Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001836.1 Hibiscus syriacus cultivar Beakdansim tig00003715_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: 2428596
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 12
Found at i:965305 original size:65 final size:63
Alignment explanation
Indices: 965186--965395 Score: 221
Period size: 65 Copynumber: 3.3 Consensus size: 63
965176 TTTTTCAGAA
* * *
965186 TGATGCACCGATGCATCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGC
1 TGATGCATCGATGCA-CAA-CCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATGC
965248 ATT
61 ATT
* *
965251 TCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCAT
965315 T
63 T
* * * * *
965316 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
965380 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
965396 TCTTAGTGCA
Statistics
Matches: 125, Mismatches: 12, Indels: 18
0.81 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 47 0.38
65 69 0.55
66 5 0.04
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.26
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:965395 original size:17 final size:19
Alignment explanation
Indices: 965367--965415 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
965357 TATTTTGAAA
965367 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
965385 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
965404 CACCGATGCACT
1 CATCGATGCACT
965416 AAGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:966383 original size:9 final size:9
Alignment explanation
Indices: 966355--966384 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
966345 TTTCCTTTAA
966355 TCTTTTTTT
1 TCTTTTTTT
*
966364 TATTTTTTT
1 TCTTTTTTT
966373 TCTTTTTTT
1 TCTTTTTTT
966382 TCT
1 TCT
966385 GATGGATGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:968897 original size:20 final size:20
Alignment explanation
Indices: 968872--968911 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
968862 AATATAAATA
*
968872 CAAATGTAAAGATGCGAATG
1 CAAATGCAAAGATGCGAATG
* *
968892 CAAATGCAAATATGTGAATG
1 CAAATGCAAAGATGCGAATG
968912 TAAAATGAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.10, G:0.23, T:0.23
Consensus pattern (20 bp):
CAAATGCAAAGATGCGAATG
Found at i:969531 original size:44 final size:44
Alignment explanation
Indices: 969477--969571 Score: 172
Period size: 44 Copynumber: 2.2 Consensus size: 44
969467 TCAACGAATT
* *
969477 GTCCTTTGTTGGTGTCCTCTTGGACTGTCAAACCCTTAATCCTG
1 GTCCATTGTTGGTGTCCTCTTGGACTGTCAAACCCTCAATCCTG
969521 GTCCATTGTTGGTGTCCTCTTGGACTGTCAAACCCTCAATCCTG
1 GTCCATTGTTGGTGTCCTCTTGGACTGTCAAACCCTCAATCCTG
969565 GTCCATT
1 GTCCATT
969572 ACAGACTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.15, C:0.28, G:0.20, T:0.37
Consensus pattern (44 bp):
GTCCATTGTTGGTGTCCTCTTGGACTGTCAAACCCTCAATCCTG
Found at i:969863 original size:45 final size:45
Alignment explanation
Indices: 969792--969893 Score: 132
Period size: 45 Copynumber: 2.2 Consensus size: 45
969782 ATGTGAGGAA
* * *
969792 AAATATAAAAGAAATAAATAATGTACAACACACAAATATAATCTTT
1 AAATAT-AAAGAAACAAATAATGTACAACAAAAAAATATAATCTTT
* * *
969838 AAATCTAAAGAAACAAATAATGTACAACAAAAAAATTTATTCTTT
1 AAATATAAAGAAACAAATAATGTACAACAAAAAAATATAATCTTT
*
969883 CAATATAAAGA
1 AAATATAAAGA
969894 CATATAATTA
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 43 0.90
46 5 0.10
ACGTcount: A:0.58, C:0.11, G:0.05, T:0.26
Consensus pattern (45 bp):
AAATATAAAGAAACAAATAATGTACAACAAAAAAATATAATCTTT
Found at i:970806 original size:16 final size:16
Alignment explanation
Indices: 970785--970815 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
970775 TCACAGGACT
970785 AAAATAAAATGAATAG
1 AAAATAAAATGAATAG
*
970801 AAAATAAAGTGAATA
1 AAAATAAAATGAATA
970816 AAAGTATTGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (16 bp):
AAAATAAAATGAATAG
Found at i:977420 original size:14 final size:14
Alignment explanation
Indices: 977397--977434 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
977387 TTCTGTCTAA
*
977397 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
977410 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
977425 TGCAGGGATT
1 TGCAGGGATT
977435 ACTTCCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:980858 original size:211 final size:212
Alignment explanation
Indices: 980494--980913 Score: 670
Period size: 211 Copynumber: 2.0 Consensus size: 212
980484 CAAACATTAA
980494 ATTTGAAAAGTTCATGAAATCATAAACTAAAAATAATGTGAAACGTAACCCATAAATTAATTTTT
1 ATTTGAAAAGTTCATGAAATCATAAACTAAAAATAATGTGAAACGTAACCCATAAATTAATTTTT
980559 ACTCGAAAGGACAAAGACAAATATAACTTCTTTCGCATAGGCTCTCTCTCAAGTACAAATCATAC
66 ACTCGAAAGGACAAAGACAAATATAACTTCTTTCGCATAGGCTCTCTCTCAAGTACAAATCATAC
*
980624 ATATAGAGATCGATAAACTATTAAATATT-AAAAAAATACAAACACTTATA-TAATAACAGACAA
131 ACATAGAGATCGATAAACTATTAAATATTAAAAAAAATACAAACACTTATATTAATAACAGACAA
980687 AATAATAAACTATTAAAT
196 AATAATAAA-TATTAAAT
*
980705 ATTTGAAAA-TGTCATGAAATCATAGACTAAAAATAATGTGAAACGTAACCCATAAATTAATTTT
1 ATTTGAAAAGT-TCATGAAATCATAAACTAAAAATAATGTGAAACGTAACCCATAAATTAATTTT
* * *
980769 TACTTGAAAGGACATATG-C-AATATAAATTTCTTTCGCATAGGCTCTCTCTCAAGTACAAATCA
65 TACTCGAAAGGACA-AAGACAAATAT-AACTTCTTTCGCATAGGCTCTCTCTCAAGTACAAATCA
* * *
980832 TACACATAGATATCGATAAACTATTAAATATTCAAAAAAAATATAAACACTTGTATTAATAACAG
128 TACACATAGAGATCGATAAACTATTAAATATT-AAAAAAAATACAAACACTTATATTAATAACAG
* *
980897 AGAAGATAATAAATATT
192 ACAAAATAATAAATATT
980914 GATCATTTAA
Statistics
Matches: 193, Mismatches: 10, Indels: 10
0.91 0.05 0.05
Matches are distributed among these distances:
210 6 0.03
211 142 0.74
212 2 0.01
213 23 0.12
214 20 0.10
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.29
Consensus pattern (212 bp):
ATTTGAAAAGTTCATGAAATCATAAACTAAAAATAATGTGAAACGTAACCCATAAATTAATTTTT
ACTCGAAAGGACAAAGACAAATATAACTTCTTTCGCATAGGCTCTCTCTCAAGTACAAATCATAC
ACATAGAGATCGATAAACTATTAAATATTAAAAAAAATACAAACACTTATATTAATAACAGACAA
AATAATAAATATTAAAT
Found at i:981885 original size:21 final size:20
Alignment explanation
Indices: 981839--981894 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
981829 AGCTTACTAG
*
981839 TTTTTCAAATTGACATTTAA
1 TTTTTCAAATTGACCTTTAA
* *
981859 TATTTCAAACTGACCTCTTAA
1 TTTTTCAAATTGACCT-TTAA
981880 TTTTTCAAATTGACC
1 TTTTTCAAATTGACC
981895 ATTCATTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (20 bp):
TTTTTCAAATTGACCTTTAA
Found at i:983808 original size:6 final size:6
Alignment explanation
Indices: 983797--983838 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
983787 AATCTTTTAC
983797 ATGAAA ATGAAA ATGAAA ATGAAA ATGAAA ATGAAA ATGAAA
1 ATGAAA ATGAAA ATGAAA ATGAAA ATGAAA ATGAAA ATGAAA
983839 TGTAAAAGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (6 bp):
ATGAAA
Found at i:990591 original size:15 final size:15
Alignment explanation
Indices: 990571--990615 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 15
990561 TAACCGGTTT
990571 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
990586 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
990603 CGGTTATAAAAAA
1 CGGTTTTAAAAAA
990616 TCGATTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 11 0.44
17 14 0.56
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:990599 original size:17 final size:17
Alignment explanation
Indices: 990574--990607 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
990564 CCGGTTTCGG
990574 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
990591 TTTTTAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
990608 ATAAAAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:991029 original size:13 final size:13
Alignment explanation
Indices: 991008--991062 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
990998 CTCAAGTATA
*
991008 AATTCAAATACTT
1 AATTGAAATACTT
991021 AATTGAAATACTT
1 AATTGAAATACTT
* *
991034 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
991048 AATTGAAATACTT
1 AATTGAAATACTT
991061 AA
1 AA
991063 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:991128 original size:32 final size:33
Alignment explanation
Indices: 991048--991145 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
991038 AACTCAACAT
* * *
991048 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
991081 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
991114 AATTC-AATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
991145 A
1 A
991146 TTGAAACAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
31 12 0.19
32 15 0.24
33 35 0.56
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:991165 original size:20 final size:20
Alignment explanation
Indices: 991135--991179 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
991125 TAAAAACTTC
991135 AAGTT-CGATAATTGAAACA
1 AAGTTACGATAATTGAAACA
*
991154 AAGTTACGATAATTGAAATA
1 AAGTTACGATAATTGAAACA
991174 AAGTTA
1 AAGTTA
991180 TAAAATAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.29
Consensus pattern (20 bp):
AAGTTACGATAATTGAAACA
Found at i:993451 original size:12 final size:12
Alignment explanation
Indices: 993434--993477 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
993424 GGATAAAAAT
993434 CGGTTTTTTAAC
1 CGGTTTTTTAAC
993446 CGGTTTTTTTCAAAC
1 CGG-TTTTTT--AAC
*
993461 CGGTTTTTTATC
1 CGGTTTTTTAAC
993473 CGGTT
