Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007860.1 Hibiscus syriacus cultivar Beakdansim tig00110223_pilon, 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: 2941097
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 16
Found at i:910151 original size:20 final size:21
Alignment explanation
Indices: 910105--910165 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
910095 TTCCCCTATG
910105 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
910128 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
910148 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
910166 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:917867 original size:199 final size:198
Alignment explanation
Indices: 917491--918129 Score: 1041
Period size: 199 Copynumber: 3.2 Consensus size: 198
917481 AATCAAAAAT
* * *
917491 AAAACATCTTACCCGGAGGTTTTACATATGACCCGGAGGACTTAATTTTCTTGA-AATTAAATGA
1 AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGACTTAATTTTCTTGAGAATTAAATGA
* *
917555 GAAACTTTGGTAATCGTTTTCTCATTTTCATGTGAAAACATCCTA-CCTAAAGGTTTTATAGATG
66 GAAACTTTGGTAATCGCTTTCTCATTTTCATGTGAAAACATCCTACCCTAAAGGTTTTACAGATG
** * *
917619 ACATGGATGACTTAATTTTCTTGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCA
131 AC-CCGAGGACTTAATTTTCTTGAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCA
*
917684 TATG
195 TGTG
* * * ** *
917688 AAAACATCCTACCCTGAGGTTTTATAGATGACCTGGAGGTCTTAATTTTAATGAGCATTAAATGA
1 AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGACTTAATTTTCTTGAGAATTAAATGA
917753 GAAACTTTGGTAATCGCTTTCTCATTTTCATGTGAAAACATCCTACCCTAAAGGTTTTAC-GAAT
66 GAAACTTTGGTAATCGCTTTCTCATTTTCATGTGAAAACATCCTACCCTAAAGGTTTTACAG-AT
917817 GACCCAGAGGACTTAATTTTCTTGAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTC
130 GACCC-GAGGACTTAATTTTCTTGAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTC
917882 ATGTG
194 ATGTG
*
917887 AAAACATCATACCCTGAGGTTTTACAGATGACCCGGAGGACTTAATTTTCTTGAGAATTAAATGA
1 AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGACTTAATTTTCTTGAGAATTAAATGA
*
917952 GAAACTTTGGTAATCGCTTTCTCATTTTCATGTGAAAACATCCTACCCTGAAGGTTTTACAGATG
66 GAAACTTTGGTAATCGCTTTCTCATTTTCATGTGAAAACATCCTACCCTAAAGGTTTTACAGATG
918017 ACCCGAAGGACTTAATTTTCTTGAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCA
131 ACCCG-AGGACTTAATTTTCTTGAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCA
918082 TGTG
195 TGTG
* *
918086 AAAACATCCTACCCTAAGGTTTTACAGATGACCTGGAGGACTTA
1 AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGACTTA
918130 TCATCTTGCT
Statistics
Matches: 409, Mismatches: 27, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
197 46 0.11
198 55 0.13
199 307 0.75
200 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (198 bp):
AAAACATCCTACCCTGAGGTTTTACAGATGACCCGGAGGACTTAATTTTCTTGAGAATTAAATGA
GAAACTTTGGTAATCGCTTTCTCATTTTCATGTGAAAACATCCTACCCTAAAGGTTTTACAGATG
ACCCGAGGACTTAATTTTCTTGAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCAT
GTG
Found at i:917877 original size:100 final size:99
Alignment explanation
Indices: 917491--918129 Score: 989
Period size: 99 Copynumber: 6.4 Consensus size: 99
917481 AATCAAAAAT
* ** *
917491 AAAACATCTTACCCGGAGGTTTTACATATGACCCGGAGGACTTAATTTTCTTGAA-ATTAAATGA
1 AAAACATCCTACCCTAAGGTTTTACAGATGACCCGGAGGACTTAATTTTCTTGAACATTAAATGA
*
917555 GAAACTTTGGTAATCGTTTTCTCATTTTCATGTG
66 GAAACTTTGGTAATCGCTTTCTCATTTTCATGTG
* ** *
917589 AAAACATCCTA-CCTAAAGGTTTTATAGATGACATGGATGACTTAATTTTCTTGAACATTAAATG
1 AAAACATCCTACCCT-AAGGTTTTACAGATGACCCGGAGGACTTAATTTTCTTGAACATTAAATG
*
917653 AGAAACTTTGGTAATCGCTTTCTCATTTTCATATG
65 AGAAACTTTGGTAATCGCTTTCTCATTTTCATGTG
* * * * ** *
917688 AAAACATCCTACCCTGAGGTTTTATAGATGACCTGGAGGTCTTAATTTTAATGAGCATTAAATGA
1 AAAACATCCTACCCTAAGGTTTTACAGATGACCCGGAGGACTTAATTTTCTTGAACATTAAATGA
917753 GAAACTTTGGTAATCGCTTTCTCATTTTCATGTG
66 GAAACTTTGGTAATCGCTTTCTCATTTTCATGTG
*
917787 AAAACATCCTACCCTAAAGGTTTTAC-GAATGACCCAGAGGACTTAATTTTCTTGAACATTAAAT
1 AAAACATCCTACCCT-AAGGTTTTACAG-ATGACCCGGAGGACTTAATTTTCTTGAACATTAAAT
*
917851 GAGAAACTTTGGTAATCACTTTCTCATTTTCATGTG
64 GAGAAACTTTGGTAATCGCTTTCTCATTTTCATGTG
* *
917887 AAAACATCATACCCTGAGGTTTTACAGATGACCCGGAGGACTTAATTTTCTTGAGA-ATTAAATG
1 AAAACATCCTACCCTAAGGTTTTACAGATGACCCGGAGGACTTAATTTTCTTGA-ACATTAAATG
917951 AGAAACTTTGGTAATCGCTTTCTCATTTTCATGTG
65 AGAAACTTTGGTAATCGCTTTCTCATTTTCATGTG
*
917986 AAAACATCCTACCCTGAAGGTTTTACAGATGACCCGAAGGACTTAATTTTCTTGAACATTAAATG
1 AAAACATCCTACCCT-AAGGTTTTACAGATGACCCGGAGGACTTAATTTTCTTGAACATTAAATG
*
918051 AGAAACTTTGGTAATCACTTTCTCATTTTCATGTG
65 AGAAACTTTGGTAATCGCTTTCTCATTTTCATGTG
*
918086 AAAACATCCTACCCTAAGGTTTTACAGATGACCTGGAGGACTTA
1 AAAACATCCTACCCTAAGGTTTTACAGATGACCCGGAGGACTTA
918130 TCATCTTGCT
Statistics
Matches: 495, Mismatches: 37, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
97 2 0.00
98 44 0.09
99 263 0.53
100 186 0.38
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (99 bp):
AAAACATCCTACCCTAAGGTTTTACAGATGACCCGGAGGACTTAATTTTCTTGAACATTAAATGA
GAAACTTTGGTAATCGCTTTCTCATTTTCATGTG
Found at i:923525 original size:17 final size:17
Alignment explanation
Indices: 923503--923542 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
923493 AGAATACTGA
923503 TATGTATAATGTATGAT
1 TATGTATAATGTATGAT
923520 TATGTATAATGTATGAT
1 TATGTATAATGTATGAT
923537 TATGTA
1 TATGTA
923543 GATATCAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.47
Consensus pattern (17 bp):
TATGTATAATGTATGAT
Found at i:925597 original size:3 final size:3
Alignment explanation
Indices: 925589--925625 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
925579 TATTTGTAAA
*
925589 AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
925626 TTATAAATAT
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:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:927997 original size:23 final size:23
Alignment explanation
Indices: 927968--928025 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
927958 TTCATTAAAA
927968 TTATAATATATTTTTTAAATAAT
1 TTATAATATATTTTTTAAATAAT
* *
927991 TTATAAT-TAAATTTTTAACTAAT
1 TTATAATAT-ATTTTTTAAATAAT
928014 TTATAATTATAT
1 TTATAA-TATAT
928026 ATTAAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 1 0.03
23 25 0.86
24 2 0.07
25 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TTATAATATATTTTTTAAATAAT
Found at i:928050 original size:29 final size:28
Alignment explanation
Indices: 927986--928044 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 28
927976 TATTTTTTAA
927986 ATAATTTATAATTAAATTTTTAACTAATTT
1 ATAA-TTATAATTAAATTTTTAAC-AATTT
928016 ATAATTATATATTAAATTTTTTAA-AATTT
1 ATAATTATA-ATTAAA-TTTTTAACAATTT
928045 TAAATTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 10 0.37
30 10 0.37
31 7 0.26
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (28 bp):
ATAATTATAATTAAATTTTTAACAATTT
Found at i:931190 original size:2 final size:2
Alignment explanation
Indices: 931179--931220 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
931169 TTTATCTAAT
931179 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
931220 T
1 T
931221 TATTTTTCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:932576 original size:56 final size:58
Alignment explanation
Indices: 932486--932601 Score: 191
Period size: 56 Copynumber: 2.0 Consensus size: 58
932476 GTCCTCTAAA
932486 TTATTTTGTTGTTTGAACAAGTGCGTTATGCATTGGAAGTTGGAACTGAAATA-TTATACC
1 TTATTTTGTTGTTTG---AAGTGCGTTATGCATTGGAAGTTGGAACTGAAATATTTATACC
932546 TTATTTTGTTGTTTG-AGTGCGTTATGCATTGGAAGTTGGAACTGAAATATTTATAC
1 TTATTTTGTTGTTTGAAGTGCGTTATGCATTGGAAGTTGGAACTGAAATATTTATAC
932602 TTGATGTTAT
Statistics
Matches: 55, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
56 34 0.62
57 6 0.11
60 15 0.27
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (58 bp):
TTATTTTGTTGTTTGAAGTGCGTTATGCATTGGAAGTTGGAACTGAAATATTTATACC
Found at i:936343 original size:14 final size:14
Alignment explanation
Indices: 936324--936352 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
936314 ATGGAAGCCA
936324 AAAAAAGTTCATAT
1 AAAAAAGTTCATAT
936338 AAAAAAGTTCATAT
1 AAAAAAGTTCATAT
936352 A
1 A
936353 CCAACAGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.28
Consensus pattern (14 bp):
AAAAAAGTTCATAT
Found at i:937758 original size:14 final size:15
Alignment explanation
Indices: 937739--937770 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
937729 CTTTTTTTAA
937739 ATAATTTTAAAA-AT
1 ATAATTTTAAAAGAT
937753 ATAATTTTAAAAGAT
1 ATAATTTTAAAAGAT
937768 ATA
1 ATA
937771 TTAATTTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
ATAATTTTAAAAGAT
Found at i:938057 original size:21 final size:21
Alignment explanation
Indices: 938031--938089 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
938021 ATTTATCGTG
938031 ATTGCGGCCGTCGCGGGCGCT
1 ATTGCGGCCGTCGCGGGCGCT
* * *
938052 ATTGCGGTCATCGCGGACGCT
1 ATTGCGGCCGTCGCGGGCGCT
938073 ATTGCGGCCGTCGCGGG
1 ATTGCGGCCGTCGCGGG
938090 TAACTCGGAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.08, C:0.31, G:0.41, T:0.20
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGGCGCT
Found at i:939515 original size:2 final size:2
Alignment explanation
Indices: 939510--939544 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
939500 TGTCATTAGG
939510 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
939545 TCTAAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:940718 original size:18 final size:18
Alignment explanation
Indices: 940666--940723 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
940656 GACAAACCCT
*
940666 AAAATAAAAGTTAAAAAC-
1 AAAAT-AAAGTAAAAAACA
940684 AAAATAATA-TAATAAAACA
1 AAAATAA-AGTAA-AAAACA
940703 AAAATAAAGTGAAAAAA-A
1 AAAATAAAGT-AAAAAACA
940721 AAA
1 AAA
