Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, whole genome shotgun sequence
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: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 8 of 125
Found at i:1084101 original size:18 final size:17
Alignment explanation
Indices: 1084066--1084102 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
1084056 GAATTTTTTA
1084066 TTAAATTTTTTATAATT
1 TTAAATTTTTTATAATT
*
1084083 TTAAATTTATTTTTAATT
1 TTAAATTT-TTTATAATT
1084101 TT
1 TT
1084103 TGATCTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTAAATTTTTTATAATT
Found at i:1085442 original size:9 final size:9
Alignment explanation
Indices: 1085428--1085453 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1085418 TCCAAGGGAG
1085428 AATTACTTA
1 AATTACTTA
1085437 AATTACTTA
1 AATTACTTA
1085446 AATTACTT
1 AATTACTT
1085454 TCAATTTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (9 bp):
AATTACTTA
Found at i:1087840 original size:49 final size:49
Alignment explanation
Indices: 1087749--1088747 Score: 919
Period size: 49 Copynumber: 20.5 Consensus size: 49
1087739 TCATCTGATT
* * * * * *
1087749 AGAGACTCAATAACTTTAAAAAAATTCATCTTAAAAAAAGCTCTTCTCAGC
1 AGAGGCTCAACAACTTT--AAAAATCCATCTTGAAAAAAGCTCCTCTAAGC
* * * *
1087800 AAAGGTTCAATAACTTTAAAAAATCCATCTT-AAAAAAGCTCCTCTAAGT
1 AGAGGCTCAACAACTTT-AAAAATCCATCTTGAAAAAAGCTCCTCTAAGC
* * * *
1087849 AGAGGCTCAACAACTTT--AAA--CTTCTTGAAAAAA-CTCTTTTCAGC
1 AGAGGCTCAACAACTTTAAAAATCCATCTTGAAAAAAGCTCCTCTAAGC
* * * * * *
1087893 AAAAGTTTAACAACTTTAAAAATCTCATCTTTG-AAAAAGCTACTCTAAAC
1 AGAGGCTCAACAACTTTAAAAATC-CATC-TTGAAAAAAGCTCCTCTAAGC
* * *
1087943 AGAGGCTCAACAACTTTAAAAATCCAT-TTTAAAAAA-ATCCTCTAAGT
1 AGAGGCTCAACAACTTTAAAAATCCATCTTGAAAAAAGCTCCTCTAAGC
*
1087990 AGAGGCTCAACAACTTTAAAAATCTCATCTTGAAAAAGGCTCCTCTCAA-C
1 AGAGGCTCAACAACTTTAAAAATC-CATCTTGAAAAAAGCTCCTCT-AAGC
* * *
1088040 AAAGGCTCAACAACTTT-AAAATTCATCTTTAAAAAAAGCTCCTCTAAGC
1 AGAGGCTCAACAACTTTAAAAATCCATC-TTGAAAAAAGCTCCTCTAAGC
* * * *
1088089 AAAGGCTCAGCAACTTTAAAAAATTCATCTT-AAAAAAGTTCCTCTAAGC
1 AGAGGCTCAACAACTTT-AAAAATCCATCTTGAAAAAAGCTCCTCTAAGC
** * * *
1088138 AGAGATTCAACAACTTT-AAAATCTAATTTTGAAAAAAGCTCCTCTCAGC
1 AGAGGCTCAACAACTTTAAAAATC-CATCTTGAAAAAAGCTCCTCTAAGC
* *
1088187 AGAGGCTCAATAACTTT-AAAATCTCATCTTAAAAAAAGCTCCTCTAAGC
1 AGAGGCTCAACAACTTTAAAAATC-CATCTTGAAAAAAGCTCCTCTAAGC
* * *
1088236 AGAGGCTCAACAACTTTAAAATAT-AATCTTGAAAAAAACTCCTCTAAAC
1 AGAGGCTCAACAACTTTAAAA-ATCCATCTTGAAAAAAGCTCCTCTAAGC
* * *
1088285 AAAGGTTCAACAACTTT-AAAATCCAATCTTGAAAAAAGCTCCTCTAAAC
1 AGAGGCTCAACAACTTTAAAAATCC-ATCTTGAAAAAAGCTCCTCTAAGC
* * * * *
1088334 AGAAGCTCAATAACTTTAAAAATCTATCTT-AAAAAAGCTCTTTTAAGC
1 AGAGGCTCAACAACTTTAAAAATCCATCTTGAAAAAAGCTCCTCTAAGC
* ** * *
1088382 AGATGCTCAACAACTTTAAACTTCTCATCTTG-GAAAAGCTCATCTAAGC
1 AGAGGCTCAACAACTTTAAAAATC-CATCTTGAAAAAAGCTCCTCTAAGC
* * * *
1088431 AGAGGCTCAACAACTTTAAAATAT-AATCTTGAAAAAAACTCCCCTAAAC
1 AGAGGCTCAACAACTTTAAAA-ATCCATCTTGAAAAAAGCTCCTCTAAGC
** * *
1088480 AGAGGCTCAACAACTTTAAAAATTTATCTTAAAAAAAGCTCCTCTCAGC
1 AGAGGCTCAACAACTTTAAAAATCCATCTTGAAAAAAGCTCCTCTAAGC
* ** * * * * *
1088529 AGAGGCTCAATAACTTTAAACTTTTCATTTTG-AAAAATCTCCTTTAAGT
1 AGAGGCTCAACAACTTTAAA-AATCCATCTTGAAAAAAGCTCCTCTAAGC
* * * *
1088578 AGAAGCTCAACAACTTT-AAAATCCAATCTTGAAAAAAACTCCTATAAAC
1 AGAGGCTCAACAACTTTAAAAATCC-ATCTTGAAAAAAGCTCCTCTAAGC
* ** * *
1088627 AGAGGCTCAACAACTTTAAAAATCTATCTT-AAAAAAAATCTTTTAAGC
1 AGAGGCTCAACAACTTTAAAAATCCATCTTGAAAAAAGCTCCTCTAAGC
* ** *
1088675 AGATGCTCAACAACTTTAAACTTCTCATCTTG-AAAAAGCTCATCTAAGC
1 AGAGGCTCAACAACTTTAAAAATC-CATCTTGAAAAAAGCTCCTCTAAGC
*
1088724 AGAGGCTCAACAACTTTTAAAATC
1 AGAGGCTCAACAACTTTAAAAATC
1088748 TAATCTTTGT
Statistics
Matches: 775, Mismatches: 138, Indels: 72
0.79 0.14 0.07
Matches are distributed among these distances:
44 25 0.03
45 6 0.01
46 6 0.01
47 42 0.05
48 106 0.14
49 474 0.61
50 88 0.11
51 28 0.04
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (49 bp):
AGAGGCTCAACAACTTTAAAAATCCATCTTGAAAAAAGCTCCTCTAAGC
Found at i:1088179 original size:147 final size:146
Alignment explanation
Indices: 1087769--1088754 Score: 1035
Period size: 147 Copynumber: 6.8 Consensus size: 146
1087759 TAACTTTAAA
* * * * * *
1087769 AAAATTCATCTTAAAAAAAGCTCTTCTCAGCAAAGGTTCAATAACTTTAAAAAATCCATCTTAAA
1 AAAATTCATCTTAAAAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAAATTCATCTTAAA
* * * * *
1087834 AAAGCTCCTCTAAGTAGAGGCTCAACAACTTT-AAA-CT--TCTTGAAAAAA-CTCTTTTCAGCA
66 AAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAATCTAATCTTGAAAAAAGCTCCTCTAAACA
* * *
1087894 AAAGTTTAACAACTTT
131 AAGGCTCAACAACTTT
** * * * *
1087910 AAAAATCTCATCTTTGAAAAAGCTACTCTAAACAGAGGCTCAACAACTTT-AAAAATCCATTTTA
1 -AAAAT-TCATCTTAAAAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAAATTCATCTTA
* * * * *
1087974 AAAAA-ATCCTCTAAGTAGAGGCTCAACAACTTTAAAAATCTCATCTTGAAAAAGGCTCCTCTCA
64 AAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTT-AAAATCTAATCTTGAAAAAAGCTCCTCTAA
1088038 ACAAAGGCTCAACAACTTT
128 ACAAAGGCTCAACAACTTT
* *
1088057 AAAATTCATCTTTAAAAAAAGCTCCTCTAAGCAAAGGCTCAGCAACTTTAAAAAATTCATCTTAA
1 AAAATTCATC-TTAAAAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAAATTCATCTTAA
* ** * * *
1088122 AAAAGTTCCTCTAAGCAGAGATTCAACAACTTTAAAATCTAATTTTGAAAAAAGCTCCTCTCAGC
65 AAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAATCTAATCTTGAAAAAAGCTCCTCTAAAC
* *
1088187 AGAGGCTCAATAACTTT
130 AAAGGCTCAACAACTTT
* *
1088204 AAAATCTCATCTTAAAAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAATA-TAATCTTGA
1 AAAAT-TCATCTTAAAAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAAATTCATCTT-A
* * * * *
1088268 AAAAAACTCCTCTAAACAAAGGTTCAACAACTTTAAAATCCAATCTTGAAAAAAGCTCCTCTAAA
64 AAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAATCTAATCTTGAAAAAAGCTCCTCTAAA
*
1088333 CAGAA-GCTCAATAACTTT
129 CA-AAGGCTCAACAACTTT
* * * * ** *
1088351 AAAAATCTATCTT-AAAAAAGCTCTTTTAAGCAGATGCTCAACAACTTT-AAACTTCTCATCTTG
1 AAAATTC-ATCTTAAAAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAAAT-TCATCTTA
* * * * *
1088414 GAAAAGCTCATCTAAGCAGAGGCTCAACAACTTTAAAATATAATCTTGAAAAAAACTCCCCTAAA
64 AAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAATCTAATCTTGAAAAAAGCTCCTCTAAA
*
1088479 CAGAGGCTCAACAACTTT
129 CAAAGGCTCAACAACTTT
* * * *** * *
1088497 AAAAATTTATCTTAAAAAAAGCTCCTCTCAGCAGAGGCTCAATAACTTTAAACTTTTCATTTTGA
1 -AAAATTCATCTTAAAAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAAATTCATCTTAA
* * * * * * *
1088562 AAAATCTCCTTTAAGTAGAAGCTCAACAACTTTAAAATCCAATCTTGAAAAAAACTCCTATAAAC
65 AAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAATCTAATCTTGAAAAAAGCTCCTCTAAAC
*
1088627 AGAGGCTCAACAACTTT
130 AAAGGCTCAACAACTTT
* * * * * ** *
1088644 AAAAATCTATCTTAAAAAAA-ATCTTTTAAGCAGATGCTCAACAACTTT-AAACTTCTCATCTTG
1 AAAATTC-ATCTTAAAAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAAAT-TCATCTTA
*
1088707 AAAAAGCTCATCTAAGCAGAGGCTCAACAACTTTTAAAATCTAATCTT
64 AAAAAGCTCCTCTAAGCAGAGGCTCAACAAC-TTTAAAATCTAATCTT
1088755 TGTAGACACC
Statistics
Matches: 714, Mismatches: 107, Indels: 41
0.83 0.12 0.05
Matches are distributed among these distances:
141 27 0.04
142 23 0.03
143 37 0.05
144 2 0.00
145 13 0.02
146 221 0.31
147 357 0.50
148 34 0.05
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (146 bp):
AAAATTCATCTTAAAAAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAAATTCATCTTAAA
AAAGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAATCTAATCTTGAAAAAAGCTCCTCTAAACA
AAGGCTCAACAACTTT
Found at i:1088370 original size:293 final size:293
Alignment explanation
Indices: 1087754--1088754 Score: 1165
Period size: 293 Copynumber: 3.4 Consensus size: 293
1087744 TGATTAGAGA
* * * *
1087754 CTCAATAACTTTAAAAAAAT-TCATCTTAAAAAAAGCTCTTCTCAGCAAAGGTTCAATAACTTTA
1 CTCAACAACTTT--AAAAATCT-ATCTTAAAAAAAGCTCTTCTAAGCAAAGGCTCAACAACTTT-
* *
1087818 AAAAATC-CATCTTAAAAAAGCTCCTCTAAGTAGAGGCTCAACAACTTT-AAA-CT--TCTTGAA
62 AAAAATCTCATCTTAAAAAAGCTCATCTAAGCAGAGGCTCAACAACTTTAAAATCTAATCTTGAA
* * * * * * ** * *
1087878 AAAACTCTTTTCAGCAAAAGTTTAACAACTTTAAAAATCTCATCTTTGAAAAAGCTACTCTAAAC
127 AAAACTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTAAAAAAAGCTCCTCTAAGC
* *
1087943 AGAGGCTCAACAACTTTAAAA-ATCCATTTTAAAAAAA-TCCTCTAAGTAGAGGCTCAACAACTT
192 AGAGGCTCAACAACTTTAAAATAT-CATTTGAAAAAAACTCCTCTAAGTAAAGGCTCAACAACTT
* *
1088006 TAAAAATCTC-ATCTTGAAAAAGGCTCCTCTCAACA-AAGG
256 T-AAAATC-CAATCTTGAAAAAAGCTCCTCTAAACAGAA-G
* * *
1088045 CTCAACAACTTTAAAATTC-ATCTTTAAAAAAAGCTCCTCTAAGCAAAGGCTCAGCAACTTTAAA
1 CTCAACAACTTTAAAAATCTATC-TTAAAAAAAGCTCTTCTAAGCAAAGGCTCAACAACTTT-AA
* * ** *
1088109 AAAT-TCATCTTAAAAAAGTTCCTCTAAGCAGAGATTCAACAACTTTAAAATCTAATTTTGAAAA
64 AAATCTCATCTTAAAAAAGCTCATCTAAGCAGAGGCTCAACAACTTTAAAATCTAATCTTGAAAA
*
1088173 AAGCTCCTCTCAGCAGAGGCTCAATAACTTT-AAAATCTCATCTTAAAAAAAGCTCCTCTAAGCA
129 AA-CTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTAAAAAAAGCTCCTCTAAGCA
* ** *
1088237 GAGGCTCAACAACTTTAAAATATAATCTTGAAAAAAACTCCTCTAAACAAAGGTTCAACAACTTT
193 GAGGCTCAACAACTTTAAAATATCAT-TTGAAAAAAACTCCTCTAAGTAAAGGCTCAACAACTTT
1088302 AAAATCCAATCTTGAAAAAAGCTCCTCTAAACAGAAG
257 AAAATCCAATCTTGAAAAAAGCTCCTCTAAACAGAAG
* * * * *
1088339 CTCAATAACTTTAAAAATCTATCTT-AAAAAAGCTCTTTTAAGCAGATGCTCAACAACTTTAAAC
1 CTCAACAACTTTAAAAATCTATCTTAAAAAAAGCTCTTCTAAGCAAAGGCTCAACAACTTTAAAA
* ** *
1088403 TTCTCATCTTGGAAAAGCTCATCTAAGCAGAGGCTCAACAACTTTAAAATATAATCTTGAAAAAA
66 ATCTCATCTTAAAAAAGCTCATCTAAGCAGAGGCTCAACAACTTTAAAATCTAATCTTG-AAAAA
* * * * *
1088468 ACTCCCCTAAACAGAGGCTCAACAACTTTAAAAAT-TTATCTTAAAAAAAGCTCCTCTCAGCAGA
130 ACTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTAAAAAAAGCTCCTCTAAGCAGA
* * * * *
1088532 GGCTCAATAACTTTAAACTTTTCATTTTG-AAAAATCTCCTTTAAGTAGAA-GCTCAACAACTTT
195 GGCTCAACAACTTTAAA-ATATCA-TTTGAAAAAAACTCCTCTAAGTA-AAGGCTCAACAACTTT
* * *
1088595 AAAATCCAATCTTGAAAAAAACTCCTATAAACAGAGG
257 AAAATCCAATCTTGAAAAAAGCTCCTCTAAACAGAAG
* * * * *
1088632 CTCAACAACTTTAAAAATCTATCTTAAAAAAA-ATCTTTTAAGCAGATGCTCAACAACTTTAAAC
1 CTCAACAACTTTAAAAATCTATCTTAAAAAAAGCTCTTCTAAGCAAAGGCTCAACAACTTTAAAA
* *
1088696 TTCTCATCTTGAAAAAGCTCATCTAAGCAGAGGCTCAACAACTTTTAAAATCTAATCTT
66 ATCTCATCTTAAAAAAGCTCATCTAAGCAGAGGCTCAACAAC-TTTAAAATCTAATCTT
1088755 TGTAGACACC
Statistics
Matches: 618, Mismatches: 70, Indels: 41
0.85 0.10 0.06
Matches are distributed among these distances:
288 3 0.00
289 82 0.13
290 3 0.00
291 13 0.02
292 4 0.01
293 363 0.59
294 121 0.20
295 29 0.05
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (293 bp):
CTCAACAACTTTAAAAATCTATCTTAAAAAAAGCTCTTCTAAGCAAAGGCTCAACAACTTTAAAA
ATCTCATCTTAAAAAAGCTCATCTAAGCAGAGGCTCAACAACTTTAAAATCTAATCTTGAAAAAA
CTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTTAAAAAAAGCTCCTCTAAGCAGAG
GCTCAACAACTTTAAAATATCATTTGAAAAAAACTCCTCTAAGTAAAGGCTCAACAACTTTAAAA
TCCAATCTTGAAAAAAGCTCCTCTAAACAGAAG
Found at i:1089007 original size:3 final size:3
Alignment explanation
Indices: 1088994--1089024 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1088984 TGGGTTTATC
1088994 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1089025 TTTAATTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:1089517 original size:20 final size:20
Alignment explanation
Indices: 1089502--1089541 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1089492 TGCCCAGTTT
1089502 TCGGCGAAAAATCCCAGAAA
1 TCGGCGAAAAATCCCAGAAA
*
1089522 TCGGCGAAGAATCCCAGAAA
1 TCGGCGAAAAATCCCAGAAA
1089542 CTGGTGGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.25, G:0.23, T:0.10
Consensus pattern (20 bp):
TCGGCGAAAAATCCCAGAAA
Found at i:1089808 original size:12 final size:12
Alignment explanation
