber: 2.4 Consensus size: 31
11707401 GGTTAAGGAG
11707411 GCATTTGATCGGGGCGCCGGGATACTAGCTGT
1 GCATTTGATCGGGGCGCCGGGATACTAGC-GT
*
11707443 GTTATTTCAGATCGGGGCGCCGGGATACTAGC-T
1 G-CATTT--GATCGGGGCGCCGGGATACTAGCGT
11707476 GCATTTGATCGGG
1 GCATTTGATCGGG
11707489 AGGGAAGCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
30 7 0.17
32 5 0.12
33 6 0.15
35 23 0.56
ACGTcount: A:0.17, C:0.21, G:0.36, T:0.27
Consensus pattern (31 bp):
GCATTTGATCGGGGCGCCGGGATACTAGCGT
Found at i:11708860 original size:23 final size:23
Alignment explanation
Indices: 11708827--11709560 Score: 646
Period size: 23 Copynumber: 32.4 Consensus size: 23
11708817 NNNNNNNNNN
* *
11708827 GGTTTTAAATTAAGTTAGCTTAG
1 GGTTTTTAATTAAGTTAGGTTAG
11708850 GGTTTTTAATTAAATTAGTTAGGTTAG
1 GGTTTTTAATT--A--AGTTAGGTTAG
* *
11708877 GGTTTTTAATTAAATTAAGTTA-
1 GGTTTTTAATTAAGTTAGGTTAG
11708899 GG-TTTTAAGTTAAGTTAGGTTAG
1 GGTTTTTAA-TTAAGTTAGGTTAG
*
11708922 TG-TTTTACATTAAGTTAGGTTAG
1 GGTTTTTA-ATTAAGTTAGGTTAG
11708945 GGTTTTTAATTAA---A--TTA-
1 GGTTTTTAATTAAGTTAGGTTAG
11708962 GGTTTTTAATTCAA-TTAGGTTAG
1 GGTTTTTAATT-AAGTTAGGTTAG
11708985 GG-TTTTACATTAAGTTAGGTTAG
1 GGTTTTTA-ATTAAGTTAGGTTAG
*
11709008 GGTTTTTAATTAAGTTAGGGTAG
1 GGTTTTTAATTAAGTTAGGTTAG
* *
11709031 GG-TTTTAAATACAGTTAGCTTAG
1 GGTTTTTAATTA-AGTTAGGTTAG
11709054 GGTTTTTAATTTAATTAAGTTAGGTTAG
1 GG---TT--TTTAATTAAGTTAGGTTAG
11709082 GG-TTTTACATTAAGTTAGGTTAG
1 GGTTTTTA-ATTAAGTTAGGTTAG
11709105 GGTTTTTAATTAA---A--TTA-
1 GGTTTTTAATTAAGTTAGGTTAG
11709122 GGTTTTTAATTCAA-TTAGGTTAG
1 GGTTTTTAATT-AAGTTAGGTTAG
11709145 GG-TTTTACATTAAGTTAGGTTAG
1 GGTTTTTA-ATTAAGTTAGGTTAG
11709168 GGTTTTTAATT-A---A-GTTAG
1 GGTTTTTAATTAAGTTAGGTTAG
11709186 GGTTTTTAATTCAA-TTAGGTTAG
1 GGTTTTTAATT-AAGTTAGGTTAG
* *
11709209 GGTTTTTAATTAAATTAAGTTA-
1 GGTTTTTAATTAAGTTAGGTTAG
11709231 GG-TTTTAAGTTAAGTTAGGTTAG
1 GGTTTTTAA-TTAAGTTAGGTTAG
*
11709254 GG-TTTTACATTAAGTTAAGTTAG
1 GGTTTTTA-ATTAAGTTAGGTTAG
11709277 GGTTTTTAATT-A---A-GTTAG
1 GGTTTTTAATTAAGTTAGGTTAG
11709295 GGTTTTTAATTCAA-TTAGGTTAG
1 GGTTTTTAATT-AAGTTAGGTTAG
11709318 GGTTTTTAATTAAGTTAGGTTAG
1 GGTTTTTAATTAAGTTAGGTTAG
* * *
11709341 GGATTTTAATTAAATTAAGTTA-
1 GGTTTTTAATTAAGTTAGGTTAG
11709363 GG-TTTTAAGTTAAGTTAGGTTAG
1 GGTTTTTAA-TTAAGTTAGGTTAG
11709386 GG-TTTTACATTAAGTTAGGTTAG
1 GGTTTTTA-ATTAAGTTAGGTTAG
11709409 GGTTTTTAATTAA---A--TTA-
1 GGTTTTTAATTAAGTTAGGTTAG
11709426 GGTTTTTAATTCAA-TTAGGTTAG
1 GGTTTTTAATT-AAGTTAGGTTAG
* *
11709449 GGTTTTTAA-CACAATTAGGTTAG
1 GGTTTTTAATTA-AGTTAGGTTAG
*
11709472 GGTTTTTAATTCAATTAAGTTAGGTTTG
1 GG--TTT--TT-AATTAAGTTAGGTTAG
*
11709500 GATTTTTAATTCAA-TTAGGTTAG
1 GGTTTTTAATT-AAGTTAGGTTAG
11709523 GGTTTTTAATTAAATTAAGTTAGGTTAG
1 GG--TTT--TT-AATTAAGTTAGGTTAG
11709551 GGTTTTTAAT
1 GGTTTTTAAT
11709561 CAAATAATGT
Statistics
Matches: 605, Mismatches: 30, Indels: 152
0.77 0.04 0.19
Matches are distributed among these distances:
17 33 0.05
18 47 0.08
19 2 0.00
20 8 0.01
21 19 0.03
22 83 0.14
23 284 0.47
24 40 0.07
25 8 0.01
26 6 0.01
27 28 0.05
28 39 0.06
29 8 0.01
ACGTcount: A:0.29, C:0.02, G:0.22, T:0.47
Consensus pattern (23 bp):
GGTTTTTAATTAAGTTAGGTTAG
Found at i:11708911 original size:17 final size:17
Alignment explanation
Indices: 11708886--11708919 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11708876 GGGTTTTTAA
11708886 TTAAATTAAGTTAGGTT
1 TTAAATTAAGTTAGGTT
*
11708903 TTAAGTTAAGTTAGGTT
1 TTAAATTAAGTTAGGTT
11708920 AGTGTTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (17 bp):
TTAAATTAAGTTAGGTT
Found at i:11708961 original size:28 final size:28
Alignment explanation
Indices: 11708831--11708902 Score: 128
Period size: 27 Copynumber: 2.6 Consensus size: 28
11708821 NNNNNNGGTT
*
11708831 TTAAATTAAGTTAGCTTAGGGTTTTTAA
1 TTAAATTAAGTTAGGTTAGGGTTTTTAA
11708859 TTAAATT-AGTTAGGTTAGGGTTTTTAA
1 TTAAATTAAGTTAGGTTAGGGTTTTTAA
11708886 TTAAATTAAGTTAGGTT
1 TTAAATTAAGTTAGGTT
11708903 TTAAGTTAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
27 26 0.62
28 16 0.38
ACGTcount: A:0.32, C:0.01, G:0.19, T:0.47
Consensus pattern (28 bp):
TTAAATTAAGTTAGGTTAGGGTTTTTAA
Found at i:11708968 original size:18 final size:17
Alignment explanation
Indices: 11708945--11708982 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
11708935 GTTAGGTTAG
11708945 GGTTTTTAATTAAATTA
1 GGTTTTTAATTAAATTA
*
11708962 GGTTTTTAATTCAATTA
1 GGTTTTTAATTAAATTA
11708979 GGTT
1 GGTT
11708983 AGGGTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.53
Consensus pattern (17 bp):
GGTTTTTAATTAAATTA
Found at i:11709026 original size:18 final size:18
Alignment explanation
Indices: 11708940--11709028 Score: 63
Period size: 18 Copynumber: 4.4 Consensus size: 18
11708930 ATTAAGTTAG
11708940 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
*
11708958 ATTA-GGTTTTTAATTCAATTA
1 GTTAGGGTTTTTAATT--A--A
*
11708979 GGTTAGGGTTTTACATTAAGTTAG
1 -GTTAGGG-TTT---TTAA-TTAA
11709003 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
11709021 GTTAGGGT
1 GTTAGGGT
11709029 AGGGTTTTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 22
0.68 0.05 0.27
Matches are distributed among these distances:
17 11 0.20
18 14 0.25
19 5 0.09
21 1 0.02
22 6 0.11
23 9 0.16
24 3 0.05
26 1 0.02
27 4 0.07
28 2 0.04
ACGTcount: A:0.27, C:0.02, G:0.24, T:0.47
Consensus pattern (18 bp):