940724 CAAAAACAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
17 4 0.12
18 16 0.47
19 12 0.35
20 2 0.06
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (18 bp):
AAAATAAAGTAAAAAACA
Found at i:940742 original size:23 final size:22
Alignment explanation
Indices: 940678--940746 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
940668 AATAAAAGTT
*
940678 AAAAACAAAATAATATAATAAAAC
1 AAAAAC-AAATAATA-AAAAAAAC
*
940702 AAAAATAAAGTGAA-AAAAAAAAC
1 AAAAACAAA-T-AATAAAAAAAAC
940725 AAAAACAAATAAGTAAAAAAAA
1 AAAAACAAATAA-TAAAAAAAA
940747 GAGAACAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
21 2 0.05
22 1 0.03
23 26 0.68
24 7 0.18
25 2 0.05
ACGTcount: A:0.78, C:0.06, G:0.04, T:0.12
Consensus pattern (22 bp):
AAAAACAAATAATAAAAAAAAC
Found at i:940745 original size:26 final size:30
Alignment explanation
Indices: 940704--940766 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 30
940694 AATAAAACAA
*
940704 AAATAAAGTGAAAAAAA-A-AAC-AA-AAAC
1 AAAT-AAGTAAAAAAAAGAGAACAAATAAAC
940731 AAATAAGTAAAAAAAAGAGAACAAATAAAC
1 AAATAAGTAAAAAAAAGAGAACAAATAAAC
940761 AAATAA
1 AAATAA
940767 AAATAAGGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 11 0.35
27 5 0.16
28 3 0.10
29 2 0.06
30 10 0.32
ACGTcount: A:0.76, C:0.06, G:0.08, T:0.10
Consensus pattern (30 bp):
AAATAAGTAAAAAAAAGAGAACAAATAAAC
Found at i:940771 original size:36 final size:37
Alignment explanation
Indices: 940702--940773 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 37
940692 ATAATAAAAC
*
940702 AAAAATAAAGTGAAAAAAAAAACAAAAACAAATAAGT
1 AAAAATAAAGAGAAAAAAAAAACAAAAACAAATAAGT
* *
940739 AAAAA-AAAGAGAACAAATAAACAAATAA-AAATAAG
1 AAAAATAAAGAGAAAAAAAAAACAAA-AACAAATAAG
940774 GAAGAAAGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 24 0.77
37 7 0.23
ACGTcount: A:0.76, C:0.06, G:0.08, T:0.10
Consensus pattern (37 bp):
AAAAATAAAGAGAAAAAAAAAACAAAAACAAATAAGT
Found at i:941036 original size:18 final size:19
Alignment explanation
Indices: 941003--941040 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
940993 AACCAAAAAG
941003 AAAATAGAGAAAAATAAAT
1 AAAATAGAGAAAAATAAAT
*
941022 AAAATAGA-TAAAATAAAT
1 AAAATAGAGAAAAATAAAT
941040 A
1 A
941041 GAAAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (19 bp):
AAAATAGAGAAAAATAAAT
Found at i:941047 original size:20 final size:20
Alignment explanation
Indices: 941001--941057 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
940991 AAAACCAAAA
*
941001 AGAAAATAGAGAAAAATAAAT
1 AGAAAATAGA-TAAAATAAAT
941022 --AAAATAGATAAAATAAAT
1 AGAAAATAGATAAAATAAAT
* *
941040 AGAAAATATATATAATAA
1 AGAAAATAGATAAAATAA
941058 TAATAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 9 0.29
19 8 0.26
20 14 0.45
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (20 bp):
AGAAAATAGATAAAATAAAT
Found at i:941069 original size:22 final size:22
Alignment explanation
Indices: 941014--941069 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
941004 AAATAGAGAA
*
941014 AAATAAATAAAATAGATAAAAT
1 AAATAAATAATATAGATAAAAT
*
941036 AAATAGAA-AATATATATAATAAT
1 AAATA-AATAATATAGATAA-AAT
941059 -AATAAATAATA
1 AAATAAATAATA
941070 ATAATAGGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 2 0.07
22 22 0.76
23 5 0.17
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.27
Consensus pattern (22 bp):
AAATAAATAATATAGATAAAAT
Found at i:943911 original size:11 final size:10
Alignment explanation
Indices: 943889--943936 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
943879 ACCCCCCTTA
943889 TTCCTTTTTT
1 TTCCTTTTTT
943899 TTCCTTCTTTT
1 TTCCTT-TTTT
943910 TTCC--TTTT
1 TTCCTTTTTT
*
943918 CT-CTTTTTT
1 TTCCTTTTTT
943927 TT-CTTTTTT
1 TTCCTTTTTT
943936 T
1 T
943937 CTTTTTTCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
7 1 0.03
8 5 0.15
9 13 0.39
10 6 0.18
11 8 0.24
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTCCTTTTTT
Found at i:943915 original size:28 final size:26
Alignment explanation
Indices: 943884--943936 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 26
943874 CTTGAACCCC
943884 CCTTATTC-CTTTTTTTTCCTTCTTTTTT
1 CCTT-TTCTCTTTTTTTT-CTT-TTTTTT
943912 CCTTTTCTCTTTTTTTTCTTTTTTT
1 CCTTTTCTCTTTTTTTTCTTTTTTT
943937 CTTTTTTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 5 0.21
27 6 0.25
28 13 0.54
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (26 bp):
CCTTTTCTCTTTTTTTTCTTTTTTTT
Found at i:943917 original size:17 final size:17
Alignment explanation
Indices: 943897--943944 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
943887 TATTCCTTTT
943897 TTTTCCTTCTTTTTTCC
1 TTTTCCTTCTTTTTTCC
943914 TTTTCTCTT-TTTTTT-C
1 TTTTC-CTTCTTTTTTCC
*
943930 TTTT-TTTCTTTTTTC
1 TTTTCCTTCTTTTTTC
943945 GATTTGGGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 2 0.07
15 6 0.22
16 5 0.19
17 11 0.41
18 3 0.11
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTCCTTCTTTTTTCC
Found at i:947365 original size:2 final size:2
Alignment explanation
Indices: 947360--947416 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
947350 AAAAAAAATA
947360 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
947402 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
947417 AAACGTTAGG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:952039 original size:20 final size:21
Alignment explanation
Indices: 952014--952055 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
952004 TTACACAAGG
952014 TAATCATTCAACTCT-TTTTT
1 TAATCATTCAACTCTGTTTTT
*
952034 TAATCATTCAGCTCTGTTTTT
1 TAATCATTCAACTCTGTTTTT
952055 T
1 T
952056 TCTTTATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.21, C:0.19, G:0.05, T:0.55
Consensus pattern (21 bp):
TAATCATTCAACTCTGTTTTT
Found at i:960530 original size:131 final size:124
Alignment explanation
Indices: 960384--960854 Score: 461
Period size: 118 Copynumber: 3.9 Consensus size: 124
960374 TATTTCAAGT
*
960384 TAACTACTAACTTTTATTTTATTACACTCTAACCATTGTTTATTTATTTACTTACTGTTTCTAAT
1 TAACTACTAACTTTTATTTTATTGCACTCTAACCA-T-TTTATTTATTTA-TTA-T-TTT-TAAT
*
960449 ATTCGATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCATATTATTATGGTTCATACTCTG
60 ATTCGATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTCA-ACTCTG
960514 C
124 C
* *
960515 TAACTACTGACTTTTATTTTATTGCACTCTAACCA--TTATTTA--T-TTATTTAT-ATATT-GA
1 TAACTACTAACTTTTATTTTATTGCACTCTAACCATTTTATTTATTTATTATTTTTAATATTCGA
* * * *
960573 TTCGACCTTGTGGTGACCAGATCCGGTGTACGATCCACATTATTTTGGTTCGGACTCTGC
66 TTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTC-AACTCTGC
* * * *
960633 TAACTACTAACTTTTATTTTATTGCACT-TAACCATTAATAATTATTTAATATTTTTATTATTCG
1 TAACTACTAACTTTTATTTTATTGCACTCTAACCATT-TTATTTATTTATTATTTTTAATATTCG
* ** *
960697 ATTCGACC-T-T-GTGATCAGATAAGGGGTATGATCCACATTATTATGGTTCGAACTCTTC
65 ATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTC-AACTCTGC
* * *
960755 TAACCACTAAC-TTT-TTATA-T--A-T-T---TATTTTA--T-TTTATT-TTGTTTGAATTATT
1 TAACTACTAACTTTTATTTTATTGCACTCTAACCATTTTATTTATTTATTATT-TTT-AA-TATT
* *
960806 CGATTCGACCTTGTGGTGACCAGATCTGGGGTATGATCCAGATTATTAT
63 CGATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTAT
960855 AATTCGGACT
Statistics
Matches: 293, Mismatches: 32, Indels: 47
0.79 0.09 0.13
Matches are distributed among these distances:
108 2 0.01
109 8 0.03
110 2 0.01
111 14 0.05
112 3 0.01
113 4 0.01
114 30 0.10
116 2 0.01
117 7 0.02
118 83 0.28
119 6 0.02
120 10 0.03
121 5 0.02
122 52 0.18
123 10 0.03
124 5 0.02
125 10 0.03
127 7 0.02
131 33 0.11
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (124 bp):
TAACTACTAACTTTTATTTTATTGCACTCTAACCATTTTATTTATTTATTATTTTTAATATTCGA
TTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTCAACTCTGC
Found at i:960893 original size:16 final size:16
Alignment explanation
Indices: 960868--960910 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
960858 TCGGACTCTA
* *
960868 CTAACCGCTAACTTTT
1 CTAACAGCTAACCTTT
960884 CTAACAGCTAACCTTT
1 CTAACAGCTAACCTTT
*
960900 CTAACTGCTAA
1 CTAACAGCTAA
960911 TTACTAACGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (16 bp):
CTAACAGCTAACCTTT
Found at i:960991 original size:16 final size:16
Alignment explanation
Indices: 960957--960990 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
960947 ATTTCTGCTA
*
960957 TTTAACTTTATGCACT
1 TTTAAATTTATGCACT
960973 TTTAAATTTATGCA-T
1 TTTAAATTTATGCACT
960988 TTT
1 TTT
960991 TTTTTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (16 bp):
TTTAAATTTATGCACT
Found at i:963391 original size:11 final size:11
Alignment explanation
Indices: 963375--963403 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
963365 GGAAAGTATT
963375 GGAAAATGAAA
1 GGAAAATGAAA
963386 GGAAAATGAAA
1 GGAAAATGAAA
963397 GGAAAAT
1 GGAAAAT
963404 AAGGGTGCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.10
Consensus pattern (11 bp):
GGAAAATGAAA
Found at i:964470 original size:29 final size:28
Alignment explanation
Indices: 964420--964479 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
964410 TAATCGAATG
*
964420 AAACGTTAGACACCAAACTAAAACGAAAA
1 AAACGTTAGACACCAAACTAAAA-AAAAA
** *
964449 AAACGTTAGACATTAAATTAAAAAAAAA
1 AAACGTTAGACACCAAACTAAAAAAAAA
964477 AAA
1 AAA
964480 GCCTACGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 7 0.26
29 20 0.74
ACGTcount: A:0.63, C:0.13, G:0.08, T:0.15
Consensus pattern (28 bp):
AAACGTTAGACACCAAACTAAAAAAAAA
Found at i:967169 original size:2 final size:2
Alignment explanation
Indices: 967164--967258 Score: 190
Period size: 2 Copynumber: 47.5 Consensus size: 2
967154 AAAAAAAAGT
967164 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
967206 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
967248 TA TA TA TA TA T
1 TA TA TA TA TA T