1 CGGTT
993478 AAAAAACCGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 10 0.36
13 6 0.21
14 6 0.21
15 6 0.21
ACGTcount: A:0.14, C:0.18, G:0.18, T:0.50
Consensus pattern (12 bp):
CGGTTTTTTAAC
Found at i:993546 original size:20 final size:20
Alignment explanation
Indices: 993521--993560 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
993511 GTTAAAATAA
* *
993521 CCGGTTTAAAAAAATCCGAT
1 CCGGTTAAAAAAAAACCGAT
993541 CCGGTTAAAAAAAAACCGAT
1 CCGGTTAAAAAAAAACCGAT
993561 TTTTCCCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (20 bp):
CCGGTTAAAAAAAAACCGAT
Found at i:994622 original size:16 final size:17
Alignment explanation
Indices: 994595--994626 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
994585 TTTGCTGAGT
994595 GAGCTCCGGTACTGTTA
1 GAGCTCCGGTACTGTTA
994612 GAGCT-CGGTACTGTT
1 GAGCTCCGGTACTGTT
994627 GAGATCCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.16, C:0.22, G:0.31, T:0.31
Consensus pattern (17 bp):
GAGCTCCGGTACTGTTA
Found at i:996787 original size:50 final size:51
Alignment explanation
Indices: 996680--996789 Score: 150
Period size: 51 Copynumber: 2.2 Consensus size: 51
996670 TAGCAGGAAA
* * *
996680 GCGCGCCCCCTGCACCGCGCTATATGCTGATTTGGCGCCACGTGGGTATAAC
1 GCGC-CCCCCTGCACCGCGATATACGCTGATCTGGCGCCACGTGGGTATAAC
* * *
996732 GCGCCCCCCTGCCCCGCGATATACGGTGATCTGGCGCCACGTGGGTAT-AG
1 GCGCCCCCCTGCACCGCGATATACGCTGATCTGGCGCCACGTGGGTATAAC
996782 GCGCCCCC
1 GCGCCCCC
996790 TGATCCACGC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 9 0.17
51 39 0.75
52 4 0.08
ACGTcount: A:0.14, C:0.38, G:0.30, T:0.18
Consensus pattern (51 bp):
GCGCCCCCCTGCACCGCGATATACGCTGATCTGGCGCCACGTGGGTATAAC
Found at i:996815 original size:51 final size:51
Alignment explanation
Indices: 996707--996804 Score: 128
Period size: 51 Copynumber: 2.0 Consensus size: 51
996697 CGCTATATGC
* * *
996707 TGATTTGGCGCCACGTGGGTATAACGCGCCCCCCTGCCCCGCGATATACGG
1 TGATCTGGCGCCACGTGGGTATAACGCGCCCCCCTGACCCACGATATACGG
* * *
996758 TGATCTGGCGCCACGTGGGTAT-AGGCG-CCCCCTGATCCACGCTATAC
1 TGATCTGGCGCCACGTGGGTATAACGCGCCCCCCTGACCCACGATATAC
996805 CTGGATATCT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
49 16 0.39
50 4 0.10
51 21 0.51
ACGTcount: A:0.16, C:0.35, G:0.29, T:0.20
Consensus pattern (51 bp):
TGATCTGGCGCCACGTGGGTATAACGCGCCCCCCTGACCCACGATATACGG
Found at i:998578 original size:30 final size:30
Alignment explanation
Indices: 998515--998597 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
998505 TCCGAAGGAC
* * * *
998515 CTATCCAGAGGTCACACAG-ACCCCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCAGCAA
*
998544 CTATCCAGAGGTCATAAAGAACCTCAGCAA
1 CTATCCAGAGGTCACAAAGAACCTCAGCAA
* *
998574 CTATCCATAGGTCCCAAAGAACCT
1 CTATCCAGAGGTCACAAAGAACCT
998598 AGGTAAACTG
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 17 0.38
30 28 0.62
ACGTcount: A:0.35, C:0.31, G:0.17, T:0.17
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCAGCAA
Found at i:998660 original size:31 final size:31
Alignment explanation
Indices: 998572--998666 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 31
998562 GAACCTCAGC
* * * *
998572 AACTATCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTTCCAAAGAACATAGGTA
**
998603 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCAAAGAACATAGGTA
* *
998634 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGT-TCCAAAGAACATAGGTA
998665 AA
1 AA
998667 ACCCTCGACT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 48 0.92
32 4 0.08
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTTCCAAAGAACATAGGTA
Found at i:999429 original size:64 final size:65
Alignment explanation
Indices: 999318--999468 Score: 182
Period size: 64 Copynumber: 2.3 Consensus size: 65
999308 TCTTTCAATG
* * * * * **
999318 AAGGTATGCATCGATGCACTA-CTTGTGCATCGGTGCATAAAATGCATTCGATGTTTTTATTTTA
1 AAGGAATGCATCGATGCATTATCTTATGCATCGATGCATAAAAGGCATTCGATGTCCTTATTTT-
999382 A
65 A
* *
999383 AAGG-ATGCATCGATGCATTATC-TATGCATCGATGCATCAAAGGCATTCGATGTCCTTCTTTTA
1 AAGGAATGCATCGATGCATTATCTTATGCATCGATGCATAAAAGGCATTCGATGTCCTTATTTTA
999446 AAGGAATGCATCGATGCACTTAT
1 AAGGAATGCATCGATGCA-TTAT
999469 GAATGTGCAT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
63 5 0.07
64 61 0.81
65 9 0.12
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (65 bp):
AAGGAATGCATCGATGCATTATCTTATGCATCGATGCATAAAAGGCATTCGATGTCCTTATTTTA
Found at i:1002366 original size:51 final size:50
Alignment explanation
Indices: 1002276--1002405 Score: 138
Period size: 51 Copynumber: 2.5 Consensus size: 50
1002266 CCCCTACGTG
* * *
1002276 GCGTATAGCGCGAATCAGGGGGCGCGCTATACCCCACGTGTAAC-CC-AGTTA
1 GCGTATAGCGCG-TTCAGGGGGCGCGCTATACCCCACGTG--ACGCCAAATCA
* * *
1002327 GCGTATAGCGCAGTTCAGGTGGCGCGCTATACTCTACGTGACGCCAAATCA
1 GCGTATAGCGC-GTTCAGGGGGCGCGCTATACCCCACGTGACGCCAAATCA
*
1002378 GCGTATAGCGCGGTGCAGGGGGCGCGCT
1 GCGTATAGCGC-GTTCAGGGGGCGCGCT
1002406 TTCCTGCTAA
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
49 2 0.03
50 2 0.03
51 62 0.93
52 1 0.01
ACGTcount: A:0.21, C:0.28, G:0.33, T:0.18
Consensus pattern (50 bp):
GCGTATAGCGCGTTCAGGGGGCGCGCTATACCCCACGTGACGCCAAATCA
Found at i:1003907 original size:38 final size:38
Alignment explanation
Indices: 1003799--1003910 Score: 111
Period size: 37 Copynumber: 3.0 Consensus size: 38
1003789 ATATGTTATA
* * * *
1003799 ATGAACTTT-TATTCGATTGAAATATGAATATGTTATTT
1 ATGAA-TTTATATTCAATTTAAATACGAATATATTATTT
* *** * *
1003837 ATAAATTTATATT-TGCTTAAATACAAAAATATTATTT
1 ATGAATTTATATTCAATTTAAATACGAATATATTATTT
1003874 ATGAATTTATATTCAATTTAAATACGAATATATTATT
1 ATGAATTTATATTCAATTTAAATACGAATATATTATT
1003911 ACAAATATAT
Statistics
Matches: 57, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
37 31 0.54
38 26 0.46
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.46
Consensus pattern (38 bp):
ATGAATTTATATTCAATTTAAATACGAATATATTATTT
Found at i:1004643 original size:21 final size:21
Alignment explanation
Indices: 1004619--1004676 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
1004609 AATCACATTG
1004619 CGATTTTCCAAATTCGTGTTA
1 CGATTTTCCAAATTCGTGTTA
*
1004640 CGATTTTCCAAATTCGTGTTG
1 CGATTTTCCAAATTCGTGTTA
*
1004661 CGATTATCCAAATTCG
1 CGATTTTCCAAATTCG
1004677 CAACACTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.40
Consensus pattern (21 bp):
CGATTTTCCAAATTCGTGTTA
Found at i:1004739 original size:40 final size:40
Alignment explanation
Indices: 1004671--1004770 Score: 137
Period size: 40 Copynumber: 2.5 Consensus size: 40
1004661 CGATTATCCA
****
1004671 AATTCGCAACACTGAATTTCAAATTCGCAACTCGATTTCTG
1 AATTCGCAACAC-GAATTTTGTTTTCGCAACTCGATTTCTG
* *
1004712 AATTCGCAACGCGAATTTTGTTTTCGCAACTCGATTTTTG
1 AATTCGCAACACGAATTTTGTTTTCGCAACTCGATTTCTG
1004752 AATTCGCAACACGAATTTT
1 AATTCGCAACACGAATTTT
1004771 TAATTTCACA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
40 41 0.79
41 11 0.21
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (40 bp):
AATTCGCAACACGAATTTTGTTTTCGCAACTCGATTTCTG
Found at i:1004782 original size:21 final size:21
Alignment explanation
Indices: 1004745--1004814 Score: 69
Period size: 18 Copynumber: 3.5 Consensus size: 21
1004735 TCGCAACTCG
*
1004745 ATTTTTGAA-TTCGCAACACGA
1 ATTTTT-AATTTCACAACACGA
1004766 ATTTTTAATTTCACAACA-G-
1 ATTTTTAATTTCACAACACGA
* *
1004785 -GTTTTAGTTTCACAACACGA
1 ATTTTTAATTTCACAACACGA
1004805 A-TTTTAATTT
1 ATTTTTAATTT
1004815 TGCAACAGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
18 15 0.37
19 1 0.02
20 11 0.27
21 14 0.34
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (21 bp):
ATTTTTAATTTCACAACACGA
Found at i:1004795 original size:18 final size:18
Alignment explanation
Indices: 1004768--1004839 Score: 72
Period size: 18 Copynumber: 3.9 Consensus size: 18
1004758 CAACACGAAT
1004768 TTTTAATTTCACAACAGG
1 TTTTAATTTCACAACAGG
* *
1004786 TTTTAGTTTCACAACACGAA
1 TTTTAATTTCACAACA-G-G
**
1004806 TTTTAATTTTGCAACAGG
1 TTTTAATTTCACAACAGG
* *
1004824 TTTTAGTTTCGCAACA
1 TTTTAATTTCACAACA
1004840 CAAATGTTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
18 29 0.66
19 2 0.05
20 13 0.30
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (18 bp):
TTTTAATTTCACAACAGG
Found at i:1004820 original size:20 final size:20
Alignment explanation
Indices: 1004673--1004840 Score: 107
Period size: 20 Copynumber: 8.5 Consensus size: 20
1004663 ATTATCCAAA
* *
1004673 TTCGCAACACTGAATTTCAAA
1 TTCGCAACAC-GAATTTTAAT
*
1004694 TTCGCAACTCG-ATTTCTGAA-
1 TTCGCAACACGAATTT-T-AAT
* **
1004714 TTCGCAACGCGAATTTTGTT
1 TTCGCAACACGAATTTTAAT
* *
1004734 TTCGCAACTCGATTTTTGAA-
1 TTCGCAACACGAATTTT-AAT
1004754 TTCGCAACACGAATTTTTAAT
1 TTCGCAACACGAA-TTTTAAT
* * *
1004775 TTCACAACA-G-GTTTTAGT
1 TTCGCAACACGAATTTTAAT
*
1004793 TTCACAACACGAATTTTAAT
1 TTCGCAACACGAATTTTAAT
* * *
1004813 TTTGCAACA-G-GTTTTAGT
1 TTCGCAACACGAATTTTAAT
1004831 TTCGCAACAC
1 TTCGCAACAC
1004841 AAATGTTTTG
Statistics
Matches: 116, Mismatches: 21, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
18 29 0.25
19 6 0.05
20 54 0.47
21 27 0.23
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCGCAACACGAATTTTAAT
Found at i:1004821 original size:38 final size:39
Alignment explanation
Indices: 1004758--1004849 Score: 132
Period size: 38 Copynumber: 2.4 Consensus size: 39
1004748 TTTGAATTCG