Indices: 1089791--1089826 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1089781 GAACCCGACC
1089791 CGACCCGAGCGT
1 CGACCCGAGCGT
1089803 CGACCCGAGCGT
1 CGACCCGAGCGT
*
1089815 CGACCCGCGCGT
1 CGACCCGAGCGT
1089827 GCTTCCCTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.14, C:0.44, G:0.33, T:0.08
Consensus pattern (12 bp):
CGACCCGAGCGT
Found at i:1089951 original size:1 final size:1
Alignment explanation
Indices: 1089945--1089978 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
1089935 CCGCTCCAGG
**
1089945 TTTTTTTTTTTTTTTTTTTTGATTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1089979 ATTAATCCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.03, C:0.00, G:0.03, T:0.94
Consensus pattern (1 bp):
T
Found at i:1090388 original size:160 final size:158
Alignment explanation
Indices: 1089961--1090589 Score: 1057
Period size: 160 Copynumber: 4.0 Consensus size: 158
1089951 TTTTTTTTTT
* * * *
1089961 TTTTGATTTTTTTTTTTTATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCT
1 TTTTGATTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGT-GAAACAGTAGTTTTTCT
*
1090026 TGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAA
65 TGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAA
1090091 TAATTTTCGATAATTAATTACTTGGCTGA
130 TAATTTTCGATAATTAATTACTTGGCTGA
*
1090120 TTTTGATTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAATAGTTTTTCTT
1 TTTTGATTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTT
*
1090185 GCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTTAATTGAGAAT
66 GCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAAT
1090250 AATTTTCGATAATTAATTACTTGGCTGA
131 AATTTTCGATAATTAATTACTTGGCTGA
* *
1090278 TTTTGATTTTTTTTTCTTTAATTAATCCGACGACGGAGCTTCTGTAAGTGAAACAGTAGTTTTTC
1 TTTTGA--TTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTC
1090343 TTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGA
64 TTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGA
* *
1090408 ATAATTTTCGATAATTAATTAATTGGTTGA
129 ATAATTTTCGATAATTAATTACTTGGCTGA
* * *
1090438 TCTTGA--TTTTTCTTTAAATAATCCGACGACGGAGCCTCTGTAAGTGAAACAGTAGTTTTTCTT
1 TTTTGATTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTT
1090501 GCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAA-
66 GCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAAT
* *
1090565 AAGTTTCCAATAATTAATTACTTGG
131 AA-TTTTCGATAATTAATTACTTGG
1090590 TAAAATTTTA
Statistics
Matches: 448, Mismatches: 19, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
155 2 0.00
156 138 0.31
158 113 0.25
159 44 0.10
160 151 0.34
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (158 bp):
TTTTGATTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTT
GCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAAT
AATTTTCGATAATTAATTACTTGGCTGA
Found at i:1090541 original size:316 final size:316
Alignment explanation
Indices: 1089961--1090589 Score: 1075
Period size: 316 Copynumber: 2.0 Consensus size: 316
1089951 TTTTTTTTTT
1089961 TTTTGATTTTTTTTTTTTATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCT
1 TTTTGATTTTTTTTTTTTATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCT
1090026 TGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAA
66 TGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAA
* * *
1090091 TAATTTTCGATAATTAATTACTTGGCTGATTTTGATTTTTTTCTTTAATTAATCCGACGACGGAG
131 TAATTTTCGATAATTAATTAATTGGCTGATCTTGA-TTTTTTCTTTAAATAATCCGACGACGGAG
1090156 CCTCTGCAAGTGAAACAATAGTTTTTCTTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTC
195 CCTCTGCAAGTGAAACAATAGTTTTTCTTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTC
* * *
1090221 TGCTAAAAGTATTAGAGTTAATTGAGAATAA-TTTTCGATAATTAATTACTTGGCTGA
260 TGCTAAAAGTATTAGAGTCAATTGAGAA-AAGTTTCCAATAATTAATTACTTGGCTGA
* ** *
1090278 TTTTGATTTTTTTTTCTTTAATTAATCCGACGACGGAGCTTCTGTAAGT-GAAACAGTAGTTTTT
1 TTTTGATTTTTTTTT-TTT-ATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTT
*
1090342 CTTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAG
64 CTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAG
*
1090407 AATAATTTTCGATAATTAATTAATTGGTTGATCTTGA-TTTTTCTTTAAATAATCCGACGACGGA
129 AATAATTTTCGATAATTAATTAATTGGCTGATCTTGATTTTTTCTTTAAATAATCCGACGACGGA
* *
1090471 GCCTCTGTAAGTGAAACAGTAGTTTTTCTTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTT
194 GCCTCTGCAAGTGAAACAATAGTTTTTCTTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTT
1090536 CTGCTAAAAGTATTAGAGTCAATTGAGAAAAGTTTCCAATAATTAATTACTTGG
259 CTGCTAAAAGTATTAGAGTCAATTGAGAAAAGTTTCCAATAATTAATTACTTGG
1090590 TAAAATTTTA
Statistics
Matches: 295, Mismatches: 14, Indels: 7
0.93 0.04 0.02
Matches are distributed among these distances:
315 2 0.01
316 137 0.46
317 15 0.05
318 115 0.39
319 26 0.09
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (316 bp):
TTTTGATTTTTTTTTTTTATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCT
TGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAA
TAATTTTCGATAATTAATTAATTGGCTGATCTTGATTTTTTCTTTAAATAATCCGACGACGGAGC
CTCTGCAAGTGAAACAATAGTTTTTCTTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCT
GCTAAAAGTATTAGAGTCAATTGAGAAAAGTTTCCAATAATTAATTACTTGGCTGA
Found at i:1091746 original size:9 final size:10
Alignment explanation
Indices: 1091720--1091745 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1091710 TTATTTTTCA
1091720 TTTTTTTATT
1 TTTTTTTATT
1091730 TTTTTTTATT
1 TTTTTTTATT
1091740 TTTTTT
1 TTTTTT
1091746 AAGCAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:1104150 original size:13 final size:13
Alignment explanation
Indices: 1104132--1104166 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1104122 ATCGGATAAG
1104132 GAAAAAGAAGAAA
1 GAAAAAGAAGAAA
*
1104145 GAAAAAAAAGAAA
1 GAAAAAGAAGAAA
*
1104158 AAAAAAGAA
1 GAAAAAGAA
1104167 AATTAATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
GAAAAAGAAGAAA
Found at i:1104182 original size:3 final size:3
Alignment explanation
Indices: 1104170--1104204 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
1104160 AAAAGAAAAT
*
1104170 TAA TAA -AA TAA TAA TAA TAA TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1104205 AAAAAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1112669 original size:20 final size:20
Alignment explanation
Indices: 1112644--1112693 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1112634 AAATTTAGTG
1112644 AACAAAGAAACTGCATAAGA
1 AACAAAGAAACTGCATAAGA
*
1112664 AACAAAGAAACTGTATAAGA
1 AACAAAGAAACTGCATAAGA
*
1112684 AATAAAGAAA
1 AACAAAGAAA
1112694 TATACTTAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.64, C:0.10, G:0.14, T:0.12
Consensus pattern (20 bp):
AACAAAGAAACTGCATAAGA
Found at i:1114269 original size:41 final size:41
Alignment explanation
Indices: 1114202--1114284 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 41
1114192 ATGCCACTAT
* *
1114202 AATGGGATAAATCATATATTTACTCAAGAA-ATACAAGAACC
1 AATGGAATAAATCATATATGTACTCAAGAATA-ACAAGAACC
* * *
1114243 AATGGAATAAATCATGTATGTGCTCAAGATTAACAAGAACC
1 AATGGAATAAATCATATATGTACTCAAGAATAACAAGAACC
1114284 A
1 A
1114285 TGTCAAAATC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
41 35 0.97
42 1 0.03
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.24
Consensus pattern (41 bp):
AATGGAATAAATCATATATGTACTCAAGAATAACAAGAACC
Found at i:1116850 original size:15 final size:16
Alignment explanation
Indices: 1116818--1116853 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1116808 TATTTTATTT
1116818 TAATTTTACACTAAAA
1 TAATTTTACACTAAAA
*
1116834 TAATTTTAGAC-AAAA
1 TAATTTTACACTAAAA
1116849 TAATT
1 TAATT
1116854 GATTGTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (16 bp):
TAATTTTACACTAAAA
Found at i:1135415 original size:14 final size:14
Alignment explanation
Indices: 1135396--1135425 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1135386 CATTTTTTCT
1135396 TTTTATAAAACATA
1 TTTTATAAAACATA
*
1135410 TTTTATAAAATATA
1 TTTTATAAAACATA
1135424 TT
1 TT
1135426 AGAAAGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTTATAAAACATA
Found at i:1144386 original size:4 final size:4
Alignment explanation
Indices: 1144373--1144409 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
1144363 TTTTTCCTTT
*
1144373 TTTA TCTA TTTA TTTA -TTA -TTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1144410 GAGTAAGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 6 0.20
4 24 0.80
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:1144398 original size:14 final size:15
Alignment explanation
Indices: 1144374--1144404 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1144364 TTTTCCTTTT
1144374 TTATCTATTTATTTA
1 TTATCTATTTATTTA
1144389 TTAT-TATTTATTTA
1 TTATCTATTTATTTA
1144403 TT
1 TT
1144405 TATTTGAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (15 bp):
TTATCTATTTATTTA
Found at i:1144400 original size:18 final size:18
Alignment explanation
Indices: 1144374--1144408 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1144364 TTTTCCTTTT
1144374 TTATCTATTTATTTATTA
1 TTATCTATTTATTTATTA
*
1144392 TTATTTATTTATTTATT
1 TTATCTATTTATTTATT
1144409 TGAGTAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATCTATTTATTTATTA
Found at i:1144488 original size:33 final size:33
Alignment explanation
Indices: 1144450--1144517 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1144440 CTCTTAAAAT
*
1144450 AAAAAATATTTTTG-AGAAAAAATTGAAAGTATC
1 AAAAAACATTTTTGAAG-AAAAATTGAAAGTATC
*
1144483 AAAAAACATTTTTGAAGAAAAGTTGAAAGTATC
1 AAAAAACATTTTTGAAGAAAAATTGAAAGTATC
1144516 AA
1 AA
1144518 TTTTTCTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 30 0.94
34 2 0.06
ACGTcount: A:0.54, C:0.04, G:0.13, T:0.28
Consensus pattern (33 bp):
AAAAAACATTTTTGAAGAAAAATTGAAAGTATC
Found at i:1144536 original size:64 final size:64
Alignment explanation
Indices: 1144481--1144989 Score: 519
Period size: 64 Copynumber: 7.7 Consensus size: 64
1144471 ATTGAAAGTA
*
1144481 TCAAAAAACATTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTTGATTAA
1 TCAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAA--TT-A--AA
1144546 AATT
61 AATT
* * * *
1144550 TCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTTTCAATTTTTCTTGAAAATAAAATACAAAAAA
1 TC-AAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAAT-TAAAAAT
1144615 T
64 T
* * * *
1144616 T-AAAAAAAAATTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTTTAAAATAAAAATAAAAATT
1 TCAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTAAAAATT
* *
1144679 TCAAATAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTTTCTTGAAAATAAAA-TAAAACA
1 TC-AA-AAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTAAAA-A
1144743 TT
63 TT
* * * * * *
1144745 TCAAAAAATATTTTTTAAGAAAAGTTGAAAATATCAAGTTTCCTTGAAACTAAAAATAAAAAATT
1 TCAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTTGAAAAT-AAAATTAAAAATT
* * * *
1144810 TCAAACAAAATATTTTTG-AGAAAAAGTTAAAAATATCAATTTTTCTT-TAAA-AAAA-TAAAGA
1 TC-AA-AAAATATTTTTGAAG-AAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTAAAAA
1144871 TT
63 TT
* * * * *
1144873 TAAAAAAAAAGGTATTCTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATGAAAAAATAA
1 T--CAAAAAA--TATTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTTGAAAAT--AAAATTAA
*
1144938 ATATT
60 AAATT
*
1144943 TCAAAAAAGGATTTTT-AAGGAAAAGTTGAAAGTATCAATTTTTCTTG
1 TCAAAAAA-TATTTTTGAA-GAAAAGTTGAAAGTATCAATTTTTCTTG
1144990 TATAAAAACA
Statistics
Matches: 373, Mismatches: 45, Indels: 46
0.80 0.10 0.10
Matches are distributed among these distances:
63 18 0.05
64 96 0.26
65 48 0.13
66 72 0.19
67 67 0.18
68 8 0.02
69 6 0.02
70 58 0.16
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.34
