Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006960.1 Hibiscus syriacus cultivar Beakdansim tig00017906_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: 84572
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:865 original size:22 final size:22
Alignment explanation
Indices: 810--879 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
800 ATTATAAATT
810 ATATTAATTATT-TA-TTAAAGTA
1 ATATTAATTATTATATTTAAA--A
*
832 ATATGTTA-TATTATATTTAAAA
1 ATAT-TAATTATTATATTTAAAA
* *
854 ATATTAATTATTAAATTT-TAA
1 ATATTAATTATTATATTTAAAA
875 ATATT
1 ATATT
880 TTTATTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
21 9 0.22
22 22 0.55
23 4 0.10
24 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (22 bp):
ATATTAATTATTATATTTAAAA
Found at i:912 original size:34 final size:34
Alignment explanation
Indices: 839--939 Score: 80
Period size: 34 Copynumber: 2.9 Consensus size: 34
829 GTAATATGTT
* * *
839 ATATTATATTTAAAAATATTAATTATTA-AATTTTAA
1 ATATTA-AATTAAAAATA-T-ATTATTATTATATTAA
**
875 ATATTTTTATTAAAAATATATTATTATTATATT-A
1 ATA-TTAAATTAAAAATATATTATTATTATATTAA
*
909 ATATTAAATATATAAATATATTATTCATTAT
1 ATATTAAAT-TAAAAATATATTATT-ATTAT
940 TATAATTACT
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
33 4 0.08
34 25 0.47
35 10 0.19
36 12 0.23
37 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (34 bp):
ATATTAAATTAAAAATATATTATTATTATATTAA
Found at i:1089 original size:21 final size:22
Alignment explanation
Indices: 1056--1110 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
1046 TTGATTACTT
1056 TATTATAATATTAAAAATA-TAA
1 TATTAT-ATATTAAAAATATTAA
*
1078 TATTATATATTAGAAATATTAA
1 TATTATATATTAAAAATATTAA
1100 TATATATATAT
1 TAT-TATATAT
1111 ATATATATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 11 0.37
22 12 0.40
23 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TATTATATATTAAAAATATTAA
Found at i:1104 original size:29 final size:27
Alignment explanation
Indices: 1056--1139 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 27
1046 TTGATTACTT
*
1056 TATTATAATATTAAAAATATAATATTATA
1 TATTA-AATATT-AATATATAATATTATA
1085 TATTAGAAATATTAATATATATATATATATA
1 TATT--AAATATTAATATATA-ATAT-TATA
1116 TATTAAATATTTAATA-ATAATATT
1 TATTAAATA-TTAATATATAATATT
1140 TTTGATTAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
27 1 0.02
28 4 0.08
29 19 0.39
30 16 0.33
31 9 0.18
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (27 bp):
TATTAAATATTAATATATAATATTATA
Found at i:2989 original size:633 final size:636
Alignment explanation
Indices: 1417--3948 Score: 4048
Period size: 629 Copynumber: 4.0 Consensus size: 636
1407 CTATCACTCA
* * *
1417 ACTCCTACAGTAAATCCAAAATAAAAAGAAAAATAAAGGAAAATAATATATTGTATGAAAAAGAT
1 ACTCCTACAATAAATCCAAAA-AAAAAAAAAAAAAAAGGAAAAT-A-ATATTGTATGAAAAAGAT
*
1482 ACATGGA-CCCAGTCCACAA-TTTCATTCCATCTTAAATACTGTAAC-ATGATTATGTAATTTAT
63 ACATGGACCCCAATCCACAATTTTCATTCCATCTTAAATACTGTAACAATGATTATGTAATTTAT
* *
1544 GTCATTGAAACATGTGACTAATTAATC-ATCAAATCATCATCGATATTTTGATTTAATCAATCAA
128 GTCATTAAAACATGTGACTAATTAATCAATCAAACCATCATCGATATTTTGATTTAATCAATCAA
* *
1608 TCGTTTAATTATTT-AATATTTCAGGTGACATGATAATT-AAATATTTTGTTATAA-TACA-ATT
193 TCGTTTAATTATTTAAATATTTCAGGTGACATGACAATTAAAATATTTTGTTATAATTATACA-T
* *
1669 AGTCATTATTACTTATATATTGTTTTAATTTGATCTTAATTTTAATAAACTAAATTAAATTTAAC
257 AGTCA-TATTACTTATATATTGTTTCAATTTGGTCTTAATTTTAATAAACTAAATT-AATTTAAC
* *
1734 TTCTCGAATCATGTGGTGTCATATGTTATTAGTGATACTATGGTTGAAAATAAATAAATCAATGC
320 -TCTCGAATCATGTGGTGTCATATGTCATTAGTGACACTATGGTTGAAAATAAATAAATCAATGC
* * * *
1799 AAACGAGGGTAAGGGGAATC-AACAAAGAACCCTTT-GGTG--ACATAAGCACCAAACCATTAAG
384 ACATGAGGGCAAGGGGAATCAAACAAAGAACCCTTTGGGTGATATATAAGCACCAAACCATTAAG
1860 TCAAGGCAACCATTTCACATAATTTAGACAATAAATATATATAATGTATCTTAGTATAT-AACAC
449 TCAAGGCAACCATTTCACATAATTTAGACAATAAATATATATAATGTATCTTAGTATATAAACAC
* *
1924 -TTACTTAAATTCAT-ATATTTTATATTCTTAATTTTAAAAATAAATTTTATTTTTGTCTTAATT
514 TTTACTTAAATTCATAATATTTTATATTCTTAATTTT-TAAATAAATTTTATTTTTGTCTTAACT
1987 TATT-AATGTA-TTTTTTATTTTAATATAAAATATATGTTTTAATCTTATCTTCACTTG
578 TATTAAATGTATTTTTTTATTTTAATATAAAATATATGTTTTAATCTTATCTTCACTTG
* *
2044 ACTCCTACAGT-AATCCAAAAATAAAAAGAAAAATAAAGGAAAATAATATTGTATGAAAAAGGAT
1 ACTCCTACAATAAATCCAAAAA-AAAAA-AAAAAAAAAGGAAAATAATATTGTATGAAAAA-GAT
*
2108 ACATGGACCCCAGTCCACAATTTTCATTCCATCTTAAATAC--TAACAATGATTATGTAATTTAT
63 ACATGGACCCCAATCCACAATTTTCATTCCATCTTAAATACTGTAACAATGATTATGTAATTTAT
* * *
2171 GTCATTGAAACATGTGACTAATTATTCAATCAAACCATCATTGATATTTTGATTTAATCAATCAA
128 GTCATTAAAACATGTGACTAATTAATCAATCAAACCATCATCGATATTTTGATTTAATCAATCAA
*
2236 TCGTTTAATTA-TTAAATATTTCAGGTGATATGACAATTAAAATATTTTGTTATAATTATACATT
193 TCGTTTAATTATTTAAATATTTCAGGTGACATGACAATTAAAATATTTTGTTATAATTATACA-T
2300 AGTCATTATTACTTATATATTGTTTCAATTTGGTCTTAATTTTAATAAACTAAATTAAATTT-AC
257 AGTCA-TATTACTTATATATTGTTTCAATTTGGTCTTAATTTTAATAAACTAAATT-AATTTAAC
*
2364 TCTCGAATCATGTGATGTCATATGTCATTAGTGACACTATGGTTGAAAAATAAATAAATC-ATGC
320 TCTCGAATCATGTGGTGTCATATGTCATTAGTGACACTATGGTTG-AAAATAAATAAATCAATGC
*
2428 ACATGAGGGCAAGGGGAATC-AACAAAGAACCCTTTGGGTGATATATAAGCACCAAATCATTAAG
384 ACATGAGGGCAAGGGGAATCAAACAAAGAACCCTTTGGGTGATATATAAGCACCAAACCATTAAG
*
2492 TCAAGGC-ACCATTTCACATAATTTAGACAATAATCATATATATAATGTATCTTAGTATCTAAAC
449 TCAAGGCAACCATTTCACATAATTTAGACAATAA--ATATATATAATGTATCTTAGTATATAAAC
2556 ACTTTACTTAAATTCATAATATTTTATATTCTT-ATTTTTAAAT-AATTTTATTTTTGTCTTAAC
512 ACTTTACTTAAATTCATAATATTTTATATTCTTAATTTTTAAATAAATTTTATTTTTGTCTTAAC
2619 TTATTAAATGTATTTTTTTA-TTTAATATAAAAATATATGTTTTAATCTTATCTTCACTTG
577 TTATTAAATGTATTTTTTTATTTTAATAT-AAAATATATGTTTTAATCTTATCTTCACTTG
2679 ACTCCTACAATAAATCCAAAAAAAAGAAAAAAAAAAAGG-AAATAATATTGTATGAAAAAGATAC
1 ACTCCTACAATAAATCCAAAAAAAA-AAAAAAAAAAAGGAAAATAATATTGTATGAAAAAGATAC
2743 ATGGA-CCCAATCCACAATTTTCATTCCATCTTAAATACTGTAACAATGATTATGTAATTTATGT
65 ATGGACCCCAATCCACAATTTTCATTCCATCTTAAATACTGTAACAATGATTATGTAATTTATGT
2807 CATTAAAACATGTGACTAAATTAATCAATCAAACCATCATCGATATTTTGATTTAATCAATCAGA
130 CATTAAAACATGTGACT-AATTAATCAATCAAACCATCATCGATATTTTGATTTAATCAATCA-A
*
2872 TTGTTTAATTATTTAAATATTTCAGGTGACATGACAATTAAAATATTTTTGTTATAATTA-ACA-
193 TCGTTTAATTATTTAAATATTTCAGGTGACATGACAATTAAAATA-TTTTGTTATAATTATACAT
*