1004758 CAACACGAATTTTTAATTTCACAACAGGTTTTAGTTTCA
1 CAACACGAATTTTTAATTTCACAACAGGTTTTAGTTTCA
** *
1004797 CAACACGAA-TTTTAATTTTGCAACAGGTTTTAGTTTCG
1 CAACACGAATTTTTAATTTCACAACAGGTTTTAGTTTCA
*
1004835 CAACACAAATGTTTT
1 CAACACGAAT-TTTT
1004850 GGGTATATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
38 34 0.72
39 9 0.19
40 4 0.09
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (39 bp):
CAACACGAATTTTTAATTTCACAACAGGTTTTAGTTTCA
Found at i:1004996 original size:14 final size:15
Alignment explanation
Indices: 1004977--1005014 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1004967 TCCCCATCTC
1004977 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
1004991 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1005007 TAATTTTT
1 TAATTTTT
1005015 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1005803 original size:24 final size:24
Alignment explanation
Indices: 1005745--1005791 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1005735 AATCAGTATT
* *
1005745 CGAAATTTGATCTTTGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
1005769 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
1005792 TCGGATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:1008381 original size:29 final size:30
Alignment explanation
Indices: 1008314--1008386 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 30
1008304 TCGCAACGCG
*
1008314 AAAGTCAAATTCACGTTGCGATTTTTTGTTGCG
1 AAAGTCAAATTCACGTTGCGA---TTTGTTGCA
*
1008347 AAAGTCAAATTCGCGTTGCGA-TTGTTGCA
1 AAAGTCAAATTCACGTTGCGATTTGTTGCA
1008376 AAAGTCAAATT
1 AAAGTCAAATT
1008387 TGAAACGCGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 18 0.47
33 20 0.53
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (30 bp):
AAAGTCAAATTCACGTTGCGATTTGTTGCA
Found at i:1008401 original size:13 final size:13
Alignment explanation
Indices: 1008383--1008415 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1008373 GCAAAAGTCA
1008383 AATTTGAAACGCG
1 AATTTGAAACGCG
*
1008396 AATTTGCAACGCG
1 AATTTGAAACGCG
1008409 AATTTGA
1 AATTTGA
1008416 CTTTCGCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.27
Consensus pattern (13 bp):
AATTTGAAACGCG
Found at i:1008581 original size:64 final size:64
Alignment explanation
Indices: 1008512--1008665 Score: 229
Period size: 64 Copynumber: 2.4 Consensus size: 64
1008502 AATTTAAAAC
1008512 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACAT-ATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTT-CATCATCAATTA
*** *
1008576 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTTTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTCATCATCAATTA
*
1008640 AACAAATCAACACTTTTATAAATCAA
1 AACAAATC-A-ACTTTTACAAATCAA
1008666 CTTTTACAAA
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
63 2 0.02
64 65 0.79
65 1 0.01
66 14 0.17
ACGTcount: A:0.52, C:0.16, G:0.02, T:0.30
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTCATCATCAATTA
Found at i:1008664 original size:16 final size:15
Alignment explanation
Indices: 1008641--1008679 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
1008631 CATCAATTAA
1008641 ACAAATCAACACTTTT
1 ACAAATCAA-ACTTTT
*
1008657 ATAAATC-AACTTTT
1 ACAAATCAAACTTTT
1008671 ACAAATCAA
1 ACAAATCAA
1008680 TTAAACAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
14 12 0.60
15 2 0.10
16 6 0.30
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.31
Consensus pattern (15 bp):
ACAAATCAAACTTTT
Found at i:1010084 original size:42 final size:41
Alignment explanation
Indices: 1010037--1010155 Score: 166
Period size: 42 Copynumber: 2.8 Consensus size: 41
1010027 GTGAATCGGG
*
1010037 CTCTTGAACGGTGGGAGGGACATCTTGAACGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGG-CCTCTTGAACGATGATAGGGGC
* *
1010079 CTCTTGAACGGTGAGAGGGGCCTCTTGAAGGATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGCCTCTTGAACGATGATAGGGGC
* *
1010121 CTCTTGAACGATAGGAGAGGCCTCTTGAACGATGA
1 CTCTTGAACGGTGGGAG-GGCCTCTTGAACGATGA
1010156 CAGATGAATC
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
41 1 0.01
42 64 0.94
43 3 0.04
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGCCTCTTGAACGATGATAGGGGC
Found at i:1010152 original size:21 final size:21
Alignment explanation
Indices: 1010037--1010155 Score: 141
Period size: 21 Copynumber: 5.7 Consensus size: 21
1010027 GTGAATCGGG
* * *
1010037 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGAGAGGGGC
* *
1010058 ATCTTGAACGATGATAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
1010079 CTCTTGAACGGTGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* *
1010100 CTCTTGAAGGATGATAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
1010121 CTCTTGAACGAT-AGGAGAGGC
1 CTCTTGAACGATGA-GAGGGGC
1010142 CTCTTGAACGATGA
1 CTCTTGAACGATGA
1010156 CAGATGAATC
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
20 1 0.01
21 80 0.98
22 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:1012203 original size:20 final size:20
Alignment explanation
Indices: 1012146--1012196 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1012136 CTAAAATCGA
1012146 GTTGCGATTTTCATTTTCGC
1 GTTGCGATTTTCATTTTCGC
1012166 GTTGCGATTTTCATTTTCGC
1 GTTGCGATTTTCATTTTCGC
1012186 GTTGCGATTTT
1 GTTGCGATTTT
1012197 AAGTTTCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.10, C:0.18, G:0.22, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGC
Found at i:1012562 original size:22 final size:22
Alignment explanation
Indices: 1012535--1012576 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1012525 GAGATAGACG
*
1012535 GATTTCGCCGGAGATGAGGACA
1 GATTTCACCGGAGATGAGGACA
*
1012557 GATTTCATCGGAGATGAGGA
1 GATTTCACCGGAGATGAGGA
1012577 TGGATGTCGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.14, G:0.36, T:0.21
Consensus pattern (22 bp):
GATTTCACCGGAGATGAGGACA
Found at i:1012726 original size:20 final size:20
Alignment explanation
Indices: 1012701--1012762 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
1012691 TTTCGAATTT
1012701 GAAAATAAAATTCGCGTTGC
1 GAAAATAAAATTCGCGTTGC
**
1012721 GAAAAT-AAACGCGCGTTGC
1 GAAAATAAAATTCGCGTTGC
* *
1012740 G-AATTACAGATTCGCGTTGC
1 GAAAATA-AAATTCGCGTTGC
1012760 GAA
1 GAA
1012763 TTTGAAAATC
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
18 3 0.09
19 12 0.36
20 17 0.52
21 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (20 bp):
GAAAATAAAATTCGCGTTGC
Found at i:1012777 original size:20 final size:21
Alignment explanation
Indices: 1012754--1012793 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
1012744 TACAGATTCG
1012754 CGTTGCGAATTT-GAAAATCA
1 CGTTGCGAATTTGGAAAATCA
1012774 CGTTGCGAATTTGGAAAATC
1 CGTTGCGAATTTGGAAAATC
1012794 GCAATGCGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (21 bp):
CGTTGCGAATTTGGAAAATCA
Found at i:1012801 original size:21 final size:20
Alignment explanation
Indices: 1012757--1012802 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
1012747 AGATTCGCGT
**
1012757 TGCGAATTTGAAAATCACGT
1 TGCGAATTTGAAAATCACAA
*
1012777 TGCGAATTTGGAAAATCGCAA
1 TGCGAATTT-GAAAATCACAA
1012798 TGCGA
1 TGCGA
1012803 TTTACACATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (20 bp):
TGCGAATTTGAAAATCACAA
Found at i:1018926 original size:10 final size:10
Alignment explanation
Indices: 1018907--1018954 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
1018897 CAAATATGTA
*
1018907 ATTATAAAAT
1 ATTATTAAAT
1018917 ATTATTAAAT
1 ATTATTAAAT
1018927 ATTATTAAAT
1 ATTATTAAAT
*
1018937 -TTATTTTAAT
1 ATTA-TTAAAT
1018947 -TTATTAAA
1 ATTATTAAA
1018955 AGTAGGACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
9 7 0.21
10 27 0.79
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
ATTATTAAAT
Found at i:1020054 original size:130 final size:130
Alignment explanation
Indices: 1019914--1020161 Score: 433
Period size: 130 Copynumber: 1.9 Consensus size: 130
1019904 TTATTATATA
*
1019914 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* *
1019979 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTTACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
1020044 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
1020109 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
1020162 GAAGAAAATT
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 111 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:1020192 original size:130 final size:129
Alignment explanation
Indices: 1019928--1020192 Score: 318
Period size: 130 Copynumber: 2.0 Consensus size: 129
1019918 ATTTGGTCCT
* *
1019928 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
1019993 TGACACGTGTCATTGGTGACACATGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
1020058 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
1020123 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
1020187 -A
128 CA
1020188 AAATT
1 AAATT
1020193 TGGGTCTTGG
Statistics
Matches: 114, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
130 101 0.89
132 8 0.07
133 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:1020512 original size:28 final size:26
Alignment explanation
Indices: 1020481--1020541 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
1020471 AGTTGATACA
*
1020481 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTT-AAA-AATAAATTTAAGAATT