GTTAGGGTTTTTAATTAA
Found at i:11709047 original size:109 final size:106
Alignment explanation
Indices: 11708862--11709495 Score: 546
Period size: 109 Copynumber: 5.8 Consensus size: 106
11708852 TTTTTAATTA
* * *
11708862 AATTAGTTAGGTTAGGGTTTTTAATTAAATTAAGTTA-GG-TTTTAAGTTAAGTTAGGTTAGTGT
1 AATTAATTAGGTTAGGGTTTTTAATT-AATTAGGTTAGGGTTTTTAA-TTAAGTTAGGTTAGGGT
* *
11708925 TTTACATTAAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTTTT
64 TTTA-AATAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTTTT
*
11708969 AATTCAATTAGGTTAGGG-TTTTACATTAAGTTAGGTTAGGGTTTTTAATTAAGTTAGGGTAGGG
1 AATT-AATTAGGTTAGGGTTTTTA-ATTAA-TTAGGTTAGGGTTTTTAATTAAGTTAGGTTAGGG
* *
11709033 TTTTAAATACAGTTAGCTTAGGGTTTTTAATTTAATTAAGTTAGGTTAGGGTTTT
63 TTTTAAATA-AATTAGGTTAGGGTTTTTAA-TT-A--AA-TTAGG-T----TTTT
11709088 ACATTAAGTTAGGTTAGGGTTTTTAATTAA--A--TTA-GGTTTTTAATTCAA-TTAGGTTAGGG
1 A-ATTAA-TTAGGTTAGGGTTTTTAATTAATTAGGTTAGGGTTTTTAATT-AAGTTAGGTTAGGG
* * *
11709147 TTTTACATTAAGTTAGGTTAGGGTTTTTAATTAAGTTAGGGTTTTT
63 TTTTA-AATAAATTAGGTTAGGGTTTTTAATTAAATTA-GGTTTTT
*
11709193 AATTCAATTAGGTTAGGGTTTTTAATTAAATTAAGTTA-GG-TTTTAAGTTAAGTTAGGTTAGGG
1 AATT-AATTAGGTTAGGGTTTTTAATT-AATTAGGTTAGGGTTTTTAA-TTAAGTTAGGTTAGGG
* * * *
11709256 TTTTACATTAAGTTAAGTTAGGGTTTTTAATTAAGTTAGGGTTTTT
63 TTTTA-AATAAATTAGGTTAGGGTTTTTAATTAAATTA-GGTTTTT
* * *
11709302 AATTCAATTAGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGATTTTAATTAAATTAAGTTA-GGT
1 AATT-AATTAGGTTAGGGTTTTTAATTAA-TTAGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGT
* * *
11709366 TTTAAGTTAAGTTAGGTTAGGG-TTTTACATTAAGTTAGGTTAGGGTTT
64 TTTAA-ATAAATTAGGTTAGGGTTTTTA-ATTAAATTAGGTT----TTT
** * *
11709414 --TTAATTAAATTA-GGTTTTTAATTCAATTAGGTTAGGGTTTTTAA-CACAATTAGGTTAGGGT
1 AATTAATTAGGTTAGGGTTTTTAATT-AATTAGGTTAGGGTTTTTAATTA-AGTTAGGTTAGGG-
* * *
11709475 TTTTAATTCAATTAAGTTAGG
63 TTTTAAATAAATTAGGTTAGG
11709496 TTTGGATTTT
Statistics
Matches: 461, Mismatches: 23, Indels: 84
0.81 0.04 0.15
Matches are distributed among these distances:
104 23 0.05
105 9 0.02
107 13 0.03
108 82 0.18
109 196 0.43
110 32 0.07
111 7 0.02
112 4 0.01
113 4 0.01
114 50 0.11
115 9 0.02
117 1 0.00
119 7 0.02
120 19 0.04
121 5 0.01
ACGTcount: A:0.29, C:0.03, G:0.22, T:0.46
Consensus pattern (106 bp):
AATTAATTAGGTTAGGGTTTTTAATTAATTAGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTT
TAAATAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTTTT
Found at i:11709075 original size:51 final size:51
Alignment explanation
Indices: 11708966--11709121 Score: 182
Period size: 51 Copynumber: 3.2 Consensus size: 51
11708956 AAATTAGGTT
* * *
11708966 TTTAATTCAA-TTAGGTTAGGGTTTTACATTAAGTTAGGTTAGGG---TT--
1 TTTAATT-AAGTTAGGGTAGGGTTTTACAATAAGTTAGCTTAGGGTTTTTAA
11709012 TTTAATTAAGTTAGGGTAGGGTTTTA-AATACAGTTAGCTTAGGGTTTTTAA
1 TTTAATTAAGTTAGGGTAGGGTTTTACAATA-AGTTAGCTTAGGGTTTTTAA
* * *
11709063 TTTAATTAAGTTAGGTTAGGGTTTTACATTAAGTTAGGTTAGGGTTTTTAA
1 TTTAATTAAGTTAGGGTAGGGTTTTACAATAAGTTAGCTTAGGGTTTTTAA
*
11709114 TTAAATTA
1 TTTAATTA
11709122 GGTTTTTAAT
Statistics
Matches: 95, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
45 5 0.05
46 34 0.36
49 2 0.02
51 51 0.54
52 3 0.03
ACGTcount: A:0.29, C:0.03, G:0.22, T:0.46
Consensus pattern (51 bp):
TTTAATTAAGTTAGGGTAGGGTTTTACAATAAGTTAGCTTAGGGTTTTTAA
Found at i:11709127 original size:17 final size:17
Alignment explanation
Indices: 11709105--11709142 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
11709095 GTTAGGTTAG
11709105 GGTTTTTAATTAAATTA
1 GGTTTTTAATTAAATTA
*
11709122 GGTTTTTAATTCAATTA
1 GGTTTTTAATTAAATTA
11709139 GGTT
1 GGTT
11709143 AGGGTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.53
Consensus pattern (17 bp):
GGTTTTTAATTAAATTA
Found at i:11709375 original size:17 final size:17
Alignment explanation
Indices: 11709350--11709383 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11709340 GGGATTTTAA
11709350 TTAAATTAAGTTAGGTT
1 TTAAATTAAGTTAGGTT
*
11709367 TTAAGTTAAGTTAGGTT
1 TTAAATTAAGTTAGGTT
11709384 AGGGTTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (17 bp):
TTAAATTAAGTTAGGTT
Found at i:11709432 original size:18 final size:17
Alignment explanation
Indices: 11709409--11709446 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
11709399 GTTAGGTTAG
11709409 GGTTTTTAATTAAATTA
1 GGTTTTTAATTAAATTA
*
11709426 GGTTTTTAATTCAATTA
1 GGTTTTTAATTAAATTA
11709443 GGTT
1 GGTT
11709447 AGGGTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.53
Consensus pattern (17 bp):
GGTTTTTAATTAAATTA
Found at i:11709465 original size:40 final size:41
Alignment explanation
Indices: 11709078--11709469 Score: 191
Period size: 41 Copynumber: 9.2 Consensus size: 41
11709068 TTAAGTTAGG
* *
11709078 TTAGGGTTTTACATTAAGTTAGGTTAGGGTTTTTAATTAAA
1 TTAGGTTTTTACATTAAGTTAGGTTAGGGTTTTTAATCAAA
* *
11709119 TTAGGTTTTTA-ATTCAA-TTAGGTTAGGG-TTTTACATTAAG
1 TTAGGTTTTTACATT-AAGTTAGGTTAGGGTTTTTA-ATCAAA
*
11709159 TTAGGTTAGGGTTT---TTAA-TTAAGTTAGGGTTTTTAATTCAATTA
1 TTAGGTT----TTTACATTAAGTTAGGTTAGGGTTTTTAA-TCAA--A
* * * * **
11709203 GGTTAGGGTTTTTA-ATTAAATTAAGTTAGGTTTTAAGTTAAGTTAGG
1 --TTA-GGTTTTTACATTAAGTTAGGTTAGGGTTT---TTAA-TCAAA
* * * *
11709250 TTAGGGTTTTACATTAAGTTAAGTTAGGGTTTTTAATTAAG
1 TTAGGTTTTTACATTAAGTTAGGTTAGGGTTTTTAATCAAA
*
11709291 TTAGGGTTTTTA-ATTCAA-TTAGGTTAGGGTTTTTAATTAAGTTA