Consensus pattern (64 bp):
TCAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTAAAAATT
Found at i:1144591 original size:130 final size:124
Alignment explanation
Indices: 1144457--1144985 Score: 504
Period size: 130 Copynumber: 4.0 Consensus size: 124
1144447 AATAAAAAAT
* * *
1144457 ATTTTTGAGAAAAAATTGAAAGTATCAAAAAACATTTTTGAAGAAAAGTTGAAAGTATCAATTTT
1 ATTTTTGA-AAAAAAAT-AAAATATCAAAAAAAATTTTTGAAGAAAAGTTGAAAGTATCAATTTT
* * * *
1144522 TCTTGAAAATAAAATTTTGATTAAAATTTCAAA-AAAATATTTTTGAGGAAAAGTTGAAAGTTTC
64 CCTTGAAAATAAAA-----ATAAAAATTTCAAACAAAATATTTTTGAGGAAAAGTTGAAAATATC
1144586 A
124 A
* * *
1144587 ATTTTTCTTGAAAATAAAATACAAAAAATTAAAAAAAAATTTTGAAGAAAAGTTGAAAGTATCAA
1 A--TTT-TTGAAAA-AAAAT--AAAATATCAAAAAAAATTTTTGAAGAAAAGTTGAAAGTATCAA
* * *
1144652 TTTTTCTTTAAAATAAAAATAAAAATTTCAAATAAAATATTTTTGAGGAAAAGTTGAAAATATCA
60 TTTTCCTTGAAAATAAAAATAAAAATTTCAAACAAAATATTTTTGAGGAAAAGTTGAAAATATCA
* * * *
1144717 ATTTTTCTTGAAAATAAAATAAAACATTTCAAAAAATATTTTTTAAGAAAAGTTGAAAATATCAA
1 A--TTT-TTGAAAA-AAAAT-AAA-ATATCAAAAAAAATTTTTGAAGAAAAGTTGAAAGTATCAA
* * * *
1144782 GTTTCCTTGAAACTAAAAATAAAAAATTTCAAACAAAATATTTTTGAGAAAAAGTTAAAAATATC
60 TTTTCCTTGAAAATAAAAAT-AAAAATTTCAAACAAAATATTTTTGAGGAAAAGTTGAAAATATC
1144847 A
124 A
** * * *
1144848 ATTTTTCTTTAAAAAAATAAAGATTTAAAAAAAAAGGTATTCTTGAGGAAAAGTTGAAAGTATCA
1 A-TTTT-TGAAAAAAAATAAA-ATATCAAAAAAAA--T-TT-TTGAAGAAAAGTTGAAAGTATCA
* ** * *
1144913 ATTTTCCTTGAAAATGAAAAAATAAATATTTCAAA-AAAGGATTTTTAAGGAAAAGTTGAAAGTA
59 ATTTTCCTTGAAAAT--AAAAATAAAAATTTCAAACAAAATATTTTTGAGGAAAAGTTGAAAATA
1144977 TCA
122 TCA
1144980 ATTTTT
1 ATTTTT
1144986 CTTGTATAAA
Statistics
Matches: 341, Mismatches: 43, Indels: 30
0.82 0.10 0.07
Matches are distributed among these distances:
128 14 0.04
129 22 0.06
130 110 0.32
131 49 0.14
132 66 0.19
133 19 0.06
134 61 0.18
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.34
Consensus pattern (124 bp):
ATTTTTGAAAAAAAATAAAATATCAAAAAAAATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCC
TTGAAAATAAAAATAAAAATTTCAAACAAAATATTTTTGAGGAAAAGTTGAAAATATCA
Found at i:1148202 original size:15 final size:15
Alignment explanation
Indices: 1148184--1148217 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1148174 GCATGCATGT
*
1148184 ATTTTCATTCATTGC
1 ATTTTCATTCATTAC
*
1148199 ATTTTTATTCATTAC
1 ATTTTCATTCATTAC
1148214 ATTT
1 ATTT
1148218 AACAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.15, G:0.03, T:0.59
Consensus pattern (15 bp):
ATTTTCATTCATTAC
Found at i:1155414 original size:10 final size:10
Alignment explanation
Indices: 1155399--1155423 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1155389 ATTTGAGCTC
1155399 AAAAAAAATA
1 AAAAAAAATA
1155409 AAAAAAAATA
1 AAAAAAAATA
1155419 AAAAA
1 AAAAA
1155424 GGCTCAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:1155587 original size:46 final size:46
Alignment explanation
Indices: 1155491--1155580 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
1155481 AAAAGAAAAG
* *
1155491 AAAAAAAAGCTCAAATTGAAAACCCGTAAAGGGCAGTTTGAGTTAA
1 AAAAAAAAGCTCAAACTGAAAACCCGTAAAGAGCAGTTTGAGTTAA
**
1155537 AAAAAAAAGCTCAAACTGAAAATTCGTAAAGAGC-GATTTGAGTT
1 AAAAAAAAGCTCAAACTGAAAACCCGTAAAGAGCAG-TTTGAGTT
1155581 CTAAAAAGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 1 0.03
46 38 0.97
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21
Consensus pattern (46 bp):
AAAAAAAAGCTCAAACTGAAAACCCGTAAAGAGCAGTTTGAGTTAA
Found at i:1156543 original size:86 final size:86
Alignment explanation
Indices: 1156373--1156805 Score: 373
Period size: 86 Copynumber: 5.0 Consensus size: 86
1156363 AACGTATTTT
* **
1156373 GGCTTAGTCC-AGATTATTCATTTCAGACTTCGATTCAATCCAGGTCATTCTATTTTCAGATTTT
1 GGCTCAGTCCAAG-TTATTCATTTCAGACTTCGATTCAATCCAGGTCATTCTATTTTTGGATTTT
*
1156437 GA-TATATG-CTAGATCTTTCTTC
65 GACT-TATGTC-AAATCTTTCTTC
* ** * * *
1156459 GGCTCAATCCAAGTTATTCATTTCAGACTTCGATTTTATCCAGGTCATTTTGTTTTTGGATTTCG
1 GGCTCAGTCCAAGTTATTCATTTCAGACTTCGATTCAATCCAGGTCATTCTATTTTTGGATTTTG
*
1156524 ACTTATGTCAAATCCTTCTTC
66 ACTTATGTCAAATCTTTCTTC
* * ** * * * **
1156545 GACTTAGTCCAAACTATTCATTTTAGACTTTGATTCAATCCAAGTCATTCTATTTTCAGATTTTG
1 GGCTCAGTCCAAGTTATTCATTTCAGACTTCGATTCAATCCAGGTCATTCTATTTTTGGATTTTG
* * * * * *
1156610 ACATACGCCATATCCTTCTTT
66 ACTTATGTCAAATCTTTCTTC
* * *
1156631 GGC-CTAGTACAAGTTATGGCACTTT-A-ACTTCGATTCAATCTCA-GTCATTCTGTTTTTGGAT
1 GGCTC-AGTCCAAGTTAT-TCA-TTTCAGACTTCGATTCAATC-CAGGTCATTCTATTTTTGGAT
1156692 TTTGACTTATGTCAAATCTTTCCTT-
62 TTTGACTTATGTCAAATCTTT-CTTC
* * * * * * *
1156717 GACTTAGTCTAAG-TACTT-GTTTCAGACTTTGGTTCAATCCAGGTCATTTTATTTTTGGATTTT
1 GGCTCAGTCCAAGTTA-TTCATTTCAGACTTCGATTCAATCCAGGTCATTCTATTTTTGGATTTT
* *
1156780 GACCTATGTCAAATCTTTCTTT
65 GACTTATGTCAAATCTTTCTTC
1156802 GGCT
1 GGCT
1156806 TTCACTTTAG
Statistics
Matches: 275, Mismatches: 58, Indels: 29
0.76 0.16 0.08
Matches are distributed among these distances:
83 3 0.01
84 6 0.02
85 53 0.19
86 198 0.72
87 12 0.04
88 3 0.01
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.44
Consensus pattern (86 bp):
GGCTCAGTCCAAGTTATTCATTTCAGACTTCGATTCAATCCAGGTCATTCTATTTTTGGATTTTG
ACTTATGTCAAATCTTTCTTC
Found at i:1156663 original size:172 final size:172
Alignment explanation
Indices: 1156375--1156782 Score: 479
Period size: 172 Copynumber: 2.4 Consensus size: 172
1156365 CGTATTTTGG
* * * *
1156375 CTTAGTCCAGATTATTCATTTCAGACTTCGATTCAATCCAGGTCATTCTATTTTCAGATTTTGAT
1 CTTAGTCCAAACTATTCATTTCAGACTTTGATTCAATCCAGGTCATTCTATTTTCAGATTTTGAC
* * * * * **
1156440 ATATGCTAGATCTTTCTTCGGCTCAATCCAAGTTATTCATTTCAGACTTCGATTTTATC-CAGGT
66 ATACGCCAGATCCTTCTTCGGCTCAATACAAGTTATGCATTTCAGACTTCGATTCAATCTCA-GT
*
1156504 CATTTTGTTTTTGGATTTCGACTTATGTCAAATCCTT-CTTCGA
130 CATTCTGTTTTTGGATTTCGACTTATGTCAAATCCTTCCTT-GA
* *
1156547 CTTAGTCCAAACTATTCATTTTAGACTTTGATTCAATCCAAGTCATTCTATTTTCAGATTTTGAC
1 CTTAGTCCAAACTATTCATTTCAGACTTTGATTCAATCCAGGTCATTCTATTTTCAGATTTTGAC
* * *
1156612 ATACGCCATATCCTTCTTTGGC-CTAGTACAAGTTATGGCACTTT-A-ACTTCGATTCAATCTCA
66 ATACGCCAGATCCTTCTTCGGCTC-AATACAAGTTAT-GCA-TTTCAGACTTCGATTCAATCTCA
* *
1156674 GTCATTCTGTTTTTGGATTTTGACTTATGTCAAATCTTTCCTTGA
128 GTCATTCTGTTTTTGGATTTCGACTTATGTCAAATCCTTCCTTGA
* * * * * **
1156719 CTTAGT-CTAAGTACTT-GTTTCAGACTTTGGTTCAATCCAGGTCATTTTATTTTTGGATTTTGA
1 CTTAGTCCAAACTA-TTCATTTCAGACTTTGATTCAATCCAGGTCATTCTATTTTCAGATTTTGA
1156782 C
65 C
1156783 CTATGTCAAA
Statistics
Matches: 202, Mismatches: 28, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
171 47 0.23
172 144 0.71
173 8 0.04
174 3 0.01
ACGTcount: A:0.23, C:0.20, G:0.13, T:0.44
Consensus pattern (172 bp):
CTTAGTCCAAACTATTCATTTCAGACTTTGATTCAATCCAGGTCATTCTATTTTCAGATTTTGAC
ATACGCCAGATCCTTCTTCGGCTCAATACAAGTTATGCATTTCAGACTTCGATTCAATCTCAGTC
ATTCTGTTTTTGGATTTCGACTTATGTCAAATCCTTCCTTGA
Found at i:1158189 original size:4 final size:4
Alignment explanation
Indices: 1158174--1158229 Score: 51
Period size: 4 Copynumber: 13.8 Consensus size: 4
1158164 TTTTCCTTTT
* * * *
1158174 TTTA TCTA TTTA TTTA -TTA TTTA TTGA TTAAA TTGAA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TT-TA TTTA TTTA TTTA
1158223 TTTA TTT
1 TTTA TTT
1158230 GAGTAAGCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
3 3 0.07
4 34 0.77
5 7 0.16
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:1158322 original size:32 final size:34
Alignment explanation
Indices: 1158269--1158334 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 34
1158259 TCTCTTAAAA
*
1158269 TAAAAAATATTTTTAAGGAAAAA-TTGAAAGTAT
1 TAAAAAACATTTTTAAGGAAAAAGTTGAAAGTAT
*
1158302 TAAAAAACATTTTTGA-GAAAAAGTTGAAAGTAT
1 TAAAAAACATTTTTAAGGAAAAAGTTGAAAGTAT
1158335 CAATTTTCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 6 0.20
33 24 0.80
ACGTcount: A:0.53, C:0.02, G:0.14, T:0.32
Consensus pattern (34 bp):
TAAAAAACATTTTTAAGGAAAAAGTTGAAAGTAT
Found at i:1158494 original size:67 final size:65
Alignment explanation
Indices: 1158303--1158754 Score: 475
Period size: 67 Copynumber: 6.8 Consensus size: 65
1158293 TGAAAGTATT
*
1158303 AAAAAACATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAAATAAAAATTTTC
1 AAAAAACATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAATAAAAA-ATTC
1158367 -
65 A
* * * *
1158367 AAAAAACATTTTTGAGGAAAAGTTAAAAGTATCAATGTTCCTTGAAAATAAAATTCAAAAAATTC
1 AAAAAACATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAAT-AAAAAATTC
1158432 AAA
65 --A
* * *
1158435 AAAAAATATTTTTGAGAAAAAGTTGAAATTATCAATTTTTCTTGAAAATAAAAATAAAAAATTTC
1 AAAAAACATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAATAAAAAA-TTC
1158500 AA
65 -A
* * * * *
1158502 AAAAAATATTTTTGAGGAAAAGTTGAATGTGTCAATTTTCGTTGAAAATAAAAA-ATAAAAA-T-
1 AAAAAACATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAATA-AAAAATTC
1158564 A
65 A
* * *
1158565 AAAAAAGCATTTTTGATG-AAAAGTTGAAAGTATTAATTTTCCTTGAAAATGAAAAAATAAAGAT
1 AAAAAA-CATTTTTGA-GAAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT--AAAAATAAAAAA
1158629 TTCA
62 TTCA
**** * * * *
1158633 AAATGGGATTTTTAAGAAAAAGTTGAAAGTATTAATTTTCCTTGAAAATGAAAAAATAAAGATTT
1 AAAAAACATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT--AAAAATAAAAAATT
1158698 CA
64 CA
**** * *
1158700 AAATGGGATTTTTAAGAAAAAGTTGAAAGTATCAATTTTGCTTGAAAATAAAAAT
1 AAAAAACATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAAT
1158755 CTTAAAATGC
Statistics
Matches: 341, Mismatches: 32, Indels: 29
0.85 0.08 0.07
Matches are distributed among these distances:
63 7 0.02
64 82 0.24
65 15 0.04
66 15 0.04
67 167 0.49
68 55 0.16
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.32
Consensus pattern (65 bp):
AAAAAACATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAATAAAAAATTCA
Found at i:1158700 original size:199 final size:197
Alignment explanation
Indices: 1158303--1158753 Score: 520
Period size: 199 Copynumber: 2.3 Consensus size: 197
1158293 TGAAAGTATT
*
1158303 AAAAAACATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT--AAAATAAAAATTTT
1 AAAAAACATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCGTTGAAAATAAAAAATAAAAA--TT
* *
1158366 CAAAAAACATTTTTGAGGAAAAGTTAAAAGTATCAATGTTCCTTGAAAATAAAATTCAAAAAATT
64 AAAAAAACATTTTTGAGGAAAAGTTAAAAGTATCAATGTTCCTTGAAAATAAAAATCAAAAAATT
* * * *
1158431 CAAAAAAAAATATTTTTGAGAAAAAGTTGAAATTATCAATTTTTCTTGAAAATAAAAATAAAAAA
129 C-AAAAAAAAGATTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAATAAAAAA
1158496 TTTCAA
193 TTTC-A
* * * *
1158502 AAAAAATATTTTTGAGGAAAAGTTGAATGTGTCAATTTTCGTTGAAAATAAAAAATAAAAA-TAA
1 AAAAAACATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCGTTGAAAATAAAAAATAAAAATTAA
* * * * * *
1158566 AAAAAGCATTTTTGATGAAAAGTTGAAAGTATTAATTTTCCTTGAAAATGAAAAAAT-AAAGATT
66 AAAAA-CATTTTTGAGGAAAAGTTAAAAGTATCAATGTTCCTTGAAAAT--AAAAATCAAAAAAT
*** *
1158630 TC-AAAATGGGATTTTTAAGAAAAAGTTGAAAGTATTAATTTTCCTTGAAAATGAAAAA-ATAAA
128 TCAAAAAAAAGATTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAAAATA-AAA
*
1158693 GATTTCA
191 AATTTCA
**** *
1158700 AAATGGGATTTTTAAGAAAAAGTTGAAAGTATCAATTTT-GCTTGAAAATAAAAA
1 AAAAAACATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCG-TTGAAAATAAAAA
1158754 TCTTAAAATG
Statistics
Matches: 214, Mismatches: 30, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
197 1 0.00
198 95 0.44
199 96 0.45
200 7 0.03
201 15 0.07
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.32
Consensus pattern (197 bp):
AAAAAACATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCGTTGAAAATAAAAAATAAAAATTAA
AAAAACATTTTTGAGGAAAAGTTAAAAGTATCAATGTTCCTTGAAAATAAAAATCAAAAAATTCA
AAAAAAAGATTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAATAAAAAATTT
CA
Found at i:1158753 original size:198 final size:197
Alignment explanation
Indices: 1158303--1158753 Score: 520