* * *
1020509 ATATTTTTAAACTAAATTTAATAATT
1 ATATTTTAAAAATAAATTTAAGAATT
1020535 ATATTTT
1 ATATTTT
1020542 CATATTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 20 0.69
27 2 0.07
28 7 0.24
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (26 bp):
ATATTTTAAAAATAAATTTAAGAATT
Found at i:1020639 original size:16 final size:18
Alignment explanation
Indices: 1020618--1020651 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1020608 ATTTCTTATT
1020618 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
1020634 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
1020652 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:1020798 original size:21 final size:21
Alignment explanation
Indices: 1020774--1020816 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1020764 TATTACCTTA
1020774 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
1020795 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
1020816 A
1 A
1020817 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:1020834 original size:35 final size:35
Alignment explanation
Indices: 1020785--1020870 Score: 93
Period size: 35 Copynumber: 2.5 Consensus size: 35
1020775 ATTGAAGTAT
** * *
1020785 TTTAGAATTTAATTGAAGTATTTTAG-AATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTGA-GG
* *
1020820 TTTAGAATAAAATTGAATTACTTTGGAAATTGAGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTGAGG
*
1020855 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
1020871 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 38 0.88
36 5 0.12
ACGTcount: A:0.38, C:0.01, G:0.20, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTGAGG
Found at i:1022557 original size:21 final size:21
Alignment explanation
Indices: 1022533--1022681 Score: 133
Period size: 21 Copynumber: 7.1 Consensus size: 21
1022523 GTTTCCAGAT
* * *
1022533 TCGCAACGCAAACTTCGATTA
1 TCGCAACGCGAACTTGGACTA
1022554 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTGGACTA
*
1022575 TCGCAATGCGAACTTGGACTA
1 TCGCAACGCGAACTTGGACTA
* * *
1022596 TCGCAATGCGAA-TATGTA-AA
1 TCGCAACGCGAACT-TGGACTA
* * *
1022616 TCGCAATGCGATA-GTCGACTA
1 TCGCAACGCGA-ACTTGGACTA
*
1022637 TCGCAATGCGAACTTGGACTA
1 TCGCAACGCGAACTTGGACTA
* * *
1022658 TCGCAATGTGAACTTCGACTA
1 TCGCAACGCGAACTTGGACTA
1022679 TCG
1 TCG
1022682 TATTGCGATT
Statistics
Matches: 110, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
20 16 0.15
21 94 0.85
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (21 bp):
TCGCAACGCGAACTTGGACTA
Found at i:1022648 original size:83 final size:84
Alignment explanation
Indices: 1022547--1022773 Score: 268
Period size: 83 Copynumber: 2.7 Consensus size: 84
1022537 AACGCAAACT
* * *
1022547 TCGATTATCGCAACGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATG
1 TCGACTATCGCAATGCGAACTTGGACTATCGCAATGTGAACTTGGACTATCGCAATGCGAAT-T-
1022612 TA-A-A-TCGCAATGCGATAG
64 TACATATTCGCAATGCGATAG
* * *
1022630 TCGACTATCGCAATGCGAACTTGGACTATCGCAATGTGAACTTCGACTATCGTATTGCG-ATTTA
1 TCGACTATCGCAATGCGAACTTGGACTATCGCAATGTGAACTTGGACTATCGCAATGCGAATTTA
*
1022694 CATATTCGCATTGCGATAG
66 CATATTCGCAATGCGATAG
* * * * *
1022713 TCGAAGT-TCGCATTGCGATA-GTCGACTATCGCATTGTGAACTTGGACTATCGCAATGCGAA
1 TCG-ACTATCGCAATGCGA-ACTTGGACTATCGCAATGTGAACTTGGACTATCGCAATGCGAA
1022774 CTTCGACTAT
Statistics
Matches: 123, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
80 2 0.02
81 2 0.02
82 3 0.02
83 112 0.91
84 4 0.03
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (84 bp):
TCGACTATCGCAATGCGAACTTGGACTATCGCAATGTGAACTTGGACTATCGCAATGCGAATTTA
CATATTCGCAATGCGATAG
Found at i:1022662 original size:104 final size:104
Alignment explanation
Indices: 1022533--1022818 Score: 332
Period size: 104 Copynumber: 2.8 Consensus size: 104
1022523 GTTTCCAGAT
* * * * * * *
1022533 TCGCAACGCAAACTTCGATTATCGCAACGCGAACTTGGACTATCGCAATGCGAACTTGGAC-TA-
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCGACTATCGCATTGCGAA-TT-GACATAT
1022596 TCGCAATGCGAATATGT-AA-ATCGCAATGCGATAGTCGACTA
64 TCGCAATGCG-ATA-GTCAAGATCGCAATGCGATAGTCGACTA
* * *
1022637 TCGCAATGCGAACTTGGACTATCGCAATGTGAACTTCGACTATCGTATTGCG-ATTTACATATTC
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCGACTATCGCATTGCGAATTGACATATTC
* * *
1022701 GCATTGCGATAGTCGAAGTTCGCATTGCGATAGTCGACTA
66 GCAATGCGATAGTC-AAGATCGCAATGCGATAGTCGACTA
* * *
1022741 TCGCATTGTGAACTTGGACTATCGCAATGCGAACTTCGACTATCGCATTGCG-ATTTACATATTC
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCGACTATCGCATTGCGAATTGACATATTC
*
1022805 GCATTGCGATAGTC
66 GCAATGCGATAGTC
1022819 GAAGTTCACA
Statistics
Matches: 160, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
101 4 0.03
102 7 0.04
103 12 0.08
104 137 0.86
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (104 bp):
TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCGACTATCGCATTGCGAATTGACATATTC
GCAATGCGATAGTCAAGATCGCAATGCGATAGTCGACTA
Found at i:1022744 original size:21 final size:21
Alignment explanation
Indices: 1022615--1022820 Score: 110
Period size: 21 Copynumber: 9.9 Consensus size: 21
1022605 GAATATGTAA
*
1022615 ATCGCAATGCGATAGTCGACT
1 ATCGCATTGCGATAGTCGACT
* * *
1022636 ATCGCAATGCGA-ACTTGGACT
1 ATCGCATTGCGATA-GTCGACT
* * *
1022657 ATCGCAATGTGA-ACTTCGACT
1 ATCGCATTGCGATA-GTCGACT
* *
1022678 ATCGTATTGCGAT--T-TACAT
1 ATCGCATTGCGATAGTCGAC-T
*
1022697 ATTCGCATTGCGATAGTCGAAGT
1 A-TCGCATTGCGATAGTCG-ACT
1022720 -TCGCATTGCGATAGTCGACT
1 ATCGCATTGCGATAGTCGACT
* * *
1022740 ATCGCATTGTGA-ACTTGGACT
1 ATCGCATTGCGATA-GTCGACT
* *
1022761 ATCGCAATGCGA-ACTTCGACT
1 ATCGCATTGCGATA-GTCGACT
*
1022782 ATCGCATTGCGAT--T-TACAT
1 ATCGCATTGCGATAGTCGAC-T
1022801 ATTCGCATTGCGATAGTCGA
1 A-TCGCATTGCGATAGTCGA
1022821 AGTTCACATT
Statistics
Matches: 148, Mismatches: 21, Indels: 30
0.74 0.11 0.15
Matches are distributed among these distances:
18 4 0.03
19 6 0.04
20 27 0.18
21 106 0.72
22 2 0.01
23 2 0.01
24 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (21 bp):
ATCGCATTGCGATAGTCGACT
Found at i:1022819 original size:104 final size:104
Alignment explanation
Indices: 1022616--1022839 Score: 385
Period size: 104 Copynumber: 2.2 Consensus size: 104
1022606 AATATGTAAA
* *
1022616 TCGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGTGAACTTCGACTATC
1 TCGCATTGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCGACTATC
*
1022681 GTATTGCGATTTACATATTCGCATTGCGATAGTCGAAGT
66 GCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGT
* *
1022720 TCGCATTGCGATAGTCGACTATCGCATTGTGAACTTGGACTATCGCAATGCGAACTTCGACTATC
1 TCGCATTGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCGACTATC
1022785 GCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGT
66 GCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGT
* *
1022824 TCACATTGAGATAGTC
1 TCGCATTGCGATAGTC
1022840 CAAAATCGCA
Statistics
Matches: 113, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
104 113 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30
Consensus pattern (104 bp):
TCGCATTGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCGACTATC
GCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGT
Found at i:1022916 original size:6 final size:6
Alignment explanation
Indices: 1022905--1022948 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
1022895 AGATAGTATT
1022905 CGACCA CGACCA CGACCA CGACCA CGA-CA CGA-CA CGA-CA CGACC
1 CGACCA CGACCA CGACCA CGACCA CGACCA CGACCA CGACCA CGACC
1022949 CTACCCGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 15 0.41
6 22 0.59
ACGTcount: A:0.34, C:0.48, G:0.18, T:0.00
Consensus pattern (6 bp):
CGACCA
Found at i:1023600 original size:23 final size:23
Alignment explanation
Indices: 1023574--1023649 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 23
1023564 GACTATCGTA
*
1023574 ACGAATTTGGAATAAATCGCAAC
1 ACGAACTTGGAATAAATCGCAAC
* *
1023597 ACGAACTTCGACT--ATCGC-A-
1 ACGAACTTGGAATAAATCGCAAC
1023616 ACGAACTTGGAATAAATCGCAAC
1 ACGAACTTGGAATAAATCGCAAC
*
1023639 GCGAACTTGGA
1 ACGAACTTGGA
1023650 CTATCGCAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
19 11 0.26
20 1 0.02
21 10 0.23
22 1 0.02
23 20 0.47
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (23 bp):
ACGAACTTGGAATAAATCGCAAC
Found at i:1023626 original size:42 final size:42
Alignment explanation
Indices: 1023564--1023658 Score: 154
Period size: 42 Copynumber: 2.3 Consensus size: 42
1023554 TGCGATTTTG
* *
1023564 GACTATCGTAACGAATTTGGAATAAATCGCAACACGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACACGAACTTC
* *
1023606 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACACGAACTTC
1023648 GACTATCGCAA
1 GACTATCGCAA
1023659 TGCGAATATG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACACGAACTTC
Found at i:1023663 original size:21 final size:21
Alignment explanation
Indices: 1023589--1023664 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
1023579 TTTGGAATAA
* *
1023589 ATCGCAACACGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
*
1023610 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTGGACT
1023629 AAATCGCAACGCGAACTTGGACT
1 --ATCGCAACGCGAACTTGGACT
*
1023652 ATCGCAATGCGAA
1 ATCGCAACGCGAA
1023665 TATGTAAATC
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
19 10 0.21
21 26 0.55
23 11 0.23
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:1024095 original size:2 final size:2