1 TTA-GGTTTTTACATT-AAGTTAGGTTAGGGTTTTTAATCAA---A
* * * * * **
11709335 GGTTAGGGATTTTA-ATTAAATTAAGTTAGGTTTTAAGTTAAGTTAGG
1 --TTA-GGTTTTTACATTAAGTTAGGTTAGGGTTT---TTAA-TCAAA
* *
11709382 TTAGGGTTTTACATTAAGTTAGGTTAGGGTTTTTAATTAAA
1 TTAGGTTTTTACATTAAGTTAGGTTAGGGTTTTTAATCAAA
11709423 TTAGGTTTTTA-ATTCAA-TTAGGTTAGGGTTTTTAA-CACAA
1 TTAGGTTTTTACATT-AAGTTAGGTTAGGGTTTTTAATCA-AA
11709463 TTAGGTT
1 TTAGGTT
11709470 AGGGTTTTTA
Statistics
Matches: 286, Mismatches: 30, Indels: 71
0.74 0.08 0.18
Matches are distributed among these distances:
39 6 0.02
40 56 0.20
41 71 0.25
42 27 0.09
43 3 0.01
44 17 0.06
45 47 0.16
46 42 0.15
47 4 0.01
49 10 0.03
50 3 0.01
ACGTcount: A:0.29, C:0.03, G:0.22, T:0.47
Consensus pattern (41 bp):
TTAGGTTTTTACATTAAGTTAGGTTAGGGTTTTTAATCAAA
Found at i:11709506 original size:91 final size:88
Alignment explanation
Indices: 11709175--11709548 Score: 270
Period size: 86 Copynumber: 4.2 Consensus size: 88
11709165 TAGGGTTTTT
** *
11709175 AATTAAGTTAGGGTTTTTAATTCAATTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTT--TA
1 AATTAAGTTA-GG-TTTTAACACAATTAGGTTAGGGTTTTTAATTCAATTAAGTTAGGTTTGGT-
** ** *
11709238 AGTTAAGTTAGGTTAGGGTTTTACATTA
63 TTTTAA-TTAAATTAGGTTTTTA-ATTA
* * * *
11709266 AGTTAAGTTAGGGTTTT----TAATTAAGTTAGGGTTTTTAATTCAATTAGGTTAGGGTTT--TT
1 AATTAAGTTA-GGTTTTAACACAATTAGGTTAGGGTTTTTAATTCAATTAAGTTA-GGTTTGGTT
* ** *
11709325 AATTAAGTTAGGTTAGGGATTTTAATTA
64 -TTTAA-TTAAATTA-GGTTTTTAATTA
*** *
11709353 AATTAAGTTAGGTTTTAAGTTAAGTTAGGTTAGGG-TTTT-A--C-ATTAAGTTAGGTTAGGGTT
1 AATTAAGTTAGGTTTTAACACAA-TTAGGTTAGGGTTTTTAATTCAATTAAGTTAGGTT-TGGTT
*
11709413 TTTAATTAAATTAGGTTTTTAATTC
64 TTTAATTAAATTAGGTTTTTAATTA
*
11709438 AATTAGGTTAGGGTTTTTAACACAATTAGGTTAGGGTTTTTAATTCAATTAAGTTAGGTTTGGAT
1 AATTAAGTTA-GG-TTTTAACACAATTAGGTTAGGGTTTTTAATTCAATTAAGTTAGGTTTGG-T
11709503 TTTTAATTCAATTAGGTTAGGGTTTTTAATTA
63 TTTTAATT-AA--A--TTA-GGTTTTTAATTA
11709535 AATTAAGTTAGGTT
1 AATTAAGTTAGGTT
11709549 AGGGTTTTTA
Statistics
Matches: 234, Mismatches: 24, Indels: 46
0.77 0.08 0.15
Matches are distributed among these distances:
85 23 0.10
86 63 0.27
87 49 0.21
88 10 0.04
89 1 0.00
90 14 0.06
91 44 0.19
92 2 0.01
94 1 0.00
95 2 0.01
96 5 0.02
97 20 0.09
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (88 bp):
AATTAAGTTAGGTTTTAACACAATTAGGTTAGGGTTTTTAATTCAATTAAGTTAGGTTTGGTTTT
TAATTAAATTAGGTTTTTAATTA
Found at i:11709518 original size:132 final size:133
Alignment explanation
Indices: 11708866--11709499 Score: 638
Period size: 132 Copynumber: 4.8 Consensus size: 133
11708856 TAATTAAATT
* *
11708866 AGTTAGGTTAGGGTTTTTAATTAAATTAAGTTAGG-TTTTAAGTT-AAGTTAGGTTAGTG-TTTT
1 AGTTAGGTTAGGGTTTTTAATTAAGTT-AG---GGTTTTTAA-TTCAA-TTAGGTTAGGGTTTTT
* * *
11708928 ACATTA-AGTTAGGTTAGGGTTTTTAATTAAATTAGGTT---TTT-AA-TTCAA-TTAGGTTAGG
60 A-ATTACAATTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTTGAAGTT-AAGTTAGATTAGG
11708986 GTTTTACATTA
123 GTTTTACATTA
* * *
11708997 AGTTAGGTTAGGGTTTTTAATTAAGTTAGGGTAGGGTTTTAAATACAGTTAGCTTAGGGTTTTTA
1 AGTTAGGTTAGGGTTTTTAATTAAGTTAGGGT----TTTT-AATTCAATTAGGTTAGGGTTTTTA
* * * *
11709062 ATTTAATTAAGTTAGGTTAGGG-TTTTACATTAAGTTAGGTTAGGGTTT----TTAA-TTAAATT
61 A-TT-A-CAA-TTAGGTTAGGGTTTTTA-ATTAAATTAAGTTA-GGTTTGAAGTTAAGTTAGATT
*
11709121 AGGTTTTTA-ATTCA
120 AGGGTTTTACATT-A
*
11709135 A-TTAGGTTAGGG-TTTTACATTAAGTTA-GGTTAGGGTTT--TT-AATTAAGTTAGGGTTTTTA
1 AGTTAGGTTAGGGTTTTTA-ATTAAGTTAGGGTT----TTTAATTCAATTAGGTTAGGGTTTTTA
* *
11709194 ATT-CAATTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTTTAAGTTAAGTTAGGTTAGGGTT
61 ATTACAATTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTTGAAGTTAAGTTAGATTAGGGTT
11709258 TTACATTA
126 TTACATTA
*
11709266 AGTTAAGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTCAATTAGGTTAGGGTTTTTAATTA-
1 AGTTAGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTCAATTAGGTTAGGGTTTTTAATTAC
* * * *
11709330 AGTTAGGTTAGGGATTTTAATTAAATTAAGTTAGGTTTTAAGTTAAGTTAGGTTAGGGTTTTACA
66 AATTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTTGAAGTTAAGTTAGATTAGGGTTTTACA
11709395 TTA
131 TTA
* *
11709398 AGTTAGGTTAGGGTTTTTAATTAAATTA-GGTTTTTAATTCAATTAGGTTAGGGTTTTTAA-CAC
1 AGTTAGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTCAATTAGGTTAGGGTTTTTAATTAC
*
11709461 AATTAGGTTAGGGTTTTTAATTCAATTAAGTTAGGTTTG
66 AATTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTTG
11709500 GATTTTTAAT
Statistics
Matches: 433, Mismatches: 31, Indels: 78
0.80 0.06 0.14
Matches are distributed among these distances:
126 5 0.01
127 25 0.06
128 7 0.02
129 3 0.01
130 7 0.02
131 112 0.26
132 168 0.39
133 20 0.05
134 1 0.00
136 17 0.04
137 46 0.11
138 17 0.04
139 2 0.00
141 3 0.01
ACGTcount: A:0.29, C:0.03, G:0.22, T:0.46
Consensus pattern (133 bp):
AGTTAGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTCAATTAGGTTAGGGTTTTTAATTAC
AATTAGGTTAGGGTTTTTAATTAAATTAAGTTAGGTTTGAAGTTAAGTTAGATTAGGGTTTTACA
TTA
Found at i:11709557 original size:28 final size:28
Alignment explanation
Indices: 11709463--11709565 Score: 126
Period size: 28 Copynumber: 3.9 Consensus size: 28
11709453 TTTAACACAA
*
11709463 TTAGGTTAGGGTTTTTAATTCAATTAAG
1 TTAGGTTAGGGTTTTTAATTAAATTAAG
* * *
11709491 TTAGGTTTGGATTTTTAA-T---TCAA-
1 TTAGGTTAGGGTTTTTAATTAAATTAAG
11709514 TTAGGTTAGGGTTTTTAATTAAATTAAG
1 TTAGGTTAGGGTTTTTAATTAAATTAAG
*