2935 AGTC-TATTATTTATATATTGTTTCAATTTGGTCTTAATTTTAATAAACTAAATTAATTTAACTC
257 AGTCATATTACTTATATATTGTTTCAATTTGGTCTTAATTTTAATAAACTAAATTAATTTAACTC
*
2999 TCGAATCGTGTGGTG---TATGTCATTAGTGACACTATGGTTGAAAATAAATAAATCAATGCACA
322 TCGAATCATGTGGTGTCATATGTCATTAGTGACACTATGGTTGAAAATAAATAAATCAATGCACA
3061 TGAGGGCAAGGGGAATCAAACAAAGAACCCTTTGGGTGATATATAAGCACCAAACCATTAAGTCA
387 TGAGGGCAAGGGGAATCAAACAAAGAACCCTTTGGGTGATATATAAGCACCAAACCATTAAGTCA
3126 AGGCAACCATTTCACATAATTTAGACAATAAATCATATATAATGTATCTTAGTATATAAACACTT
452 AGGCAACCATTTCACATAATTTAGACAATAAAT-ATATATAATGTATCTTAGTATATAAACACTT
3191 TACTTAAATTCATAATA-TTTATATTC-TAATTTTTAAATAAATTTTATTTTTGTCTTAACTTAT
516 TACTTAAATTCATAATATTTTATATTCTTAATTTTTAAATAAATTTTATTTTTGTCTTAACTTAT
3254 TAAATGTATTTTTTTTATTTTAATATAAAAATATATGTTTTAATCTTATCTTCACTTG
581 TAAATGTA-TTTTTTTATTTTAATAT-AAAATATATGTTTTAATCTTATCTTCACTTG
3312 ACTCCTACAATAAATCCAAAAAAAAAAAAGAAAAAAAAGG---A-AATATTGTATG-AAAAGATA
1 ACTCCTACAATAAATCC-AAAAAAAAAAA-AAAAAAAAGGAAAATAATATTGTATGAAAAAGATA
3372 CA-GGACCCCAATCCACAATTTTCATTCCATCTTAAATACTGT-ACAATGATTATGTAATTTATG
64 CATGGACCCCAATCCACAATTTTCATTCCATCTTAAATACTGTAACAATGATTATGTAATTTATG
3435 TCATTAAAACATGTGACTAAATTAATCAATCAAACCATCATCGATATTTTGATTTAATCAATCAG
129 TCATTAAAACATGTGACT-AATTAATCAATCAAACCATCATCGATATTTTGATTTAATCAATCA-
*
3500 ATTGTTTAATTATTTAAATATTTCAGGTGACATGACAATTAAAATATTTTGTTATAATTATACAA
192 ATCGTTTAATTATTTAAATATTTCAGGTGACATGACAATTAAAATATTTTGTTATAATTATAC-A
3565 TTAGTCATTATTACTTATATATTGTTTCAATTT-GTCTTAATTTTAATAAAACTAAATTAATTTA
256 -TAGTCA-TATTACTTATATATTGTTTCAATTTGGTCTTAATTTTAAT-AAACTAAATTAATTTA
*
3629 ACTCTCGAAATCGTGTGGTGTCATATGTCATTAGTGACACTATGGTTGAAAAT-AAT-AATCAAT
318 ACTCTCG-AATCATGTGGTGTCATATGTCATTAGTGACACTATGGTTGAAAATAAATAAATCAAT
*
3692 GCACAT-AGGGCAAGGGGAATCAAACAAAGAACCCTTTGGGTGATATATAAGCACCAAACCAGTA
382 GCACATGAGGGCAAGGGGAATCAAACAAAGAACCCTTTGGGTGATATATAAGCACCAAACCATTA
*
3756 ATTCAAGGC-ACCATTTCACATAATTTAGACAATAAATCATATATATAATGTATCTTAGTATATA
447 AGTCAAGGCAACCATTTCACATAATTTAGACAAT-AA--ATATATATAATGTATCTTAGTATATA
3820 AACACTTTACTTAAATTCATAATATTTTATATTCTTAATTTTTAAAAATAAATTTTATTTTTGTC
509 AACACTTTACTTAAATTCATAATATTTTATATTCTTAATTTTT--AAATAAATTTTATTTTTGTC
3885 TTAACTTATTAAATGTATTTTTTTATTTTAATATAAAATATATGTTTTAATCTTATCTTCACTT
572 TTAACTTATTAAATGTATTTTTTTATTTTAATATAAAATATATGTTTTAATCTTATCTTCACTT
3949 ACAAGTATTT
Statistics
Matches: 1808, Mismatches: 36, Indels: 111
0.92 0.02 0.06
Matches are distributed among these distances:
625 16 0.01
626 28 0.02
627 84 0.05
628 102 0.06
629 246 0.14
630 140 0.08
631 229 0.13
632 103 0.06
633 198 0.11
634 172 0.10
635 206 0.11
636 99 0.05
637 49 0.03
638 82 0.05
639 17 0.01
640 37 0.02
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (636 bp):
ACTCCTACAATAAATCCAAAAAAAAAAAAAAAAAAAGGAAAATAATATTGTATGAAAAAGATACA
TGGACCCCAATCCACAATTTTCATTCCATCTTAAATACTGTAACAATGATTATGTAATTTATGTC
ATTAAAACATGTGACTAATTAATCAATCAAACCATCATCGATATTTTGATTTAATCAATCAATCG
TTTAATTATTTAAATATTTCAGGTGACATGACAATTAAAATATTTTGTTATAATTATACATAGTC
ATATTACTTATATATTGTTTCAATTTGGTCTTAATTTTAATAAACTAAATTAATTTAACTCTCGA
ATCATGTGGTGTCATATGTCATTAGTGACACTATGGTTGAAAATAAATAAATCAATGCACATGAG
GGCAAGGGGAATCAAACAAAGAACCCTTTGGGTGATATATAAGCACCAAACCATTAAGTCAAGGC
AACCATTTCACATAATTTAGACAATAAATATATATAATGTATCTTAGTATATAAACACTTTACTT
AAATTCATAATATTTTATATTCTTAATTTTTAAATAAATTTTATTTTTGTCTTAACTTATTAAAT
GTATTTTTTTATTTTAATATAAAATATATGTTTTAATCTTATCTTCACTTG
Found at i:3967 original size:27 final size:27
Alignment explanation
Indices: 3929--3986 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
3919 AAAATATATG
* *
3929 TTTTAATCTTATCTTCACTTACAAGTA
1 TTTTAATCTTATCTTCACTTAAAAATA
*
3956 TTTTAA-CTTTATCTTCATTTAAAAATA
1 TTTTAATC-TTATCTTCACTTAAAAATA
3983 TTTT
1 TTTT
3987 TTTTATCTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.31, C:0.14, G:0.02, T:0.53
Consensus pattern (27 bp):
TTTTAATCTTATCTTCACTTAAAAATA
Found at i:4000 original size:25 final size:26
Alignment explanation
Indices: 3963--4015 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
3953 GTATTTTAAC
* *
3963 TTTATCTTCA-TTTAAAAATATTTTT
1 TTTATCTTAATTTTAAAAATATATTT
*
3988 TTTATCTTAATTTTTAAAATATATTT
1 TTTATCTTAATTTTAAAAATATATTT
4014 TT
1 TT
4016 CTAATTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTATCTTAATTTTAAAAATATATTT
Found at i:4089 original size:31 final size:27
Alignment explanation
Indices: 4042--4146 Score: 79
Period size: 31 Copynumber: 3.7 Consensus size: 27
4032 AAAATATATT
*
4042 ATATAGTTTATTCTTATTTCAATATAATAA
1 ATATATTTTA-TCTTATTTCAAT-TAA-AA
* *
4072 TATATATTTTGTCCTTATATTCACTTAAAA
1 -ATATATTTTAT-CTTAT-TTCAATTAAAA
*
4102 ATATATTTTATCTTATTTTAAATT--AA
1 ATATATTTTATCTTA-TTTCAATTAAAA
*
4128 AGATATTTTATTCTTATTT
1 ATATATTTTA-TCTTATTT
4147 TAAATAATAT
Statistics
Matches: 63, Mismatches: 7, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
26 14 0.22
27 5 0.08
28 9 0.14
29 11 0.17
30 3 0.05
31 16 0.25
32 5 0.08
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.54
Consensus pattern (27 bp):
ATATATTTTATCTTATTTCAATTAAAA
Found at i:7559 original size:11 final size:11
Alignment explanation
Indices: 7543--7569 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
7533 TTCATAGCCA
7543 TTTTATGAAAG
1 TTTTATGAAAG
7554 TTTTATGAAAG
1 TTTTATGAAAG
7565 TTTTA
1 TTTTA
7570 GCTGAAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (11 bp):
TTTTATGAAAG
Found at i:7853 original size:260 final size:261
Alignment explanation
Indices: 7141--12085 Score: 4715
Period size: 260 Copynumber: 19.2 Consensus size: 261
7131 CATTTATGCA
* *
7141 CCAGAATATCACGGTTCTAAAGGAAATAGGTTGCGACTTTTAATGTCAACTTGTGTATTAACAGA
1 CCAGAATATCACGGTTCTAAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGA
* * * * * * * * *
7206 ATAGATTGCGTCCAGAGTATCATGACCCCAAAGAAAACATGTTGCAATCTGAAATATTAACATTT
66 ATAGATTGCGCCCAAAGTGTCATGGCCCCAAAGAAAGCAAGTTGCAATATGGAATATTATCATTT
* ** *
7271 T-AAAAATAAAAGCGATTGCGCCTAAAGTATTATGAGTGTTTTAGCTC-AAGGAGCCTTGGCGTT
131 TAAAAAATAAAAGCGATTGCACCTAAAGTATTATGAAAGTTTTAG-TCGATGGAGCCTTGGCGTT
* * * *
7334 CC-C-CTACAATCAAATAGATTAAGAGCACAAAGTATTACGATTAAGC-AAATAGAAATGGTTGC
195 CCACACGACAATCAAATAGGTTAAGAGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTTGC
7396 ACC
260 -CC
* * * * * *