Period size: 198 Copynumber: 2.3 Consensus size: 197
1158293 TGAAAGTATT
*
1158303 AAAAAACATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT--AAAATAAAAATTTT
1 AAAAAAGATTTTTGAGAAAAAGTTGAAAGTATCAATTTT-CTTGAAAATAAAAAATAAAAA--TT
* *
1158366 CAAAAAACATTTTTGAGGAAAAGTTAAAAGTATCAATGTTCCTTGAAAATAAAATTCAAAAAATT
63 AAAAAAACATTTTTGAGGAAAAGTTAAAAGTATCAATGTTCCTTGAAAATAAAAATCAAAAAATT
* * * *
1158431 CAAAAAAAAATATTTTTGAGAAAAAGTTGAAATTATCAATTTTTCTTGAAAATAAAAATAAAAAA
128 C-AAAAAAAAGATTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAATAAAAAA
1158496 TTTCAA
192 TTTCAA
* * * *
1158502 AAAAAATATTTTTGAGGAAAAGTTGAATGTGTCAATTTTCGTTGAAAATAAAAAATAAAAA-TAA
1 AAAAAAGATTTTTGAGAAAAAGTTGAAAGTATCAATTTTC-TTGAAAATAAAAAATAAAAATTAA
* * * * * *
1158566 AAAAAGCATTTTTGATGAAAAGTTGAAAGTATTAATTTTCCTTGAAAATGAAAAAAT-AAAGATT
65 AAAAA-CATTTTTGAGGAAAAGTTAAAAGTATCAATGTTCCTTGAAAAT--AAAAATCAAAAAAT
*** *
1158630 TC-AAAATGGGATTTTTAAGAAAAAGTTGAAAGTATTAATTTTCCTTGAAAATGAAAAA-ATAAA
127 TCAAAAAAAAGATTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAAAATA-AAA
*
1158693 GATTTC-A
190 AATTTCAA
*** *
1158700 AAATGGGATTTTTAAGAAAAAGTTGAAAGTATCAATTTTGCTTGAAAATAAAAA
1 AAAAAAGATTTTTGAGAAAAAGTTGAAAGTATCAATTTT-CTTGAAAATAAAAA
1158754 TCTTAAAATG
Statistics
Matches: 214, Mismatches: 29, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
198 96 0.45
199 96 0.45
200 7 0.03
201 15 0.07
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.32
Consensus pattern (197 bp):
AAAAAAGATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTGAAAATAAAAAATAAAAATTAAA
AAAACATTTTTGAGGAAAAGTTAAAAGTATCAATGTTCCTTGAAAATAAAAATCAAAAAATTCAA
AAAAAAGATTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAATAAAAAATTTC
AA
Found at i:1159582 original size:3 final size:3
Alignment explanation
Indices: 1159576--1159612 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1159566 AATGATGATG
*
1159576 ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1159613 CGTAATACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1159905 original size:64 final size:64
Alignment explanation
Indices: 1159835--1159980 Score: 195
Period size: 64 Copynumber: 2.3 Consensus size: 64
1159825 AAAGTGACAA
*
1159835 GGATGAAACCACGAGTCAAGAATGAAATGACCAAGA-TCGAGTCAAGGTAAAAAATAAATGATCG
1 GGATGAAACCACGAGTCAAGAATGAAATGACCAAGACT-GAGTCAAGGTAAAAAATAAATGACCG
* * * ** * *
1159899 GGATGAAACCATGAGTCAGGAATGAAGTGACCAAGACTGAGTTGAGGTCAAAAGTAAATGACCG
1 GGATGAAACCACGAGTCAAGAATGAAATGACCAAGACTGAGTCAAGGTAAAAAATAAATGACCG
*
1159963 GGATGAAATCACGAGTCA
1 GGATGAAACCACGAGTCA
1159981 TAAGAAATGA
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
64 70 0.99
65 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.27, T:0.16
Consensus pattern (64 bp):
GGATGAAACCACGAGTCAAGAATGAAATGACCAAGACTGAGTCAAGGTAAAAAATAAATGACCG
Found at i:1160153 original size:118 final size:118
Alignment explanation
Indices: 1159900--1160483 Score: 525
Period size: 118 Copynumber: 4.9 Consensus size: 118
1159890 AAATGATCGG
* * * *
1159900 GATGAAACCATGAGTCAGGAATGAAGTGACCAAGA-CTGAGTTGAGGTCAAAAGTAAATGACCGG
1 GATGAAACCACGAGTCA-AAATGAAGTGACCAAGATC-GAGTCGAGGTCAAAAGTAAATGA-CGA
* * * ***
1159964 GATGAAATCACGAGTCATAAGAAATGATCTGGACTAAGCCAAGATCAAGTGACCGG
63 GATGAAACCACTAGTCATAAGAAATGATCTAGACTAAGCCAAGATCAAGTGACTAA
* ** * *
1160020 GATAAAACTTC-AGTCAAAATGAAGTGACCAAAATCGAGTCGAGGTCGAAAGTAAATGATCGAGA
1 GATGAAACCACGAGTCAAAATGAAGTGACCAAGATCGAGTCGAGGTCAAAAGTAAATGA-CGAGA
** *
1160084 CAAAACCACTAGTCATAAGAAATAATCTAG-CTAAGCCAAGATCAAGTGACTAA
65 TGAAACCACTAGTCATAAGAAATGATCTAGACTAAGCCAAGATCAAGTGACTAA
* * *
1160137 GATGAAACCACGAGTCAAAATAAAGTGACCAAAATCGAGTCGAGGTCAAAAGTAAATGACCAGGA
1 GATGAAACCACGAGTCAAAATGAAGTGACCAAGATCGAGTCGAGGTCAAAAGTAAATGACGA-GA
* * * * * * *
1160202 TGAAACCACAAGTCATAAAAAATTATCTAGATTGAGCTAAGATCAAGTGATCGAA
65 TGAAACCACTAGTCATAAGAAATGATCTAGACTAAGCCAAGATCAAGTGA-CTAA
* * * * * * * * *
1160257 -ATGAAACCATGAGTCAAAAATGAAGCGACTAGGACCGAGTTGAGATAAAAAAATAAATGACTGA
1 GATGAAACCACGAGTC-AAAATGAAGTGACCAAGATCGAGTCGAGGT-CAAAAGTAAATGAC-GA
* * * *
1160321 GATTG-AACCA-TGAGTCATAAGAAATGATCTGGACTGAGCCAAGATCAGGTGACTGA
63 GA-TGAAACCACT-AGTCATAAGAAATGATCTAGACTAAGCCAAGATCAAGTGACTAA
* * * **
1160377 GACGAAATCACGAGTCAAAATAAAGTGACCAAGATCGAGTCGAGGTTGAAAGTAAATGATCGAGA
1 GATGAAACCACGAGTCAAAATGAAGTGACCAAGATCGAGTCGAGGTCAAAAGTAAATGA-CGAGA
* ** * * * * *
1160442 CGATGCCACGAGTCAGAA-AAGTGATTTAGACTAAGCTAAGAT
65 TGAAACCACTAGTCATAAGAAATGATCTAGACTAAGCCAAGAT
1160484 AAAAAATGAG
Statistics
Matches: 372, Mismatches: 78, Indels: 30
0.77 0.16 0.06
Matches are distributed among these distances:
117 30 0.08
118 156 0.42
119 60 0.16
120 58 0.16
121 65 0.17
122 3 0.01
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.18
Consensus pattern (118 bp):
GATGAAACCACGAGTCAAAATGAAGTGACCAAGATCGAGTCGAGGTCAAAAGTAAATGACGAGAT
GAAACCACTAGTCATAAGAAATGATCTAGACTAAGCCAAGATCAAGTGACTAA
Found at i:1160422 original size:240 final size:236
Alignment explanation
Indices: 1159903--1160435 Score: 595
Period size: 236 Copynumber: 2.2 Consensus size: 236
1159893 TGATCGGGAT
* * * * *
1159903 GAAACCATGAGTCAGGAATGAAGTGACCAAGA-CTGAGTTGAGGTCAAAAGTAAATGACCGGGAT
1 GAAACCACGAGTCA-AAATAAAGTGACCAAGATC-GAGTCGAGGTCAAAAGTAAATGACCAGGAT
* * * * ** *
1159967 GAAATCACGAGTCATAAGAAATGATCTGGACTAAGCCAAGATCAAGTGACCGGGATAAAACTTCA
64 GAAACCACAAGTCATAAAAAATGATCTAGACTAAGCCAAGATCAAGTGACCGAAATAAAACATCA
* * * ** *
1160032 GTCAAAATGAAGTGACCAAAATCGAGTCGAGGTCGAAAGTAAATGATCGAGACAAAACCACTAGT
129 GTCAAAATGAAGCGACCAAAACCGAGTCGAGATAAAAAATAAATGATCGAGACAAAACCACTAGT
*
1160097 CATAAGAAATAATCTAGCTAAGCCAAGATCAAGTGACTAAGAT
194 CATAAGAAATAATCTAGCTAAGCCAAGATCAAGTGACTAAGAC
*
1160140 GAAACCACGAGTCAAAATAAAGTGACCAAAATCGAGTCGAGGTCAAAAGTAAATGACCAGGATGA
1 GAAACCACGAGTCAAAATAAAGTGACCAAGATCGAGTCGAGGTCAAAAGTAAATGACCAGGATGA
* * * * * * *
1160205 AACCACAAGTCATAAAAAATTATCTAGATTGAGCTAAGATCAAGTGATCGAAATGAAACCATGAG
66 AACCACAAGTCATAAAAAATGATCTAGACTAAGCCAAGATCAAGTGACCGAAAT-AAAACATCAG
* ** * ***
1160270 TCAAAAATGAAGCGACTAGGACCGAGTTGAGATAAAAAAATAAATGA-CTGAGATTGAACCA-TG
130 TC-AAAATGAAGCGACCAAAACCGAGTCGAGAT-AAAAAATAAATGATC-GAGACAAAACCACT-
* * * * *
1160333 AGTCATAAGAAATGATCTGGACTGAGCCAAGATCAGGTGACTGAGAC
191 AGTCATAAGAAATAATCTAG-CTAAGCCAAGATCAAGTGACTAAGAC
* **
1160380 GAAATCACGAGTCAAAATAAAGTGACCAAGATCGAGTCGAGGTTGAAAGTAAATGA
1 GAAACCACGAGTCAAAATAAAGTGACCAAGATCGAGTCGAGGTCAAAAGTAAATGA
1160436 TCGAGACGAT
Statistics
Matches: 246, Mismatches: 43, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
236 87 0.35
237 23 0.09
238 25 0.10
239 37 0.15
240 74 0.30
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.18
Consensus pattern (236 bp):
GAAACCACGAGTCAAAATAAAGTGACCAAGATCGAGTCGAGGTCAAAAGTAAATGACCAGGATGA
AACCACAAGTCATAAAAAATGATCTAGACTAAGCCAAGATCAAGTGACCGAAATAAAACATCAGT
CAAAATGAAGCGACCAAAACCGAGTCGAGATAAAAAATAAATGATCGAGACAAAACCACTAGTCA
TAAGAAATAATCTAGCTAAGCCAAGATCAAGTGACTAAGAC
Found at i:1165243 original size:19 final size:19
Alignment explanation
Indices: 1165221--1165257 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1165211 AATGGGTTGA
1165221 AAAAATAAAATCAAAAAAT
1 AAAAATAAAATCAAAAAAT
*
1165240 AAAAATAAAATGAAAAAA
1 AAAAATAAAATCAAAAAA
1165258 AAATCTACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.81, C:0.03, G:0.03, T:0.14
Consensus pattern (19 bp):
AAAAATAAAATCAAAAAAT
Found at i:1165599 original size:31 final size:31
Alignment explanation
Indices: 1165496--1165599 Score: 118
Period size: 31 Copynumber: 3.3 Consensus size: 31
1165486 GCGGTTTCTG
* * **
1165496 AAAAATCCTATCAAAAAGTTCATACTTCACCA
1 AAAAATTC-ATCAAAAAATTCATACTTCGTCA
* *
1165528 AAAAATTTATCAAAAAATTCTTACTTCGTCA
1 AAAAATTCATCAAAAAATTCATACTTCGTCA
* **
1165559 GAATTTTCATCAAAAAATTCATACTTCGTCA
1 AAAAATTCATCAAAAAATTCATACTTCGTCA
1165590 AAAAATTCAT
1 AAAAATTCAT
1165600 TCATAACCCA
Statistics
Matches: 58, Mismatches: 14, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
31 52 0.90
32 6 0.10
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (31 bp):
AAAAATTCATCAAAAAATTCATACTTCGTCA
Found at i:1166119 original size:3 final size:3
Alignment explanation
Indices: 1166111--1166139 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1166101 AATAAAAATA
1166111 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1166140 AATAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:1166144 original size:3 final size:3
Alignment explanation
Indices: 1166138--1166187 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
1166128 GATGATGATG
*
1166138 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1166186 AT
1 AT
1166188 GTAATACTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1167088 original size:21 final size:21
Alignment explanation
Indices: 1167064--1167105 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1167054 CTTATAGCAA
1167064 TTGATAT-AGGAGTTTAAACAT
1 TTGATATAAGG-GTTTAAACAT
1167085 TTGATATAAAGGGTTTAAACA
1 TTGATAT-AAGGGTTTAAACA
1167106 AAACGGGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 9 0.47
23 3 0.16
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (21 bp):
TTGATATAAGGGTTTAAACAT
Found at i:1167851 original size:3 final size:3
Alignment explanation
Indices: 1167843--1168003 Score: 149
Period size: 3 Copynumber: 54.3 Consensus size: 3
1167833 ATTTTCTTTG
*
1167843 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1167891 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTGCA -TG TTA -TC TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT--A TTA TTA TTA TTA TTA
* * * *
1167935 GTA -TA GTCTA GTA GTA TTA TTA TTA -TA TTA TCA TTTA TTA TTA TTA
1 TTA TTA -T-TA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
1167981 TTA TTTA TT- TTA TT- TTA TT- TTA T
1 TTA -TTA TTA TTA TTA TTA TTA TTA T
1168004 GTTATTTTTT
Statistics
Matches: 133, Mismatches: 11, Indels: 28
0.77 0.06 0.16
Matches are distributed among these distances:
2 13 0.10
3 111 0.83
4 6 0.05
5 3 0.02
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1167981 original size:16 final size:16
Alignment explanation
Indices: 1167954--1167994 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
1167944 AGTAGTATTA
1167954 TTATTA-TATTATCAT
1 TTATTATTATTATCAT
*
1167969 TTATTATTATTATTAT
1 TTATTATTATTATCAT
1167985 TTATT-TTATT
1 TTATTATTATT
1167995 TTATTTTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTATTATTATCAT
Found at i:1168000 original size:5 final size:5
Alignment explanation
Indices: 1167968--1168011 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
1167958 TATATTATCA
*
1167968 TTTAT TATTAT TATTA- TTTAT TTTAT TTTAT TTTAT GTTAT TTT
1 TTTAT T-TTAT T-TTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1168012 TTATTTCCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 3 0.09
5 23 0.66
6 9 0.26
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:1171662 original size:2 final size:2
Alignment explanation
Indices: 1171643--1171689 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
1171633 ATCAGTAAGG
* * * *
1171643 AT AT AT AC AT AT AA AT AT AT AT AT GT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1171685 AT AT A
1 AT AT A
1171690 ACAAGAAACA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1179286 original size:13 final size:13
Alignment explanation
Indices: 1179264--1179293 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1179254 AAATACAAGT
*
1179264 TAAAGTTAAAAGC
1 TAAAGCTAAAAGC
1179277 TAAAGCTAAAAGC
1 TAAAGCTAAAAGC
1179290 TAAA
1 TAAA
1179294 ACTGTGGTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.10, G:0.13, T:0.20
Consensus pattern (13 bp):
TAAAGCTAAAAGC