11709542 TTAGGTTAGGGTTTTTAATCAAAT
1 TTAGGTTAGGGTTTTTAATTAAAT
11709566 AATGTCAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
23 16 0.25
24 4 0.06
27 4 0.06
28 39 0.62
ACGTcount: A:0.29, C:0.03, G:0.20, T:0.48
Consensus pattern (28 bp):
TTAGGTTAGGGTTTTTAATTAAATTAAG
Found at i:11711715 original size:14 final size:15
Alignment explanation
Indices: 11711698--11711731 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
11711688 AATAAATATC
11711698 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
11711712 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
11711727 TAAAA
1 TAAAA
11711732 TATAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:11711957 original size:22 final size:22
Alignment explanation
Indices: 11711927--11711968 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
11711917 ATTTGGAGAT
*
11711927 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
11711949 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
11711969 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:11711976 original size:30 final size:30
Alignment explanation
Indices: 11711940--11711996 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
11711930 TTGAAGGAAA
* *
11711940 TTGAGAGGATTTTGGAAGGAATTTGAGAGT
1 TTGAGAGAATTTTGGAAGGAAATTGAGAGT
11711970 TTGAGAGAATTTTGGAAGGAAATTGAG
1 TTGAGAGAATTTTGGAAGGAAATTGAG
11711997 GGAATTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.32
Consensus pattern (30 bp):
TTGAGAGAATTTTGGAAGGAAATTGAGAGT
Found at i:11711989 original size:52 final size:51
Alignment explanation
Indices: 11711918--11712020 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 51
11711908 TTAATATGGA
* * *
11711918 TTTGGAGATTTTTTGAAGGAAATTGAGAGG-ATTTTGGAAGGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGGAAATTGAG-GGAATTTTGGAAGGAAATTGAGAG
*
11711969 TTTGAGAGAATTTTGGAAGGAAATTGAGGGAATTTTTGAAGGAAATTGAGAG
1 TTTG-GAGAATTTTGGAAGGAAATTGAGGGAATTTTGGAAGGAAATTGAGAG
11712021 AATTTGTTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
51 6 0.13
52 40 0.87
ACGTcount: A:0.34, C:0.00, G:0.33, T:0.33
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGGAAATTGAGGGAATTTTGGAAGGAAATTGAGAG
Found at i:11711995 original size:22 final size:22
Alignment explanation
Indices: 11711970--11712025 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
11711960 ATTTGAGAGT
11711970 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
* *
11711992 TTGAGGGAATTTTTGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
11712014 TTGAGAGAATTT
1 TTGAGAGAATTT
11712026 GTTTGTGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.38, C:0.00, G:0.30, T:0.32
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:11713306 original size:21 final size:21
Alignment explanation
Indices: 11713282--11713323 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
11713272 ATTTTCAAAT
*
11713282 TAATTGCACATTGATTTGTAA
1 TAATTGCACATTAATTTGTAA
*
11713303 TAATTGCATATTAATTTGTAA
1 TAATTGCACATTAATTTGTAA
11713324 ATTTTTGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (21 bp):
TAATTGCACATTAATTTGTAA
Found at i:11715764 original size:11 final size:10
Alignment explanation
Indices: 11715748--11715808 Score: 59
Period size: 10 Copynumber: 5.7 Consensus size: 10
11715738 TTTCTCCTTC
11715748 TTTCTTTCCTT
1 TTTCTTT-CTT
*
11715759 TTTCTTTCTG
1 TTTCTTTCTT
*
11715769 TTTCATTTCAT
1 TTTC-TTTCTT
*
11715780 TTTGTTTCTT
1 TTTCTTTCTT
11715790 TTTCTATTTCTT
1 TTTC--TTTCTT
11715802 TTTCTTT
1 TTTCTTT
11715809 TATTTTGTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
10 17 0.41
11 14 0.34
12 10 0.24
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:11715772 original size:21 final size:20
Alignment explanation
Indices: 11715748--11715808 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
11715738 TTTCTCCTTC
11715748 TTTCTTTCCTTTTTCTTTCTG
1 TTTCTTT-CTTTTTCTTTCTG
* * *
11715769 TTTCATTTCATTTTGTTTCTT
1 TTTC-TTTCTTTTTCTTTCTG
11715790 TTTCTATTTCTTTTTCTTT
1 TTTC--TTTCTTTTTCTTT
11715809 TATTTTGTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (20 bp):
TTTCTTTCTTTTTCTTTCTG
Found at i:11717321 original size:21 final size:22
Alignment explanation
Indices: 11717287--11717340 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
11717277 ACATGTGGAT
*
11717287 TATAAAAATA-ACATAAAATAA
1 TATATAAATATACATAAAATAA
***
11717308 TATAT-AATATACATATTTTAA
1 TATATAAATATACATAAAATAA
11717329 TATATAAATATA
1 TATATAAATATA
11717341 TATATATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 4 0.15
21 17 0.63
22 6 0.22
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
TATATAAATATACATAAAATAA
Found at i:11717534 original size:21 final size:21
Alignment explanation
Indices: 11717502--11717583 Score: 51
Period size: 21 Copynumber: 3.6 Consensus size: 21
11717492 AATAAAAACC
11717502 TAACAATAATAACAAA-AATAT
1 TAACAATAATAA-AAATAATAT
11717523 TAACGAAT-ATAAAAATAATAAT
1 TAAC-AATAATAAAAATAAT-AT
* *
11717545 AGTAAAGACAATAATAATAATAATAA
1 --T--A-ACAATAATAAAAATAATAT
*
11717571 TAATAATAATAAA
1 TAACAATAATAAA
11717584 TTGACCAGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 18
0.69 0.06 0.26
Matches are distributed among these distances:
20 3 0.06
21 20 0.42
22 6 0.12
24 2 0.04
26 5 0.10
27 12 0.25
ACGTcount: A:0.66, C:0.05, G:0.04, T:0.26