967259 TGGTATTTGT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 93 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:974291 original size:2 final size:2
Alignment explanation
Indices: 974280--974345 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
974270 AAAAGGAAAA
*
974280 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
974322 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
974346 CAAAGTATTA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:974586 original size:24 final size:23
Alignment explanation
Indices: 974532--974587 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
974522 AAGGTTTTTT
* *
974532 TAAAAAA-AAAATAATATAATAA
1 TAAAAAATAAAAAAATAAAATAA
**
974554 TAATGAATAAAAAAATGAAAATAA
1 TAAAAAATAAAAAAAT-AAAATAA
974578 TAAAAAATAA
1 TAAAAAATAA
974588 TAAATATATA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 5 0.19
23 7 0.27
24 14 0.54
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (23 bp):
TAAAAAATAAAAAAATAAAATAA
Found at i:974589 original size:27 final size:26
Alignment explanation
Indices: 974536--974591 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
974526 TTTTTTTAAA
* *
974536 AAAAAAATAATATAATAATAATGAAT
1 AAAAAAATAAAATAATAAAAATGAAT
974562 AAAAAAATGAAAATAATAAAAAAT-AAT
1 AAAAAAAT-AAAATAAT-AAAAATGAAT
974589 AAA
1 AAA
974592 TATATAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 8 0.31
27 13 0.50
28 5 0.19
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (26 bp):
AAAAAAATAAAATAATAAAAATGAAT
Found at i:975269 original size:37 final size:36
Alignment explanation
Indices: 975219--975356 Score: 172
Period size: 37 Copynumber: 3.8 Consensus size: 36
975209 GTGCTTGTGG
* * * * *
975219 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA-AAATCT
* *
975256 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAAT-CT
*
975293 ATCCTATTTTTAGGAGTTTGAATCCTA--AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
975327 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
975357 GGATGAAAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
34 28 0.31
35 4 0.04
36 4 0.04
37 53 0.60
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
Found at i:975330 original size:34 final size:35
Alignment explanation
Indices: 975253--975353 Score: 161
Period size: 34 Copynumber: 2.9 Consensus size: 35
975243 TTAGTAGAAC
975253 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATG
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAATG
975291 T-TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
975324 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
975354 GTAGGATGAA
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
33 1 0.02
34 33 0.53
37 27 0.44
38 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
Found at i:976202 original size:105 final size:105
Alignment explanation
Indices: 975902--976733 Score: 1278
Period size: 105 Copynumber: 8.0 Consensus size: 105
975892 CATTGTTCCA
* * * * ** * * *
975902 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGTTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * * * *
975967 CAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
976008 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
976068 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
976108 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
976173 AGCGGTCCCTTCATCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
976213 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTATTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
976278 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCTTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
976318 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
976383 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
976423 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
976488 AGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
976528 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
976593 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
976633 AGTCCAATATCATTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * *
976698 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
976734 CCTCGAGTGC
Statistics
Matches: 675, Mismatches: 45, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
100 82 0.12
101 1 0.00
102 4 0.01
103 4 0.01
104 3 0.00
105 504 0.75
106 77 0.11
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:977511 original size:67 final size:66
Alignment explanation
Indices: 977376--977532 Score: 199
Period size: 68 Copynumber: 2.4 Consensus size: 66
977366 AAGATATCTG
* * * **
977376 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAAGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA-
977441 TT
65 TT
* * * *
977443 TGTGTTTCAAGAGTAACTGTCTCAAAGGAGACAAAATT-TGTTTTAGGGGAAATAAATTCAAAGG
1 T-TGTTTCAAGAGAAACTGTCTCAAAGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA
977507 TT
65 TT
*
977509 TTGTTTCAAGGGAAACTGTCTCAA
1 TTGTTTCAAGAGAAACTGTCTCAA
977533 GATAAACGAA
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 21 0.27
66 3 0.04
67 23 0.29
68 31 0.40
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAAGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAT
T
Found at i:977549 original size:36 final size:35
Alignment explanation
Indices: 977509--977789 Score: 252
Period size: 36 Copynumber: 8.0 Consensus size: 35
977499 TTCAAAGGTT
* *
977509 TTGTTTCAAGGGAAACTGTCTCAAGATAAACGAAAA
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAA
*
977545 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* ** * * *
977580 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAAT
1 -TT-GTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAA
* * * * * **
977618 TTGTTTTAAAGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAA
*
977647 TTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
977682 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAA
*
977719 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
977754 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
977790 CTCTTCTAGT
Statistics
Matches: 200, Mismatches: 31, Indels: 28
0.77 0.12 0.11
Matches are distributed among these distances:
28 2 0.01
29 18 0.09
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 8 0.04
36 132 0.66
37 33 0.17
38 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:977549 original size:65 final size:66
Alignment explanation
Indices: 977376--977769 Score: 219
Period size: 65 Copynumber: 5.8 Consensus size: 66
977366 AAGATATCTG
* * * ** *
977376 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAAACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGAG
977441 TT
65 TT
* * *
977443 TGTGTTTCAAGAGTAACTGTCTCAA-AGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAG-
1 T-TGTTTCAAGAGAAACTGTCTCAAGA-GAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGA
977506 GTT
64 GTT
* * * * *
977509 TTGTTTCAAGGGAAACTGTCTCAAGATAAACGAAAA-TTGTTTCAAGAGAAACT--GTCTCAAGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAAAC-AAAATTTGTTTTAAGGGAAA-TAAAT-TCAA-A
*
977571 GAGACAAAACT
62 GAG------TT
* * * * * ** * * * * *
977582 TAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAATTTGTTTTAAAGAAAACATATTCAAATA-T
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGT
977646 T
66 T
* * * * * *
977647 TTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACT--GTCTCAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAAACAAAATTTGTTTTAAGGGAAA-TAAAT-TC-A-A-
*
977710 AGACGAAAT
61 AGA-G--TT
* *
977719 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAAACAAAATTTGTTTTAAGGGAAA
977770 CTGTCTCAAG
Statistics
Matches: 247, Mismatches: 54, Indels: 47
0.71 0.16 0.14
Matches are distributed among these distances:
64 2 0.01
65 82 0.33
66 12 0.05
67 25 0.10
68 32 0.13
72 53 0.21
73 40 0.16
74 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.29
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGT
T
Found at i:977619 original size:138 final size:137
Alignment explanation
Indices: 977457--977770 Score: 405
Period size: 138 Copynumber: 2.3 Consensus size: 137
977447 TTTCAAGAGT
* * * *
977457 AACTGTCTCAAAGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* *
977522 AACTGTCTCAAGATAAACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
66 AACTGTCTCAAGAGAAAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGT
977586 TCCAAAAGA
129 TCCAAAAGA
** * * * * *
977595 AACTGTCTCAAGGGAGACGGAATTTGTTTTAAAGAAAACATATTCAAATATTTTGTTTTAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* * * * * *
977660 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTT
66 AACTGTCTCAAGAGAAACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
*
977725 CAAGAGA
131 CAAAAGA
* *
977732 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
1 AACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAAC
977771 TGTCTCAAGA
Statistics
Matches: 149, Mismatches: 26, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
137 48 0.32
138 101 0.68
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (137 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAAACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
CAAAAGA
Found at i:977677 original size:102 final size:102
Alignment explanation
Indices: 977545--977733 Score: 272
Period size: 102 Copynumber: 1.9 Consensus size: 102
977535 TAAACGAAAA
*
977545 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAACTGTCTCAAGAGA
* *
977610 GACGGAATTTGTTTTAA-AGAAAACATATTCAAATATT
65 GACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
* * * * ** *
977647 TTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAG
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGAG
977712 ACGAAATTTGTTTCAAGAGAAA
66 ACGAAATTTGTTTCAAGAGAAA
977734 CTGTCTCAAG
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
101 35 0.46
102 41 0.54
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (102 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGAG
ACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
Found at i:977811 original size:35 final size:36
Alignment explanation
Indices: 977654--977823 Score: 166
Period size: 36 Copynumber: 4.8 Consensus size: 36
977644 ATTTTGTTTT
* * **
977654 AAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTC
1 AAGGAAAACTGTCTCAAGAGAGACAAAATCTGCTTC
* * * * *
977690 AAGGGAAACTGTCTCAAGATAGACGAAATTTGTTTC
1 AAGGAAAACTGTCTCAAGAGAGACAAAATCTGCTTC
* *
977726 AA-GAGAAACTGTCTCAAGAGAGACAAAATTTGTTTC
1 AAGGA-AAACTGTCTCAAGAGAGACAAAATCTGCTTC
*
977762 AAGGGAAACTGTCTCAAGAGAGACAAAA-CT-CTTC
1 AAGGAAAACTGTCTCAAGAGAGACAAAATCTGCTTC
* * *
977796 TAGTGAAAACGGTCTCAAGCGAGACAAA
1 AAG-GAAAACTGTCTCAAGAGAGACAAA
977824 TCTTGTTTTA
Statistics
Matches: 118, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
34 5 0.04
35 23 0.19
36 89 0.75
37 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
AAGGAAAACTGTCTCAAGAGAGACAAAATCTGCTTC
Found at i:978292 original size:18 final size:18
Alignment explanation
Indices: 978269--978304 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
978259 TGTTGAATCC
*
978269 CCAAAAATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
978287 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
978305 TTGATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.31, G:0.06, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:978745 original size:22 final size:22
Alignment explanation
Indices: 978719--978767 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
978709 TTGTGTTTGG
* *
978719 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
978741 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
978763 TCAAA
1 TCAAA
978768 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:978774 original size:22 final size:22
Alignment explanation
Indices: 978731--978774 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
978721 AAAGGTTTGG
* * *
978731 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
978753 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
978775 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:979437 original size:15 final size:15
Alignment explanation
Indices: 979419--979498 Score: 56
Period size: 15 Copynumber: 5.1 Consensus size: 15
979409 TCTTTTTGAT
979419 TTTTGTTTTTTTTTC
1 TTTTGTTTTTTTTTC
*
979434 TTTTGTTCTTGTTTCTC
1 TTTTGTT-TT-TTTTTC
*
979451 TTTT-TCTTTATTTT-
1 TTTTGT-TTTTTTTTC
*
979465 TTTTGCTTTTTTGCTTC
1 TTTTG-TTTTTT-TTTC
* *
979482 TTTTCTTTTTTGTTC
1 TTTTGTTTTTTTTTC
979497 TT
1 TT
979499 GATTGGATCT
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
14 4 0.08
15 19 0.37
16 14 0.27
17 14 0.27
ACGTcount: A:0.01, C:0.12, G:0.07, T:0.79
Consensus pattern (15 bp):
TTTTGTTTTTTTTTC
Found at i:979491 original size:16 final size:16
Alignment explanation
Indices: 979419--979498 Score: 55
Period size: 16 Copynumber: 5.1 Consensus size: 16
979409 TCTTTTTGAT
*
979419 TTTTG-TTTTTTTTTC
1 TTTTGCTTTTTTGTTC
979434 TTTTG-TTCTTGTT-TCTC
1 TTTTGCTT-TT-TTGT-TC
* *
979451 TTTTTCTTTATT-TT-
1 TTTTGCTTTTTTGTTC
979465 TTTTGCTTTTTTGCTTC
1 TTTTGCTTTTTTG-TTC
979482 TTTT-CTTTTTTGTTC
1 TTTTGCTTTTTTGTTC
979497 TT
1 TT
979499 GATTGGATCT
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.19
15 13 0.24
16 16 0.30
17 13 0.24
18 2 0.04
ACGTcount: A:0.01, C:0.12, G:0.07, T:0.79
Consensus pattern (16 bp):
TTTTGCTTTTTTGTTC
Found at i:980668 original size:8 final size:8
Alignment explanation
Indices: 980652--980690 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
980642 AATGTAGATG
980652 AAAATGCA
1 AAAATGCA
*
980660 AAAAGGCA
1 AAAATGCA
980668 AAAATGC-
1 AAAATGCA
980675 AAAATGCA
1 AAAATGCA
*
980683 AGAATGCA
1 AAAATGCA
980691 CGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:980678 original size:15 final size:15
Alignment explanation
Indices: 980652--980690 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
980642 AATGTAGATG
980652 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
980668 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
980683 AGAATGCA
1 AAAATGCA
980691 CGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:981234 original size:18 final size:18
Alignment explanation
Indices: 981211--981250 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
981201 ATTAGTCTTT
981211 CAGAAGTGGATGTGAATC
1 CAGAAGTGGATGTGAATC
981229 CAGAAGTGGATGTGAATC
1 CAGAAGTGGATGTGAATC
981247 CAGA
1 CAGA
981251 CTTGAAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.33, T:0.20
Consensus pattern (18 bp):
CAGAAGTGGATGTGAATC
Found at i:983808 original size:18 final size:17
Alignment explanation
Indices: 983787--983829 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
983777 ATATATACAT
983787 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
* *
983805 ATAATAAAAATAAGTGA
1 ATAATAATAATAAATGA
983822 ATAA-AATA
1 ATAATAATA
983830 TCTATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:984235 original size:37 final size:36
Alignment explanation
Indices: 984185--984322 Score: 172
Period size: 37 Copynumber: 3.8 Consensus size: 36
984175 GTGCTTGTGG
* * * * *
984185 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA-AAATCT
* *
984222 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAAT-CT
*
984259 ATCCTATTTTTAGGAGTTTGAATCCTA--AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
984293 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
984323 GGACAAAAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
34 28 0.31
35 4 0.04
36 4 0.04
37 53 0.60
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
Found at i:984296 original size:34 final size:35
Alignment explanation
Indices: 984219--984319 Score: 161
Period size: 34 Copynumber: 2.9 Consensus size: 35
984209 TTAGTAGAAC
984219 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATG
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAATG
984257 T-TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
984290 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
984320 GTAGGACAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
33 1 0.02
34 33 0.53
37 27 0.44
38 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
Found at i:985515 original size:24 final size:24
Alignment explanation
Indices: 985484--985580 Score: 131
Period size: 24 Copynumber: 4.0 Consensus size: 24
985474 GTGCTTCCTG
* *
985484 TTCTTGATTAATCTGGCATATTGG
1 TTCTTGATTATTCTGGCATATTGC
*
985508 TTCTTGATTGTTCTGGCATATTGC
1 TTCTTGATTATTCTGGCATATTGC
* *
985532 TTCTTGATTTTTCTGGCATACTGC
1 TTCTTGATTATTCTGGCATATTGC
* *
985556 TTCTTGATTAGTCTGGTATATTGC
1 TTCTTGATTATTCTGGCATATTGC
985580 T
1 T
985581 GCCTTGTTGT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.15, C:0.15, G:0.20, T:0.49
Consensus pattern (24 bp):
TTCTTGATTATTCTGGCATATTGC
Found at i:986741 original size:27 final size:26
Alignment explanation
Indices: 986710--986791 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 26
986700 TCACCCATCA
986710 ACAGCTCCTCAAGCTCATCAGTTTTCT
1 ACAGCTCCTCAAG-TCATCAGTTTTCT
** *
986737 ACAGCTCCTCTTGTTCACCAGTTTTCT
1 ACAGCTCCTCAAG-TCATCAGTTTTCT
* * *
986764 GCAGTTCCTCAAAGTCCTCAGTTTTCT
1 ACAGCTCCTC-AAGTCATCAGTTTTCT
986791 A
1 A
986792 TTTTTCCACC
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
27 42 0.98
28 1 0.02
ACGTcount: A:0.20, C:0.32, G:0.12, T:0.37
Consensus pattern (26 bp):
ACAGCTCCTCAAGTCATCAGTTTTCT
Found at i:988478 original size:15 final size:15
Alignment explanation
Indices: 988442--988483 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
988432 ATCCACTACA
*
988442 TCATCAACATCATTG
1 TCATCACCATCATTG
*
988457 TCTTCACCA-CATATG
1 TCATCACCATCAT-TG
988472 TCATCACCATCA
1 TCATCACCATCA
988484 CAACAACTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 3 0.14
15 17 0.77
16 2 0.09
ACGTcount: A:0.31, C:0.33, G:0.05, T:0.31
Consensus pattern (15 bp):
TCATCACCATCATTG
Found at i:991683 original size:36 final size:36
Alignment explanation
Indices: 991643--991774 Score: 169
Period size: 36 Copynumber: 3.7 Consensus size: 36
991633 GTACGAAAAT
** *
991643 GAAGCATCAGCACTTTTAATTCAAAGTGAACGGAAG
1 GAAGCATCAGCACTTTCGATTCAAAGTGAACGAAAG
*
991679 GAAGCATC-GACACTTTCGATTCAATA-AGAACGAAAG
1 GAAGCATCAG-CACTTTCGATTCAA-AGTGAACGAAAG
* *
991715 GAAGCATCAGCACTTTCGATTCAAAGTGAATGAAAT
1 GAAGCATCAGCACTTTCGATTCAAAGTGAACGAAAG
*
991751 GAAGCATCAGCACTTTCGACTCAA
1 GAAGCATCAGCACTTTCGATTCAA
991775 TTGTTCATCT
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
35 2 0.02
36 80 0.95
37 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (36 bp):
GAAGCATCAGCACTTTCGATTCAAAGTGAACGAAAG
Found at i:993091 original size:34 final size:32
Alignment explanation
Indices: 993046--993115 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
993036 TTTTATAAAG
* *
993046 GGGAAAAGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAAGTTCTAGCTTAGCCCG-G-AAAAACTA
* *
993080 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAAGTTCTAGCTTAGCCCGGAAAAACTA
993112 GGGA
1 GGGA
993116 GTTGTAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.23
Consensus pattern (32 bp):
GGGAAAAGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:995872 original size:34 final size:30
Alignment explanation
Indices: 995834--995902 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
995824 TTGATATAAA
995834 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
995868 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
995897 AATTTA
1 AATTTA