Found at i:1182192 original size:44 final size:44
Alignment explanation
Indices: 1182142--1182230 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
1182132 CAATCTTATT
* * *
1182142 TATATGGAATTATATCATATTATCGCTGAATGAAAGTTGATACA
1 TATATGGAATTATATCACATTATCACTCAATGAAAGTTGATACA
*
1182186 TATATGGAATTATATCACATTATCACTCAATGACAGTTGATACA
1 TATATGGAATTATATCACATTATCACTCAATGAAAGTTGATACA
1182230 T
1 T
1182231 CACTCTGACA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (44 bp):
TATATGGAATTATATCACATTATCACTCAATGAAAGTTGATACA
Found at i:1190037 original size:17 final size:18
Alignment explanation
Indices: 1190011--1190048 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1190001 TACACTAATA
1190011 TTTATTTTTG-AAA-ATT
1 TTTATTTTTGTAAATATT
1190027 TTTAGTTTTTGTAAATATT
1 TTTA-TTTTTGTAAATATT
1190046 TTT
1 TTT
1190049 GGAAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.21
17 6 0.32
18 3 0.16
19 6 0.32
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (18 bp):
TTTATTTTTGTAAATATT
Found at i:1205203 original size:16 final size:16
Alignment explanation
Indices: 1205164--1205224 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
1205154 TTAACAAGTG
* **
1205164 ATATATTTAATTAACC
1 ATATAATTAATTAATA
* *
1205180 ATAAAATTAATTAATT
1 ATATAATTAATTAATA
1205196 ATATAATTAAATTAAATA
1 ATATAATT-AATT-AATA
*
1205214 ATATCATTAAT
1 ATATAATTAAT
1205225 CCACATGGTG
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
16 19 0.53
17 7 0.19
18 10 0.28
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATAATTAATTAATA
Found at i:1206108 original size:15 final size:15
Alignment explanation
Indices: 1206088--1206118 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1206078 GTTGTCTTGC
1206088 ATCAATACAAAATGG
1 ATCAATACAAAATGG
1206103 ATCAATACAAAATGG
1 ATCAATACAAAATGG
1206118 A
1 A
1206119 CAAAGATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.13, G:0.13, T:0.19
Consensus pattern (15 bp):
ATCAATACAAAATGG
Found at i:1209027 original size:2 final size:2
Alignment explanation
Indices: 1209020--1209050 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1209010 TAGGGTTCTA
1209020 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 A
1209051 CACACAATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1213436 original size:13 final size:13
Alignment explanation
Indices: 1213413--1213467 Score: 65
Period size: 13 Copynumber: 4.1 Consensus size: 13
1213403 ATTTTTTTCG
*
1213413 TATTTTTTTATAT
1 TATTTTATTATAT
*
1213426 TATATTATTATAT
1 TATTTTATTATAT
1213439 CATATTTTATTATAT
1 --TATTTTATTATAT
*
1213454 TATTTTATTCTAT
1 TATTTTATTATAT
1213467 T
1 T
1213468 TTAAATTAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
13 24 0.67
15 12 0.33
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTTTATTATAT
Found at i:1213453 original size:23 final size:23
Alignment explanation
Indices: 1213423--1213470 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1213413 TATTTTTTTA
1213423 TATTATATTATTATA-TCATATTT
1 TATTATATTATTATATTC-TATTT
*
1213446 TATTATATTATTTTATTCTATTT
1 TATTATATTATTATATTCTATTT
1213469 TA
1 TA
1213471 AATTAGTCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (23 bp):
TATTATATTATTATATTCTATTT
Found at i:1222785 original size:27 final size:27
Alignment explanation
Indices: 1222755--1222809 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
1222745 TAATTTTTTT
* * *
1222755 AAATATATA-AAATATATTAATAATAAA
1 AAATAAATACAAACATA-TAATAACAAA
1222782 AAATAAATACAAACATATAATAACAAA
1 AAATAAATACAAACATATAATAACAAA
1222809 A
1 A
1222810 TTTATAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.25
Consensus pattern (27 bp):
AAATAAATACAAACATATAATAACAAA
Found at i:1223078 original size:22 final size:20
Alignment explanation
Indices: 1223026--1223079 Score: 54
Period size: 22 Copynumber: 2.6 Consensus size: 20
1223016 ATATTTTTTA
1223026 AATAAATTAAAATTTAAAAC
1 AATAAATTAAAATTTAAAAC
** * *
1223046 AATAAGGTAAAAGCTTTGATAC
1 AATAAATTAAAA--TTTAAAAC
1223068 AATAAATTAAAA
1 AATAAATTAAAA
1223080 CCTTCTAATT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 10 0.38
22 16 0.62
ACGTcount: A:0.59, C:0.06, G:0.07, T:0.28
Consensus pattern (20 bp):
AATAAATTAAAATTTAAAAC
Found at i:1224373 original size:27 final size:27
Alignment explanation
Indices: 1224332--1224411 Score: 83
Period size: 27 Copynumber: 2.9 Consensus size: 27
1224322 AAAAAAATTT
* *
1224332 TAAAAATATGAAAAAAATCCAAAAAAA-TC
1 TAAAAAT-T-AAAA-AATCTAAAAAAACCC
*
1224361 TAAAATTTTAAAAAAT-TAAAAAAACCC
1 TAAAA-ATTAAAAAATCTAAAAAAACCC
1224388 TAAAAATTAAAAAATCTAAAAAAA
1 TAAAAATTAAAAAATCTAAAAAAA
1224412 GAATTATGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
26 16 0.36
27 17 0.39
28 4 0.09
29 6 0.14
30 1 0.02
ACGTcount: A:0.69, C:0.09, G:0.01, T:0.21
Consensus pattern (27 bp):
TAAAAATTAAAAAATCTAAAAAAACCC
Found at i:1224444 original size:21 final size:21
Alignment explanation
Indices: 1224420--1224459 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1224410 AAGAATTATG
*
1224420 AAAAAATTTAAAAACTAAAAA
1 AAAAAATTTAAAAAATAAAAA
1224441 AAAAAATTTAAAAAATAAA
1 AAAAAATTTAAAAAATAAA
1224460 TTTCTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (21 bp):
AAAAAATTTAAAAAATAAAAA
Found at i:1224455 original size:31 final size:32
Alignment explanation
Indices: 1224389--1224455 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
1224379 AAAAAACCCT
* *
1224389 AAAAATTAAAAAATCTAAAAAAAGAATTATGA
1 AAAAATTAAAAAATCTAAAAAAAAAATTATAA
*
1224421 AAAAATTTAAAAA-CTAAAAAAAAAAATT-TAA
1 AAAAATTAAAAAATCT-AAAAAAAAAATTATAA
1224452 AAAA
1 AAAA
1224456 TAAATTTCTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 8 0.26
32 23 0.74
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (32 bp):
AAAAATTAAAAAATCTAAAAAAAAAATTATAA
Found at i:1224477 original size:13 final size:13
Alignment explanation
Indices: 1224438--1224479 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1224428 TAAAAACTAA
1224438 AAAAAAAAATT-T
1 AAAAAAAAATTCT
1224450 AAAAAATAAATTTCT
1 AAAAAA-AAA-TTCT
*
1224465 GAAAAAAAATTCT
1 AAAAAAAAATTCT
1224478 AA
1 AA
1224480 TTTTTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 6 0.24
13 8 0.32
14 5 0.20
15 6 0.24
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (13 bp):
AAAAAAAAATTCT
Found at i:1224705 original size:25 final size:26
Alignment explanation
Indices: 1224675--1224724 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
1224665 AAATATTAGC
*
1224675 TTTTCAAAATTTTTT-GAAATTTTAA
1 TTTTCAAAATTTTTTAAAAATTTTAA
1224700 TTTTCAAAATTTTTTAAAAATTTTA
1 TTTTCAAAATTTTTTAAAAATTTTA
1224725 GATATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (26 bp):
TTTTCAAAATTTTTTAAAAATTTTAA
Found at i:1224713 original size:26 final size:25
Alignment explanation
Indices: 1224675--1224724 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
1224665 AAATATTAGC
**
1224675 TTTTCAAAATTTTTTGAAATTTTAA
1 TTTTCAAAATTTTTAAAAATTTTAA
1224700 TTTTCAAAATTTTTTAAAAATTTTA
1 TTTTCAAAA-TTTTTAAAAATTTTA
1224725 GATATTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (25 bp):
TTTTCAAAATTTTTAAAAATTTTAA
Found at i:1224919 original size:26 final size:24
Alignment explanation
Indices: 1224883--1224940 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
1224873 AATTTTCATT
**
1224883 ATTTTTTATATTTCTTTTCATTTTC
1 ATTTTTTATATTT-TTTAAATTTTC
1224908 ATTTTTATATATTTTTTAAATTTTC
1 ATTTTT-TATATTTTTTAAATTTTC
1224933 ATATTTTT
1 AT-TTTTT
1224941 TTATAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 18 0.62
26 11 0.38
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (24 bp):
ATTTTTTATATTTTTTAAATTTTC
Found at i:1224936 original size:19 final size:18
Alignment explanation
Indices: 1224908--1224943 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1224898 TTTCATTTTC
*
1224908 ATTTTTATATATTTTTTAA
1 ATTTTCATAT-TTTTTTAA
1224927 ATTTTCATATTTTTTTA
1 ATTTTCATATTTTTTTA
1224944 TAAAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTTCATATTTTTTTAA
Found at i:1224947 original size:20 final size:19
Alignment explanation
Indices: 1224908--1224961 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 19
1224898 TTTCATTTTC
* *
1224908 ATTTTTATATATTTTTTAA
1 ATTTTAATATTTTTTTTAA
*
1224927 ATTTTCATATTTTTTTATAA
1 ATTTTAATATTTTTTT-TAA
* *
1224947 AATTTAAGATTTTTT
1 ATTTTAATATTTTTT
1224962 AATTTGCAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
ATTTTAATATTTTTTTTAA
Found at i:1225036 original size:9 final size:9
Alignment explanation
Indices: 1225015--1225056 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
1225005 TTTTTGGAAT
1225015 TTTTATTAAA
1 TTTT-TTAAA
*
1225025 TTTTTTAGA
1 TTTTTTAAA
*
1225034 TTTTCTAAA
1 TTTTTTAAA
1225043 TTTTTTAAA
1 TTTTTTAAA
1225052 TTTTT
1 TTTTT
1225057 CATGAGTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
9 24 0.86
10 4 0.14
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:1225116 original size:22 final size:22
Alignment explanation
Indices: 1225072--1225119 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1225062 GTTTCAATAA
* *
1225072 TTTTTTAATTTCAAAATTTTTT
1 TTTTTTAATTTCAAAAGTATTT
**
1225094 TTTTTTAATTTTTAAAGTATTT
1 TTTTTTAATTTCAAAAGTATTT
1225116 TTTT
1 TTTT
1225120 AATGCTAATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTTTAATTTCAAAAGTATTT
Found at i:1225116 original size:23 final size:22
Alignment explanation
Indices: 1225072--1225119 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
1225062 GTTTCAATAA
*
1225072 TTTTTTAATTTCAAAATTTTTT
1 TTTTTTAATTTCAAAATATTTT
* *
1225094 TTTTTTAATTTTTAAAGTATTTT
1 TTTTTTAA-TTTCAAAATATTTT
1225117 TTT
1 TTT
1225120 AATGCTAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTTTAATTTCAAAATATTTT
Found at i:1225589 original size:24 final size:24
Alignment explanation
Indices: 1225570--1225655 Score: 68
Period size: 24 Copynumber: 3.5 Consensus size: 24
1225560 TGATATTATT
*
1225570 ATAATAGTGAAATTAAATATAATA
1 ATAATAGTAAAATTAAATATAATA
*
1225594 ATAATATTAAAATT-AATAATAA-A
1 ATAATAGTAAAATTAAAT-ATAATA
* **
1225617 ATATATATTTGAATATAAATATAATA
1 ATA-ATAGTAAAAT-TAAATATAATA
* *
1225643 GTAATAGTGAAAT
1 ATAATAGTAAAAT
1225656 ATAATGAGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
23 7 0.14
24 24 0.49
25 12 0.24
26 6 0.12
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (24 bp):
ATAATAGTAAAATTAAATATAATA
Found at i:1225602 original size:18 final size:18
Alignment explanation
Indices: 1225581--1225660 Score: 57
Period size: 18 Copynumber: 4.7 Consensus size: 18
1225571 TAATAGTGAA
1225581 ATTAAATATAATAATAAT
1 ATTAAATATAATAATAAT
1225599 ATTAAA-AT--TAATAAT
1 ATTAAATATAATAATAAT
*
1225614 A--AAATAT-ATATTTGAAT
1 ATTAAATATAATA-AT-AAT
*
1225631 A-TAAATATAATAGTAAT
1 ATTAAATATAATAATAAT
*
1225648 AGTGAAATATAAT
1 A-TTAAATATAAT
1225661 GAGAAAAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
13 3 0.06
14 2 0.04
15 10 0.20
16 1 0.02
17 10 0.20
18 13 0.25
19 12 0.24
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (18 bp):
ATTAAATATAATAATAAT
Found at i:1225762 original size:9 final size:9
Alignment explanation
Indices: 1225735--1225781 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
1225725 GATATTTATG
*
1225735 AAATTAATA
1 AAATTATTA
*
1225744 AAA-AATTA
1 AAATTATTA
1225752 AAATTATTA
1 AAATTATTA
1225761 AAATTATTA
1 AAATTATTA
*
1225770 ATATATATTA
1 AAAT-TATTA
1225780 AA
1 AA
1225782 TAATATTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
8 6 0.19
9 19 0.61
10 6 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
AAATTATTA
Found at i:1225806 original size:14 final size:14
Alignment explanation
Indices: 1225778--1225825 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