7399 CCAGAATATTATGGTTCTCAAGGAAATAGGTT--AAATTATATAT-T--A--T-T-TATCT-A-A
1 CCAGAATATCACGGTTCTAAAGGAAATAGGTTGCGACTTGTA-ATGTCAACTTGTGTAT-TAATA
* ** ** * ** ** * * * * * *
7453 CAAT-GA-ACCAAACCAAA-TGT-ATGATCTGC-TTGAATGGCTTAGTACTCCTAGAT-G-TTCA
64 GAATAGATTGC-GCCCAAAGTGTCATG-GCCCCAAAGAA-AGC-AAGT--TGCAATATGGAAT-A
* *** * * * ** *
7511 TTATAATTTAGGTACAATTCCCTTCATAGCCATTTTA--TGAAAGTTTTATGAAAGTTTTAG-CT
122 TTATCATTT---TA-AA---AAATAAAAGCGATTGCACCT-AAAGTATTATGAAAGTTTTAGTC-
* * * * * *
7573 GAAGGAACCTTGACGTTCCACACGACAATCAAATAGATTAAGAGCACAAAAATATTATGATTAGG
178 GATGGAGCCTTGGCGTTCCACACGACAATCAAATAGGTTAAGAGCAC-AAAGTATTACGATTAGG
*
7638 CAAAATAGAAACGGTTGCTTC
242 CAAAATAGAAACGGTTGC-CC
* * *
7659 CTAGAATATCATGGTTCTCAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAG-
1 CCAGAATATCACGGTTCTAAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGA
* * * *
7723 ATAGATTGCACCCAAAGTGTCATGGCCCCAAAGAAAGCAAGTTGTAATATGGACTATTAACATTT
66 ATAGATTGCGCCCAAAGTGTCATGGCCCCAAAGAAAGCAAGTTGCAATATGGAATATTATCATTT
** * *
7788 T-AAAAATAAAAGCGATTGTGCCTAAAGTGTTTTGAAAG-TTTAGTCGATGGAGCCTTGGCGTTC
131 TAAAAAATAAAAGCGATTGCACCTAAAGTATTATGAAAGTTTTAGTCGATGGAGCCTTGGCGTTC
* * * * * *
7851 CACATGGCAATTAAATAGGTTAAGAACACAAAGTATTACGATTAGGCAAAACAGAAACGATTGCG
196 CACACGACAATCAAATAGGTTAAGAGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTTGC-
7916 CC
260 CC
* *
7918 CC---ATA--A------T-----ACAT-GGTTGCGACTTGTAATGTCAACTTGTGTACTAATAGA
1 CCAGAATATCACGGTTCTAAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGA
* * * * * *
7966 ACAGATTGCACCC-AA-TTTCATGTCCCCCAAAGAAAGCACGTTGCAATATGAAATATTATCATT
66 ATAGATTGCGCCCAAAGTGTCATG-GCCCCAAAGAAAGCAAGTTGCAATATGGAATATTATCATT
* * *
8029 TTAAAAAATAAAAGCGATTGAACGTAAAGTATTATGCAAGTTTTAGTCGATGGAGCCTTGGCGTT
130 TTAAAAAATAAAAGCGATTGCACCTAAAGTATTATGAAAGTTTTAGTCGATGGAGCCTTGGCGTT
** * *
8094 CTGCACGACAAACAAATAGGTTAAGAGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTT-A
195 CCACACGACAATCAAATAGGTTAAGAGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTTGC
8158 CC
260 CC
* *
8160 CCAAAATATCACGGTTCTAAAGGAAATATGTTGCGACTTGTAATGTC-ACTTGTGTATTAATAGA
1 CCAGAATATCACGGTTCTAAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGA
* * * * *
8224 ATAGATTGCGCCCAGAGTGTCATTGCCCCCAAAAAGAAAGCACGTTGCAATCTAGAATATTATCA
66 ATAGATTGCGCCCAAAGTGTCA-TGGCCCC--AAAGAAAGCAAGTTGCAATATGGAATATTATCA
* ** *
8289 TTTTAAAAAATAAAAGCGATTGAATGTAAAGTATTATGAAAGTTTTAGTTGATGGAGCCTTGGCG
128 TTTTAAAAAATAAAAGCGATTGCACCTAAAGTATTATGAAAGTTTTAGTCGATGGAGCCTTGGCG
** * * *
8354 TTCTGCACAACAAACAAATAGGTTAAGAGCACAAAGTATTACGATTAGGAAAAATAGAAACGGTT
193 TTCCACACGACAATCAAATAGGTTAAGAGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTT
*
8419 ACGCC
258 GC-CC
* * * * *
8424 CCAAAATATCACAGTTCTAAAGGGAATAGGTTGTGACTTGTAATGTCAACTTGTGTATTATTAGA
1 CCAGAATATCACGGTTCTAAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGA
* * * * * *
8489 ATAGATTGCTCCCAGAGTGTCATGGCCCCTAAGGTAAGCACGTTGCAATATGTAATATTATCATT
66 ATAGATTGCGCCCAAAGTGTCATGGCCCC-AAAGAAAGCAAGTTGCAATATGGAATATTATCATT
* * ** * * *
8554 TTTAAAAATAAAAGCAATTGCAATTAAAGAATTATGAAAGTTGTAGTCGATGAAGCCTTGGCGTT
130 TTAAAAAATAAAAGCGATTGCACCTAAAGTATTATGAAAGTTTTAGTCGATGGAGCCTTGGCGTT
* * * * * **
8619 CCCCACAAAAATCAAATAGGTTAATAGCACAAAATATTACGA-TAGGCAAAATAGAAACTATTGT
195 CCACACGACAATCAAATAGGTTAAGAGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTTG-
*
8683 GCC
259 CCC
* * * *
8686 CTAGAATATCAC-GTTCTAAAGGAAATAGGTTGCAACTCGTAATGTC-ACTTGTGTATTAATTG-
1 CCAGAATATCACGGTTCTAAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGA
* * *
8748 ATAGATTGCGCTCAGAGTATCATGGCCCCCAAAGAAAGTGC-A-TTGCAATATGGAATATTATCA
66 ATAGATTGCGCCCAAAGTGTCATGG-CCCCAAAGAAA--GCAAGTTGCAATATGGAATATTATCA
* *
8811 TTTTAAAAAATAAAAGTGATTGCATCTAAAGTATTATGAAAGTTTTA-TCTGATGGAGCCTTGGC
128 TTTTAAAAAATAAAAGCGATTGCACCTAAAGTATTATGAAAGTTTTAGTC-GATGGAGCCTTGGC
* * * * * *
8875 GTTCCCCACGACAATCAAATAGGTTAATAACACAAAGTATTACGATTAGGTAAAACAGAAATGGT
192 GTTCCACACGACAATCAAATAGGTTAAGAGCACAAAGTATTACGATTAGGCAAAATAGAAACGGT
8940 TGCGCC
257 TGC-CC
* * *
8946 CCAG-A-ATCACGGTTCTAAAGAAAATAGGTTACGACTTGTAATGTCAACTTGTGTATTAACAGA
1 CCAGAATATCACGGTTCTAAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGA
* * *
9009 ATAGATTGCGCCCAAAGTGTCATGGCCCACAAAGAAA-CACGTTGCAATCTAGAATA-TATCATT
66 ATAGATTGCGCCCAAAGTGTCATGGCCC-CAAAGAAAGCAAGTTGCAATATGGAATATTATCATT
* * *** * * * *
9072 TTAAAAAAT-AAAGCAATTACGTGTAAAGTATTATGAAAGTTTTCGTTGATGGACCCTTGGCATT
130 TTAAAAAATAAAAGCGATTGCACCTAAAGTATTATGAAAGTTTTAGTCGATGGAGCCTTGGCGTT
* * *
9136 CCACACAACAAACAAATAGGTTAAGAGCA-AAAGTATTATGATTAGGCAAAATAGAAACGGTTAT
195 CCACACGACAATCAAATAGGTTAAGAGCACAAAGTATTACGATTAGGCAAAATAGAAACGG-T-T
9200 G-CC
258 GCCC
* * * * * * * *
9203 CCATAATATCACGATCCTAAA--AAATAGGTTGTGATTTGTAATGTCAACCTATGTATTATTAGA
1 CCAGAATATCACGGTTCTAAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGA
* * * ** * *
9266 ATAGGTTGC-TCCAAGAGTGTCATGGCCTCTC-AGGAAAGCTCGTTGCAATATGAAATATTATAA
66 ATAGATTGCGCCCAA-AGTGTCATGGCC-C-CAAAGAAAGCAAGTTGCAATATGGAATATTATCA
* ** * *
9329 TTTTAAAAAATAAAAGCAATTGCAATTAAAGTATTATGAAAGTTTTAGCCGATGGAGCCTTGGCA
128 TTTTAAAAAATAAAAGCGATTGCACCTAAAGTATTATGAAAGTTTTAGTCGATGGAGCCTTGGCG
* * * *
9394 TTCCCCATGACAATCAAATAGGTTAAGAGCA-AAATTATTACGATTAGGAAAAATAGAAACGGTT
193 TTCCACACGACAATCAAATAGGTTAAGAGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTT
9458 GCACC
258 GC-CC
* * * *
9463 CC--AATATCATGGTTCT-AAGG-AATAAGTTGTGAATTG-AACTGTCAACTTGTGTATTAATAG
1 CCAGAATATCACGGTTCTAAAGGAAATAGGTTGCGACTTGTAA-TGTCAACTTGTGTATTAATAG
* *
9523 -ATAGATTGTGCCCAGAGTGTCATGGCCCCAAAGAAATCGC-A-TTGCAATATGGAATATTATCA
65 AATAGATTGCGCCCAAAGTGTCATGGCCCCAAAGAAA--GCAAGTTGCAATATGGAATATTATCA
* * * *
9585 -TTT-AAAAATAAAAGTGATTGCA-CTAAAAGTATTATGAAAGTTATAGCCGATGGAGCCTTGGT
128 TTTTAAAAAATAAAAGCGATTGCACCT-AAAGTATTATGAAAGTTTTAGTCGATGGAGCCTTGGC
* * * * *
9647 GTTCCCCACGACAATCAAATAGGTTAAGAACACAAAGTATTACGATTAGGTAAAAACAGAAATGG
192 GTTCCACACGACAATCAAATAGGTTAAGAGCACAAAGTATTACGATTAGG-CAAAATAGAAACGG
9712 TTGCGCC
256 TTGC-CC
* *
9719 CCAGAATATCACGATTCTAAAGGAAATAGGTTGCGACTTGTAATGTCAACTTATGTATTAATAGA
1 CCAGAATATCACGGTTCTAAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGA
* * * *
9784 ATAGATTGCGTCCAGAGTGTCATGGCCCCCAAAGAAA-C-CGTTACAATATGGAATATTATCATT