995903 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:995914 original size:29 final size:30
Alignment explanation
Indices: 995843--995902 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
995833 AAATTTAAGG
995843 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
995874 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
995903 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:996053 original size:22 final size:20
Alignment explanation
Indices: 995983--996103 Score: 131
Period size: 22 Copynumber: 5.8 Consensus size: 20
995973 AGGGTGTCAA
995983 AGTGCATCCATGCACCT-CTGC
1 AGTGCATCCATGCACCTGC--C
996004 AGTGCATCCATGCATCCCTG-C
1 AGTGCATCCATGCA--CCTGCC
996025 AGTGCATCCATGCACCTGCAC
1 AGTGCATCCATGCACCTGC-C
996046 TAGTGCATCCATGCACCTGCAC
1 -AGTGCATCCATGCACCTGC-C
*
996068 TAGTGCATCGATGCACCATG-C
1 -AGTGCATCCATGCACC-TGCC
996089 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
996104 TCAAACACCG
Statistics
Matches: 91, Mismatches: 2, Indels: 15
0.84 0.02 0.14
Matches are distributed among these distances:
19 4 0.04
20 14 0.15
21 31 0.34
22 37 0.41
23 5 0.05
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACCTGCC
Found at i:996090 original size:64 final size:64
Alignment explanation
Indices: 995983--996103 Score: 183
Period size: 64 Copynumber: 1.9 Consensus size: 64
995973 AGGGTGTCAA
* *
995983 AGTGCATCCATGCACCTCTGCAGTGCATCCATGCATCCCTGCAGTGCATCCATGCACCTGCACT
1 AGTGCATCCATGCACCTCTACAGTGCATCCATGCATCCATGCAGTGCATCCATGCACCTGCACT
*
996047 AGTGCATCCATGCACCTGC-ACTAGTGCATCGATGCA-CCATGCAGTGCATCCATGCAC
1 AGTGCATCCATGCACCT-CTAC-AGTGCATCCATGCATCCATGCAGTGCATCCATGCAC
996104 TCAAACACCG
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
64 38 0.73
65 14 0.27
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.22
Consensus pattern (64 bp):
AGTGCATCCATGCACCTCTACAGTGCATCCATGCATCCATGCAGTGCATCCATGCACCTGCACT
Found at i:996103 original size:42 final size:38
Alignment explanation
Indices: 995983--996103 Score: 134
Period size: 42 Copynumber: 2.9 Consensus size: 38
995973 AGGGTGTCAA
995983 AGTGCATCCATGCACCTCTGCAGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-C-CTGCAGTGCATCCATGCA--CCTGC
996025 AGTGCATCCATGCACCTGCACTAGTGCATCCATGCACCTGCAC
1 AGTGCATCCATGCACCTG--C-AGTGCATCCATGCACCTG--C
*
996068 TAGTGCATCGATGCACCATGCAGTGCATCCATGCAC
1 -AGTGCATCCATGCACC-TGCAGTGCATCCATGCAC
996104 TCAAACACCG
Statistics
Matches: 71, Mismatches: 1, Indels: 14
0.83 0.01 0.16
Matches are distributed among these distances:
40 3 0.04
41 5 0.07
42 30 0.42
43 16 0.23
44 15 0.21
45 2 0.03
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.22
Consensus pattern (38 bp):
AGTGCATCCATGCACCTGCAGTGCATCCATGCACCTGC
Found at i:996190 original size:41 final size:41
Alignment explanation
Indices: 996124--996206 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
996114 AATGCAATTA
* *
996124 GTGCATCGATGCATCCTTATGTGCATCGATGCATC-AAGGCT
1 GTGCATCGATGCATCCTGATCTGCATCGATGCA-CGAAGGCT
* *
996165 GTGCATCGATGCATCCTGCTCTGCATCTATGCACGAAGGCT
1 GTGCATCGATGCATCCTGATCTGCATCGATGCACGAAGGCT
996206 G
1 G
996207 CAACGGCTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
40 1 0.03
41 36 0.97
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.28
Consensus pattern (41 bp):
GTGCATCGATGCATCCTGATCTGCATCGATGCACGAAGGCT
Found at i:996191 original size:20 final size:20
Alignment explanation
Indices: 996124--996197 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
996114 AATGCAATTA
**
996124 GTGCATCGATGCATCCTTAT
1 GTGCATCGATGCATCCTGCT
**
996144 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-CTGCT
996165 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
* *
996185 CTGCATCTATGCA
1 GTGCATCGATGCA
996198 CGAAGGCTGC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:996277 original size:21 final size:21
Alignment explanation
Indices: 996253--996306 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
996243 GAAGGGGTAT
996253 CGATGCACCATGATAGTGCAC
1 CGATGCACCATGATAGTGCAC
996274 CGATGCACCATGATAGTGCAC
1 CGATGCACCATGATAGTGCAC
996295 CGATGCACCATG
1 CGATGCACCATG
996307 TTATGGGCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.19
Consensus pattern (21 bp):
CGATGCACCATGATAGTGCAC
Found at i:996369 original size:20 final size:22
Alignment explanation
Indices: 996331--996370 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
996321 TTTGAGTAGA
996331 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
996353 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
996371 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:996624 original size:34 final size:32
Alignment explanation
Indices: 996585--996654 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
996575 TTTTGTAAAG
* *
996585 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
996619 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
996651 GGGA
1 GGGA
996655 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:997687 original size:16 final size:16
Alignment explanation
Indices: 997666--997698 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
997656 TAATAAATAA
997666 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
997682 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
997698 A
1 A
997699 ATTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:997745 original size:31 final size:31
Alignment explanation
Indices: 997707--997783 Score: 154
Period size: 31 Copynumber: 2.5 Consensus size: 31
997697 CAATTTTTTT
997707 TTGTTCATGTTCGTTTATTAAAGAATATAAC
1 TTGTTCATGTTCGTTTATTAAAGAATATAAC
997738 TTGTTCATGTTCGTTTATTAAAGAATATAAC
1 TTGTTCATGTTCGTTTATTAAAGAATATAAC
997769 TTGTTCATGTTCGTT
1 TTGTTCATGTTCGTT
997784 CATTTAATAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.48
Consensus pattern (31 bp):
TTGTTCATGTTCGTTTATTAAAGAATATAAC
Found at i:997819 original size:16 final size:16
Alignment explanation
Indices: 997790--997878 Score: 137
Period size: 16 Copynumber: 5.7 Consensus size: 16
997780 CGTTCATTTA
997790 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
997804 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
*
997820 ATAAACGAACACGAAC
1 ATAAATGAACACGAAC
*
997836 ATAAATGAACAAGAAC
1 ATAAATGAACACGAAC
997852 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
*
997868 ATAAACGAACA
1 ATAAATGAACA
997879 TAAATGTTGG
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
14 6 0.09
15 2 0.03
16 60 0.88
ACGTcount: A:0.60, C:0.18, G:0.11, T:0.11
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:998601 original size:14 final size:14
Alignment explanation
Indices: 998584--998620 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
998574 GATTGGGTTA
* *
998584 AACATAAATGAATG
1 AACATAAACGAACG
998598 AACATAAACGAACG
1 AACATAAACGAACG
998612 AACATAAAC
1 AACATAAAC
998621 AAACATAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.59, C:0.16, G:0.11, T:0.14
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:999249 original size:23 final size:23
Alignment explanation
Indices: 999223--999267 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
999213 CTAAAAAACA
*
999223 TAATATTATATTATTAA-AATTAT
1 TAATAATATATT-TTAATAATTAT
999246 TAATAATATATTTTAATAATTA
1 TAATAATATATTTTAATAATTA
999268 ATATTCTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TAATAATATATTTTAATAATTAT
Found at i:999473 original size:19 final size:19
Alignment explanation
Indices: 999449--999489 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
999439 TGTTTTGGTG
999449 AGTTGTCAGCCACGTCGAA
1 AGTTGTCAGCCACGTCGAA
*
999468 AGTTGTCAGCCACGTCGGA
1 AGTTGTCAGCCACGTCGAA
999487 AGT
1 AGT
999490 CATCAATCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.22
Consensus pattern (19 bp):
AGTTGTCAGCCACGTCGAA
Found at i:1000608 original size:16 final size:15
Alignment explanation
Indices: 1000572--1000610 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
1000562 TTTCTGCGTG
1000572 AGGTTTAATTTGTTT
1 AGGTTTAATTTGTTT
*
1000587 ATGTTTAATTTAGTTT
1 AGGTTTAATTT-GTTT
1000603 AGGTTTAA
1 AGGTTTAA
1000611 GATTTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (15 bp):
AGGTTTAATTTGTTT
Found at i:1012354 original size:8 final size:8
Alignment explanation
Indices: 1012341--1012547 Score: 63
Period size: 7 Copynumber: 26.0 Consensus size: 8
1012331 TGAAGAAGAG
1012341 ATGAAAAA
1 ATGAAAAA
1012349 ATGAAAAGA
1 ATGAAAA-A
1012358 A--AAGAGAA
1 ATGAA-A-AA
1012366 AT-AAAAA
1 ATGAAAAA
*
1012373 ATGTTGAAAA
1 ATG--AAAAA
1012383 A-GAAAAA
1 ATGAAAAA
* *
1012390 AAGGA-AA
1 ATGAAAAA
1012397 ATGAGAAAA
1 ATGA-AAAA
1012406 ATAGAAGAAA
1 AT-GAA-AAA
1012416 A-G-AAAA
1 ATGAAAAA
1012422 ATGAAAAAA
1 ATG-AAAAA
*
1012431 ATGATAAATG
1 ATGA-AAA-A
*
1012441 ATAAAAAAA
1 AT-GAAAAA
*
1012450 ATGAAAAG
1 ATGAAAAA
1012458 A-G-AAAA
1 ATGAAAAA
1012464 A-GAGAAAA
1 ATGA-AAAA
*
1012472 AT-AGAAA
1 ATGAAAAA
1012479 AT-AAGAAA
1 ATGAA-AAA
1012487 ATGGAAGAAAA
1 AT-G-A-AAAA
1012498 ATG-AAAA
1 ATGAAAAA
1012505 ATGAAAAA
1 ATGAAAAA
1012513 ATG--AAA
1 ATGAAAAA
*
1012519 A-GGAAAA
1 ATGAAAAA
1012526 ATGAAAAA
1 ATGAAAAA
1012534 A-GAAAAA
1 ATGAAAAA
1012541 A-GAAAAA
1 ATGAAAAA
1012548 GGAAATAAAA
Statistics
Matches: 155, Mismatches: 14, Indels: 61
0.67 0.06 0.27
Matches are distributed among these distances:
5 1 0.01
6 13 0.08
7 48 0.31
8 45 0.29
9 23 0.15
10 17 0.11
11 7 0.05
12 1 0.01
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.10
Consensus pattern (8 bp):
ATGAAAAA
Found at i:1012389 original size:7 final size:7
Alignment explanation
Indices: 1012379--1012552 Score: 93
Period size: 7 Copynumber: 23.3 Consensus size: 7
1012369 AAAAATGTTG
1012379 AAAAAGAA
1 AAAAAG-A
1012387 AAAAAGGA
1 AAAAA-GA
*
1012395 AAATGAGA
1 AAA-AAGA
1012403 AAAATAGA