1225768 TAATATATAT
*
1225778 TAAATAATATTTTTA
1 TAAATAA-ATATTTA
1225793 TAAATAAATATTTA
1 TAAATAAATATTTA
* *
1225807 CAAATAAATATTAA
1 TAAATAAATATTTA
1225821 TAAAT
1 TAAAT
1225826 GATTAAAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.76
15 7 0.24
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAATAAATATTTA
Found at i:1226591 original size:43 final size:43
Alignment explanation
Indices: 1226543--1226628 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
1226533 TAATTGAGTT
*
1226543 GGAATATCAAAAGATGGGTTGTACCGGTTATAACGTTTATATA
1 GGAATACCAAAAGATGGGTTGTACCGGTTATAACGTTTATATA
* * **
1226586 GGAATACCAAAAGATTGGTTGTACCTGTTATGGCGTTTATATA
1 GGAATACCAAAAGATGGGTTGTACCGGTTATAACGTTTATATA
1226629 CAATAAACGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.34
Consensus pattern (43 bp):
GGAATACCAAAAGATGGGTTGTACCGGTTATAACGTTTATATA
Found at i:1228373 original size:28 final size:26
Alignment explanation
Indices: 1228341--1228403 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 26
1228331 ATTACTTTAA
*
1228341 AAATTATAAGTACTA-ATTATTATTATT
1 AAATTATAAGTACTACATT-TTA-TAGT
*
1228368 ATAATTATAATTACTACATTTTATAGT
1 A-AATTATAAGTACTACATTTTATAGT
1228395 AAATTATAA
1 AAATTATAA
1228404 AAAATTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 8 0.25
27 5 0.16
28 16 0.50
29 3 0.09
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (26 bp):
AAATTATAAGTACTACATTTTATAGT
Found at i:1229785 original size:12 final size:12
Alignment explanation
Indices: 1229768--1229793 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1229758 TATTTGTTTT
1229768 AAATTTTTATTA
1 AAATTTTTATTA
1229780 AAATTTTTATTA
1 AAATTTTTATTA
1229792 AA
1 AA
1229794 TAATTTAAAA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
AAATTTTTATTA
Found at i:1234046 original size:35 final size:34
Alignment explanation
Indices: 1234002--1234073 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
1233992 TTTGTATAAT
**
1234002 AAAACGTCACTAAAATTAATGGTGTTCTTATCATA
1 AAAACGTCAC-AAAATTAATGACGTTCTTATCATA
*
1234037 AAAATGTCACAAAATTAATGACGTTCTTATCATA
1 AAAACGTCACAAAATTAATGACGTTCTTATCATA
1234071 AAA
1 AAA
1234074 GCCCCACTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 25 0.74
35 9 0.26
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (34 bp):
AAAACGTCACAAAATTAATGACGTTCTTATCATA
Found at i:1234086 original size:34 final size:34
Alignment explanation
Indices: 1234009--1234087 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
1233999 AATAAAACGT
** ***
1234009 CACTAAAATTAATGGTGTTCTTATCATAAAAATGT
1 CACT-AAATTAATGACGTTCTTATCATAAAAACCC
* *
1234044 CACAAAATTAATGACGTTCTTATCATAAAAGCCC
1 CACTAAATTAATGACGTTCTTATCATAAAAACCC
1234078 CACTAAATTA
1 CACTAAATTA
1234088 GTCATGTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
34 33 0.92
35 3 0.08
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.32
Consensus pattern (34 bp):
CACTAAATTAATGACGTTCTTATCATAAAAACCC
Found at i:1237221 original size:14 final size:14
Alignment explanation
Indices: 1237204--1237248 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
1237194 AAAAAATAAT
1237204 TATTAAAAATTTTA
1 TATTAAAAATTTTA
1237218 TATT-AAAATTTTA
1 TATTAAAAATTTTA
* * *
1237231 TAATAAATATTTGA
1 TATTAAAAATTTTA
1237245 TATT
1 TATT
1237249 TATGAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 12 0.46
14 14 0.54
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
TATTAAAAATTTTA
Found at i:1237225 original size:13 final size:13
Alignment explanation
Indices: 1237204--1237248 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
1237194 AAAAAATAAT
1237204 TATTAAAAATTTTA
1 TATT-AAAATTTTA
1237218 TATTAAAATTTTA
1 TATTAAAATTTTA
* *
1237231 TAATAAATATTTGA
1 TATTAAA-ATTTTA
1237245 TATT
1 TATT
1237249 TATGAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (13 bp):
TATTAAAATTTTA
Found at i:1237273 original size:47 final size:43
Alignment explanation
Indices: 1237219--1237304 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 43
1237209 AAAATTTTAT
*
1237219 ATTAAAATTTTATAATAAATATTTGATATTTATGAAATTAATAAAAA
1 ATTAAAATTAT-TAA-AAATATTT-ATATTTATGAAA-TAATAAAAA
* *
1237266 ATTAAAATTATTAAAATTATTTATATTTATTAAATAATA
1 ATTAAAATTATTAAAAATATTTATATTTATGAAATAATA
1237305 CTTTTATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 5 0.14
44 11 0.31
45 7 0.19
46 3 0.08
47 10 0.28
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (43 bp):
ATTAAAATTATTAAAAATATTTATATTTATGAAATAATAAAAA
Found at i:1237485 original size:12 final size:12
Alignment explanation
Indices: 1237455--1237497 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1237445 GAAGTTTATG
*
1237455 AATTTTTTAAAA
1 AATTTATTAAAA
1237467 TAATTTATTAAAA
1 -AATTTATTAAAA
* *
1237480 AATTTAATAAAG
1 AATTTATTAAAA
1237492 AATTTA
1 AATTTA
1237498 AAATAATAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (12 bp):
AATTTATTAAAA
Found at i:1237643 original size:14 final size:14
Alignment explanation
Indices: 1237624--1237656 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1237614 AACATTTTTA
*
1237624 CTAAAAATATCTAT
1 CTAAAAATATATAT
1237638 CTAAAAATATATAT
1 CTAAAAATATATAT
1237652 C-AAAA
1 CTAAAA
1237657 TTTATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (14 bp):
CTAAAAATATATAT
Found at i:1239889 original size:11 final size:11
Alignment explanation
Indices: 1239873--1239897 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1239863 TTGAAAATCG
1239873 GGGGTCGGGTC
1 GGGGTCGGGTC
1239884 GGGGTCGGGTC
1 GGGGTCGGGTC
1239895 GGG
1 GGG
1239898 TAGGATGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.68, T:0.16
Consensus pattern (11 bp):
GGGGTCGGGTC
Found at i:1240064 original size:21 final size:23
Alignment explanation
Indices: 1240038--1240091 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
1240028 TGATATTTTA
*
1240038 AATATTTTATA-TTT-AAAAATT
1 AATATTTTATATTTTAAAAAAAT
1240059 AATATTTTATATTTTAAAAAAAT
1 AATATTTTATATTTTAAAAAAAT
1240082 AATATTTTAT
1 AATATTTTAT
1240092 TAATTTCGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 11 0.37
22 3 0.10
23 16 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTTATATTTTAAAAAAAT
Found at i:1240429 original size:10 final size:9
Alignment explanation
Indices: 1240392--1240427 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
1240382 AAAATATAAA
1240392 TTAAAA-TT
1 TTAAAATTT
1240400 TT-AAATTT
1 TTAAAATTT
1240408 TTAAAATTT
1 TTAAAATTT
1240417 TTAAAATTT
1 TTAAAATTT
1240426 TT
1 TT
1240428 TAGATAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 3 0.12
8 6 0.23
9 17 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TTAAAATTT
Found at i:1240731 original size:27 final size:28
Alignment explanation
Indices: 1240703--1240754 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
1240693 ATTAATTTAT
* *
1240703 TTTTATTT-TTGTGTAAT-TATTGAATA
1 TTTTATTTATTATATAATATATTGAATA
1240729 TTTTATTTATTATATAATATATTGAA
1 TTTTATTTATTATATAATATATTGAA
1240755 AGTAATTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
27 7 0.32
28 7 0.32
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.60
Consensus pattern (28 bp):
TTTTATTTATTATATAATATATTGAATA
Found at i:1240860 original size:7 final size:7
Alignment explanation
Indices: 1240848--1240885 Score: 67
Period size: 7 Copynumber: 5.3 Consensus size: 7
1240838 TATTACTTTA
1240848 AAAATTT
1 AAAATTT
1240855 AAAATTT
1 AAAATTT
1240862 AAAATTT
1 AAAATTT
1240869 AAAAATTT
1 -AAAATTT
1240877 AAAATTT
1 AAAATTT
1240884 AA
1 AA
1240886 TGTAGATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 23 0.77
8 7 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AAAATTT
Found at i:1240862 original size:15 final size:15
Alignment explanation
Indices: 1240848--1240885 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
1240838 TATTACTTTA
1240848 AAAATTT-AAAATTT
1 AAAATTTAAAAATTT
1240862 AAAATTTAAAAATTT
1 AAAATTTAAAAATTT
1240877 AAAATTTAA
1 AAAATTTAA
1240886 TGTAGATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATTTAAAAATTT
Found at i:1240870 original size:22 final size:22
Alignment explanation
Indices: 1240844--1240885 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1240834 GATCTATTAC
1240844 TTTAAAAATTTAAAATTTAAAA
1 TTTAAAAATTTAAAATTTAAAA
1240866 TTTAAAAATTTAAAATTTAA
1 TTTAAAAATTTAAAATTTAA
1240886 TGTAGATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTAAAAATTTAAAATTTAAAA
Found at i:1244849 original size:18 final size:18
Alignment explanation
Indices: 1244826--1244917 Score: 82
Period size: 18 Copynumber: 5.3 Consensus size: 18
1244816 TATCTACCAT
1244826 AAATGTATCCTCCACCTC
1 AAATGTATCCTCCACCTC
* ** *
1244844 AAATGTATCATTTACCAC
1 AAATGTATCCTCCACCTC
* *
1244862 AAATGTATCCCCCACCAC
1 AAATGTATCCTCCACCTC
*
1244880 AAATGTATCAT---CCTC
1 AAATGTATCCTCCACCTC
* *
1244895 AAATATATCCTCTACCTC
1 AAATGTATCCTCCACCTC
1244913 AAATG
1 AAATG
1244918 CATCAAGAAC
Statistics
Matches: 57, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
15 12 0.21
18 45 0.79
ACGTcount: A:0.35, C:0.32, G:0.05, T:0.28
Consensus pattern (18 bp):
AAATGTATCCTCCACCTC
Found at i:1244860 original size:36 final size:34
Alignment explanation
Indices: 1244816--1244922 Score: 112
Period size: 36 Copynumber: 3.1 Consensus size: 34
1244806 GTATAGTTAT
1244816 TATC-TACCATAAATGTATCCTCCACCTCAAATG
1 TATCATACCATAAATGTATCCTCCACCTCAAATG
* * *
1244849 TATCATTTACCACAAATGTATCCCCCACCACAAATG
1 TATCA--TACCATAAATGTATCCTCCACCTCAAATG
* *
1244885 TATCAT-CC-TCAAATATATCCTCTACCTCAAATG
1 TATCATACCAT-AAATGTATCCTCCACCTCAAATG
*
1244918 CATCA
1 TATCA
1244923 AGAACAAAAG
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
33 29 0.48
34 1 0.02
36 31 0.51
ACGTcount: A:0.35, C:0.32, G:0.05, T:0.29
Consensus pattern (34 bp):
TATCATACCATAAATGTATCCTCCACCTCAAATG
Found at i:1246314 original size:52 final size:52
Alignment explanation
Indices: 1246195--1246327 Score: 133
Period size: 52 Copynumber: 2.6 Consensus size: 52
1246185 TTTGGTTCGG
* * * **
1246195 GCCCAATTGGGCCCATCCTCGTCCAAGCTCAGTTGGATTCATTCTAGTCCAA
1 GCCCAATTGGGCCCATTCTGGTCCAAGCCCAGTTGGACCCATTCTAGTCCAA
* ** * * **
1246247 GCCTAGGTGGACCCATTCTGGTCCAAGCCCAGTTGGACCCATTCTGGT-CTT
1 GCCCAATTGGGCCCATTCTGGTCCAAGCCCAGTTGGACCCATTCTAGTCCAA
*
1246298 GACCCAATTGGGCCCATTCTGGTTCAAGCC
1 G-CCCAATTGGGCCCATTCTGGTCCAAGCC
1246328 TAATTGGTCC
Statistics
Matches: 63, Mismatches: 17, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
51 2 0.03
52 61 0.97
ACGTcount: A:0.19, C:0.32, G:0.23, T:0.26
Consensus pattern (52 bp):
GCCCAATTGGGCCCATTCTGGTCCAAGCCCAGTTGGACCCATTCTAGTCCAA
Found at i:1246332 original size:26 final size:26
Alignment explanation
Indices: 1246195--1246367 Score: 118
Period size: 26 Copynumber: 6.7 Consensus size: 26
1246185 TTTGGTTCGG
* * *
1246195 GCCCAATTGGGCCCATCCTCGTCCAA
1 GCCCAATTGGACCCATTCTGGTCCAA
* * ** *
1246221 GCTCAGTTGGATTCATTCTAGTCCAA
1 GCCCAATTGGACCCATTCTGGTCCAA
* **
1246247 GCCTAGGTGGACCCATTCTGGTCCAA
1 GCCCAATTGGACCCATTCTGGTCCAA
* **
1246273 GCCCAGTTGGACCCATTCTGGT-CTT
1 GCCCAATTGGACCCATTCTGGTCCAA
* *
1246298 GACCCAATTGGGCCCATTCTGGTTCAA
1 G-CCCAATTGGACCCATTCTGGTCCAA
* *
1246325 GCCTAATTGGTCCCA-TCTTGGT-CAGA
1 GCCCAATTGGACCCATTC-TGGTCCA-A
* *
1246351 GCCCAACTGAACCCATT
1 GCCCAATTGGACCCATT
1246368 TTTGTTAATC
Statistics
Matches: 115, Mismatches: 27, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
25 6 0.05
26 106 0.92
27 3 0.03
ACGTcount: A:0.20, C:0.32, G:0.21, T:0.27
Consensus pattern (26 bp):
GCCCAATTGGACCCATTCTGGTCCAA
Found at i:1246430 original size:3 final size:3
Alignment explanation
Indices: 1246422--1246666 Score: 301
Period size: 3 Copynumber: 81.7 Consensus size: 3