Consensus pattern (21 bp):
TAACAATAATAAAAATAATAT
Found at i:11717544 original size:3 final size:3
Alignment explanation
Indices: 11717531--11717582 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
11717521 ATTAACGAAT
* * *
11717531 ATA AAA ATA ATA ATA GTA A-A GACA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
11717576 ATA ATA A
1 ATA ATA A
11717583 ATTGACCAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
2 1 0.02
3 40 0.95
4 1 0.02
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:11719428 original size:46 final size:44
Alignment explanation
Indices: 11719319--11719445 Score: 166
Period size: 46 Copynumber: 2.8 Consensus size: 44
11719309 AGATAAGATC
* * * *
11719319 CTTTAATCCGCTCCACTGTAATCTCAGGGAAATAGGATTACTAT
1 CTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAT
*
11719363 CTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACT-T
1 CTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-T--ACTAT
*
11719409 CTTTGGTCTGCTCCACTGTAATCTCAGGGAGATAAGA
1 CTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGA
11719446 CCTGTATAAT
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
44 33 0.45
45 1 0.01
46 36 0.49
47 3 0.04
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.31
Consensus pattern (44 bp):
CTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAT
Found at i:11731863 original size:21 final size:22
Alignment explanation
Indices: 11731829--11731882 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
11731819 ACATGTGGAT
*
11731829 TATAAAAATA-ACATAAAATAA
1 TATATAAATATACATAAAATAA
***
11731850 TATAT-AATATACATATTTTAA
1 TATATAAATATACATAAAATAA
11731871 TATATAAATATA
1 TATATAAATATA
11731883 TATATATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 4 0.15
21 17 0.63
22 6 0.22
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
TATATAAATATACATAAAATAA
Found at i:11732076 original size:21 final size:21
Alignment explanation
Indices: 11732044--11732084 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
11732034 AATAAAAACC
11732044 TAACAATAATAACAAA-AATAT
1 TAACAATAATAA-AAATAATAT
11732065 TAACGAAT-ATAAAAATAATA
1 TAAC-AATAATAAAAATAATA
11732085 ATAGTAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 3 0.17
21 12 0.67
22 3 0.17
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.24
Consensus pattern (21 bp):
TAACAATAATAAAAATAATAT
Found at i:11732099 original size:18 final size:18
Alignment explanation
Indices: 11732073--11732123 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
11732063 ATTAACGAAT
*
11732073 ATAAAAATAATAATAGTA
1 ATAACAATAATAATAGTA
*
11732091 A-AGACAATAATAGTAGTA
1 ATA-ACAATAATAATAGTA
*
11732109 ATAATAATAATAATA
1 ATAACAATAATAATA
11732124 AATTGACCAG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 1 0.04
18 25 0.93
19 1 0.04
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (18 bp):
ATAACAATAATAATAGTA
Found at i:11760221 original size:13 final size:13
Alignment explanation
Indices: 11760205--11760237 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
11760195 TTTAAACCAA
11760205 ACTTTTCACAAAT-
1 ACTTTTCA-AAATC
11760218 ACTTTTCAAAATC
1 ACTTTTCAAAATC
11760231 ACTTTTC
1 ACTTTTC
11760238 TACAGGACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.42
Consensus pattern (13 bp):
ACTTTTCAAAATC
Found at i:11760737 original size:20 final size:20
Alignment explanation
Indices: 11760691--11760737 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
11760681 TGCTAAACAT
* *
11760691 TAATTT-AATTAAGTTTAAT
1 TAATTTAAATTAAGATTAAG
11760710 TAGA-TTAAATTAAGATTAAG
1 TA-ATTTAAATTAAGATTAAG
11760730 TAATTTAA
1 TAATTTAA
11760738 TTATAAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.45
Consensus pattern (20 bp):
TAATTTAAATTAAGATTAAG
Found at i:11764538 original size:50 final size:50
Alignment explanation
Indices: 11764423--11764721 Score: 391
Period size: 50 Copynumber: 5.8 Consensus size: 50
11764413 GATAATAACA
* ** *
11764423 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTTGG
* * *
11764474 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
* *
11764524 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
* * *
11764574 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
* * *
11764624 TGCCCATGCCACGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTT--GG
*
11764679 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
11764722 TTACCCAAAT
Statistics
Matches: 219, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
50 143 0.65
51 33 0.15
53 3 0.01
55 2 0.01
56 38 0.17
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
Found at i:11764837 original size:13 final size:13
Alignment explanation
Indices: 11764816--11764846 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
11764806 GCTTAGATCA
*
11764816 TCATCAAATAAAT
1 TCATAAAATAAAT
11764829 TCATAAAATAAAT
1 TCATAAAATAAAT
11764842 TCATA
1 TCATA
11764847 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:11765118 original size:29 final size:30
Alignment explanation
Indices: 11765059--11765115 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
11765049 CCTCGACTCT
*
11765059 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
11765089 AACTTTTACATAATTACATTTTTGCCC
1 AACTTTTACAAAATTACAATTTTGCCC
11765116 TAAGGCTCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.42