1 AAAA-AGA
1012411 AGAAAAGA
1 A-AAAAGA
*
1012419 AAAATGAA
1 AAAAAG-A
1012427 AAAAATGA
1 AAAAA-GA
* *
1012435 TAAATG-
1 AAAAAGA
*
1012441 ATAAA-A
1 AAAAAGA
*
1012447 AAAATGA
1 AAAAAGA
*
1012454 AAAGAGA
1 AAAAAGA
1012461 AAAAGAGA
1 AAAA-AGA
1012469 AAAATAGA
1 AAAA-AGA
1012477 AAATAAGA
1 AAA-AAGA
1012485 AAATGGAAGA
1 AAA---AAGA
*
1012495 AAAATGA
1 AAAAAGA
*
1012502 AAAATGA
1 AAAAAGA
1012509 AAAAATG-
1 AAAAA-GA
*
1012516 AAAAGGA
1 AAAAAGA
*
1012523 AAAATGA
1 AAAAAGA
1012530 AAAAAGA
1 AAAAAGA
1012537 AAAAAGA
1 AAAAAGA
*
1012544 AAAAGGA
1 AAAAAGA
1012551 AA
1 AA
1012553 TAAAAGGGGG
Statistics
Matches: 130, Mismatches: 22, Indels: 29
0.72 0.12 0.16
Matches are distributed among these distances:
6 6 0.05
7 59 0.45
8 51 0.39
9 7 0.05
10 7 0.05
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.09
Consensus pattern (7 bp):
AAAAAGA
Found at i:1012405 original size:16 final size:16
Alignment explanation
Indices: 1012400--1012547 Score: 93
Period size: 16 Copynumber: 9.4 Consensus size: 16
1012390 AAGGAAAATG
1012400 AGAAAAAT-AGAAGAAA
1 AGAAAAATGAGAA-AAA
1012416 AGAAAAATGA-AAAAA
1 AGAAAAATGAGAAAAA
* *
1012431 ATGATAAATGATAAAAA
1 A-GAAAAATGAGAAAAA
*
1012448 A-AATGAAAAGAGAAAAA
1 AGAA--AAATGAGAAAAA
1012465 GAGAAAAAT-AGAAAATA
1 -AGAAAAATGAGAAAA-A
1012482 AG-AAAATGGAAGAAAAA
1 AGAAAAAT-G-AGAAAAA
*
1012499 TGAAAAATGA-AAAAA
1 AGAAAAATGAGAAAAA
*
1012514 TG-AAAA-G-GAAAAA
1 AGAAAAATGAGAAAAA
*
1012527 TGAAAAA--AGAAAAA
1 AGAAAAATGAGAAAAA
1012541 AGAAAAA
1 AGAAAAA
1012548 GGAAATAAAA
Statistics
Matches: 110, Mismatches: 7, Indels: 32
0.74 0.05 0.21
Matches are distributed among these distances:
13 8 0.07
14 20 0.18
15 17 0.15
16 27 0.25
17 24 0.22
18 12 0.11
19 2 0.02
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (16 bp):
AGAAAAATGAGAAAAA
Found at i:1012430 original size:41 final size:40
Alignment explanation
Indices: 1012379--1012547 Score: 165
Period size: 41 Copynumber: 4.3 Consensus size: 40
1012369 AAAAATGTTG
*
1012379 AAAAAGAAAAAAAGGAAAATGAGAAAAATAGAAGAAAAGA
1 AAAAAGAAAAAAATGAAAATGAGAAAAATAGAAGAAAAGA
* *
1012419 AAAATGAAAAAAATGATAAATGATAAAAA-A-AATGAAAAGA
1 AAAAAGAAAAAAATGA-AAATGAGAAAAATAGAA-GAAAAGA
* * *
1012459 GAAAAAGAGAAAAATAGAAAATAAG-AAAATGGAAGAAAAATGA
1 -AAAAAGAAAAAAAT-GAAAATGAGAAAAATAGAAG-AAAA-GA
*
1012502 AAAATG-AAAAAATGAAAA-G-GAAAAAT-GAA-AAAAGA
1 AAAAAGAAAAAAATGAAAATGAGAAAAATAGAAGAAAAGA
1012537 AAAAAGAAAAA
1 AAAAAGAAAAA
1012548 GGAAATAAAA
Statistics
Matches: 107, Mismatches: 12, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
35 7 0.07
36 8 0.07
38 4 0.04
39 7 0.07
40 31 0.29
41 35 0.33
42 13 0.12
43 2 0.02
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (40 bp):
AAAAAGAAAAAAATGAAAATGAGAAAAATAGAAGAAAAGA
Found at i:1012449 original size:66 final size:66
Alignment explanation
Indices: 1012379--1012546 Score: 170
Period size: 66 Copynumber: 2.5 Consensus size: 66
1012369 AAAAATGTTG
* * *
1012379 AAAAAGAAAAAAAG-GAAAATGAGAAAAATAGAAGAA-AAGAAAAAT-GAA-AAAAATGATAAAT
1 AAAAAAAAAAAAAGAGAAAAAGAGAAAAATAGAA-AATAAG-AAAATGGAAGAAAAATGAAAAAT
1012440 GATA
64 GA-A
**
1012444 AAAAAAATGAAAAGAGAAAAAGAGAAAAATAGAAAATAAGAAAATGGAAGAAAAATGAAAAATGA
1 AAAAAAAAAAAAAGAGAAAAAGAGAAAAATAGAAAATAAGAAAATGGAAGAAAAATGAAAAATGA
1012509 A
66 A
*
1012510 AAAATGAAAAGGAAAAA-TGAAAAA-AGAAAAA-AGAAAA
1 AAAA--AAAA--AAAAAGAGAAAAAGAGAAAAATAGAAAA
1012547 AGGAAATAAA
Statistics
Matches: 87, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
65 18 0.21
66 29 0.33
67 20 0.23
68 10 0.11
69 6 0.07
70 4 0.05
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (66 bp):
AAAAAAAAAAAAAGAGAAAAAGAGAAAAATAGAAAATAAGAAAATGGAAGAAAAATGAAAAATGA
A
Found at i:1013957 original size:55 final size:55
Alignment explanation
Indices: 1013901--1014382 Score: 519
Period size: 55 Copynumber: 8.9 Consensus size: 55
1013891 GAAGCAAACC
* * * *
1013901 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTTTGAAGGACTAGAGAGCAGACC
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCAGACA
* *
1013956 CGTTT-TATTAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGT-TGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCAGACA
* * *
1014011 CGTTTGTTGAAGA----TCGAGTCCTATACTCTCTGAAGAAATAGGGAGC-GAACC
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCAG-ACA
** *
1014062 CGTTT-TATGAAGATTGTTCGAGTTCTATACTCTCTGAAAAAATAGGGAGCGGACA
1 CGTTTGT-TGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCAGACA
* *
1014117 CGTTTGTTGAAGA---TT-GAG-TCTTATACTCTCTGAAGGAATAGGGAGCATACC
1 CGTTTGTTGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGGGAGCAGACA
* * * *
1014168 CGTTTATTGAAGATTGTTCAAGTTATATACTCTCTGAAGGAATAGGGAAC-GTACA
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCAG-ACA
* * *
1014223 CGTTTTTTGAAGATTGTTCGAGTTCTATACTCCCTGAACGAATAGGGAGCAGACA
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCAGACA
* * * * *
1014278 CTTTTGCTGATGATTGTTCGAG-TCTTATACTCCCTGAACGAATAGGGAGCAGACA
1 CGTTTGTTGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGGGAGCAGACA
* * *
1014333 CATTTGCTAAAGATTGTTCGAG-TCTTATACTC-CTTGAAGGAATAGGGAGC
1 CGTTTGTTGAAGATTGTTCGAGTTC-TATACTCTC-TGAAGGAATAGGGAGC
1014383 GGACCCGTCA
Statistics
Matches: 369, Mismatches: 38, Indels: 40
0.83 0.09 0.09
Matches are distributed among these distances:
50 4 0.01
51 84 0.23
52 2 0.01
54 6 0.02
55 268 0.73
56 5 0.01
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.31
Consensus pattern (55 bp):
CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCAGACA
Found at i:1014090 original size:106 final size:107
Alignment explanation
Indices: 1013901--1014390 Score: 544
Period size: 106 Copynumber: 4.5 Consensus size: 107
1013891 GAAGCAAACC
* * * * *
1013901 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTTTGAAGGACTAGAGAGCAGACCCGTTTTATTA
1 CGTTTGTTGAAGA---TTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACCCGTTTTATGA
1013966 AGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
63 AGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
*
1014011 CGTTTGTTGAAGA-TCGAGTCCTATACTCTCTGAAGAAATAGGGAGC-GAACCCGTTTTATGAAG
1 CGTTTGTTGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAG-ACCCGTTTTATGAAG
**
1014074 ATTGTTCGAGTTCTATACTCTCTGAAAAAATAGGGAGCGGACA
65 ATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
* *
1014117 CGTTTGTTGAAGATT-GAGTCTTATACTCTCTGAAGGAATAGGGAGCATACCCG-TTTATTGAAG
1 CGTTTGTTGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACCCGTTTTA-TGAAG
* * * *
1014180 ATTGTTCAAGTTATATACTCTCTGAAGGAATAGGGAACGTACA
65 ATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * * * *
1014223 CGTTTTTTGAAGATTGTTCGAGTTCTATACTCCCTGAACGAATAGGGAGCAGACAC-TTTTGCTG
1 CGTTTGTTGAAGA---TTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACCCGTTTT-ATG
* * * *
1014287 ATGATTGTTCGAG-TCTTATACTCCCTGAACGAATAGGGAGCAGACA
62 AAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGGGAGCGGACA
* * * * *
1014333 CATTTGCTAAAGATTGTTCGAGTCTTATACTC-CTTGAAGGAATAGGGAGCGGACCCGT
1 CGTTTGTTGAAGA---TTCGAGTCCTATACTCTC-TGAAGGAATAGGGAGCAGACCCGT
1014391 CATTCAAAGA
Statistics
Matches: 325, Mismatches: 42, Indels: 25
0.83 0.11 0.06
Matches are distributed among these distances:
105 5 0.02
106 184 0.57
107 1 0.00
109 4 0.01
110 130 0.40
111 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (107 bp):
CGTTTGTTGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACCCGTTTTATGAAGA
TTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
Found at i:1014199 original size:161 final size:161
Alignment explanation
Indices: 1013897--1014390 Score: 547
Period size: 161 Copynumber: 3.0 Consensus size: 161
1013887 TAGTGAAGCA
* * * * *
1013897 AACCCGTTTGTTGAAGATTGTTCGAGTTCTATACTCTTTGAAGGACTAGAGAGCAGACCCGTTT-
1 AACCCGTTT-TTGAAGATTGTTCGAGTTCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTG
* *
1013961 TATTAAGATTGTTCGAGT-TCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGA-
65 T-TGAAGA-T-TTCGAGTCT-TATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGAT
* *
1014024 ---TCGAGTCCTATACTCTCTGAAGAAATAGGGAGCG
126 TGTTCGAGT-TTATACTCTCTGAAGGAATAGGGAGCG
* *
1014058 AACCCGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAAAAATAGGGAGCGGACACGTTTG
1 AACCCGTTTT-TGAAGATTGTTCGAGTTCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTG
* * *
1014123 TTGAAGA-TT-GAGTCTTATACTCTCTGAAGGAATAGGGAGCATACCCGTTTATTGAAGATTGTT
65 TTGAAGATTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGTT
* *
1014186 CAAGTTATATACTCTCTGAAGGAATAGGGAACG
130 CGAGTT-TATACTCTCTGAAGGAATAGGGAGCG
* * * * *
1014219 TACACGTTTTTTGAAGATTGTTCGAGTTCTATACTCCCTGAACGAATAGGGAGCAGACACTTTTG
1 AACCCG-TTTTTGAAGATTGTTCGAGTTCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTG
* * * * * * *
1014284 CTGATGATTGTTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACATTTGCTAAAGATTG
65 TTGAAGA-T-TTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTG
1014349 TTCGAGTCTTATACTC-CTTGAAGGAATAGGGAGCG
128 TTCGAGT-TTATACTCTC-TGAAGGAATAGGGAGCG
*
1014384 GACCCGT
1 AACCCGT
1014391 CATTCAAAGA
Statistics
Matches: 281, Mismatches: 37, Indels: 27
0.81 0.11 0.08
Matches are distributed among these distances:
157 43 0.15
158 3 0.01
160 1 0.00
161 147 0.52
162 5 0.02
164 4 0.01
165 77 0.27
166 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (161 bp):
AACCCGTTTTTGAAGATTGTTCGAGTTCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTTGT
TGAAGATTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGTTC
GAGTTTATACTCTCTGAAGGAATAGGGAGCG
Found at i:1015574 original size:16 final size:15
Alignment explanation
Indices: 1015538--1015576 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
1015528 TTTCTGTGTG
1015538 AGGTTTAATTTGTTT
1 AGGTTTAATTTGTTT
*
1015553 ATGTTTAATTTAGTTT
1 AGGTTTAATTT-GTTT