Alignment explanation
Indices: 1024088--1024120 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1024078 ATTTTTCAAG
1024088 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1024121 ATTGTTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1029056 original size:16 final size:17
Alignment explanation
Indices: 1029035--1029070 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1029025 TTTTTAATTT
*
1029035 AATCACT-TAACTTTCA
1 AATCACTCTAACTTTAA
1029051 AATCACTCTAACTTTAA
1 AATCACTCTAACTTTAA
1029068 AAT
1 AAT
1029071 AATAATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.42, C:0.22, G:0.00, T:0.36
Consensus pattern (17 bp):
AATCACTCTAACTTTAA
Found at i:1034392 original size:54 final size:54
Alignment explanation
Indices: 1034310--1034417 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
1034300 TTCAAGGAAG
1034310 TCTGTTTCTGGTTTCTGCATTAAGCTTGGAAGTTCATTGATTTCATGGAAATCC
1 TCTGTTTCTGGTTTCTGCATTAAGCTTGGAAGTTCATTGATTTCATGGAAATCC
*
1034364 TCTGTTTCTGGTTTCTGCATTAAGCTTGGAAGTTCGTTGATTTCATGGAAATCC
1 TCTGTTTCTGGTTTCTGCATTAAGCTTGGAAGTTCATTGATTTCATGGAAATCC
1034418 AAGAAGCAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (54 bp):
TCTGTTTCTGGTTTCTGCATTAAGCTTGGAAGTTCATTGATTTCATGGAAATCC
Found at i:1041941 original size:21 final size:21
Alignment explanation
Indices: 1041904--1041943 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1041894 TCTGCTGAAA
**
1041904 CTCCACCTGTTTTGGAGTATG
1 CTCCACCTGTTGCGGAGTATG
1041925 CTCCACCTGTTGCGGAGTA
1 CTCCACCTGTTGCGGAGTA
1041944 CTACTTGTCT
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:0.15, C:0.28, G:0.25, T:0.33
Consensus pattern (21 bp):
CTCCACCTGTTGCGGAGTATG
Found at i:1047512 original size:10 final size:10
Alignment explanation
Indices: 1047494--1047588 Score: 55
Period size: 10 Copynumber: 8.5 Consensus size: 10
1047484 AATGATAGAT
1047494 GAACATAAAC
1 GAACATAAAC
*
1047504 GAACGTAAAC
1 GAACATAAAC
*
1047514 GAACACAAACAAAC
1 G-A-AC--ATAAAC
1047528 GAACATAAAC
1 GAACATAAAC
* *
1047538 AAACATAATAAAT
1 GAAC---ATAAAC
*
1047551 GAACATAGAC
1 GAACATAAAC
1047561 GAACACAATAAAC
1 G-A-AC-ATAAAC
1047574 GAACATAAAC
1 GAACATAAAC
1047584 GAACA
1 GAACA
1047589 ATACAAACAC
Statistics
Matches: 65, Mismatches: 10, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
10 34 0.52
11 4 0.06
12 7 0.11
13 15 0.23
14 5 0.08
ACGTcount: A:0.60, C:0.20, G:0.11, T:0.09
Consensus pattern (10 bp):
GAACATAAAC
Found at i:1047529 original size:14 final size:14
Alignment explanation
Indices: 1047510--1047541 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1047500 AAACGAACGT
1047510 AAACGAACACAAAC
1 AAACGAACACAAAC
*
1047524 AAACGAACATAAAC
1 AAACGAACACAAAC
1047538 AAAC
1 AAAC
1047542 ATAATAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.66, C:0.25, G:0.06, T:0.03
Consensus pattern (14 bp):
AAACGAACACAAAC
Found at i:1047565 original size:23 final size:23
Alignment explanation
Indices: 1047498--1047588 Score: 119
Period size: 23 Copynumber: 3.9 Consensus size: 23
1047488 ATAGATGAAC
*
1047498 ATAAACGAACGTAAACGAACACAA
1 ATAAACGAACATAAACGAACAC-A
* * *
1047522 ACAAACGAACATAAACAAACATA
1 ATAAACGAACATAAACGAACACA
* *
1047545 ATAAATGAACATAGACGAACACA
1 ATAAACGAACATAAACGAACACA
1047568 ATAAACGAACATAAACGAACA
1 ATAAACGAACATAAACGAACA
1047589 ATACAAACAC
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
23 38 0.68
24 18 0.32
ACGTcount: A:0.60, C:0.20, G:0.10, T:0.10
Consensus pattern (23 bp):
ATAAACGAACATAAACGAACACA
Found at i:1047870 original size:14 final size:16
Alignment explanation
Indices: 1047851--1047882 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1047841 GCCCTCTGTT
1047851 CGAACATA-AAT-GAA
1 CGAACATATAATCGAA
1047865 CGAACATATAATCGAA
1 CGAACATATAATCGAA
1047881 CG
1 CG
1047883 TTCACGAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.50, C:0.19, G:0.16, T:0.16
Consensus pattern (16 bp):
CGAACATATAATCGAA
Found at i:1050283 original size:252 final size:252
Alignment explanation
Indices: 1049826--1050331 Score: 739
Period size: 252 Copynumber: 2.0 Consensus size: 252
1049816 AAGATTAACA
* * * * *
1049826 AGTGGGATTACCTTTTCTGTCTCCATAGTTATAGGATCATCTGATTTAGCATTTCCTTCTTCTGG
1 AGTGGGATTACCTTTCCTGTCACCATAGTTATAGGATCAGCTGAGTTAGCATTTCCTTCTTCTGA
* * *
1049891 TTTTGATGGATCAGTTCCAGAGTTATGTTCAGTCCGTTTTTCTGATCCTCCAAGATGCTCGTTAC
66 TTTTGATGGATCAGTTCCAGAGTTATGTTCAGTCAGTTTTTCTGATCCTCCAAGATGCTCGATAA
* * * * * *
1049956 AATCAGGATTACTTTCACAAGATGGTTCTGATTGTTCTTTTGCATCCGTTGACCTCATCGAAATT
131 AATCAGGATTACTTTCACAAGATGGTTCTAATGGTTCATTCGCATCCATTGAACTCATCGAAATT
*
1050021 TTTAATTCATCTTTACTGGATTTTATAGAAGAATCTTCCTTGCCATGTGTGCCTTCT
196 TTTAATTCATCTTTACTGGATTTTATAGAAGAATCTTCCTTGCCATGAGTGCCTTCT
*
1050078 AGTGGGATTACCTTTCCTGTCACCATAGTGT-TAGGATCAGCTGAGTTAGCATTTTCTTCATT-T
1 AGTGGGATTACCTTTCCTGTCACCATAGT-TATAGGATCAGCTGAGTTAGCATTTCCTTC-TTCT
*
1050141 GATTTTGATGGATCAGTTCCAGAGTTATGTTCAGTCAGTTTTTCTGATCCTCCAAGATGCTTGAT
64 GATTTTGATGGATCAGTTCCAGAGTTATGTTCAGTCAGTTTTTCTGATCCTCCAAGATGCTCGAT
* * * * **
1050206 AAAATCAGGATTACTTTCACCATATGGTTTTAATGGTTCATTCGCATCCATTGAATTTGTCGAAG
129 AAAATCAGGATTACTTTCACAAGATGGTTCTAATGGTTCATTCGCATCCATTGAACTCATCGAA-
* *
1050271 A-TTTTGATTCATCTTTACTGGATTTTATAGAAGAATTTTCCTTGCCATGAGTGCCTTCT
193 ATTTTTAATTCATCTTTACTGGATTTTATAGAAGAATCTTCCTTGCCATGAGTGCCTTCT
1050330 AG
1 AG
1050332 GACAAGTTCA
Statistics
Matches: 226, Mismatches: 25, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
252 222 0.98
253 4 0.02
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (252 bp):
AGTGGGATTACCTTTCCTGTCACCATAGTTATAGGATCAGCTGAGTTAGCATTTCCTTCTTCTGA
TTTTGATGGATCAGTTCCAGAGTTATGTTCAGTCAGTTTTTCTGATCCTCCAAGATGCTCGATAA
AATCAGGATTACTTTCACAAGATGGTTCTAATGGTTCATTCGCATCCATTGAACTCATCGAAATT
TTTAATTCATCTTTACTGGATTTTATAGAAGAATCTTCCTTGCCATGAGTGCCTTCT
Found at i:1053830 original size:245 final size:236
Alignment explanation
Indices: 1053360--1053828 Score: 666
Period size: 245 Copynumber: 2.0 Consensus size: 236
1053350 ATTTTTATTC
* *
1053360 AATATATGAATTAGAAATCCGACCCGACATGACACAAAATAATAAAAAAATTACTTTTATTCAAT
1 AATATATGAATTAGAAATCCGACCCGACACGACACAAAATAATAAAAAAAATACTTTTATTCAAT
*
1053425 AAAAACAGACTTAATTGGAAAAAAAATATATAGAGGGGTATTATTGTAATTATTCCTAAATATAT
66 AAAAACAGACTTAATTGGAAAAAAAATATATAGAGCGGTATTATTGTAATTATTCCTAAATATAT
* * * * * *
1053490 AAGGTAAAATTATATTTTTTTTCTGGTCGGTTTGATTGTTTTCACCCTAAACTCGAACCCGACCC
131 AAGGTAAAATTATATATATTTTCGGGTCGGTGTGATTGATTTCACCCTAAACCCGAACCCGACCC
1053555 GACCCGAGTATCACACTTAAAAAAACCCGACCCGACCCGTCCCG
196 GA--C-AGTATCACACTTAAAAAAACCCGACCCGACCCGTCCCG
* * *
1053599 AATATATGAATTAGAAATCCGACCCGACCCGACCCGACCCGAAATAATAAAAAAAATATTTTTAT
1 AATATATGAATTAGAAATCCGACCCGA--C-A--CGACACAAAATAATAAAAAAAATACTTTTAT
1053664 TCAATAAAAACAGTGACTTAATT-GAAAAAAAATATATAGAGCGGTATTATTGTAATTATTCCTA
61 TCAATAAAAACA--GACTTAATTGGAAAAAAAATATATAGAGCGGTATTATTGTAATTATTCCTA
*
1053728 AATATATAAGGTAAAATTATATATATTTTCGGGTCGG-GT-A-T-ATTTCATCCTAAACCCGAAC
124 AATATATAAGGTAAAATTATATATATTTTCGGGTCGGTGTGATTGATTTCACCCTAAACCCGAAC
*
1053789 TCGACCCGA-A-TATCACACTTAAAAAAA-CCGACCCGACCCG
189 CCGACCCGACAGTATCACACTTAAAAAAACCCGACCCGACCCG
1053829 ACTGAAATAA
Statistics
Matches: 209, Mismatches: 14, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
235 13 0.06
236 17 0.08
237 1 0.00
239 27 0.13
241 26 0.12
242 2 0.01
243 1 0.00
244 39 0.19
245 74 0.35
246 9 0.04
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (236 bp):
AATATATGAATTAGAAATCCGACCCGACACGACACAAAATAATAAAAAAAATACTTTTATTCAAT
AAAAACAGACTTAATTGGAAAAAAAATATATAGAGCGGTATTATTGTAATTATTCCTAAATATAT
AAGGTAAAATTATATATATTTTCGGGTCGGTGTGATTGATTTCACCCTAAACCCGAACCCGACCC
GACAGTATCACACTTAAAAAAACCCGACCCGACCCGTCCCG
Found at i:1058286 original size:2 final size:2
Alignment explanation
Indices: 1058279--1058323 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1058269 TAAAACATAG
1058279 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
1058321 TA T
1 TA T
1058324 GTTGTATAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1058329 original size:123 final size:123
Alignment explanation
Indices: 1058177--1058403 Score: 445
Period size: 123 Copynumber: 1.8 Consensus size: 123
1058167 CAAATAGGGA
1058177 ATATATATATATATATATATATATGTTGTATAGAAAATTCCAGATGTTTCAATGAAATGATGATT
1 ATATATATATATATATATATATATGTTGTATAGAAAATTCCAGATGTTTCAATGAAATGATGATT
1058242 TAAAACTGATTCAATTCTTAAGTGATATAAAACATAGTATATATATATATATATATAT
66 TAAAACTGATTCAATTCTTAAGTGATATAAAACATAGTATATATATATATATATATAT
*
1058300 ATATATATATATATATATATATATGTTGTATAGAAAATTCTAGATGTTTCAATGAAATGATGATT
1 ATATATATATATATATATATATATGTTGTATAGAAAATTCCAGATGTTTCAATGAAATGATGATT
1058365 TAAAACTGATTCAATTCTTAAGTGATATAAAACATAGTA
66 TAAAACTGATTCAATTCTTAAGTGATATAAAACATAGTA
1058404 CATAGATCTA
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
123 103 1.00
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.40
Consensus pattern (123 bp):
ATATATATATATATATATATATATGTTGTATAGAAAATTCCAGATGTTTCAATGAAATGATGATT
TAAAACTGATTCAATTCTTAAGTGATATAAAACATAGTATATATATATATATATATAT
Found at i:1059598 original size:2 final size:2
Alignment explanation
Indices: 1059591--1059616 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1059581 TGGCGAGCTC
1059591 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