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:11768249 original size:2 final size:2
Alignment explanation
Indices: 11768242--11768274 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
11768232 GTATACATAC
11768242 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11768275 AAAACCAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11769238 original size:20 final size:20
Alignment explanation
Indices: 11769213--11769254 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
11769203 TCGGTGCCGC
11769213 CATCTGACAATCTGCACAAA
1 CATCTGACAATCTGCACAAA
11769233 CATCTGACAATCTGCACAAA
1 CATCTGACAATCTGCACAAA
11769253 CA
1 CA
11769255 CTGTGCCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.31, G:0.10, T:0.19
Consensus pattern (20 bp):
CATCTGACAATCTGCACAAA
Found at i:11770178 original size:20 final size:22
Alignment explanation
Indices: 11770155--11770197 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
11770145 AAACCCGAAT
*
11770155 TTAACTCAA-AAAA-ATAAAAA
1 TTAAATCAACAAAAGATAAAAA
*
11770175 TTAAATTAACAAAAGATAAAAA
1 TTAAATCAACAAAAGATAAAAA
11770197 T
1 T
11770198 ATTATAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.23
Consensus pattern (22 bp):
TTAAATCAACAAAAGATAAAAA
Found at i:11772481 original size:19 final size:19
Alignment explanation
Indices: 11772444--11772481 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
11772434 AAGCACCATC
*
11772444 ATAAAATTATAGTTTTTTA
1 ATAAAATTATAGTTATTTA
11772463 ATAAAATTAT-GATTATTTA
1 ATAAAATTATAG-TTATTTA
11772482 TAATAATCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
ATAAAATTATAGTTATTTA
Found at i:11774396 original size:30 final size:30
Alignment explanation
Indices: 11774334--11774397 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
11774324 TATTATATTT
*
11774334 AAATAAGTCTTTAAATTTTAATTAGTACTC
1 AAATAAGTCTTTAAATTTTAATTAGCACTC
* *
11774364 AAATAAGTTTTTAAATTTTAAGTTA-CATTC
1 AAATAAGTCTTTAAATTTTAA-TTAGCACTC
11774394 AAAT
1 AAAT
11774398 TATAAGTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 27 0.90
31 3 0.10
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (30 bp):
AAATAAGTCTTTAAATTTTAATTAGCACTC
Found at i:11787433 original size:18 final size:18
Alignment explanation
Indices: 11787412--11787469 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
11787402 AATGCAAAGA
11787412 TTAATAAAAATAAATAAT
1 TTAATAAAAATAAATAAT
*
11787430 TTAATAATATATAAA-AA-
1 TTAATAA-AAATAAATAAT
** *
11787447 TTGGTAAAAATCAATAAT
1 TTAATAAAAATAAATAAT
11787465 TTAAT
1 TTAAT
11787470 CATTTATATG
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
16 5 0.17
17 7 0.23
18 12 0.40
19 6 0.20
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (18 bp):
TTAATAAAAATAAATAAT
Found at i:11790888 original size:17 final size:16
Alignment explanation
Indices: 11790866--11790898 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
11790856 TGAAAGATTG
11790866 ATGTAAATATATGTTAA
1 ATGTAAATATAT-TTAA
11790883 ATGTAAATATATTTAA
1 ATGTAAATATATTTAA
11790899 TTTTTTAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (16 bp):
ATGTAAATATATTTAA
Found at i:11791177 original size:20 final size:20
Alignment explanation
Indices: 11791139--11791190 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
11791129 TTTCTCTTCC
*
11791139 AATTATAAAAAAATAAAAA-
1 AATTATAAAAATATAAAAAG
*
11791158 AATTATTAAAAATATGAAAAG
1 AATTA-TAAAAATATAAAAAG
*
11791179 AGTTATAAAAAT
1 AATTATAAAAAT
11791191 TAATGGCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 5 0.18
20 19 0.68
21 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (20 bp):
AATTATAAAAATATAAAAAG
Found at i:11791717 original size:125 final size:124
Alignment explanation
Indices: 11791494--11791739 Score: 359
Period size: 125 Copynumber: 2.0 Consensus size: 124
11791484 AAATAGTGGG
** * * * *
11791494 AAATCGCTTTTACCAGGATGCTATTTGAGAAAAAATTGTGAAATAATGGCCTCGTGGACGCGATT
1 AAATCGCTGATACCAGGATGCTATATGAGAAAAAATTGTGAAATAACGCCCTCGTGGACGCGATA
* *
11791559 TCGCTACAGTGGTCATGTAAGAAATAATTTTTTTTTGACTTTTACTGAGCAAATAGTATA
66 TCGCTACAGTGGTCATGTAAGAAATAATATTTTTTTGACGTTT-CTGAGCAAATAGTATA
* **
11791619 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATA
1 AAATCGCTGATACCAGGATGCTATATGAGAAAAAATTGTGAAATAACGCCCTCGTGGACGCGATA
*
11791684 TCGCTACAGTTGGTCATGTAGGAAATAA-ATTTTTTTGACGTTTCTGAGCAAATAGT
66 TCGCTACAG-TGGTCATGTAAGAAATAATATTTTTTTGACGTTTCTGAGCAAATAGT
11791740 GTCAAATCAC
Statistics
Matches: 108, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
124 13 0.12
125 78 0.72
126 17 0.16
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (124 bp):
AAATCGCTGATACCAGGATGCTATATGAGAAAAAATTGTGAAATAACGCCCTCGTGGACGCGATA
TCGCTACAGTGGTCATGTAAGAAATAATATTTTTTTGACGTTTCTGAGCAAATAGTATA
Found at i:11795035 original size:23 final size:23
Alignment explanation
Indices: 11795009--11795211 Score: 127
Period size: 23 Copynumber: 7.9 Consensus size: 23
11794999 TTTTTAATTA
* * * *
11795009 AATTAGGTTAGCTTAGGGATTTC
1 AATTAAGTTAGGTTAGGGTTTTT
*
11795032 AATTAAGTTAGGTTACGGTTTTT
1 AATTAAGTTAGGTTAGGGTTTTT
11795055 AATTAAGTTAGGTTAGGGTTTTT
1 AATTAAGTTAGGTTAGGGTTTTT
11795078 AATTAAAATATGTTAGGGTTAGGGTTTTCATGT
1 AATT---A-A-GTTA-GGTTAGGG-TTT--T-T
* *
11795111 AAAATAGGTTAGGGTTAGGGTTTTTAATT
1 -AATTAAGTTA-GGTTAGGG-TT-T--TT
11795140 AAATTAAGTTAGGTTAGGGTTTTTAATT