1015569 AGGTTTAA
1 AGGTTTAA
1015577 GATTTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (15 bp):
AGGTTTAATTTGTTT
Found at i:1016940 original size:29 final size:30
Alignment explanation
Indices: 1016874--1016941 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
1016864 TTTCGGCAAG
*
1016874 TGGTATAATTGAAACGAACATCAAAGTTCAG
1 TGGTATAATTGAAAC-AACATCAAAGTTCAC
* *
1016905 TGTTATAATTGAAA-AA-ATTGAAAGTTCAC
1 TGGTATAATTGAAACAACA-TCAAAGTTCAC
1016934 TGGTATAA
1 TGGTATAA
1016942 ACGATACATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 1 0.03
29 18 0.56
31 13 0.41
ACGTcount: A:0.43, C:0.09, G:0.18, T:0.31
Consensus pattern (30 bp):
TGGTATAATTGAAACAACATCAAAGTTCAC
Found at i:1021205 original size:11 final size:11
Alignment explanation
Indices: 1021189--1021228 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1021179 CTGAGCTGAG
1021189 CCGTTGACCGA
1 CCGTTGACCGA
1021200 CCGTTGACC-A
1 CCGTTGACCGA
*
1021210 CCTTTGACCGA
1 CCGTTGACCGA
*
1021221 CCATTGAC
1 CCGTTGAC
1021229 TTTTTTCGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.20, C:0.38, G:0.20, T:0.23
Consensus pattern (11 bp):
CCGTTGACCGA
Found at i:1022911 original size:19 final size:21
Alignment explanation
Indices: 1022887--1022933 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
1022877 CACTCTGATT
1022887 TCTGTTTTGATTTATG-T-TC
1 TCTGTTTTGATTTATGATATC
* *
1022906 TCTGTTCTGATTTCTGATATC
1 TCTGTTTTGATTTATGATATC
1022927 TCTGTTT
1 TCTGTTT
1022934 ATTGACTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 14 0.61
20 1 0.04
21 8 0.35
ACGTcount: A:0.11, C:0.15, G:0.15, T:0.60
Consensus pattern (21 bp):
TCTGTTTTGATTTATGATATC
Found at i:1028620 original size:23 final size:21
Alignment explanation
Indices: 1028575--1028621 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
1028565 AACTTTAAAA
*
1028575 TTATCTTTTTAAAATAAATTT
1 TTATCTTTTTAAAAAAAATTT
*
1028596 TTATTTTTTTAAAAAATAATGTT
1 TTATCTTTTTAAAAAA-AAT-TT
1028619 TTA
1 TTA
1028622 ATTGTTCGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 14 0.64
22 3 0.14
23 5 0.23
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TTATCTTTTTAAAAAAAATTT
Found at i:1031869 original size:30 final size:30
Alignment explanation
Indices: 1031829--1031898 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
1031819 TTTAAGTTAG
*
1031829 AGGGGACGAACTTAAATTTATAAAATTTCAA
1 AGGGG-CGAACTTAAACTTATAAAATTTCAA
* * *
1031860 AGGGGCGAACTTGAACTTATAAAATTTTAG
1 AGGGGCGAACTTAAACTTATAAAATTTCAA
1031890 AGGGGCGAA
1 AGGGGCGAA
1031899 AACAGGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
30 30 0.86
31 5 0.14
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.26
Consensus pattern (30 bp):
AGGGGCGAACTTAAACTTATAAAATTTCAA
Found at i:1036774 original size:15 final size:15
Alignment explanation
Indices: 1036754--1036813 Score: 68
Period size: 15 Copynumber: 3.9 Consensus size: 15
1036744 AAAAACCGGG
1036754 TATCGGGTACCCGAT
1 TATCGGGTACCCGAT
*
1036769 TATCGGGTACCCGCAA
1 TATCGGGTACCCG-AT
*
1036785 AATCCGGGTACCCGAT
1 TAT-CGGGTACCCGAT
1036801 TA-CTGGGTACCCG
1 TATC-GGGTACCCG
1036814 TAACATCCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
14 1 0.03
15 22 0.58
16 5 0.13
17 10 0.26
ACGTcount: A:0.22, C:0.30, G:0.27, T:0.22
Consensus pattern (15 bp):
TATCGGGTACCCGAT
Found at i:1036798 original size:32 final size:32
Alignment explanation
Indices: 1036757--1036825 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
1036747 AACCGGGTAT
1036757 CGGGTACCCGATTA-TCGGGTACCCGCAAAATC
1 CGGGTACCCGATTACT-GGGTACCCGCAAAATC
* *
1036789 CGGGTACCCGATTACTGGGTACCCGTAACATC
1 CGGGTACCCGATTACTGGGTACCCGCAAAATC
1036821 CGGGT
1 CGGGT
1036826 CGGGACACGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 33 0.97
33 1 0.03
ACGTcount: A:0.22, C:0.30, G:0.28, T:0.20
Consensus pattern (32 bp):
CGGGTACCCGATTACTGGGTACCCGCAAAATC
Found at i:1037250 original size:30 final size:30
Alignment explanation
Indices: 1037191--1037319 Score: 145
Period size: 30 Copynumber: 4.3 Consensus size: 30
1037181 CTCGAAGGAC
* * *
1037191 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCATAGGTCATAAAGATCCTCGGTAA
1037220 CTATCCATAGGTCATAAAGATCCTCGGTAA
1 CTATCCATAGGTCATAAAGATCCTCGGTAA
* *
1037250 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCATAGGTCATAAAGATCCTCGGTAA
* * * *
1037280 CTGTCCATAGGTCCA-GAAGAACCTAGGTAAA
1 CTATCCATAGGT-CATAAAGATCCTCGGT-AA
1037311 CTATCCATA
1 CTATCCATA
1037320 TGTCTCGAAA
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
29 18 0.21
30 57 0.66
31 12 0.14
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (30 bp):
CTATCCATAGGTCATAAAGATCCTCGGTAA
Found at i:1041586 original size:15 final size:15
Alignment explanation
Indices: 1041557--1041589 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1041547 AGAAAATACA
1041557 AAAAAGATAAATCCT
1 AAAAAGATAAATCCT
*
1041572 AAAAAGATAATTCCT
1 AAAAAGATAAATCCT
1041587 AAA
1 AAA
1041590 CTTGAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.61, C:0.12, G:0.06, T:0.21
Consensus pattern (15 bp):
AAAAAGATAAATCCT
Found at i:1051744 original size:40 final size:40
Alignment explanation
Indices: 1051624--1051749 Score: 193
Period size: 40 Copynumber: 3.2 Consensus size: 40
1051614 TTATAATATA
1051624 TATGTGTAATACACTTCGGTGTATATGGTGGGCACGACCT
1 TATGTGTAATACACTTCGGTGTATATGGTGGGCACGACCT
* *
1051664 TATGTGTAATACACTAC-G-ATATATGGTGGGCACGACCT
1 TATGTGTAATACACTTCGGTGTATATGGTGGGCACGACCT
* * *
1051702 TATGTGTAATTCACTTCGGTGTATATGGTGGGAACGAACT
1 TATGTGTAATACACTTCGGTGTATATGGTGGGCACGACCT
1051742 TATGTGTA
1 TATGTGTA
1051750 GCACTACGGT
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
38 34 0.44
39 2 0.03
40 41 0.53
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.33
Consensus pattern (40 bp):
TATGTGTAATACACTTCGGTGTATATGGTGGGCACGACCT
Found at i:1059024 original size:40 final size:40
Alignment explanation
Indices: 1058972--1059130 Score: 282
Period size: 40 Copynumber: 4.0 Consensus size: 40
1058962 TGCAGGTTTA
*
1058972 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTT
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1059012 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
1059052 TAATACACTACGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
1059092 TAATACACTTCGGTGTATATGGTGGGAACGAACTTATGT
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGT
1059131 TTAGTACTAC
Statistics
Matches: 114, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 114 1.00
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:1065977 original size:20 final size:20
Alignment explanation
Indices: 1065952--1066008 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
1065942 CTCTCAAGGG
1065952 GTATCGATACTCGTGGTCTA
1 GTATCGATACTCGTGGTCTA
* ** **
1065972 GTATCGATAATCAAGGGGTA
1 GTATCGATACTCGTGGTCTA
*
1065992 GTATCGATACTGGTGGT
1 GTATCGATACTCGTGGT
1066009 AATTTTCAGA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.14, G:0.30, T:0.32
Consensus pattern (20 bp):
GTATCGATACTCGTGGTCTA
Found at i:1066711 original size:15 final size:15
Alignment explanation
Indices: 1066693--1066724 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1066683 TAAATTCAAG
1066693 TTTAGGAATTATCTT
1 TTTAGGAATTATCTT
*
1066708 TTTAGGATTTATCTT
1 TTTAGGAATTATCTT
1066723 TT
1 TT
1066725 GTATTTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.06, G:0.12, T:0.59
Consensus pattern (15 bp):
TTTAGGAATTATCTT
Found at i:1084358 original size:39 final size:39
Alignment explanation
Indices: 1084304--1084394 Score: 137
Period size: 39 Copynumber: 2.3 Consensus size: 39
1084294 AAAATAGCAA
** *
1084304 TAGTTTAGATTAACTAGAGTTCTATCTTACTTGATTTAG
1 TAGTTTAGATTAACTAGAACTCTATCGTACTTGATTTAG
*
1084343 TAGTTTAGATTAACTAGAACTCTATCGTATTTGATTTAG
1 TAGTTTAGATTAACTAGAACTCTATCGTACTTGATTTAG
*
1084382 TAGTTTAAATTAA
1 TAGTTTAGATTAA
1084395 TTATAACTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (39 bp):
TAGTTTAGATTAACTAGAACTCTATCGTACTTGATTTAG
Found at i:1088501 original size:17 final size:17
Alignment explanation
Indices: 1088479--1088536 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
1088469 GGTAAAGTTG
1088479 AAAAGATTTAATAAAAT
1 AAAAGATTTAATAAAAT
*
1088496 AAAAGATAATAAT-AAAT
1 AAAAGAT-TTAATAAAAT
*
1088513 AAAAGGGAAATTAATAAAAT
1 AAAA--G-ATTTAATAAAAT
1088533 AAAA
1 AAAA
1088537 TAAAATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 15 0.45
18 4 0.12
19 5 0.15
20 9 0.27
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (17 bp):
AAAAGATTTAATAAAAT
Found at i:1088510 original size:18 final size:17
Alignment explanation
Indices: 1088487--1088548 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 17
1088477 TGAAAAGATT
1088487 TAATAAAATAAAAGATAA
1 TAATAAAATAAAAGA-AA
1088505 TAAT-AAATAAAAGGGAAA
1 TAATAAAATAAAA--GAAA
*
1088523 TTAATAAAATAAAATAAAA
1 -TAATAAAATAAAA-GAAA
1088542 TAATAAA
1 TAATAAA
1088549 TAATAGTAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 8 0.21
18 13 0.34
19 9 0.24
20 8 0.21
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (17 bp):
TAATAAAATAAAAGAAA
Found at i:1097330 original size:29 final size:29
Alignment explanation
Indices: 1097287--1097369 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
1097277 CTCACTTAGC
1097287 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
1097317 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
*
1097346 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
1097370 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:1102024 original size:29 final size:29
Alignment explanation
Indices: 1101988--1102063 Score: 143
Period size: 29 Copynumber: 2.6 Consensus size: 29
1101978 AACTAAATAT
1101988 ATGTAAGCAATGACATCATTACTTAAATG
1 ATGTAAGCAATGACATCATTACTTAAATG