1059617 GTGTTTGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1061715 original size:17 final size:17
Alignment explanation
Indices: 1061695--1061739 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1061685 TTCACCTTAC
1061695 TATTTCTTTTATTATAT
1 TATTTCTTTTATTATAT
* *
1061712 TATTTCTCTTATTCTAT
1 TATTTCTTTTATTATAT
*
1061729 TGTTTCTTTTA
1 TATTTCTTTTA
1061740 CTGATTCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.18, C:0.11, G:0.02, T:0.69
Consensus pattern (17 bp):
TATTTCTTTTATTATAT
Found at i:1062125 original size:39 final size:36
Alignment explanation
Indices: 1062026--1062132 Score: 119
Period size: 39 Copynumber: 2.9 Consensus size: 36
1062016 AAATGTATGG
1062026 CACATTTAGTG-CATTGTGATTGCACTATAGGTGCGA
1 CACATTTAGTGCCA-TGTGATTGCACTATAGGTGCGA
* * * *
1062062 CGCA-TCAGTGCCCTATGATTGCACTATAGATGATGCGA
1 CACATTTAGTGCCATGTGATTGCACTATAG--G-TGCGA
*
1062100 CACATTTAATGCCATGTGATTGCACTATAGGTG
1 CACATTTAGTGCCATGTGATTGCACTATAGGTG
1062133 TGGTATATTC
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
35 20 0.35
36 6 0.11
37 2 0.04
38 8 0.14
39 21 0.37
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (36 bp):
CACATTTAGTGCCATGTGATTGCACTATAGGTGCGA
Found at i:1062227 original size:54 final size:54
Alignment explanation
Indices: 1062143--1062247 Score: 183
Period size: 54 Copynumber: 1.9 Consensus size: 54
1062133 TGGTATATTC
* *
1062143 AGTGCCCTGTGAATGTACAAATATTGTAGAACACAACAACAATGTACCTATAAT
1 AGTGCCCTGTGAATGTACAAATACTATAGAACACAACAACAATGTACCTATAAT
*
1062197 AGTGCCCTGTGAATGTACAAGTACTATAGAACACAACAACAATGTACCTAT
1 AGTGCCCTGTGAATGTACAAATACTATAGAACACAACAACAATGTACCTAT
1062248 GATCCCGAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (54 bp):
AGTGCCCTGTGAATGTACAAATACTATAGAACACAACAACAATGTACCTATAAT
Found at i:1062294 original size:26 final size:26
Alignment explanation
Indices: 1062232--1062284 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
1062222 ATAGAACACA
*
1062232 ACAACAATGTACCTATGATCCCGAAT
1 ACAACAATGTACCTATGATCCCAAAT
1062258 ACAACAATGTACCTATGATCCCAAAT
1 ACAACAATGTACCTATGATCCCAAAT
1062284 A
1 A
1062285 TATAAATGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.26, G:0.09, T:0.23
Consensus pattern (26 bp):
ACAACAATGTACCTATGATCCCAAAT
Found at i:1065659 original size:40 final size:40
Alignment explanation
Indices: 1065622--1065701 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
1065612 GTGTGGAATC
* *
1065622 CTCTGGAATATTCTGGAAGAGTGTGGAACCTTATGGAAGA
1 CTCTGGAACATTATGGAAGAGTGTGGAACCTTATGGAAGA
* * *
1065662 GTGTGGAACCTTATGGAAGAGTGTGGAACCTTATGGAAGA
1 CTCTGGAACATTATGGAAGAGTGTGGAACCTTATGGAAGA
1065702 ATATGGAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.30, C:0.11, G:0.33, T:0.26
Consensus pattern (40 bp):
CTCTGGAACATTATGGAAGAGTGTGGAACCTTATGGAAGA
Found at i:1065669 original size:30 final size:30
Alignment explanation
Indices: 1065603--1065669 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
1065593 TCTAGAAGTT
* * * *
1065603 TGTGGAATAGTGTGGAATCCTCTGGAATAT
1 TGTGGAAGAGTGTGGAATCCTATGGAAGAG
*
1065633 TCTGGAAGAGTGTGGAA-CCTTATGGAAGAG
1 TGTGGAAGAGTGTGGAATCC-TATGGAAGAG
1065663 TGTGGAA
1 TGTGGAA
1065670 CCTTATGGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 2 0.07
30 28 0.93
ACGTcount: A:0.28, C:0.09, G:0.34, T:0.28
Consensus pattern (30 bp):
TGTGGAAGAGTGTGGAATCCTATGGAAGAG
Found at i:1065709 original size:20 final size:20
Alignment explanation
Indices: 1065635--1065701 Score: 134
Period size: 20 Copynumber: 3.4 Consensus size: 20
1065625 TGGAATATTC
1065635 TGGAAGAGTGTGGAACCTTA
1 TGGAAGAGTGTGGAACCTTA
1065655 TGGAAGAGTGTGGAACCTTA
1 TGGAAGAGTGTGGAACCTTA
1065675 TGGAAGAGTGTGGAACCTTA
1 TGGAAGAGTGTGGAACCTTA
1065695 TGGAAGA
1 TGGAAGA
1065702 ATATGGAATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.31, C:0.09, G:0.36, T:0.24
Consensus pattern (20 bp):
TGGAAGAGTGTGGAACCTTA
Found at i:1065719 original size:40 final size:39
Alignment explanation
Indices: 1065635--1065725 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 39
1065625 TGGAATATTC
* * *
1065635 TGGAAGAGTGTGGAACCTTATGGAAGAGTGTGGAACCTTA
1 TGGAAGAGTGTGGAACCTTATGGAAGAATATGGAA-CTGA
1065675 TGGAAGAGTGTGGAACCTTATGGAAGAATATGGAA-TGGA
1 TGGAAGAGTGTGGAACCTTATGGAAGAATATGGAACT-GA
1065714 GTGGAAGAGTGT
1 -TGGAAGAGTGT
1065726 ATAGTTTCTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 1 0.02
40 44 0.96
ACGTcount: A:0.32, C:0.07, G:0.37, T:0.24
Consensus pattern (39 bp):
TGGAAGAGTGTGGAACCTTATGGAAGAATATGGAACTGA
Found at i:1067826 original size:23 final size:23
Alignment explanation
Indices: 1067750--1067826 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
1067740 TCGTATAAAT
1067750 TTGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
* * *
1067773 TTATC-CCAAAG-GACCGCGTAGAA
1 TT-GCACCGAAGTG-CCACGTAGAA
* *
1067796 ATGTACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
1067819 TTGCACCG
1 TTGCACCG
1067827 TGGTGCCATA
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
22 1 0.03
23 37 0.93
24 2 0.05
ACGTcount: A:0.31, C:0.26, G:0.25, T:0.18
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:1067896 original size:20 final size:20
Alignment explanation
Indices: 1067873--1067920 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1067863 GAAATTCCTT
1067873 AAGAATCATATACATATACC
1 AAGAATCATATACATATACC
1067893 AAGAATCATATACATATACC
1 AAGAATCATATACATATACC
*
1067913 AAGGATCA
1 AAGAATCA
1067921 AATAGGTGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (20 bp):
AAGAATCATATACATATACC
Found at i:1068126 original size:30 final size:31
Alignment explanation
Indices: 1068085--1068155 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
1068075 TCACATAGTG
* * *
1068085 TATCTCATAGACATATTA-TTTCTATACCTT
1 TATCACATAGACATATCATTTTCCATACCTT
1068115 TATCACATAGACATATCATTTTCCATACCTT
1 TATCACATAGACATATCATTTTCCATACCTT
1068146 TATCACATAG
1 TATCACATAG
1068156 CTCATATAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 16 0.43
31 21 0.57
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.41
Consensus pattern (31 bp):
TATCACATAGACATATCATTTTCCATACCTT
Found at i:1075580 original size:126 final size:125
Alignment explanation
Indices: 1075340--1075596 Score: 426
Period size: 126 Copynumber: 2.0 Consensus size: 125
1075330 TAGTCTGTTC
*
1075340 AATGATGACTAGTAGAGGTATTTATGAAGAAATGTTTTCTTTAAAAAGGGTTAACATTGTTCCAT
1 AATGATGACTAGTAGAGGTATTTATCAAGAAATGTTTTCTTTAAAAAGGGTTAACATTGTTCCAT
*
1075405 ACCTTGATTAAACTGCAAAGTTGGCTTCAAATATGCCTAAAAATTGGTTGTCAGAGTGTA
66 ACCTTGATTAAACTGCAAAGTTGGCTTCAAATATGCCTAAAAAATGGTTGTCAGAGTGTA
* * *
1075465 AATGATGACTAGTGGAAGGTATTTATCAAGAAATGTTTTCTTTGAGAAGGGTTAACATTG-TCTC
1 AATGATGACTAGTAG-AGGTATTTATCAAGAAATGTTTTCTTTAAAAAGGGTTAACATTGTTC-C
*
1075529 ATACCTTGATTAAACTGCAAAGTTGGCTTCAAATATGCCTAAAAAATGGTTGTCGGAGTGTA
64 ATACCTTGATTAAACTGCAAAGTTGGCTTCAAATATGCCTAAAAAATGGTTGTCAGAGTGTA
*
1075591 TATGAT
1 AATGAT
1075597 AGGCAGTTCT
Statistics
Matches: 123, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
125 16 0.13
126 107 0.87
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.34
Consensus pattern (125 bp):
AATGATGACTAGTAGAGGTATTTATCAAGAAATGTTTTCTTTAAAAAGGGTTAACATTGTTCCAT
ACCTTGATTAAACTGCAAAGTTGGCTTCAAATATGCCTAAAAAATGGTTGTCAGAGTGTA
Found at i:1080117 original size:40 final size:41
Alignment explanation
Indices: 1080039--1080127 Score: 96
Period size: 40 Copynumber: 2.2 Consensus size: 41
1080029 TGAGATCGAT
*
1080039 AATTCGCAACGCGATCTCTGGTATCGCAAATCAGTTT-CCA
1 AATTCGCAACGCGATCTCTGCTATCGCAAATCAGTTTCCCA
* *
1080079 GATTCGCAACGCGAT-TCTGACTATCGC-ATTGC-GATTTCCCA
1 AATTCGCAACGCGATCTCTG-CTATCGCAAAT-CAG-TTTCCCA
1080120 AATTCGCA
1 AATTCGCA
1080128 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
39 7 0.17
40 24 0.59
41 10 0.24
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (41 bp):
AATTCGCAACGCGATCTCTGCTATCGCAAATCAGTTTCCCA
Found at i:1080128 original size:21 final size:21
Alignment explanation
Indices: 1080102--1080148 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1080092 ATTCTGACTA
1080102 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* *
1080123 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
1080144 TCGCA
1 TCGCA
1080149 ACGCGATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1080154 original size:21 final size:21
Alignment explanation
Indices: 1080109--1080156 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1080099 CTATCGCATT
**
1080109 GCGATTTCCCAAATTCGCATT
1 GCGATTTCCCAAATTCGCAAC
* *
1080130 GCGATTTTCCTAATTCGCAAC
1 GCGATTTCCCAAATTCGCAAC
1080151 GCGATT
1 GCGATT
1080157 ACGTAAATCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (21 bp):
GCGATTTCCCAAATTCGCAAC
Found at i:1080747 original size:20 final size:20
Alignment explanation
Indices: 1080722--1080818 Score: 99
Period size: 20 Copynumber: 4.8 Consensus size: 20
1080712 TTCTAAACTT
*
1080722 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
*
1080742 AAAATCGCAACACGAAAATT
1 AAAATCGCAACACGAAAATG
** *
1080762 ACTATTGCAACGA-GAGAAATG
1 AAAATCGCAAC-ACGA-AAATG
*
1080783 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
*
1080802 AAAATCGCAACGCGAAA
1 AAAATCGCAACACGAAA
1080819 CCAAAATCGC
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