66 ATAGATTGCGCCCAAAGTGTCATGG-CCCCAAAGAAAGCAAGTTGCAATATGGAATATTATCATT
* * ** * *
9847 TTAAAAAAT-AAAGCTATTGTATGTAAAGTATTATGAAAGTTTTAG-C-AGTCAGAGCC-TGGTG
130 TTAAAAAATAAAAGCGATTGCACCTAAAGTATTATGAAAGTTTTAGTCGA-T-GGAGCCTTGGCG
** * * * * *
9908 TT-CGTACGACAATCAAATAGTTTAAGAG-ATAAAAGTATTACGATTAGACAAAAATAGAAGCGA
193 TTCCACACGACAATCAAATAGGTTAAGAGCA-CAAAGTATTACGATTAGGC-AAAATAGAAACGG
* *
9971 TTGTGCT
256 TTG-CCC
* * * * * *
9978 CCAGAATATCAGGGATCT-AAGGAAGTAGGTTGTGACTTGTAATGTCAAACTTGTGTATTATTAT
1 CCAGAATATCACGGTTCTAAAGGAAATAGGTTGCGACTTGTAATGTC-AACTTGTGTATTAATAG
* * *** *
10042 AATTA-ATTGCTCCCAGAGTGTCATGGACTTTAAAGAAAGCATGTTGCAATATGGAATATTATCA
65 AA-TAGATTGCGCCCAAAGTGTCATGG-CCCCAAAGAAAGCAAGTTGCAATATGGAATATTATCA
** * *
10106 TTTTAAAAAATAAAAGCGATTGCAATTAAAGTATTATGAAAGTTTTAGCCGATGGAGCCTTGGTG
128 TTTTAAAAAATAAAAGCGATTGCACCTAAAGTATTATGAAAGTTTTAGTCGATGGAGCCTTGGCG
* * **
10171 TTCCCCACGACAATCAAATAGGTTAAGGGCACAAAGTATTACGATTAGGC---A-AGAAATTGTT
193 TTCCACACGACAATCAAATAGGTTAAGAGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTT
* *
10232 ACACT
258 GC-CC
* * *
10237 TCAGAACATAACGGTTCTAAAGGAAATAGGTTGCGACTTGTAATGTCAA----TGTATTAATAG-
1 CCAGAATATCACGGTTCTAAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGA
* * * *
10297 AT--ATTGCTCCCAAAGTGTCATGCCCCCCAAAGAAAGCGCA-TTGCAATCTGGAATATTATCAT
66 ATAGATTGCGCCCAAAGTGTCATG-GCCCCAAAGAAAGC-AAGTTGCAATATGGAATATTATCAT
* * *
10359 TTTAAAAAATAAAAGTGATTGCGCCTAAAGTATTATGAAAGTTTTAGTCGATGGAGACTTGGCGT
129 TTTAAAAAATAAAAGCGATTGCACCTAAAGTATTATGAAAGTTTTAGTCGATGGAGCCTTGGCGT
** * * * * *** * *
10424 T-CGTAGGACAATAAAATAAGTTAAGAGCACAAAGTATTATGATTATTTAAACTAGAAACGGTTA
194 TCCACACGACAATCAAATAGGTTAAGAGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTTG
10488 CGCC
259 C-CC
* *
10492 GCAGAATATCACGGTT-TAAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAACAGA
1 CCAGAATATCACGGTTCTAAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGA
* * * * * *
10556 ATAGATTGCACCCACAGTGTCATGGCCCCAAAGAAAGCATGTTGCAATCTAGTATATTATCATTT
66 ATAGATTGCGCCCAAAGTGTCATGGCCCCAAAGAAAGCAAGTTGCAATATGGAATATTATCATTT
* * * * * * *
10621 TAAAAAATAAAAG-TATTGTACGTGAAGTATTATGAAAGTTTTCA-CCGGTGGAGCCTTGGCATT
131 TAAAAAATAAAAGCGATTGCACCTAAAGTATTATGAAAGTTTT-AGTCGATGGAGCCTTGGCGTT
* *
10684 CC-CTACGAAAATCAAATAGGTTAAGAGCACAAA-TATTACGATTAGGCAAAATAGAAACGGTTA
195 CCAC-ACGACAATCAAATAGGTTAAGAGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTTG
10747 CGCC
259 C-CC
* * * * * *
10751 CCAAAATATCACGTTTCTAAAGGAAATAGGTTGCGACTTGTAATTTCTACTTGTGTATTAACATA
1 CCAGAATATCACGGTTCTAAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGA
* * * * * * * *
10816 ATCGATTTC-ACC--AGTGTCAT-TCCCCAAAGAAAGCATGTTACAATCTGAAATATT-TACATT
66 ATAGATTGCGCCCAAAGTGTCATGGCCCCAAAGAAAGCAAGTTGCAATATGGAATATTAT-CATT
** * *
10876 TTAAAAAATAAAAATGATTGCATCTAAAGTATTATGAAAGTTTTAG-CTGATGGAGCCTTGGTGT
130 TTAAAAAATAAAAGCGATTGCACCTAAAGTATTATGAAAGTTTTAGTC-GATGGAGCCTTGGCGT
* * * * * *
10940 TCC-CTATGATAATCAAATAGATTAAGAGCACAAAGCATTACGATTAGGCAAAATAAAAACGATT
194 TCCAC-ACGACAATCAAATAGGTTAAGAGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTT
11004 GCGCC
258 GC-CC
* * * * * *
11009 CCAAAATATAACAGTTCTCAATGAAATAGGTTGCGACTTGTAATTTCAACTTGTGTATTAATAGA
1 CCAGAATATCACGGTTCTAAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGA
* *
11074 ATAGATTGCGCTCAGAA-TGTCATGGCCCCAAAGAAAGCACA-TTGCAATCTGGAATATTATCAT
66 ATAGATTGCGCCCA-AAGTGTCATGGCCCCAAAGAAAGCA-AGTTGCAATATGGAATATTATCAT
* *
11137 TTTAAAAAATAAAAGCGATTGCACGTAAAG--TTATGAAAGTTTTAGTTGATGGAGCCTTGGCGT
129 TTTAAAAAATAAAAGCGATTGCACCTAAAGTATTATGAAAGTTTTAGTCGATGGAGCCTTGGCGT
* * *
11200 TCCACACGACAATCAAATAGGTTAAGAGCACAAAATACTACGATTAGGCAAAATAGACACGGTTG
194 TCCACACGACAATCAAATAGGTTAAGAGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTTG
*
11265 TGCC
259 -CCC
* *
11269 CCATAATATCACGG-T-TAAAGGAAATAGGTTGAGACTTGTAA--TCAACTTGTGTATTAATAGA
1 CCAGAATATCACGGTTCTAAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGA
11330 ATAGATTGCGCCCAAAGTGTCATGGCCCCAAAGAAAG-AATGTTGCAACTAT--AATATTATCAT
66 ATAGATTGCGCCCAAAGTGTCATGGCCCCAAAGAAAGCAA-GTTGCAA-TATGGAATATTATCAT
* * * *** *
11392 TTTAAAATAGAAAAGAGATTGCGTGTAAAGTATTATGAAAGTTTTA-ACGATGGAGCCTTGGCGT
129 TTTAAAAAATAAAAGCGATTGCACCTAAAGTATTATGAAAGTTTTAGTCGATGGAGCCTTGGCGT
* * * * * ** *
11456 TTCATACGATAATCAAATAGGTTAAGAGCAAAAAGTATTACAATTAAACAAAATAGAAGCGGTTG
194 TCCACACGACAATCAAATAGGTTAAGAGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTTG
*
11521 CACT
259 C-CC
* * * *
11525 CCAGAATATCACAGTTCTAAAGAAAATAGGTTGTGAC-T-TATTGTCAACTTGTGTATTAATAGA
1 CCAGAATATCACGGTTCTAAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGA
** * * * * * * *
11588 ATAGATTG-AACCAAGGGTTTCATGGCCCCTAAGGAAAGCAACTTGCAATTTAGAATACTATCAT
66 ATAGATTGCGCCCAA-AGTGTCATGGCCCC-AAAGAAAGCAAGTTGCAATATGGAATATTATCAT
* * ** * * * *
11652 TTTAAAATATAAAAGCAATTGTGCTTAAAGTTTTATGAAAGTTTTAGCCGATAGAGCCTTGGCGT
129 TTTAAAAAATAAAAGCGATTGCACCTAAAGTATTATGAAAGTTTTAGTCGATGGAGCCTTGGCGT
* *
11717 TCC-CACAACAATCAAATAGGTTAAGAGCACAAAGTATTACGATTAGGCAAAATAGAAACTGTTG
194 TCCACACGACAATCAAATAGGTTAAGAGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTTG
11781 -CC
259 CCC
* *
11783 CCAGAATATCACAGTTCTAAAGGAAATAGGTTTCGACTTGTAATGTCAACTTGTGTATTAATAGA
1 CCAGAATATCACGGTTCTAAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGA
* * * *
11848 ATAGATTGTGCCCAAAGTGTCATGGCCCCTAAAGAAAGCACGTTGCAATCTAGAATATTTATCAT
66 ATAGATTGCGCCCAAAGTGTCATGGCCCC-AAAGAAAGCAAGTTGCAATATGGAATA-TTATCAT
* ** * * *
11913 TTTAAAAAATAAAATCGATTGCATGTAAAATATTATGAAAG-TTTAG-CCATCGGAGCCTTGGTG
129 TTTAAAAAATAAAAGCGATTGCACCTAAAGTATTATGAAAGTTTTAGTCGAT-GGAGCCTTGGCG
** * * * * * *
11976 TTCCGTACGACAATCAAATAGTTTAAGAGCACAAAGTAATACAATTAGAC-AAATAGAAGCAGTT
193 TTCCACACGACAATCAAATAGGTTAAGAGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTT
*
12040 GCGCT
258 GC-CC
* * * *
12045 CCAGGATATCACGATTCTAAAGGAAATAAGTTGTGACTTGT
1 CCAGAATATCACGGTTCTAAAGGAAATAGGTTGCGACTTGT
12086 TCTCTTTAAA
Statistics
Matches: 3898, Mismatches: 594, Indels: 386
0.80 0.12 0.08
Matches are distributed among these distances:
241 6 0.00
242 77 0.02
243 46 0.01
244 78 0.02
245 3 0.00
246 6 0.00
247 7 0.00
248 10 0.00
249 12 0.00
250 8 0.00
251 39 0.01