1 -AATTAAGTTAGGTTAGGG--TTT--TT
*
11795168 AAATTAAGTTAAGTTAGGGTTTTT
1 -AATTAAGTTAGGTTAGGGTTTTT
*
11795192 AATTAAATTAGGTTAGGGTT
1 AATTAAGTTAGGTTAGGGTT
11795212 AGGGTTTTTA
Statistics
Matches: 153, Mismatches: 14, Indels: 26
0.79 0.07 0.13
Matches are distributed among these distances:
23 62 0.41
24 2 0.01
26 4 0.03
27 1 0.01
28 35 0.23
29 37 0.24
30 6 0.04
31 1 0.01
32 1 0.01
33 1 0.01
34 3 0.02
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.44
Consensus pattern (23 bp):
AATTAAGTTAGGTTAGGGTTTTT
Found at i:11795036 original size:28 final size:28
Alignment explanation
Indices: 11794973--11795246 Score: 275
Period size: 28 Copynumber: 10.0 Consensus size: 28
11794963 AATTATTACA
*
11794973 TTAATTCAAA-TAGGTTAGGGTTGGGGTTT
1 TTAATT-AAATTAGGTTA-GGTTAGGGTTT
* *
11795002 TTAATTAAATTAGGTTAGCTTAGGGATT
1 TTAATTAAATTAGGTTAGGTTAGGGTTT
* *
11795030 TCAATT--A--A-GTTAGGTTACGGTTT
1 TTAATTAAATTAGGTTAGGTTAGGGTTT
11795053 TTAATT--A--A-GTTAGGTTAGGGTTT
1 TTAATTAAATTAGGTTAGGTTAGGGTTT
* *
11795076 TTAATTAAAATATGTTAGGGTTAGGG-TT
1 TTAATTAAATTAGGTTA-GGTTAGGGTTT
* *
11795104 TTCATGTAAAATAGGTTAGGGTTAGGGTTT
1 TTAAT-TAAATTAGGTTA-GGTTAGGGTTT
*
11795134 TTAATTAAATTAAGTTAGGTTAGGGTTT
1 TTAATTAAATTAGGTTAGGTTAGGGTTT
* *
11795162 TTAATTAAATTAAGTTAAGTTAGGGTTT
1 TTAATTAAATTAGGTTAGGTTAGGGTTT
11795190 TTAATTAAATTAGGTTAGGGTTAGGGTTT
1 TTAATTAAATTAGGTTA-GGTTAGGGTTT
** *
11795219 TTAATTAAATTAAATTAGGGTAGGGTTT
1 TTAATTAAATTAGGTTAGGTTAGGGTTT
11795247 NNNNNNNNNN
Statistics
Matches: 215, Mismatches: 20, Indels: 21
0.84 0.08 0.08
Matches are distributed among these distances:
23 39 0.18
24 1 0.00
25 1 0.00
26 1 0.00
27 1 0.00
28 90 0.42
29 76 0.35
30 6 0.03
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.44
Consensus pattern (28 bp):
TTAATTAAATTAGGTTAGGTTAGGGTTT
Found at i:11797527 original size:14 final size:15
Alignment explanation
Indices: 11797510--11797543 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
11797500 AATAAATATC
11797510 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
11797524 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
11797539 TAAAA
1 TAAAA
11797544 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:11797661 original size:11 final size:10
Alignment explanation
Indices: 11797641--11797684 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
11797631 TGAAAATATT
11797641 AAAAATTTTA
1 AAAAATTTTA
11797651 AAAATATTTTA
1 AAAA-ATTTTA
***
11797662 AAAAAAAATA
1 AAAAATTTTA
11797672 AAAAATTTTA
1 AAAAATTTTA
11797682 AAA
1 AAA
11797685 TTTTCTTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
10 17 0.63
11 10 0.37
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAAATTTTA
Found at i:11797770 original size:22 final size:22
Alignment explanation
Indices: 11797740--11797781 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
11797730 ATTTGGAGAT
*
11797740 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
11797762 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
11797782 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:11797789 original size:30 final size:30
Alignment explanation
Indices: 11797753--11797811 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
11797743 TTGAAGGAAA
* * *
11797753 TTGAGAGGATTTTGGAAGGAATTTGAGAGT
1 TTGAGAGAATTTTGGAAGAAAATTGAGAGT
11797783 TTGAGAGAATTTTGGAAGAAAATTGAGAG
1 TTGAGAGAATTTTGGAAGAAAATTGAGAG
11797812 AATTCTTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.34, T:0.31
Consensus pattern (30 bp):
TTGAGAGAATTTTGGAAGAAAATTGAGAGT
Found at i:11797806 original size:52 final size:51
Alignment explanation
Indices: 11797731--11797833 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 51
11797721 TTAATATGGA
* * * *
11797731 TTTGGAGATTTTTTGAAGGAAATTGAGAGGATT-TTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGAAAATTGAGAGAATTCTT-GAAGGGAA-TTGAGAG
11797782 TTTGAGAGAATTTTGGAAGAAAATTGAGAGAATTCTTGAAGGGAATTGAGAG
1 TTTG-GAGAATTTTGGAAGAAAATTGAGAGAATTCTTGAAGGGAATTGAGAG
11797834 AATTTTTGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
51 4 0.09
52 35 0.78
53 6 0.13
ACGTcount: A:0.35, C:0.01, G:0.32, T:0.32
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGAAAATTGAGAGAATTCTTGAAGGGAATTGAGAG
Found at i:11797808 original size:22 final size:21
Alignment explanation
Indices: 11797783--11797852 Score: 95
Period size: 22 Copynumber: 3.2 Consensus size: 21
11797773 ATTTGAGAGT
*
11797783 TTGAGAGAATTTTGGAAGAAAA
1 TTGAGAGAATTTT-GAAGGAAA
*
11797805 TTGAGAGAATTCTTGAAGGGAA
1 TTGAGAGAATT-TTGAAGGAAA
11797827 TTGAGAGAATTTTTGAAGGAAA
1 TTGAGAGAA-TTTTGAAGGAAA
11797849 TTGA
1 TTGA
11797853 TATTGAATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
22 39 0.91
23 4 0.09
ACGTcount: A:0.40, C:0.01, G:0.29, T:0.30
Consensus pattern (21 bp):
TTGAGAGAATTTTGAAGGAAA
Found at i:11799389 original size:31 final size:31
Alignment explanation
Indices: 11799354--11799415 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
11799344 GCAATAAGAA
11799354 AGAACCAGTATATTGATTCATTGTGCTTACT
1 AGAACCAGTATATTGATTCATTGTGCTTACT
11799385 AGAACCAGTATATTGATTCATTGTGCTTACT
1 AGAACCAGTATATTGATTCATTGTGCTTACT
11799416 CAGAGGAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (31 bp):
AGAACCAGTATATTGATTCATTGTGCTTACT
Found at i:11802084 original size:29 final size:29