19 19 0.30
20 30 0.48
21 14 0.22
ACGTcount: A:0.51, C:0.19, G:0.18, T:0.13
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:1080801 original size:19 final size:19
Alignment explanation
Indices: 1080722--1080829 Score: 90
Period size: 19 Copynumber: 5.5 Consensus size: 19
1080712 TTCTAAACTT
**
1080722 AAAATCGCAACATGAAAATG
1 AAAATCGCAACGCG-AAATG
* *
1080742 AAAATCGCAACACGAAAATT
1 AAAATCGCAACGCG-AAATG
** * *
1080762 ACTATTGCAACGAGAGAAATG
1 AAAATCGCAAC--GCGAAATG
1080783 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
**
1080802 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATG
1080821 AAAATCGCA
1 AAAATCGCA
1080830 TTGCGATTTT
Statistics
Matches: 72, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
19 33 0.46
20 26 0.36
21 12 0.17
22 1 0.01
ACGTcount: A:0.50, C:0.20, G:0.17, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:1080847 original size:19 final size:19
Alignment explanation
Indices: 1080825--1080950 Score: 119
Period size: 19 Copynumber: 7.1 Consensus size: 19
1080815 GAAACCAAAA
*
1080825 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1080844 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1080858 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1080877 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1080891 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1080910 TCGCGTTGCGATTCTCTTT
1 TCGCGTTGCGATTTTCATT
*
1080929 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1080949 TC
1 TC
1080951 AACCAAAAGA
Statistics
Matches: 86, Mismatches: 10, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 38 0.44
20 16 0.19
ACGTcount: A:0.10, C:0.25, G:0.19, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1080866 original size:14 final size:14
Alignment explanation
Indices: 1080847--1080903 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1080837 TTTCATTTCG
1080847 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1080861 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1080880 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1080894 CGTTGCGATT
1 CGTTGCGATT
1080904 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1080938 original size:20 final size:20
Alignment explanation
Indices: 1080887--1080948 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
1080877 TCGCGTTGCG
*
1080887 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTCTC
*
1080907 ATT-TCGCGTTGCGATTCTC
1 ATTCTCTCGTTGCGATTCTC
* *
1080926 TTTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTCTC
1080946 ATT
1 ATT
1080949 TCAACCAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 16 0.46
20 19 0.54
ACGTcount: A:0.10, C:0.24, G:0.16, T:0.50
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTCTC
Found at i:1080950 original size:39 final size:33
Alignment explanation
Indices: 1080830--1080926 Score: 194
Period size: 33 Copynumber: 2.9 Consensus size: 33
1080820 CAAAATCGCA
1080830 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1080863 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1080896 TTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCT
1080927 TTCTCTCGTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1082806 original size:94 final size:94
Alignment explanation
Indices: 1082643--1083018 Score: 595
Period size: 94 Copynumber: 4.1 Consensus size: 94
1082633 TAGATTGCTT
* * *
1082643 AGTAAATTTATTCGGTTGCTGTCAATAT-TGTTAAAC--TGT-TT-ATTAACACTGTGAAGTTAG
1 AGTAAATTTATTCGGTTGCTGCCAAT-TCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAG
1082703 TATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
65 TATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
1082733 AGTAAATTTATTTGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1082798 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1082827 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1082892 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * * *
1082921 AGTAAATTTGTTCGTTTGGTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1082986 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1083014 AGTAA
1 AGTAA
1083019 TGCAATCCAT
Statistics
Matches: 270, Mismatches: 10, Indels: 9
0.93 0.03 0.03
Matches are distributed among these distances:
89 1 0.00
90 31 0.11
92 3 0.01
93 28 0.10
94 207 0.77
ACGTcount: A:0.21, C:0.11, G:0.19, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1083151 original size:38 final size:39
Alignment explanation
Indices: 1083109--1083189 Score: 146
Period size: 38 Copynumber: 2.1 Consensus size: 39
1083099 TCTTTTGGTT
*
1083109 GAAATGAAAATCGCAACGCGAAA-CAAAAATCGCAACGG
1 GAAATGAAAATCGCAACGCGAAACCAAAAATCGCAACGC
1083147 GAAATGAAAATCGCAACGCGAAACCAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAACCAAAAATCGCAACGC
1083186 GAAA
1 GAAA
1083190 CTATAATCGC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 23 0.56
39 18 0.44
ACGTcount: A:0.51, C:0.22, G:0.20, T:0.07
Consensus pattern (39 bp):
GAAATGAAAATCGCAACGCGAAACCAAAAATCGCAACGC
Found at i:1083199 original size:19 final size:19
Alignment explanation
Indices: 1083115--1083190 Score: 116
Period size: 19 Copynumber: 3.9 Consensus size: 19
1083105 GGTTGAAATG
1083115 AAAATCGCAACGCGAAACA
1 AAAATCGCAACGCGAAACA
* **
1083134 AAAATCGCAACGGGAAATG
1 AAAATCGCAACGCGAAACA
1083153 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAA-CA
1083173 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
1083191 TATAATCGCG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
19 33 0.66
20 17 0.34
ACGTcount: A:0.50, C:0.25, G:0.18, T:0.07
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACA
Found at i:1083286 original size:39 final size:39
Alignment explanation
Indices: 1083206--1083286 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
1083196 TCGCGTTGCG
* **
1083206 ATTCTCTCGTTGCGATTTTCGTTTCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTCATTTCGCGTTGCGATAGTC
1083245 ATTCTCTCGTTGCGATTTTCATTTCGCGTTGCGATAGTC
1 ATTCTCTCGTTGCGATTTTCATTTCGCGTTGCGATAGTC
1083284 ATT
1 ATT
1083287 TTTCACGTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.47
Consensus pattern (39 bp):
ATTCTCTCGTTGCGATTTTCATTTCGCGTTGCGATAGTC
Found at i:1083287 original size:19 final size:19
Alignment explanation
Indices: 1083213--1083279 Score: 107
Period size: 19 Copynumber: 3.5 Consensus size: 19
1083203 GCGATTCTCT
*
1083213 CGTTGCGATTTTCGTTTCG
1 CGTTGCGATTTTCATTTCG
*
1083232 CGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
1083252 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
1083271 CGTTGCGAT
1 CGTTGCGAT
1083280 AGTCATTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 26 0.59
20 18 0.41
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1083778 original size:42 final size:42
Alignment explanation
Indices: 1083702--1083790 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
1083692 GACTCGCCTG
* * *
1083702 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
1083744 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
1083786 TCATC
1 TCATC
1083791 GTTGAAGAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:1085190 original size:14 final size:14
Alignment explanation
Indices: 1085171--1085206 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1085161 ATTGTTTAAT
1085171 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1085185 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1085199 TGATTTGT
1 TGATTTGT
1085207 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1085373 original size:19 final size:19
Alignment explanation
Indices: 1085351--1085501 Score: 89
Period size: 19 Copynumber: 8.7 Consensus size: 19
1085341 CGAAACTAAA
1085351 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1085370 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1085385 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1085403 TTCGCATTGTGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1085418 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1085436 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1085451 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
1085469 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
1085488 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1085502 AGACATTAAG
Statistics
Matches: 96, Mismatches: 20, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 25 0.26
16 9 0.09
17 9 0.09
19 43 0.45
20 10 0.10
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1085397 original size:33 final size:33
Alignment explanation
Indices: 1085355--1085481 Score: 227
Period size: 33 Copynumber: 3.8 Consensus size: 33
1085345 ACTAAATTCG
* *
1085355 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1085388 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1085421 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1085454 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1085482 AGTCATTTCC
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1085461 original size:14 final size:14
Alignment explanation
Indices: 1085376--1085463 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
1085366 TCATTTCGCT
*
1085376 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