252 111 0.03
253 3 0.00
254 120 0.03
255 94 0.02
256 284 0.07
257 224 0.06
258 489 0.13
259 528 0.14
260 800 0.21
261 298 0.08
262 341 0.09
263 134 0.03
264 92 0.02
265 39 0.01
266 1 0.00
267 6 0.00
268 15 0.00
269 13 0.00
270 8 0.00
271 6 0.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (261 bp):
CCAGAATATCACGGTTCTAAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGA
ATAGATTGCGCCCAAAGTGTCATGGCCCCAAAGAAAGCAAGTTGCAATATGGAATATTATCATTT
TAAAAAATAAAAGCGATTGCACCTAAAGTATTATGAAAGTTTTAGTCGATGGAGCCTTGGCGTTC
CACACGACAATCAAATAGGTTAAGAGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTTGCC
C
Found at i:9374 original size:518 final size:522
Alignment explanation
Indices: 7550--12085 Score: 4611
Period size: 518 Copynumber: 8.8 Consensus size: 522
7540 CCATTTTATG
* * * * * * * *
7550 AAAGTTTTATGAAAGTTTTAGCTGAAGGAACCTTGACGTTCCACACGACAATCAAATAGATTAAG
1 AAAGTATTATGAAAGTTTTAGCCGATGGAGCCTTGGCGTTCCCCACAACAATCAAATAGGTTAAG
* * * * *
7615 AGCACAAAAATATTATGATTAGGCAAAATAGAAACGG-T-TGCTTCCTAGAATATCATGGTTCTC
66 AGCAC-AAAGTATTACGATTAGGCAAAATAGAAACGGTTATGC--CCCAGAATATCACGATTCT-
* *
7678 AAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAG-ATAGATTGCACCCAA-AGT
127 AAAGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGAATAGATTGC-TCCAAGAGT
** * * * *
7741 GTCATGG-CCCCAAAGAAAGCAAGTTGTAATATGGACTATTAACATTTT-AAAAATAAAAGCGAT
191 GTCATGGCCCCCAAAGAAAGCTCGTTGCAATATGAAATATTATCATTTTAAAAAATAAAAGCGAT
* * ** * * *
7804 TG--TGCCTAAAGTGTTTTGAAAG-TTTAGTCGATGGAGCCTTGGCGTTCCACATGGCAATTAAA
256 TGCATG--TAAAGTATTATGAAAGTTTTAG-CGATGGAGCCTTGGCGTTCCGTACGACAATCAAA
* * * *
7866 TAGGTTAAGAACACAAAGTATTACGATTAGGCAAAACAGAAACGATTGCGCCCC--ATA--A---
318 TAGGTTAAGAGCACAAAGTATTACGATTAGGAAAAATAGAAACGGTTGCGCCCCAGATATCACGG
* * *
7924 ---T-----ACAT-GGTTGCGACTTGTAATGTCAACTTGTGTACTAATAGAACAGATTGCACCC-
383 TTCTAAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGAATAGATTGCACCCA
* *
7979 AA-TTTCATGTCCCCCAAAGAAAGCACGTTGCAATAT-GAAATATTATCATTTTAAAAAATAAAA
448 AAGTGTCATG-GCCCCAAAGAAAGCACGTTGCAATATAG-AATATTATCATTTTAAAAAATAAAA
* *
8042 GCGATTGA-ACGT
511 GCAATT-ACATGT
* * ** * *
8054 AAAGTATTATGCAAGTTTTAGTCGATGGAGCCTTGGCGTTCTGCACGACAAACAAATAGGTTAAG
1 AAAGTATTATGAAAGTTTTAGCCGATGGAGCCTTGGCGTTCCCCACAACAATCAAATAGGTTAAG
* *
8119 AGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTTA--CCCCAAAATATCACGGTTCTAAAG
66 AGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTTATGCCCCAGAATATCACGATTCTAAA-
* * *
8182 GAAATATGTTGCGACTTGTAATGTC-ACTTGTGTATTAATAGAATAGATTGCGCCCAGAGTGTCA
130 GAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGAATAGATTGCTCCAAGAGTGTCA
* * *
8246 TTGCCCCCAAAAAGAAAGCACGTTGCAATCT-AGAATATTATCATTTTAAAAAATAAAAGCGATT
195 TGGCCCCC--AAAGAAAGCTCGTTGCAATATGA-AATATTATCATTTTAAAAAATAAAAGCGATT
* * * * * *
8310 GAATGTAAAGTATTATGAAAGTTTTAGTTGATGGAGCCTTGGCGTTCTGCACAACAAACAAATAG
257 GCATGTAAAGTATTATGAAAGTTTTAG-CGATGGAGCCTTGGCGTTCCGTACGACAATCAAATAG
* * *
8375 GTTAAGAGCACAAAGTATTACGATTAGGAAAAATAGAAACGGTTACGCCCCAAAATATCACAGTT
321 GTTAAGAGCACAAAGTATTACGATTAGGAAAAATAGAAACGGTTGCGCCCC-AGATATCACGGTT
* * * * *
8440 CTAAAGGGAATAGGTTGTGACTTGTAATGTCAACTTGTGTATTATTAGAATAGATTGCTCCCAGA
385 CTAAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGAATAGATTGCACCCAAA
* * *
8505 GTGTCATGGCCCCTAAGGTAAGCACGTTGCAATAT-GTAATATTATCATTTTTAAAAATAAAAGC
450 GTGTCATGGCCCC-AAAGAAAGCACGTTGCAATATAG-AATATTATCATTTTAAAAAATAAAAGC
*
8569 AATTGCAAT-T
513 AATTAC-ATGT
* * * * * *
8579 AAAGAATTATGAAAGTTGTAGTCGATGAAGCCTTGGCGTTCCCCACAAAAATCAAATAGGTTAAT
1 AAAGTATTATGAAAGTTTTAGCCGATGGAGCCTTGGCGTTCCCCACAACAATCAAATAGGTTAAG
* ** * *
8644 AGCACAAAATATTACGA-TAGGCAAAATAGAAACTATTGTGCCCTAGAATATCACG-TTCTAAAG
66 AGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTTATGCCCCAGAATATCACGATTCTAAA-
* * * * *
8707 GAAATAGGTTGCAACTCGTAATGTC-ACTTGTGTATTAATTG-ATAGATTGCGCTC-AGAGTATC
130 GAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGAATAGATTGCTC-CAAGAGTGTC
* * *
8769 ATGGCCCCCAAAGAAAG-TGCATTGCAATATGGAATATTATCATTTTAAAAAATAAAAGTGATTG
194 ATGGCCCCCAAAGAAAGCT-CGTTGCAATATGAAATATTATCATTTTAAAAAATAAAAGCGATTG
* * **
8833 CATCTAAAGTATTATGAAAGTTTTATCTGATGGAGCCTTGGCGTTCCCCACGACAATCAAATAGG
258 CATGTAAAGTATTATGAAAGTTTTAGC-GATGGAGCCTTGGCGTTCCGTACGACAATCAAATAGG
* * * * *
8898 TTAATAACACAAAGTATTACGATTAGGTAAAACAGAAATGGTTGCGCCCCAGA-ATCACGGTTCT
322 TTAAGAGCACAAAGTATTACGATTAGGAAAAATAGAAACGGTTGCGCCCCAGATATCACGGTTCT
* * * *
8962 AAAGAAAATAGGTTACGACTTGTAATGTCAACTTGTGTATTAACAGAATAGATTGCGCCCAAAGT
387 AAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGAATAGATTGCACCCAAAGT
*
9027 GTCATGGCCCACAAAGAAA-CACGTTGCAATCTAGAATA-TATCATTTTAAAAAAT-AAAGCAAT
452 GTCATGGCCC-CAAAGAAAGCACGTTGCAATATAGAATATTATCATTTTAAAAAATAAAAGCAAT
*
9089 TACGTGT
516 TACATGT
* ** * * * *
9096 AAAGTATTATGAAAGTTTTCGTTGATGGACCCTTGGCATTCCACACAACAAACAAATAGGTTAAG
1 AAAGTATTATGAAAGTTTTAGCCGATGGAGCCTTGGCGTTCCCCACAACAATCAAATAGGTTAAG
* * *
9161 AGCA-AAAGTATTATGATTAGGCAAAATAGAAACGGTTATGCCCCATAATATCACGATCCTAAA-
66 AGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTTATGCCCCAGAATATCACGATTCTAAAG
* * * * * *
9224 AAATAGGTTGTGATTTGTAATGTCAACCTATGTATTATTAGAATAGGTTGCTCCAAGAGTGTCAT
131 AAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGAATAGATTGCTCCAAGAGTGTCAT
* * * *
9289 GGCCTCTC-AGGAAAGCTCGTTGCAATATGAAATATTATAATTTTAAAAAATAAAAGCAATTGCA
196 GGCC-CCCAAAGAAAGCTCGTTGCAATATGAAATATTATCATTTTAAAAAATAAAAGCGATTGC-
* ** *
9353 AT-TAAAGTATTATGAAAGTTTTAGCCGATGGAGCCTTGGCATTCCCCATGACAATCAAATAGGT
259 ATGTAAAGTATTATGAAAGTTTTAG-CGATGGAGCCTTGGCGTTCCGTACGACAATCAAATAGGT
* * *
9417 TAAGAGCA-AAATTATTACGATTAGGAAAAATAGAAACGGTTGCACCCCA-ATATCATGGTTCT-
323 TAAGAGCACAAAGTATTACGATTAGGAAAAATAGAAACGGTTGCGCCCCAGATATCACGGTTCTA
* * * ** *
9479 AAGG-AATAAGTTGTGAATTG-AACTGTCAACTTGTGTATTAATAG-ATAGATTGTGCCCAGAGT
388 AAGGAAATAGGTTGCGACTTGTAA-TGTCAACTTGTGTATTAATAGAATAGATTGCACCCAAAGT
* * * * **
9541 GTCATGGCCCCAAAGAAATCGCATTGCAATATGGAATATTATCA-TTT-AAAAATAAAAGTGATT
452 GTCATGGCCCCAAAGAAAGCACGTTGCAATATAGAATATTATCATTTTAAAAAATAAAAGCAATT
* *
9604 GCACT-A
517 ACA-TGT
* * *
9610 AAAGTATTATGAAAGTTATAGCCGATGGAGCCTTGGTGTTCCCCACGACAATCAAATAGGTTAAG
1 AAAGTATTATGAAAGTTTTAGCCGATGGAGCCTTGGCGTTCCCCACAACAATCAAATAGGTTAAG