Alignment explanation
Indices: 11802026--11802084 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
11802016 TGGGCAACAG
* * * *
11802026 AAAATAGTTTAGGTATCACTTGTGACAAA
1 AAAAAAGTTTAGGTATAACTAGGGACAAA
11802055 AAAAAAGTTTAGGTACTAACTAGGGA-AAA
1 AAAAAAGTTTAGGTA-TAACTAGGGACAAA
11802084 A
1 A
11802085 TGGTATAGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.25
Consensus pattern (29 bp):
AAAAAAGTTTAGGTATAACTAGGGACAAA
Found at i:11803081 original size:8 final size:8
Alignment explanation
Indices: 11803068--11803092 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
11803058 ATTGGACAAC
11803068 AAAATTTT
1 AAAATTTT
11803076 AAAATTTT
1 AAAATTTT
11803084 AAAATTTT
1 AAAATTTT
11803092 A
1 A
11803093 TAATATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AAAATTTT
Found at i:11805084 original size:11 final size:11
Alignment explanation
Indices: 11805068--11805097 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
11805058 ATTGACCCAT
11805068 ATACAGAAATC
1 ATACAGAAATC
11805079 ATACAGAAATC
1 ATACAGAAATC
11805090 ATACAGAA
1 ATACAGAA
11805098 CATGCTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.57, C:0.17, G:0.10, T:0.17
Consensus pattern (11 bp):
ATACAGAAATC
Found at i:11814570 original size:25 final size:24
Alignment explanation
Indices: 11814542--11814619 Score: 66
Period size: 25 Copynumber: 3.2 Consensus size: 24
11814532 ATGCTTATAC
*
11814542 GAGCACATAAACGGGAAGCTCATGT
1 GAGC-CATAAACGGGAAGCTCATGA
* * * *
11814567 GAGCCATGTAACGGAAAGCTTATAA
1 GAGCCAT-AAACGGGAAGCTCATGA
* * *
11814592 GAGTCATAATCGGGAAGCTCATGC
1 GAGCCATAAACGGGAAGCTCATGA
11814616 GAGC
1 GAGC
11814620 TAATATTAAG
Statistics
Matches: 39, Mismatches: 13, Indels: 3
0.71 0.24 0.05
Matches are distributed among these distances:
24 17 0.44
25 22 0.56
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.18
Consensus pattern (24 bp):
GAGCCATAAACGGGAAGCTCATGA
Found at i:11819138 original size:15 final size:16
Alignment explanation
Indices: 11819120--11819154 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
11819110 ACATAGAAAT
*
11819120 AATAAGAAT-AATAAA
1 AATAAAAATAAATAAA
11819135 AATAAAAATAAATAAA
1 AATAAAAATAAATAAA
11819151 AATA
1 AATA
11819155 CTAAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (16 bp):
AATAAAAATAAATAAA
Found at i:11819226 original size:31 final size:29
Alignment explanation
Indices: 11819162--11819244 Score: 78
Period size: 31 Copynumber: 2.7 Consensus size: 29
11819152 ATACTAAAAC
* *
11819162 TAATAAGAATAAAATTACTATCTAGGATAAA
1 TAATAA-AATAAAAATA-AATCTAGGATAAA
11819193 TAAAATAAAATAAAAATAAATCTAGGCAT-AA
1 T--AATAAAATAAAAATAAATCTAGG-ATAAA
11819224 TAATAAAATAAATAAATAAAT
1 TAATAAAAT-AA-AAATAAAT
11819245 AAAATAAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
29 8 0.18
30 2 0.04
31 19 0.42
32 11 0.24
33 5 0.11
ACGTcount: A:0.63, C:0.05, G:0.06, T:0.27
Consensus pattern (29 bp):
TAATAAAATAAAAATAAATCTAGGATAAA
Found at i:11819240 original size:8 final size:8
Alignment explanation
Indices: 11819229--11819260 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
11819219 CATAATAATA
11819229 AAATAAAT
1 AAATAAAT
11819237 AAATAAAT
1 AAATAAAT
11819245 AAAATAAAT
1 -AAATAAAT
11819254 AAATAAA
1 AAATAAA
11819261 GAGGGAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAATAAAT
Found at i:11819247 original size:17 final size:17
Alignment explanation
Indices: 11819225--11819260 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
11819215 TAGGCATAAT
11819225 AATAAAATAAATAAATA
1 AATAAAATAAATAAATA
11819242 AATAAAATAAATAAATA
1 AATAAAATAAATAAATA
11819259 AA
1 AA
11819261 GAGGGAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (17 bp):
AATAAAATAAATAAATA
Found at i:11820218 original size:12 final size:12
Alignment explanation
Indices: 11820191--11820233 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
11820181 TTATTTCAAA
11820191 AAAAG-AAAAAC
1 AAAAGAAAAAAC
11820202 AAAAGAAGAAAAC
1 AAAAGAA-AAAAC
*
11820215 -AAAGAAAAAAG
1 AAAAGAAAAAAC
11820226 AAAAGAAA
1 AAAAGAAA
11820234 TTGTGAACAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 9 0.32
12 14 0.50
13 5 0.18
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAC
Found at i:11822933 original size:31 final size:31
Alignment explanation
Indices: 11822895--11822988 Score: 91
Period size: 31 Copynumber: 3.0 Consensus size: 31
11822885 TAAATAGTGA
**
11822895 AAACCATCATTGTTGGGCAATCCAGGGTGGT
1 AAACCATCATTGTAAGGCAATCCAGGGTGGT
* *
11822926 AAACCATCATTGTAAGGCAATCCGGGGTCGT
1 AAACCATCATTGTAAGGCAATCCAGGGTGGT
*** * *
11822957 ATGTCATCATTGCTAA-TCAATCCAGGATGGT
1 AAACCATCATTG-TAAGGCAATCCAGGGTGGT
11822988 A
1 A
11822989 GAATTGAATG
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 48 0.94
32 3 0.06
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (31 bp):
AAACCATCATTGTAAGGCAATCCAGGGTGGT
Found at i:11823153 original size:31 final size:31
Alignment explanation
Indices: 11823081--11823140 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
11823071 AATGAAAAAA
* * *
11823081 CCATCATAGCCGGGCAATCTAGGGTGGTAAG
1 CCATCATTGCCAGGCAATCTAGGGTAGTAAG
11823112 CCATCATTGCCAGGCAATCTAGGGTAGTA
1 CCATCATTGCCAGGCAATCTAGGGTAGTA
11823141 GATCATCGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (31 bp):
CCATCATTGCCAGGCAATCTAGGGTAGTAAG
Done.