1246412 TTAGATTCTG
1246422 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1246470 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
1246518 TTA TTA TCA TTA TTA CTA TTC TCA TCA TTA TTA TTA TTA TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * * *
1246566 TTA TTA CTA TTA TCA TCA TCA TCA TCA TCA TCA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
1246614 TTA TTA TCA TCA TCA TCA TCA TCA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1246662 TTA TT
1 TTA TT
1246667 TTGTTTCTTT
Statistics
Matches: 224, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 224 1.00
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1260884 original size:35 final size:35
Alignment explanation
Indices: 1260838--1260907 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
1260828 TATACATGTG
* *
1260838 AAGTCAGTTGTAATTTTATGCCCAGAAAATATTTA
1 AAGTCAGTTGTAAGTTTATGCCCAGAAAACATTTA
* * *
1260873 AAGTCAGTTGTAGGTTTATGTCTAGAAAACATTTA
1 AAGTCAGTTGTAAGTTTATGCCCAGAAAACATTTA
1260908 GTTTATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (35 bp):
AAGTCAGTTGTAAGTTTATGCCCAGAAAACATTTA
Found at i:1263945 original size:25 final size:25
Alignment explanation
Indices: 1263914--1263986 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
1263904 CAGCAATGTG
1263914 TTCAGAAACACCATTCAACAAACTA
1 TTCAGAAACACCATTCAACAAACTA
* * *
1263939 TTTAGAAACACAATTTAGA-AAACTA
1 TTCAGAAACACCATTCA-ACAAACTA
** *
1263964 TTCAGAAATGCCATTCAGCAAAC
1 TTCAGAAACACCATTCAACAAAC
1263987 CAATATCATA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
25 36 0.97
26 1 0.03
ACGTcount: A:0.47, C:0.22, G:0.08, T:0.23
Consensus pattern (25 bp):
TTCAGAAACACCATTCAACAAACTA
Found at i:1264879 original size:64 final size:63
Alignment explanation
Indices: 1264692--1264879 Score: 150
Period size: 64 Copynumber: 2.9 Consensus size: 63
1264682 CTTAAAATTT
* * * **
1264692 AAAGGGATTATTGAAGGCATATTATCCAAAAAAAACACCTTCAATTAATTCTTTT-AAA-AGATT
1 AAAGGGATTATTGAAGGCATATTATGC--AAAAAATACCTTCAA-TAATT-TTTTCAAATAAAAA
1264755 TG
62 TG
* * * * * * * * *
1264757 -AATGTATTAGTGAAGGCAT-TTTTAGTAGAAAATCACCTTCACTGATGTTTTTCCAATAAAAAT
1 AAAGGGATTATTGAAGGCATATTAT-GCAAAAAAT-ACCTTCAATAAT-TTTTTCAAATAAAAAT
1264820 G
63 G
1264821 AAAGGGATTATTGAAGGCATATTATGCAAAAAATACCTTCAATAAATTTTTTCAAATAA
1 AAAGGGATTATTGAAGGCATATTATGCAAAAAATACCTTCAAT-AATTTTTTCAAATAA
1264880 TTTGAAAGAA
Statistics
Matches: 92, Mismatches: 23, Indels: 17
0.70 0.17 0.13
Matches are distributed among these distances:
62 12 0.13
63 13 0.14
64 39 0.42
65 25 0.27
66 3 0.03
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (63 bp):
AAAGGGATTATTGAAGGCATATTATGCAAAAAATACCTTCAATAATTTTTTCAAATAAAAATG
Found at i:1265414 original size:64 final size:63
Alignment explanation
Indices: 1265346--1265467 Score: 149
Period size: 63 Copynumber: 1.9 Consensus size: 63
1265336 CAAAAATGCC
** * *
1265346 TTCAA-AAATCTCTTTCTTAAAATTTAAGGGGGATTATTAAAGGCGTATTAT-GCAAAAAAACAC
1 TTCAATAAAT-TCTTTCAAAAAATTTAA-GGGAATTAGTAAAGGCGT-TTATAGCAAAAAAACAC
1265409 A
63 A
* *
1265410 TTCAATAAATTCTTTCAAAAAATTTGAGGGAATTAGTAAAGGCGTTTATAGTAAAAAA
1 TTCAATAAATTCTTTCAAAAAATTTAAGGGAATTAGTAAAGGCGTTTATAGCAAAAAA
1265468 TGCCTATAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
62 4 0.08
63 23 0.46
64 19 0.38
65 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (63 bp):
TTCAATAAATTCTTTCAAAAAATTTAAGGGAATTAGTAAAGGCGTTTATAGCAAAAAAACACA
Found at i:1265733 original size:555 final size:556
Alignment explanation
Indices: 1264821--1266087 Score: 1704
Period size: 555 Copynumber: 2.3 Consensus size: 556
1264811 AATAAAAATG
* * * *
1264821 AAAGGGATTATTGAAGGCATATTATGCAAAAAATACCTTCAATAAATTTTTTCAAATAATTTGAA
1 AAAGGGATTATTAAAGGCATATTATGCAAAAAATACCTTCAATAAATTCTTTCAAAAAATTTGAG
* * * ** ** * *
1264886 AGAATTAATGAAA-ATGTTTGCAGTCGAAAACACCTATAATAATCT-CA--TAAAAATTTAAGAG
66 AGAATTAGT-AAAGGTGTTTGTAGTAAAAAATGCCTATAATAATCTCCATGTCAAAATTTAAAAG
*
1264947 GATTTTCGAAGGCGTTTTTAGTAGAAAA-CTGCCTTCACTAATATAAAAATTATAAGTGAAGGCA
130 GATTATCGAAGGCGTTTTTAGTAGAAAATCTGCCTTCACTAATATAAAAATTATAAGTGAAGGCA
* * * *
1265011 TTTTTTTGTCAAAAAACACTTTCAATAATTCCCTTAAAATTTGACCACAAGATTATTGAATGCGT
195 TTTTTCTGTCAAAAAACACTTTCAATAATTCCCTTAAAATTTGACCACAAGATTATTAAAGGCAT
* * * *
1265076 TTTTACTAAAAGATGCCTTTAATAATTCCAAAAAAAATTTAAAAGAAAATTATTGAAGGTTTTTT
260 TTTTACTAAAAAATGCCTTTAATAATCCCAAAAAAAATTTAAAAGAAAATTATTAAAGGATTTTT
* * ** * *
1265141 TTTTTAAAAAATACCTTCAATAATCTGGTCTATTTTTTCAATAGTTTGTTTATTGGAGGTGTTTT
325 TTTTTAAAAAATACCTTCAATAATCTAGTCAATTTTTTCAATAACTTGTTTATTAGAGATGTTTT
* * * *
1265206 ATGCTAAAAACACTTTCAATAATCCTATCCAAAAATATTAAGATGATTATTGAAGGTATTTTAT-
390 ATGCCAAAAACACCTTCAATAATCCTATCCAAAAATATTAAAAGGATTATTGAAGGTATTTTATA
* * *
1265270 AAAAAAAATACCTCTAATAA-TTTCTTTTAAAAATTTTGAAAA-GCGATTATTGAATGTA-TTTT
455 AAAAAAAATACCTCTAATAATTTTC-TTTAAAAATTTTAAAAATGAGATTATTGAAGGTATTTTT
*
1265332 TAGTCAAAAATGCCTTCAAAAATCTCTT-TC-TTAAAATTT
519 TACT-AAAAATGCCTTCAAAAAT-T-TTCTCATTAAAATTT
* *
1265371 AAGGGGGATTATTAAAGGCGTATTATGCAAAAAA-ACACATTCAATAAATTCTTTCAAAAAATTT
1 AA-AGGGATTATTAAAGGCATATTATGCAAAAAATAC-C-TTCAATAAATTCTTTCAAAAAATTT
* * *
1265435 GAGGGAATTAGTAAAGGCGTTTATAGTAAAAAATGCCTATAATAATCTCCATGTCAAAATTTAAA
63 GAGAGAATTAGTAAAGGTGTTTGTAGTAAAAAATGCCTATAATAATCTCCATGTCAAAATTTAAA
** * *
1265500 AGGATTATCGAAGGTATTTTTTGTAGAAAATC-GCTTTCACTAATATAAAAATTATAA-TCGAAG
128 AGGATTATCGAAGGCGTTTTTAGTAGAAAATCTGCCTTCACTAATATAAAAATTATAAGT-GAAG
* * * * **
1265563 GTATTTTTCTG-CCAAAAATACTTTCAATAA-TCTCCTTAAAATTTGACTATGAGATTATTAAAG
192 GCATTTTTCTGTCAAAAAACACTTTCAATAATTC-CCTTAAAATTTGACCACAAGATTATTAAAG
* * **
1265626 GTATTTTTACTAAAAAATGCCTTTAATAATCCCAACAAATTTTTGAAAAG-AAATTATTAAAGGC
256 GCATTTTTACTAAAAAATGCCTTTAATAATCCCAAAAAAAATTT-AAAAGAAAATTATTAAAGG-
* *
1265690 ATTTTTTTTTTAGAAAATGCCTTCAATAATCTAGTCAATTTTTTCAATAACTTGTTTATTAGAGA
319 ATTTTTTTTTTAAAAAATACCTTCAATAATCTAGTCAATTTTTTCAATAACTTGTTTATTAGAGA
*
1265755 TGTTTTATGCCAAAAATACCTTCAATAATCCTATCCAAAAATATTAAAAGGATTATTGAAGGTAT
384 TGTTTTATGCCAAAAACACCTTCAATAATCCTATCCAAAAATATTAAAAGGATTATTGAAGGTAT
1265820 TTTATAAAAAAAAAATACCTCTAATAATTTTCTTTAAAAATTTTAAAAATGAGATTATTGAAGGT
449 TTTAT-AAAAAAAAATACCTCTAATAATTTTCTTTAAAAATTTTAAAAATGAGATTATTGAAGGT
*
1265885 ATTTTTTACTAAAAATGCGTTCAAAAATTTTCTCATTAAAATTT
513 ATTTTTTACTAAAAATGCCTTCAAAAATTTTCTCATTAAAATTT
**
1265929 AAAGGGATTATTAAAGGTTTATTATGCAAAAAATACCTTCAATAAATTCTTTCAAAAAATTTGAG
1 AAAGGGATTATTAAAGGCATATTATGCAAAAAATACCTTCAATAAATTCTTTCAAAAAATTTGAG
**
1265994 AGAATTAGTAAAGGTGTTTGTAGTAAAAAATGCCTATAATAATCTCTTTGTCAAAATTTAAAAGG
66 AGAATTAGTAAAGGTGTTTGTAGTAAAAAATGCCTATAATAATCTCCATGTCAAAATTTAAAAGG
* * *
1266059 ATTATCAAAGGCGTTTTTGGTAAAAAATC
131 ATTATCGAAGGCGTTTTTAGTAGAAAATC
1266088 ATCTTCAGTG
Statistics
Matches: 625, Mismatches: 72, Indels: 34
0.85 0.10 0.05
Matches are distributed among these distances:
550 4 0.01
551 32 0.05
552 56 0.09
553 4 0.01
554 92 0.15
555 199 0.32
556 115 0.18
557 68 0.11
558 48 0.08
559 7 0.01
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.37
Consensus pattern (556 bp):
AAAGGGATTATTAAAGGCATATTATGCAAAAAATACCTTCAATAAATTCTTTCAAAAAATTTGAG
AGAATTAGTAAAGGTGTTTGTAGTAAAAAATGCCTATAATAATCTCCATGTCAAAATTTAAAAGG
ATTATCGAAGGCGTTTTTAGTAGAAAATCTGCCTTCACTAATATAAAAATTATAAGTGAAGGCAT
TTTTCTGTCAAAAAACACTTTCAATAATTCCCTTAAAATTTGACCACAAGATTATTAAAGGCATT
TTTACTAAAAAATGCCTTTAATAATCCCAAAAAAAATTTAAAAGAAAATTATTAAAGGATTTTTT
TTTTAAAAAATACCTTCAATAATCTAGTCAATTTTTTCAATAACTTGTTTATTAGAGATGTTTTA
TGCCAAAAACACCTTCAATAATCCTATCCAAAAATATTAAAAGGATTATTGAAGGTATTTTATAA
AAAAAAATACCTCTAATAATTTTCTTTAAAAATTTTAAAAATGAGATTATTGAAGGTATTTTTTA
CTAAAAATGCCTTCAAAAATTTTCTCATTAAAATTT
Found at i:1265834 original size:64 final size:67
Alignment explanation
Indices: 1265766--1265889 Score: 157
Period size: 64 Copynumber: 1.9 Consensus size: 67
1265756 GTTTTATGCC
1265766 AAAAATACCT-TCAATAATCCTATCCAAAAATATT-AAAA-G-GATTATTGAAGGTATTTTATAA
1 AAAAATACCTCT-AATAATCCTATCCAAAAATATTAAAAATGAGATTATTGAAGGTATTTTATAA
1265827 AAA
65 AAA
** * ** *
1265830 AAAAATACCTCTAATAATTTTCTTTAAAAATTTTAAAAATGAGATTATTGAAGGTATTTT
1 AAAAATACCTCTAATAATCCTATCCAAAAATATTAAAAATGAGATTATTGAAGGTATTTT
1265890 TTACTAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
64 26 0.52
65 5 0.10
66 1 0.02
67 18 0.36
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (67 bp):
AAAAATACCTCTAATAATCCTATCCAAAAATATTAAAAATGAGATTATTGAAGGTATTTTATAAA
AA
Found at i:1265988 original size:62 final size:62
Alignment explanation
Indices: 1265757--1265990 Score: 174
Period size: 62 Copynumber: 3.7 Consensus size: 62
1265747 ATTAGAGATG
* * * * * *
1265757 TTTTATGCCAAAAATACCTTCAAT-AATCCTATCCAAAAATATTAAAAGGATTATTGAAGGTA
1 TTTTATACAAAAAATACCTTCAATAAATTCTTTCAAAAAAT-TTAAAGGGATTATTGAAGGTA
* * * *
1265819 TTTTATAAAAAAAAAATACC-TCTAATAATTTTCTTT-AAAAATTTTAAAAATGAGATTATTGAA
1 TTTTAT--ACAAAAAATACCTTC-AATAA-ATTCTTTCAAAAAATTT--AAA-GGGATTATTGAA
1265882 GGTA
59 GGTA
* * * * * *
1265886 TTTTTTACTAAAAATGCGTTCAA-AAATT-TTCTCATTAAAATTTAAAGGGATTATTAAAGGT-
1 TTTTATACAAAAAATACCTTCAATAAATTCTT-TCA-AAAAATTTAAAGGGATTATTGAAGGTA
*
1265947 TTATTATGCAAAAAATACCTTCAATAAATTCTTTCAAAAAATTT
1 TT-TTATACAAAAAATACCTTCAATAAATTCTTTCAAAAAATTT
1265991 GAGAGAATTA
Statistics
Matches: 131, Mismatches: 26, Indels: 30
0.70 0.14 0.16
Matches are distributed among these distances:
61 2 0.02
62 44 0.34
63 16 0.12
64 19 0.15
65 22 0.17
66 9 0.07
67 19 0.15
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (62 bp):
TTTTATACAAAAAATACCTTCAATAAATTCTTTCAAAAAATTTAAAGGGATTATTGAAGGTA
Found at i:1266817 original size:13 final size:13
Alignment explanation
Indices: 1266801--1266825 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1266791 CATGTTCATT
1266801 TTTATATAAATTA
1 TTTATATAAATTA
1266814 TTTATATAAATT
1 TTTATATAAATT
1266826 TGGTCTGATA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTATATAAATTA
Found at i:1268543 original size:21 final size:21
Alignment explanation
Indices: 1268519--1268558 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1268509 CTCATATCAT
1268519 TCAAGTTGGTGATATTGATAC
1 TCAAGTTGGTGATATTGATAC
* *
1268540 TCAAGTTGGTTATCTTGAT
1 TCAAGTTGGTGATATTGAT
1268559 GTTTAAAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (21 bp):
TCAAGTTGGTGATATTGATAC
Found at i:1278754 original size:191 final size:187
Alignment explanation
Indices: 1278468--1278813 Score: 442
Period size: 191 Copynumber: 1.8 Consensus size: 187
1278458 CTTAAAATTT
* * *
1278468 AAAGGGATTATTGAAGGCATATTATGCAAAAAAACGCCTTTAATTAATTCTTTTAAAAAATTTGA
1 AAAGGGATTATTGAAGGCATATTATGCAAAAAAACGCCTTCAATAAATTCTTTCAAAAAATTTGA
* * * ** ** * * *
1278533 ATGTATTAGTGAAGGCATTTTTAGTCAAAAAAATACCTAGAATAATCTTATTGTTAAAATTTTAA
66 AAGAATTAATGAAAACATTTACAGTC--AAAAACACCTAGAATAATCTCA---TAAAAATTTTAA
** *
1278598 TGGATTATTGAAGGCATTTTTAGTAGAAAATCACCTTCACTGATGTTTTTCTGATAAAAATG
126 AAGATTATCGAAGGCATTTTTAGTAGAAAATCACCTTCACTGATGTTTTTCTGATAAAAATG
* * *
1278660 AAAGGGATTATTGAAGGCGTATTATGC-AAAAAATGCCTTCAATAAATTCTTTCAAATAATTTGA
1 AAAGGGATTATTGAAGGCATATTATGCAAAAAAACGCCTTCAATAAATTCTTTCAAAAAATTTGA
* *
1278724 AAGAATTAATGAAAACGTTTACAGTCAAAAACACCTATAATAATCTCATAAAAATTTTAAAAGAT
66 AAGAATTAATGAAAACATTTACAGTCAAAAACACCTAGAATAATCTCATAAAAATTTTAAAAGAT
*
1278789 TATCGAAGGCATTTTTGGTAGAAAA
131 TATCGAAGGCATTTTTAGTAGAAAA
1278814 ACTGCCTTCA
Statistics
Matches: 132, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
186 37 0.28
189 19 0.14
191 50 0.38
192 26 0.20
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (187 bp):
AAAGGGATTATTGAAGGCATATTATGCAAAAAAACGCCTTCAATAAATTCTTTCAAAAAATTTGA
AAGAATTAATGAAAACATTTACAGTCAAAAACACCTAGAATAATCTCATAAAAATTTTAAAAGAT
TATCGAAGGCATTTTTAGTAGAAAATCACCTTCACTGATGTTTTTCTGATAAAAATG