* * * * **
9675 AACACAAAGTATTACGATTAGGTAAAAACAGAAATGGTTGCGCCCCAGAATATCACGATTCTAAA
66 AGCACAAAGTATTACGATTAGG-CAAAATAGAAACGGTTATGCCCCAGAATATCACGATTCTAAA
*
9740 GGAAATAGGTTGCGACTTGTAATGTCAACTTATGTATTAATAGAATAGATTGCGTCC-AGAGTGT
130 -GAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGAATAGATTGC-TCCAAGAGTGT
* * *
9804 CATGGCCCCCAAAGAAA-C-CGTTACAATATGGAATATTATCATTTTAAAAAAT-AAAGCTATTG
193 CATGGCCCCCAAAGAAAGCTCGTTGCAATATGAAATATTATCATTTTAAAAAATAAAAGCGATTG
* * *
9866 TATGTAAAGTATTATGAAAGTTTTAGC-AGTCAGAGCC-TGGTGTT-CGTACGACAATCAAATAG
258 CATGTAAAGTATTATGAAAGTTTTAGCGA-T-GGAGCCTTGGCGTTCCGTACGACAATCAAATAG
* * * * * * * *
9928 TTTAAGAG-ATAAAAGTATTACGATTAGACAAAAATAGAAGCGATTGTGCTCCAGAATATCAGGG
321 GTTAAGAGCA-CAAAGTATTACGATTAG-GAAAAATAGAAACGGTTGCGCCCCAG-ATATCACGG
* * * * * *
9992 ATCT-AAGGAAGTAGGTTGTGACTTGTAATGTCAAACTTGTGTATTATTATAATTA-ATTGCTCC
383 TTCTAAAGGAAATAGGTTGCGACTTGTAATGTC-AACTTGTGTATTAATAGAA-TAGATTGCACC
* *** * *
10055 CAGAGTGTCATGGACTTTAAAGAAAGCATGTTGCAATATGGAATATTATCATTTTAAAAAATAAA
446 CAAAGTGTCATGG-CCCCAAAGAAAGCACGTTGCAATATAGAATATTATCATTTTAAAAAATAAA
* *
10120 AGCGATTGCAAT-T
510 AGCAATTAC-ATGT
* *
10133 AAAGTATTATGAAAGTTTTAGCCGATGGAGCCTTGGTGTTCCCCACGACAATCAAATAGGTTAAG
1 AAAGTATTATGAAAGTTTTAGCCGATGGAGCCTTGGCGTTCCCCACAACAATCAAATAGGTTAAG
* ** ** ** * * *
10198 GGCACAAAGTATTACGATTAGGC---A-AGAAATTGTTACACTTCAGAACATAACGGTTCTAAAG
66 AGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTTATGCCCCAGAATATCACGATTCTAAA-
10259 GAAATAGGTTGCGACTTGTAATGTCAA----TGTATTAATAG-AT--ATTGCTCCCAA-AGTGTC
130 GAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGAATAGATTGCT-CCAAGAGTGTC
* * * * * *
10316 ATGCCCCCCAAAGAAAGCGCATTGCAATCTGGAATATTATCATTTTAAAAAATAAAAGTGATTGC
194 ATGGCCCCCAAAGAAAGCTCGTTGCAATATGAAATATTATCATTTTAAAAAATAAAAGCGATTGC
*** * * * *
10381 GCCTAAAGTATTATGAAAGTTTTAGTCGATGGAGACTTGGCGTT-CGTAGGACAATAAAATAAGT
259 ATGTAAAGTATTATGAAAGTTTTAG-CGATGGAGCCTTGGCGTTCCGTACGACAATCAAATAGGT
* *** * * *
10445 TAAGAGCACAAAGTATTATGATTATTTAAACTAGAAACGGTTACGCCGCAGAATATCACGGTT-T
323 TAAGAGCACAAAGTATTACGATTAGGAAAAATAGAAACGGTTGCGCCCCAG-ATATCACGGTTCT
* *
10509 AAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAACAGAATAGATTGCACCCACAGT
387 AAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGAATAGATTGCACCCAAAGT
* * * * *
10574 GTCATGGCCCCAAAGAAAGCATGTTGCAATCTAGTATATTATCATTTTAAAAAATAAAAGTATTG
452 GTCATGGCCCCAAAGAAAGCACGTTGCAATATAGAATATTATCATTTTAAAAAATAAAAGCAAT-
10639 TAC--GT
516 TACATGT
* * * *
10644 GAAGTATTATGAAAGTTTTCA-CCGGTGGAGCCTTGGCATTCCCTACGAA-AATCAAATAGGTTA
1 AAAGTATTATGAAAGTTTT-AGCCGATGGAGCCTTGGCGTTCCCCAC-AACAATCAAATAGGTTA
* * *
10707 AGAGCACAAA-TATTACGATTAGGCAAAATAGAAACGGTTACGCCCCAAAATATCACGTTTCTAA
64 AGAGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTTATGCCCCAGAATATCACGATTCTAA
* * * * * **
10771 AGGAAATAGGTTGCGACTTGTAATTTCTACTTGTGTATTAACATAATCGATT--T-CACCAGTGT
129 A-GAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGAATAGATTGCTCCAAGAGTGT
* * * **
10833 CAT--TCCCCAAAGAAAGCAT-GTTACAATCTGAAATATT-TACATTTTAAAAAATAAAAATGAT
193 CATGGCCCCCAAAGAAAGC-TCGTTGCAATATGAAATATTAT-CATTTTAAAAAATAAAAGCGAT
* * * * *
10894 TGCATCTAAAGTATTATGAAAGTTTTAGCTGATGGAGCCTTGGTGTTCCCTATGATAATCAAATA
256 TGCATGTAAAGTATTATGAAAGTTTTAGC-GATGGAGCCTTGGCGTTCCGTACGACAATCAAATA
* * * * * * * *
10959 GATTAAGAGCACAAAGCATTACGATTAGGCAAAATAAAAACGATTGCGCCCCAAAATATAACAGT
320 GGTTAAGAGCACAAAGTATTACGATTAGGAAAAATAGAAACGGTTGCGCCCC-AGATATCACGGT
* * * * *
11024 TCTCAATGAAATAGGTTGCGACTTGTAATTTCAACTTGTGTATTAATAGAATAGATTGCGCTCAG
384 TCTAAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGAATAGATTGCACCCA-
* * *
11089 AA-TGTCATGGCCCCAAAGAAAGCACATTGCAATCTGGAATATTATCATTTTAAAAAATAAAAGC
448 AAGTGTCATGGCCCCAAAGAAAGCACGTTGCAATATAGAATATTATCATTTTAAAAAATAAAAGC
* * *
11153 GATTGCACGT
513 AATTACATGT
** * *
11163 AAAG--TTATGAAAGTTTTAGTTGATGGAGCCTTGGCGTTCCACACGACAATCAAATAGGTTAAG
1 AAAGTATTATGAAAGTTTTAGCCGATGGAGCCTTGGCGTTCCCCACAACAATCAAATAGGTTAAG
* * * * * *
11226 AGCACAAAATACTACGATTAGGCAAAATAGACACGGTTGTGCCCCATAATATCACG-GT-TAAAG
66 AGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTTATGCCCCAGAATATCACGATTCTAAA-
* *
11289 GAAATAGGTTGAGACTTGTAA--TCAACTTGTGTATTAATAGAATAGATTGCGCCCAA-AGTGTC
130 GAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGAATAGATTGC-TCCAAGAGTGTC
* * * *
11351 ATGG-CCCCAAAGAAAGAAT-GTTGCAACTAT--AATATTATCATTTTAAAATAGAAAAGAGATT
194 ATGGCCCCCAAAGAAAG-CTCGTTGCAA-TATGAAATATTATCATTTTAAAAAATAAAAGCGATT
* * * * *
11412 GCGTGTAAAGTATTATGAAAGTTTTAACGATGGAGCCTTGGCGTTTCATACGATAATCAAATAGG
257 GCATGTAAAGTATTATGAAAGTTTTAGCGATGGAGCCTTGGCGTTCCGTACGACAATCAAATAGG
* * * * * * *
11477 TTAAGAGCAAAAAGTATTACAATTA-AACAAAATAGAAGCGGTTGCACTCCAGAATATCACAGTT
322 TTAAGAGCACAAAGTATTACGATTAGGA-AAAATAGAAACGGTTGCGCCCCAG-ATATCACGGTT
* * * *
11541 CTAAAGAAAATAGGTTGTGAC-T-TATTGTCAACTTGTGTATTAATAGAATAGATTG-AACCAAG
385 CTAAAGGAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGAATAGATTGCACCCAA-
* * * * * *
11603 GGTTTCATGGCCCCTAAGGAAAGCAAC-TTGCAATTTAGAATACTATCATTTTAAAATATAAAAG
449 AGTGTCATGGCCCC-AAAGAAAGC-ACGTTGCAATATAGAATATTATCATTTTAAAAAATAAAAG
*
11667 CAATT--GTGCTT
512 CAATTACATG--T
* *
11678 AAAGTTTTATGAAAGTTTTAGCCGATAGAGCCTTGGCGTT-CCCACAACAATCAAATAGGTTAAG
1 AAAGTATTATGAAAGTTTTAGCCGATGGAGCCTTGGCGTTCCCCACAACAATCAAATAGGTTAAG
*
11742 AGCACAAAGTATTACGATTAGGCAAAATAGAAACTG-T-TGCCCCAGAATATCAC-AGTTCTAAA
66 AGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTTATGCCCCAGAATATCACGA-TTCTAAA
*
11804 GGAAATAGGTTTCGACTTGTAATGTCAACTTGTGTATTAATAGAATAGATTG-TGCCCAA-AGTG
130 -GAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGAATAGATTGCT--CCAAGAGTG
* * * *
11867 TCATGGCCCCTAAAGAAAGCACGTTGCAATCT-AGAATATTTATCATTTTAAAAAATAAAATCGA
192 TCATGGCCCCCAAAGAAAGCTCGTTGCAATATGA-AATA-TTATCATTTTAAAAAATAAAAGCGA
* * *
11931 TTGCATGTAAAATATTATGAAAG-TTTAGCCATCGGAGCCTTGGTGTTCCGTACGACAATCAAAT
255 TTGCATGTAAAGTATTATGAAAGTTTTAGCGAT-GGAGCCTTGGCGTTCCGTACGACAATCAAAT
* * * * * * * *
11995 AGTTTAAGAGCACAAAGTAATACAATTA-GACAAATAGAAGCAGTTGCGCTCCAGGATATCACGA
319 AGGTTAAGAGCACAAAGTATTACGATTAGGAAAAATAGAAACGGTTGCGCCCCA-GATATCACGG
* *
12059 TTCTAAAGGAAATAAGTTGTGACTTGT
383 TTCTAAAGGAAATAGGTTGCGACTTGT
12086 TCTCTTTAAA
Statistics