1085390 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
1085407 CATTGTGATTCTCTCG
1 --TTGCGATTCTCTCG
*
1085423 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1085440 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
1085456 TTGCGATT
1 TTGCGATT
1085464 TTCATTTCGC
Statistics
Matches: 57, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 19 0.33
16 14 0.25
17 13 0.23
19 11 0.19
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1085500 original size:20 final size:19
Alignment explanation
Indices: 1085454--1085508 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1085444 GCGATTCTCT
**
1085454 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
1085473 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
1085493 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
1085509 AAGATGATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:1085547 original size:20 final size:20
Alignment explanation
Indices: 1085475--1085547 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
1085465 TCATTTCGCA
* *
1085475 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTACGTG
* *
1085495 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTACG-TG
*
1085515 ATTGCGA-ACGTCATTTTCGTG
1 -TTGCGATA-GTCATTTACGTG
1085536 TTGCGATAGTCA
1 TTGCGATAGTCA
1085548 AATGAATGCC
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.56
21 12 0.29
22 3 0.07
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCATTTACGTG
Found at i:1087810 original size:14 final size:14
Alignment explanation
Indices: 1087791--1087818 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1087781 CTCCCGTGGC
1087791 ATTTTCTTTGGGGA
1 ATTTTCTTTGGGGA
1087805 ATTTTCTTTGGGGA
1 ATTTTCTTTGGGGA
1087819 TTTCTTCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.29, T:0.50
Consensus pattern (14 bp):
ATTTTCTTTGGGGA
Found at i:1088052 original size:24 final size:24
Alignment explanation
Indices: 1088025--1088071 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1088015 ATCATAAAAA
1088025 TCCGAGTATTGACCAAGATCAAAG
1 TCCGAGTATTGACCAAGATCAAAG
*
1088049 TCCGGGTATTGACCAAGATCAAA
1 TCCGAGTATTGACCAAGATCAAA
1088072 TTTCGAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
TCCGAGTATTGACCAAGATCAAAG
Found at i:1088085 original size:24 final size:24
Alignment explanation
Indices: 1088025--1088085 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
1088015 ATCATAAAAA
* *
1088025 TCCGAGTATTGACCAAGATCAAAG
1 TCCGAATACTGACCAAGATCAAAG
** * *
1088049 TCCGGGTATTGACCAAGATCAAAT
1 TCCGAATACTGACCAAGATCAAAG
*
1088073 TTCGAATACTGAC
1 TCCGAATACTGAC
1088086 TAGTACTCAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (24 bp):
TCCGAATACTGACCAAGATCAAAG
Found at i:1088923 original size:41 final size:40
Alignment explanation
Indices: 1088875--1089000 Score: 130
Period size: 41 Copynumber: 3.1 Consensus size: 40
1088865 GAAATCGAGT
*
1088875 TGCGAATTTGAAATTCAGCATTGCGATTACGTAAATCGCAA
1 TGCGAATTAGAAATTC-GCATTGCGATTACGTAAATCGCAA
* * * * *
1088916 TGTGAATTAGGAAAATCGCAATACAATTACGTAAATCGCAA
1 TGCGAATTA-GAAATTCGCATTGCGATTACGTAAATCGCAA
* * *
1088957 TGCG-ATTACATATTCGCATTGCGATTTACGT-AATCGCAT
1 TGCGAATTAGAAATTCGCATTGCGA-TTACGTAAATCGCAA
1088996 TGCGA
1 TGCGA
1089001 TTTTCCTAAT
Statistics
Matches: 68, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
39 21 0.31
40 10 0.15
41 31 0.46
42 6 0.09
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (40 bp):
TGCGAATTAGAAATTCGCATTGCGATTACGTAAATCGCAA
Found at i:1088964 original size:20 final size:20
Alignment explanation
Indices: 1088896--1089150 Score: 106
Period size: 20 Copynumber: 12.3 Consensus size: 20
1088886 AATTCAGCAT
1088896 TGCGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
* * *
1088916 TGTGAATTAGGAAAATCGCAA
1 TGCG-ATTACGTAAATCGCAA
* *
1088937 TACAATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
* * *
1088957 TGCGATTACAT-ATTCGCAT
1 TGCGATTACGTAAATCGCAA
*
1088976 TGCGATTTACGT-AATCGCAT
1 TGCGA-TTACGTAAATCGCAA
* * *
1088996 TGCGATTTTCCTAATTCGCATCACAA
1 TGCGA-TTACGTAA-----ATCGCAA
*
1089022 TGCGATTTACGT-AATCGCAT
1 TGCGA-TTACGTAAATCGCAA
* * * * *
1089042 TACGATTTTCCTAATTCGCAT
1 TGCGA-TTACGTAAATCGCAA
*
1089063 TGCGATTTACGT-AATCGCAT
1 TGCGA-TTACGTAAATCGCAA
* *
1089083 TGCGATTTACGT-ATTCGCAT
1 TGCGA-TTACGTAAATCGCAA
* *
1089103 TGCGAATTAGGAAAATCGCAA
1 TGCG-ATTACGTAAATCGCAA
* ** *
1089124 CGCGAATTTGGGAAATCGCAA
1 TGCG-ATTACGTAAATCGCAA
1089145 TGCGAT
1 TGCGAT
1089151 AGTCAGAATC
Statistics
Matches: 184, Mismatches: 40, Indels: 22
0.75 0.16 0.09
Matches are distributed among these distances:
19 11 0.06
20 97 0.53
21 60 0.33
25 1 0.01
26 15 0.08
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (20 bp):
TGCGATTACGTAAATCGCAA
Found at i:1089122 original size:41 final size:41
Alignment explanation
Indices: 1088942--1089107 Score: 203
Period size: 46 Copynumber: 4.0 Consensus size: 41
1088932 CGCAATACAA
* *
1088942 TTACGTAAATCGCAATGCGA-TTACAT-ATTCGCATTGCGAT
1 TTACGT-AATCGCATTGCGATTTACCTAATTCGCATTGCGAT
*
1088982 TTACGTAATCGCATTGCGATTTTCCTAATTCGCATCACAATGCGAT
1 TTACGTAATCGCATTGCGATTTACCTAATTCGCAT-----TGCGAT
* *
1089028 TTACGTAATCGCATTACGATTTTCCTAATTCGCATTGCGAT
1 TTACGTAATCGCATTGCGATTTACCTAATTCGCATTGCGAT
*
1089069 TTACGTAATCGCATTGCGATTTACGT-ATTCGCATTGCGA
1 TTACGTAATCGCATTGCGATTTACCTAATTCGCATTGCGA
1089108 ATTAGGAAAA
Statistics
Matches: 112, Mismatches: 7, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
39 12 0.11
40 23 0.21
41 37 0.33
46 40 0.36
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.36
Consensus pattern (41 bp):
TTACGTAATCGCATTGCGATTTACCTAATTCGCATTGCGAT
Found at i:1089128 original size:21 final size:21
Alignment explanation
Indices: 1089104--1089149 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1089094 TATTCGCATT
1089104 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
1089125 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1089146 GCGA
1 GCGA
1089150 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
Found at i:1095119 original size:19 final size:19
Alignment explanation
Indices: 1095095--1095144 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
1095085 TTTATGGGGT
1095095 TTCTTTGATTGATGTCTAC
1 TTCTTTGATTGATGTCTAC
*
1095114 TTCTTTGATTGATGTCTGC
1 TTCTTTGATTGATGTCTAC
*
1095133 TTTTTTGATTGA
1 TTCTTTGATTGA
1095145 ATTGGTGATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.14, C:0.12, G:0.18, T:0.56
Consensus pattern (19 bp):
TTCTTTGATTGATGTCTAC
Found at i:1097007 original size:26 final size:23
Alignment explanation
Indices: 1096949--1097008 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 23
1096939 TTTTAATTTT
*
1096949 AATATCAATTTTTAAATAAATTA
1 AATATTAATTTTTAAATAAATTA
*
1096972 AATATTAATTTTTAATATATATTA
1 AATATTAATTTTTAA-ATAAATTA
1096996 TAGATATTAATTT
1 -A-ATATTAATTT
1097009 AATATTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
23 14 0.44
24 7 0.22
25 1 0.03
26 10 0.31
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
AATATTAATTTTTAAATAAATTA
Found at i:1097019 original size:60 final size:63
Alignment explanation
Indices: 1096927--1097078 Score: 235
Period size: 60 Copynumber: 2.5 Consensus size: 63
1096917 ATATTTAATT
1096927 TATTATATT-T-GAT-TTTAATTTTAATATCAATTTTTAAATAAATTAAATATTAA-TTTTTAA
1 TATTATATTATAGATATTTAA-TTTAATATCAATTTTTAAATAAATTAAATATTAATTTTTTAA
*
1096987 TA-TATATTATAGATA-TTAATTTAATATTAATTTTTAAATAAATTAAATATTAATTTTTTAA
1 TATTATATTATAGATATTTAATTTAATATCAATTTTTAAATAAATTAAATATTAATTTTTTAA
*
1097048 TATTATATTATAGATATTTAATTTTATATCA
1 TATTATATTATAGATATTTAATTTAATATCA
1097079 TATAAATTAT
Statistics
Matches: 83, Mismatches: 3, Indels: 9
0.87 0.03 0.09
Matches are distributed among these distances:
59 6 0.07
60 36 0.43
61 16 0.19
62 13 0.16
63 12 0.14
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (63 bp):
TATTATATTATAGATATTTAATTTAATATCAATTTTTAAATAAATTAAATATTAATTTTTTAA
Found at i:1097035 original size:23 final size:23
Alignment explanation
Indices: 1097004--1097049 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1096994 TATAGATATT
*
1097004 AATTTAATATTAATTTTTAAATA
1 AATTAAATATTAATTTTTAAATA
*
1097027 AATTAAATATTAATTTTTTAATA
1 AATTAAATATTAATTTTTAAATA
1097050 TTATATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATTAAATATTAATTTTTAAATA
Found at i:1097052 original size:37 final size:37
Alignment explanation
Indices: 1096967--1097042 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
1096957 TTTTTAAATA
* *
1096967 AATTAAATATTAATTTTTAATATATATTATAGATATT
1 AATTTAATATTAATTTTTAATATAAATTATAGATATT
1097004 AATTTAATATTAATTTTTAA-ATAAATTA-A-ATATT
1 AATTTAATATTAATTTTTAATATAAATTATAGATATT
1097038 AATTT
1 AATTT
1097043 TTTAATATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
34 10 0.27
35 1 0.03
36 7 0.19
37 19 0.51
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (37 bp):
AATTTAATATTAATTTTTAATATAAATTATAGATATT
Found at i:1097633 original size:31 final size:31
Alignment explanation
Indices: 1097575--1097634 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1097565 TAGTTGTATG
* **
1097575 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTACAAAACTAA
1097606 AATTATTTAAATCTCAGTATTACAAAACT
1 AATTATTTAAATCTCAGTATTACAAAACT
1097635 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTACAAAACTAA
Done.