Found at i:1279865 original size:557 final size:553
Alignment explanation
Indices: 1278660--1279969 Score: 1656
Period size: 558 Copynumber: 2.4 Consensus size: 553
1278650 GATAAAAATG
* *
1278660 AAAGGGATTATTGAAGGCGTATTATGCAAAAAATGCCTTCAATAAATTCTTTCAAATAATTTGAA
1 AAAGGGATTATTGAAGGCGTATTATGCAAAAAATACCTTCAATAAATTCTTTCAAA-AATTTGAG
* * ** * * * * * *
1278725 AGAATTAATGAAAACGTTTACAGTCAAAAACACCTATAATAATCT-C-ATAAAAATTTTAAAAGA
65 GGAATTAGTGAAGGCGTTTATAGTAAAAAATACCTATAATAATCTCCTGTCAAAATTTAAAAAGA
* *
1278788 TTATCGAAGGCATTTTTGGTAGAAAAACTGCCTTCACTACTATAAAAATTATAAGTGAAGGCATT
130 TTATCGAA-GCGTTTTTGGTAGAAAAAC-GCCTTCACTAATATAAAAATTATAAGTGAAGGCA-T
* * * *
1278853 TTTTTTGCCAAAAAACACTTTCAATAATCTCTTTAAAATTTGACCATAAGATTATTGAATGGGTT
192 TTTTCTGCCAAAAAACACTTTCAATAATCTCCTTAAAATTTGACCATAAGATTATTGAAAGGATT
* ** *
1278918 TTTACTAAAAAATGCCTTTAATAATTTCAAAAAAATTTTAAAAGAAAATTATTGAAGGTTTTTTT
257 TTTACTAAAAAATACCTTTAATAATCCCAAAAAAATTTTAAAAGAAAATTATTAAAGGTTTTTTT
* * * *
1278983 TTTTTAAATACCTTCAATAATCCGGTCTATTTTTTCAATAATTTGTTTATTGGAGGTGTTTTATG
322 TTTTTAAATACCTTCAATAATCCAGTCTATTTTTTCAATAACTTGTTTATTAGAGATGTTTTATG
* *
1279048 CAAAAAAACACTTTCAATAATCCTATCCAAAAATATTAATATGATTATTGAAGGCATTTTATAAA
387 CAAAAAAACACTTTCAATAATCCTATCCAAAAATATTAAGAGGATTATTGAAGGCATTTTATAAA
** * * * *
1279113 AAAAAAAAACACCTCTAATAATTTCTTTTAAAAATTTTGAAAAGCGATTATTGAATGTGTTTTTA
452 AAAAAAAAACACCTCTAATAATTTCTTAAAAAAATTTTGAAAAGAGATTATTAAAGGTATTTTTA
* * **
1279178 GTCAAAAATGCCTTCAAAAATCTCTTTTTTAAAATTT
517 GTCAAAAATACCTTCAAAAATCTCCTCGTTAAAATTT
* * * * *
1279215 AAAGGGATTATTAAAAGCGTATTATGC-AAAAACACATTCAATAAATTCTTTCAAAAAATTTAAG
1 AAAGGGATTATTGAAGGCGTATTATGCAAAAAATACCTTCAATAAATTCTTTC-AAAAATTTGAG
*
1279279 GGAATTAGTGAAGGCGTTTATAGTAAAAAATGCCTATAATAATCTCCTTGTCAAAATTTAAAAAG
65 GGAATTAGTGAAGGCGTTTATAGTAAAAAATACCTATAATAATCTCC-TGTCAAAATTTAAAAAG
* * *
1279344 ATTATCGAATGTGTTTTTGGTAGAAAATCGCTTTCACTAATATAAAAATTATAA-TCGAAGGCAT
129 ATTATCGAA-GCGTTTTTGGTAGAAAAACGCCTTCACTAATATAAAAATTATAAGT-GAAGGCAT
* * * *
1279408 TTTTCTGTCAAAAATA-TCTTT-AATAATCTCCTTAAAATTTGACTATGAGATTATT-AAAGGCA
192 TTTTCTGCCAAAAA-ACACTTTCAATAATCTCCTTAAAATTTGACCATAAGATTATTGAAAGG-A
* *
1279470 TTTTTACTAAAAAATACCTTTAATAATCCCAACAAATTTTTGAAAAG-AAATTATTAAAGGTATT
255 TTTTTACTAAAAAATACCTTTAATAATCCCAAAAAAATTTT-AAAAGAAAATTATTAAAGGT-TT
* *
1279534 TTTTTTTTTAGAAAATGCCTTCAATAATCTAGT-TAATTTTTTCAATAACTTGTTTATTAGAGAT
318 TTTTTTTTT---AAATACCTTCAATAATCCAGTCT-ATTTTTTCAATAACTTGTTTATTAGAGAT
** * **
1279598 GTTTTATGCCAAAAATGC-C-TTCAATAATCCTATCTAAAAATATTGCGAGGATTATTGAAGGCA
379 GTTTTATG-CAAAAAAACACTTTCAATAATCCTATCCAAAAATATTAAGAGGATTATTGAAGGCA
* *
1279661 TTTTAT-AAAAAAAAAAATACCTCTAATAATTT-TTAAAAAAATTTTGAATAGGAGATTATTAAA
443 TTTTATAAAAAAAAAAAACACCTCTAATAATTTCTTAAAAAAATTTTGAA-AAGAGATTATTAAA
*
1279724 GGTATTTTTAGTCAAAAATACCTTTAAAAATCTCCTCGTTAAAATTT
507 GGTATTTTTAGTCAAAAATACCTTCAAAAATCTCCTCGTTAAAATTT
* * *
1279771 AAAGGGATTATTGAAGGCATATTATGCAAAAAATACCTTCAATAAATTTTTTCAAAAATTTTGGG
1 AAAGGGATTATTGAAGGCGTATTATGCAAAAAATACCTTCAATAAATTCTTTCAAAAA-TTTGAG
* * * *
1279836 GGAATTAGTCAAGGCGTTTGTAGTAAAAAAATACCTATAATAATCTCCTCGTCAAAATTTAAGAG
65 GGAATTAGTGAAGGCGTTTATAGT-AAAAAATACCTATAATAATCTCCT-GTCAAAATTTAAAAA
** * * *
1279901 GATTATCGAAGACGTTTTTGGTAGAAAGCCACCTTCAATGATATAAAAATTATAAGTGAAGGCAT
128 GATTATCGAAG-CGTTTTTGGTAGAAAAACGCCTTCACTAATATAAAAATTATAAGTGAAGGCAT
1279966 TTTT
192 TTTT
1279970 GGTAGTGAAG
Statistics
Matches: 650, Mismatches: 84, Indels: 39
0.84 0.11 0.05
Matches are distributed among these distances:
553 4 0.01
554 145 0.22
555 77 0.12
556 136 0.21
557 134 0.21
558 146 0.22
559 8 0.01
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.36
Consensus pattern (553 bp):
AAAGGGATTATTGAAGGCGTATTATGCAAAAAATACCTTCAATAAATTCTTTCAAAAATTTGAGG
GAATTAGTGAAGGCGTTTATAGTAAAAAATACCTATAATAATCTCCTGTCAAAATTTAAAAAGAT
TATCGAAGCGTTTTTGGTAGAAAAACGCCTTCACTAATATAAAAATTATAAGTGAAGGCATTTTT
CTGCCAAAAAACACTTTCAATAATCTCCTTAAAATTTGACCATAAGATTATTGAAAGGATTTTTA
CTAAAAAATACCTTTAATAATCCCAAAAAAATTTTAAAAGAAAATTATTAAAGGTTTTTTTTTTT
TAAATACCTTCAATAATCCAGTCTATTTTTTCAATAACTTGTTTATTAGAGATGTTTTATGCAAA
AAAACACTTTCAATAATCCTATCCAAAAATATTAAGAGGATTATTGAAGGCATTTTATAAAAAAA
AAAAACACCTCTAATAATTTCTTAAAAAAATTTTGAAAAGAGATTATTAAAGGTATTTTTAGTCA
AAAATACCTTCAAAAATCTCCTCGTTAAAATTT
Found at i:1281115 original size:13 final size:13
Alignment explanation
Indices: 1281099--1281123 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1281089 CATGTTCATT
1281099 TTTATATAAATTA
1 TTTATATAAATTA
1281112 TTTATATAAATT
1 TTTATATAAATT
1281124 TGGTTAGAAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTATATAAATTA
Found at i:1289319 original size:22 final size:23
Alignment explanation
Indices: 1289263--1289321 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
1289253 AATATTATAT
*
1289263 ATTTAAAATAATTATATAAATTA
1 ATTTAAAAAAATTATATAAATTA
* ** *
1289286 ATTGAATTAAATTATA-AATTTA
1 ATTTAAAAAAATTATATAAATTA
1289308 ATTTAAAAAAATTA
1 ATTTAAAAAAATTA
1289322 ATGAACCAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
22 16 0.57
23 12 0.43
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
ATTTAAAAAAATTATATAAATTA
Found at i:1293372 original size:9 final size:10
Alignment explanation
Indices: 1293360--1293413 Score: 53
Period size: 9 Copynumber: 5.5 Consensus size: 10
1293350 TTTTTTCTTT
1293360 TGTATT-TTA
1 TGTATTATTA
1293369 TGTATT-TTA
1 TGTATTATTA
1293378 T-TATTTATTA
1 TGTA-TTATTA
1293388 T-TATTATTA
1 TGTATTATTA
1293397 TGTATTAATATA
1 TGTATT-AT-TA
1293409 TGTAT
1 TGTAT
1293414 ATCTTTATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.05
9 19 0.47
10 10 0.25
11 2 0.05
12 7 0.17
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (10 bp):
TGTATTATTA
Found at i:1293384 original size:16 final size:16
Alignment explanation
Indices: 1293365--1293509 Score: 72
Period size: 16 Copynumber: 8.8 Consensus size: 16
1293355 TCTTTTGTAT
1293365 TTTATGTATT-TTATTA
1 TTTAT-TATTATTATTA
1293381 TTTATTATTATTATTA
1 TTTATTATTATTATTA
*
1293397 TGTATTAATATATGTA-TA
1 TTTATT-AT-TAT-TATTA
*
1293415 TCT-TTATTTATTTATTTA
1 TTTATTA-TTA-TTA-TTA
* *
1293433 TTTATT-TTGTTAATA
1 TTTATTATTATTATTA
1293448 TTTA-TATGTATT-TTA
1 TTTATTAT-TATTATTA
1293463 TTTA-TA-TAGTTATATA
1 TTTATTATTA-TTAT-TA
*
1293479 TTTATTATTATATTATAA
1 TTTATTA-T-TATTATTA
1293497 TTTATTTATTATT
1 TTTA-TTATTATT
1293510 CTTTTTTTCT
Statistics
Matches: 102, Mismatches: 8, Indels: 37
0.69 0.05 0.25
Matches are distributed among these distances:
13 2 0.02
14 3 0.03
15 20 0.20
16 33 0.32
17 14 0.14
18 17 0.17
19 11 0.11
20 2 0.02
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (16 bp):
TTTATTATTATTATTA
Found at i:1293426 original size:4 final size:4
Alignment explanation
Indices: 1293417--1293506 Score: 60
Period size: 4 Copynumber: 21.5 Consensus size: 4
1293407 TATGTATATC
*
1293417 TTTA TTTA TTTA TTTA TTTA TTT- TGTTA -ATA TTTA TATGTA TTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA T-T-TA -TTTA
* * *
1293463 TTTA TATA GTTA TATA TTTA -TTA TTATA TTATAA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TT-T-A TTTA TTTA TT
1293507 ATTCTTTTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
3 6 0.09
4 46 0.67
5 10 0.14
6 6 0.09
7 1 0.01
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:1293469 original size:21 final size:19
Alignment explanation
Indices: 1293417--1293469 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
1293407 TATGTATATC
1293417 TTTATTTATTTATTTATTTAT
1 TTTATTTA--TATTTATTTAT
* *
1293438 TTTGTTAATATTTATATGTAT
1 TTTATTTATATTTAT-T-TAT
1293459 TTTATTTATAT
1 TTTATTTATAT
1293470 AGTTATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 7 0.27
20 1 0.04
21 18 0.69
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (19 bp):
TTTATTTATATTTATTTAT
Found at i:1293999 original size:31 final size:31
Alignment explanation
Indices: 1293963--1294021 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1293953 CGGTTGAATT
* *
1293963 TTCTGG-CGAAACTTGAATTTTTCGATGAAAA
1 TTCTGGTC-AAACTTGAAGTTTCCGATGAAAA
*
1293994 TTCTGGTCAACCTTGAAGTTTCCGATGA
1 TTCTGGTCAAACTTGAAGTTTCCGATGA
1294022 CTTGCCCAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.96
32 1 0.04
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (31 bp):
TTCTGGTCAAACTTGAAGTTTCCGATGAAAA
Found at i:1294474 original size:17 final size:16
Alignment explanation
Indices: 1294449--1294496 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 16
1294439 CTCCAAGTTT
*
1294449 TTTTTTTATTTGTTTA
1 TTTTTTTATTTATTTA
1294465 TTTGTTTTATTTATTTA
1 TTT-TTTTATTTATTTA
1294482 TTTTATTTATTTATT
1 TTTT-TTTATTTATT
1294497 AGATTAGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 4 0.14
17 25 0.86
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (16 bp):
TTTTTTTATTTATTTA
Found at i:1294479 original size:13 final size:13
Alignment explanation
Indices: 1294461--1294496 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1294451 TTTTTATTTG
*
1294461 TTTATTTGTTTTA
1 TTTATTTATTTTA
1294474 TTTATTTATTTTA
1 TTTATTTATTTTA
1294487 TTTATTTATT
1 TTTATTTATT
1294497 AGATTAGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:1294512 original size:4 final size:4
Alignment explanation
Indices: 1294453--1294496 Score: 52
Period size: 4 Copynumber: 10.5 Consensus size: 4
1294443 AAGTTTTTTT
* *
1294453 TTTA TTTG TTTA TTTGT TTTA TTTA TTTA TTTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTT-A TTTA TTTA TTTA -TTTA TTTA TTTA TT
1294497 AGATTAGATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
4 27 0.79
5 7 0.21
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1294560 original size:21 final size:21
Alignment explanation
Indices: 1294525--1294570 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1294515 ATTTTTTATC
*
1294525 TTTATTTTATCTTTATTTTTGT
1 TTTACTTTATCTTTATTTTT-T
1294547 TTTACTTT-TCTTTATTTTTT
1 TTTACTTTATCTTTATTTTTT
1294567 TTTA
1 TTTA
1294571 TCATTATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.22
21 11 0.48
22 7 0.30
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.78
Consensus pattern (21 bp):
TTTACTTTATCTTTATTTTTT
Found at i:1294601 original size:5 final size:5
Alignment explanation
Indices: 1294518--1294606 Score: 56
Period size: 5 Copynumber: 16.8 Consensus size: 5
1294508 ATTTAAAATT
* * *
1294518 TTTTA TCTTTA TTTTA TCTTTA TTTTTG TTTTA CTTTT- CTTTA TTTTT
1 TTTTA T-TTTA TTTTA T-TTTA -TTTTA TTTTA -TTTTA TTTTA TTTTA
* *
1294566 TTTTA TCATTA -TTTA TTTTCA CTTTTA TTTTG TTTTA TTTT
1 TTTTA T-TTTA TTTTA TTTT-A -TTTTA TTTTA TTTTA TTTT
1294607 CTTTAAATAA
Statistics
Matches: 65, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
4 6 0.09
5 33 0.51
6 21 0.32
7 5 0.08
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:1298580 original size:14 final size:14
Alignment explanation
Indices: 1298561--1298593 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1298551 ACAATGGATG
1298561 AAAAATGA-GCAAAA
1 AAAAATGATG-AAAA
1298575 AAAAATGATGAAAA
1 AAAAATGATGAAAA
1298589 AAAAA
1 AAAAA
1298594 AAAAGAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.94
15 1 0.06
ACGTcount: A:0.76, C:0.03, G:0.12, T:0.09
Consensus pattern (14 bp):
AAAAATGATGAAAA
Found at i:1298589 original size:15 final size:14
Alignment explanation
Indices: 1298561--1298594 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1298551 ACAATGGATG
*
1298561 AAAAATGAGCAAAA
1 AAAAATGAGAAAAA
1298575 AAAAATGATGAAAAA
1 AAAAATGA-GAAAAA
1298590 AAAAA
1 AAAAA
1298595 AAAGAAAGAA
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:0.76, C:0.03, G:0.12, T:0.09
Consensus pattern (14 bp):
AAAAATGAGAAAAA
Done.