Matches: 3399, Mismatches: 477, Indels: 294
0.82 0.11 0.07
Matches are distributed among these distances:
500 21 0.01
501 58 0.02
502 4 0.00
503 30 0.01
504 90 0.03
505 31 0.01
506 81 0.02
507 2 0.00
509 3 0.00
510 15 0.00
511 92 0.03
512 56 0.02
513 112 0.03
514 367 0.11
515 209 0.06
516 398 0.12
517 392 0.12
518 531 0.16
519 72 0.02
520 162 0.05
521 135 0.04
522 154 0.05
523 147 0.04
524 50 0.01
525 173 0.05
526 14 0.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.28
Consensus pattern (522 bp):
AAAGTATTATGAAAGTTTTAGCCGATGGAGCCTTGGCGTTCCCCACAACAATCAAATAGGTTAAG
AGCACAAAGTATTACGATTAGGCAAAATAGAAACGGTTATGCCCCAGAATATCACGATTCTAAAG
AAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGAATAGATTGCTCCAAGAGTGTCAT
GGCCCCCAAAGAAAGCTCGTTGCAATATGAAATATTATCATTTTAAAAAATAAAAGCGATTGCAT
GTAAAGTATTATGAAAGTTTTAGCGATGGAGCCTTGGCGTTCCGTACGACAATCAAATAGGTTAA
GAGCACAAAGTATTACGATTAGGAAAAATAGAAACGGTTGCGCCCCAGATATCACGGTTCTAAAG
GAAATAGGTTGCGACTTGTAATGTCAACTTGTGTATTAATAGAATAGATTGCACCCAAAGTGTCA
TGGCCCCAAAGAAAGCACGTTGCAATATAGAATATTATCATTTTAAAAAATAAAAGCAATTACAT
GT
Found at i:15151 original size:25 final size:25
Alignment explanation
Indices: 15102--15151 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
15092 ACTTCTATTC
* *
15102 AAAAATAATAAAAAAAAATTTAATT
1 AAAAATAATAAAAAAAAAATCAATT
15127 AAAAA-AATTAAAAAAAAAATCAATT
1 AAAAATAA-TAAAAAAAAAATCAATT
15152 GTTAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (25 bp):
AAAAATAATAAAAAAAAAATCAATT
Found at i:15745 original size:17 final size:16
Alignment explanation
Indices: 15718--15753 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
15708 TTAAATATTA
*
15718 TTTTAAATAATTATAT
1 TTTTAAATAATAATAT
15734 TTTTATAATAATAATAT
1 TTTTA-AATAATAATAT
15751 TTT
1 TTT
15754 CACATCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTAAATAATAATAT
Found at i:21995 original size:12 final size:13
Alignment explanation
Indices: 21978--22006 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
21968 TTTAATTGCG
21978 AAAATTAAAA-TT
1 AAAATTAAAATTT
21990 AAAATTAAAATTT
1 AAAATTAAAATTT
22003 AAAA
1 AAAA
22007 CATTTGATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:23447 original size:3 final size:3
Alignment explanation
Indices: 23439--23504 Score: 64
Period size: 3 Copynumber: 21.0 Consensus size: 3
23429 CTGCACAAAT
*
23439 ATA ATA ATA ATTA ATTA ATA ATA AGTA GTA ATA ATA ATA ATAA ATAA
1 ATA ATA ATA A-TA A-TA ATA ATA A-TA ATA ATA ATA ATA AT-A AT-A
23486 ATA ATA AT- ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA
23505 TTTTTTGTAG
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
2 4 0.07
3 36 0.64
4 16 0.29
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:23475 original size:16 final size:14
Alignment explanation
Indices: 23439--23504 Score: 75
Period size: 14 Copynumber: 4.6 Consensus size: 14
23429 CTGCACAAAT
23439 ATAATAATAAT-TA
1 ATAATAATAATATA
23452 ATTAATAATAAGTAGTA
1 A-TAATAATAA-TA-TA
23469 ATAATAATAATA-A
1 ATAATAATAATATA
23482 ATAAATAATAATATA
1 AT-AATAATAATATA
23497 ATAA-AATA
1 ATAATAATA
23505 TTTTTTGTAG
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
13 8 0.17
14 21 0.45
15 6 0.13
16 9 0.19
17 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (14 bp):
ATAATAATAATATA
Found at i:23475 original size:30 final size:28
Alignment explanation
Indices: 23439--23504 Score: 89
Period size: 30 Copynumber: 2.3 Consensus size: 28
23429 CTGCACAAAT
* *
23439 ATAATAATAATTAATTAATAATAAGTAGTA
1 ATAATAATAATAAATAAATAATAA-TA-TA
23469 ATAATAATAATAAATAAATAATAATATA
1 ATAATAATAATAAATAAATAATAATATA
23497 ATAA-AATA
1 ATAATAATA
23505 TTTTTTGTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 4 0.12
28 6 0.18
29 2 0.06
30 22 0.65
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (28 bp):
ATAATAATAATAAATAAATAATAATATA
Found at i:23476 original size:19 final size:20
Alignment explanation
Indices: 23444--23501 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 20
23434 CAAATATAAT
*
23444 AATAATTAATTAATAATAAGT-
1 AATAA-TAA-TAATAATAAATA
*
23465 AGTAATAATAATAATAAATA
1 AATAATAATAATAATAAATA
23485 AATAATAAT-ATAATAAA
1 AATAATAATAATAATAAA
23502 ATATTTTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 18 0.55
20 11 0.33
21 4 0.12
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
AATAATAATAATAATAAATA
Found at i:27262 original size:19 final size:19
Alignment explanation
Indices: 27238--27276 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
27228 CGCAAAGTTC
27238 AAGTTAAGCGTACATCCAT
1 AAGTTAAGCGTACATCCAT
*
27257 AAGTTATGCGTACATCCAT
1 AAGTTAAGCGTACATCCAT
27276 A
1 A
27277 GATACTCGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (19 bp):
AAGTTAAGCGTACATCCAT
Found at i:29837 original size:11 final size:11
Alignment explanation
Indices: 29821--29848 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
29811 GAAGCGCAAC
29821 AAGGCGAGCCT
1 AAGGCGAGCCT
29832 AAGGCGAGCCT
1 AAGGCGAGCCT
29843 AAGGCG
1 AAGGCG
29849 CACCAGGAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.25, G:0.39, T:0.07
Consensus pattern (11 bp):
AAGGCGAGCCT
Found at i:30846 original size:15 final size:16
Alignment explanation
Indices: 30828--30860 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
30818 TTATTATGTA
30828 AATATTTT-TTAATTT
1 AATATTTTATTAATTT
*
30843 AATATTTTATTATTTT
1 AATATTTTATTAATTT
30859 AA
1 AA
30861 AATTAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
AATATTTTATTAATTT
Found at i:32109 original size:14 final size:14
Alignment explanation
Indices: 32092--32132 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
32082 CATCCGAAGC
32092 CATCCGACCGAGGG
1 CATCCGACCGAGGG
32106 CATCCGACCGAGGG
1 CATCCGACCGAGGG
32120 CATCCGACCGAGG
1 CATCCGACCGAGG
32133 CCATTCGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.22, C:0.37, G:0.34, T:0.07
Consensus pattern (14 bp):
CATCCGACCGAGGG
Found at i:32145 original size:14 final size:14
Alignment explanation
Indices: 32085--32136 Score: 77
Period size: 14 Copynumber: 3.7 Consensus size: 14
32075 TGTTGGGCAT
*
32085 CCGAAGCCATCCGA
1 CCGAGGCCATCCGA
*
32099 CCGAGGGCATCCGA
1 CCGAGGCCATCCGA
*
32113 CCGAGGGCATCCGA
1 CCGAGGCCATCCGA
32127 CCGAGGCCAT
1 CCGAGGCCAT