*
1102017 ATGTAAGCAATGACATCTTTACTTAAATG
1 ATGTAAGCAATGACATCATTACTTAAATG
1102046 ATGTAAGCAATGACATCA
1 ATGTAAGCAATGACATCA
1102064 ATTTAGTTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (29 bp):
ATGTAAGCAATGACATCATTACTTAAATG
Found at i:1104316 original size:13 final size:15
Alignment explanation
Indices: 1104290--1104336 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 15
1104280 GTCGATAGAT
1104290 TATTTAA-AAAATTA
1 TATTTAAGAAAATTA
1104304 TATTT-AG-AAATTA
1 TATTTAAGAAAATTA
*
1104317 TTTTTAAGATAAATTA
1 TATTTAAGA-AAATTA
1104333 TATT
1 TATT
1104337 AGTGCTCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 11 0.41
14 7 0.26
16 9 0.33
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (15 bp):
TATTTAAGAAAATTA
Found at i:1104664 original size:6 final size:6
Alignment explanation
Indices: 1104653--1104684 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1104643 TCCTCTTTCG
1104653 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT AT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT AT
1104685 AAATTAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATTTAT
Found at i:1108365 original size:59 final size:59
Alignment explanation
Indices: 1108281--1108395 Score: 169
Period size: 59 Copynumber: 1.9 Consensus size: 59
1108271 AAACTATGAC
** *
1108281 TCTCATTTTAAATTAGTCTCTAAACTTTTAAATATTATAATTTCATCCTCAAACTAATA
1 TCTCATTCCAAATTAGTCTCTAAACTTTTAAACATTATAATTTCATCCTCAAACTAATA
* *
1108340 TCTCATTCCAAATTAGTC-CTCAAACTTTTGAACATTCTAATTTCATCCTCAAACTA
1 TCTCATTCCAAATTAGTCTCT-AAACTTTTAAACATTATAATTTCATCCTCAAACTA
1108396 TGACCCTTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
58 2 0.04
59 48 0.96
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.41
Consensus pattern (59 bp):
TCTCATTCCAAATTAGTCTCTAAACTTTTAAACATTATAATTTCATCCTCAAACTAATA
Found at i:1114245 original size:21 final size:21
Alignment explanation
Indices: 1114216--1114268 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1114206 ATTCTGATTA
1114216 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
1114237 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
1114258 TCGCAATGCGA
1 TCGCATTGCGA
1114269 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1114283 original size:20 final size:20
Alignment explanation
Indices: 1114258--1114349 Score: 139
Period size: 20 Copynumber: 4.5 Consensus size: 20
1114248 TTTTCCTAAT
1114258 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* **
1114278 TCGCAACGCGAATTTGGTAAA
1 TCGCAATGCGAA-TACGTAAA
*
1114299 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
1114319 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1114339 TCGCAATGCGA
1 TCGCAATGCGA
1114350 TTTACATAGC
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 47 0.75
21 16 0.25
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1114304 original size:41 final size:40
Alignment explanation
Indices: 1114258--1114349 Score: 139
Period size: 41 Copynumber: 2.3 Consensus size: 40
1114248 TTTTCCTAAT
**
1114258 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAA-TACGTAAA
* *
1114299 TCGCAATGCGATTACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATACGTAAA
1114339 TCGCAATGCGA
1 TCGCAATGCGA
1114350 TTTACATAGC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 17 0.36
41 30 0.64
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.22
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATACGTAAA
Found at i:1114557 original size:22 final size:21
Alignment explanation
Indices: 1114529--1114590 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
1114519 GGCGACATCC
1114529 GTCCCCATCTCTGACGAAATCA
1 GTCCCCATCTC-GACGAAATCA
*
1114551 GTCCCCA---CGACGATATCA
1 GTCCCCATCTCGACGAAATCA
* *
1114569 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCT-CGACGAAATCA
1114591 TTCACGGTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 15 0.47
19 1 0.03
22 16 0.50
ACGTcount: A:0.26, C:0.37, G:0.16, T:0.21
Consensus pattern (21 bp):
GTCCCCATCTCGACGAAATCA
Found at i:1114999 original size:20 final size:20
Alignment explanation
Indices: 1114926--1115015 Score: 94
Period size: 20 Copynumber: 4.5 Consensus size: 20
1114916 GCAATTCTGT
1114926 TGTTGCGATTTTCATTTT--
1 TGTTGCGATTTTCATTTTCG
** **
1114944 TCGTTGCGATAGTCAAATTCG
1 T-GTTGCGATTTTCATTTTCG
* **
1114965 CGTTGCGATAGTCATTTTCG
1 TGTTGCGATTTTCATTTTCG
1114985 TGTTGCGATTTTCATTTTCG
1 TGTTGCGATTTTCATTTTCG
1115005 TGTTGCGATTT
1 TGTTGCGATTT
1115016 AAAGTTTTGC
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
18 1 0.02
19 13 0.22
20 45 0.76
ACGTcount: A:0.14, C:0.16, G:0.22, T:0.48
Consensus pattern (20 bp):
TGTTGCGATTTTCATTTTCG
Found at i:1116925 original size:20 final size:20
Alignment explanation
Indices: 1116900--1117009 Score: 166
Period size: 20 Copynumber: 5.5 Consensus size: 20
1116890 AGAATAGTTT
1116900 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
1116920 ACTATCACAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
1116940 ACTATCGCAACGCGAAAATA
1 ACTATCGCAATGCGAAAATG
1116960 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
1116980 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
1117000 ACTATCGCAA
1 ACTATCGCAA
1117010 CGAAAGAATT
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 82 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:1117081 original size:20 final size:20
Alignment explanation
Indices: 1117056--1117122 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
1117046 GATTCTCTCG
**
1117056 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
1117076 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1117096 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
1117116 TTGCGAT
1 TTGCGAT
1117123 TTTGTTGTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1119316 original size:33 final size:34
Alignment explanation
Indices: 1119259--1119354 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 34
1119249 AAAACAGACT
* * ** *
1119259 ATCGCAACGCGGAAATGACTATCGCAATGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
*
1119293 ATCGCAATGC-AAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
*
1119326 ATCGCAATTCGAAAATGAAAATCGCAACG
1 ATCGCAATGCGAAAATGAAAATCGCAACG
1119355 CGAAATTAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 27 0.50
34 27 0.50
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.16
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:1119433 original size:19 final size:19
Alignment explanation
Indices: 1119364--1119450 Score: 94
Period size: 19 Copynumber: 4.8 Consensus size: 19
1119354 GCGAAATTAG
* *
1119364 TTTCGCGTTGCTATTTTCA
1 TTTCGCATTGCGATTTTCA
1119383 TTTTCGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
* *
1119401 -CTCG--TTGCGCTTTTCA
1 TTTCGCATTGCGATTTTCA
1119417 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
1119436 TTTCGCATTGCGATT
1 TTTCGCATTGCGATT
1119451 CTCTTGTTGC
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
14 5 0.09
16 7 0.12
17 3 0.05
18 4 0.07
19 26 0.46
20 11 0.20
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.47
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:1119500 original size:20 final size:20
Alignment explanation
Indices: 1119475--1119557 Score: 114
Period size: 20 Copynumber: 4.2 Consensus size: 20
1119465 CTCTCATTGT
* *
1119475 GATAGTCGTTTCTGCGTTGC
1 GATAGTCATTTCCGCGTTGC
*
1119495 GATAGTCAATTCCGCGTTGC
1 GATAGTCATTTCCGCGTTGC
*
1119515 GATAGTCATTTCCGTGTTGC
1 GATAGTCATTTCCGCGTTGC
1119535 GATAGTCATATT-CGCGTTGC
1 GATAGTCAT-TTCCGCGTTGC
1119555 GAT
1 GAT
1119558 TTCTGCGTTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 54 0.96
21 2 0.04
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.36
Consensus pattern (20 bp):
GATAGTCATTTCCGCGTTGC
Found at i:1122022 original size:24 final size:24
Alignment explanation
Indices: 1121988--1122041 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1121978 CTAAAAAATC
1121988 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1122012 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1122036 ATCAAA
1 ATCAAA
1122042 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1122055 original size:24 final size:24
Alignment explanation
Indices: 1121988--1122055 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1121978 CTAAAAAATC
* * *
1121988 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1122012 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1122036 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1122056 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1122928 original size:20 final size:20
Alignment explanation
Indices: 1122905--1123028 Score: 151
Period size: 20 Copynumber: 6.2 Consensus size: 20
1122895 AATCTTGTTA
1122905 CGATTTACAG-ATTCGCATTG
1 CGATTTAC-GTATTCGCATTG
1122925 CGATTTACGTATTCGCATTG
1 CGATTTACGTATTCGCATTG
*
1122945 CAATTTACGTATTCGCATTG
1 CGATTTACGTATTCGCATTG
*
1122965 CGATTTACGTAATCGCATTG
1 CGATTTACGTATTCGCATTG
* ** * * *
1122985 CGATTTTCCAAATTCACGTTT
1 CGA-TTTACGTATTCGCATTG
1123006 CGATTTACGTATTCGCATTG
1 CGATTTACGTATTCGCATTG
1123026 CGA
1 CGA
1123029 ATTAGGAAAA
Statistics
Matches: 86, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
19 1 0.01
20 72 0.84
21 13 0.15
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (20 bp):
CGATTTACGTATTCGCATTG
Found at i:1123049 original size:21 final size:21
Alignment explanation
Indices: 1123025--1123070 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1123015 TATTCGCATT
1123025 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
1123046 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1123067 GCGA
1 GCGA
1123071 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Done.