32137 TCGAACGAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.23, C:0.38, G:0.31, T:0.08
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:32145 original size:28 final size:28
Alignment explanation
Indices: 32092--32145 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
32082 CATCCGAAGC
* *
32092 CATCCGACCGAGGGCATCCGACCGAGGG
1 CATCCGACCGAGGCCATCCGAACGAGGG
*
32120 CATCCGACCGAGGCCATTCGAACGAG
1 CATCCGACCGAGGCCATCCGAACGAG
32146 CTATGCGAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.24, C:0.35, G:0.31, T:0.09
Consensus pattern (28 bp):
CATCCGACCGAGGCCATCCGAACGAGGG
Found at i:32235 original size:29 final size:29
Alignment explanation
Indices: 32192--32384 Score: 359
Period size: 29 Copynumber: 6.7 Consensus size: 29
32182 GAGGAGCAGG
*
32192 AGGAGTGCATAGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
32221 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
32250 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
32279 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
32308 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
*
32337 CGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
*
32366 CGGAGTGCATGGCGACCTA
1 AGGAGTGCATGGCGACCTA
32385 TGCTGGGAAG
Statistics
Matches: 162, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 162 1.00
ACGTcount: A:0.24, C:0.28, G:0.34, T:0.14
Consensus pattern (29 bp):
AGGAGTGCATGGCGACCTACAAGGTCGCC
Found at i:35469 original size:3 final size:3
Alignment explanation
Indices: 35463--35494 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
35453 CCTTTTTTTT
35463 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
35495 GCGGAGAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:37777 original size:21 final size:20
Alignment explanation
Indices: 37753--37791 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
37743 AATAATTATT
*
37753 TAAAAAATTATTATTTTTACC
1 TAAAAAATTAAT-TTTTTACC
*
37774 TAAAATATTAATTTTTTA
1 TAAAAAATTAATTTTTTA
37792 ACATATCCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAAAAATTAATTTTTTACC
Found at i:45648 original size:2 final size:2
Alignment explanation
Indices: 45641--45686 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
45631 GCTTGTAACA
* *
45641 AT AT AT AT AT AT AA AC 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
45683 AT AT
1 AT AT
45687 TTTAAAATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:46324 original size:31 final size:31
Alignment explanation
Indices: 46289--46367 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
46279 AATTTTAAAA
* * *
46289 GTAACAAATTGGTCATTGATATTATCGATTT
1 GTAACAAAATGGTCATTAACATTATCGATTT
** * *
46320 GTAACAAAATAATCACTAACGTTATCGATTT
1 GTAACAAAATGGTCATTAACATTATCGATTT
46351 GTAACAAAATGGTCATT
1 GTAACAAAATGGTCATT
46368 CCACCGTAAT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (31 bp):
GTAACAAAATGGTCATTAACATTATCGATTT
Found at i:79023 original size:35 final size:35
Alignment explanation
Indices: 78974--79040 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
78964 GGGTTAAAGG
* * *
78974 CATTAAACTCTATTTAGGGTTAAAAACAAATTATA
1 CATTAAAATATATTTAGAGTTAAAAACAAATTATA
*
79009 CATTAAAATATATTTAGAGTTAAAGACAAATT
1 CATTAAAATATATTTAGAGTTAAAAACAAATT
79041 CCAACTCTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (35 bp):
CATTAAAATATATTTAGAGTTAAAAACAAATTATA
Found at i:83557 original size:212 final size:209
Alignment explanation
Indices: 83240--83846 Score: 559
Period size: 212 Copynumber: 2.8 Consensus size: 209
83230 TAAGTGTGAT
*
83240 TCGGGTCGAGTTAGGGTTTAGGGTGAAAATACCCGACCCGAAAATATATAATTTATCTTATATTA
1 TCGGGTCGAGTTAGGGTTTAGGGTGAAAATACCCGACCCGAAAATATATAATTTACCTTATATTA
83305 GGAATAATTACAATAATACCTCTTTATATATAATTTTTTTCCAATTAAGTCACTG-TTTTATTGA
66 GGAATAATTACAATAATACCTC--T-TATATAATTTTTTT-CAATTAAGTCACTGTTTTTATTGA
* *
83369 ATAAATAT-AATATTTTTTATTATTTCAGGTCGGGTTTCTAATTCATATTCGGGTCGGTCAATTT
127 ATAAAAATAAAT-TTTTTTATTATTTCAGGTCGGATTTCTAATTCATATTCGGGTCGGTCAATTT
83433 TTTAAGTGTGATATTCGGG
191 TTTAAGTGTGATATTCGGG
*
83452 TCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCC-AAATATATATAATTTTACCTTATA
1 TCGGGTCGAGTTAGGGTTTAGGGTG-AAAATACCCGACCCGAAA-ATATATAA-TTTACC-T-TA
* * *
83516 TATTTA-GAATAATTATAATATATTCCTC-TATATAA-TTTTTTCAATTAAGTCATTGTTTTTAT
61 TA-TTAGGAATAATTACAATA-ATACCTCTTATATAATTTTTTTCAATTAAGTCACTGTTTTTAT
* *
83578 TGAATAAAAATAAATTTTTTTATTATTTCGGGTCGGATTTCTAATTCATATATTCGTGTCGGGTC
124 TGAATAAAAATAAATTTTTTTATTATTTCAGGTCGGATTTCTAATTC--ATATTCGGGTC-GGTC
* ** ** * **
83643 GAGTCGGGTGAAACT-T--TATTTTGG
186 -AAT--TTTTTAAGTGTGATATTCGGG
* * *
83667 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACACGACCCGACCCGACCCAAAAATATATATTTT
1 TCGGGTCGAGTTAGGGTTTAGGGTG-AAAAT-----ACCCGACCCG-----AAAATATATAATTT
*
83732 ACCTTATATTTAGGAATAATTACAATACTACCTCTATATATATATATATATATATTTTTCAATTA
55 ACCTTATA-TTAGGAATAATTACAATAATACCTC------T-TATATA-AT-T-TTTTTCAATTA
* * * *
83797 AGTCACTGTTTATATTAAATAAAAAT-AATTTTCTTATTATTTCGGGTCGG
109 AGTCACTGTTTTTATTGAATAAAAATAAATTTTTTTATTATTTCAGGTCGG
83847 GTCGGGTGAA
Statistics
Matches: 330, Mismatches: 26, Indels: 57
0.80 0.06 0.14
Matches are distributed among these distances:
211 13 0.04
212 79 0.24
213 32 0.10
214 15 0.05
215 41 0.12
216 19 0.06
217 10 0.03
218 4 0.01
220 9 0.03
222 13 0.04
223 14 0.04
224 6 0.02
225 7 0.02
226 3 0.01
230 6 0.02
231 1 0.00
233 24 0.07
234 34 0.10
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.41
Consensus pattern (209 bp):
TCGGGTCGAGTTAGGGTTTAGGGTGAAAATACCCGACCCGAAAATATATAATTTACCTTATATTA
GGAATAATTACAATAATACCTCTTATATAATTTTTTTCAATTAAGTCACTGTTTTTATTGAATAA
AAATAAATTTTTTTATTATTTCAGGTCGGATTTCTAATTCATATTCGGGTCGGTCAATTTTTTAA
GTGTGATATTCGGG
Found at i:84237 original size:21 final size:21
Alignment explanation
Indices: 84211--84268 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
84201 ATGGTGTTAA
84211 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
84232 AGTGCATCCATGCACTCCTGC
1 AGTGCATCCATGCACCCCTGC
84253 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
84269 TACCACTAGT
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:0.21, C:0.40, G:0.19, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Done.