Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013317.1 Kokia drynarioides strain JFW-HI SEQ_128339, 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: 142592
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 39 characters in sequence are not A, C, G, or T
Found at i:134 original size:12 final size:12
Alignment explanation
Indices: 117--144 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
107 AATGCACTGA
117 TTAAATCATATC
1 TTAAATCATATC
129 TTAAATCATATC
1 TTAAATCATATC
141 TTAA
1 TTAA
145 CTCAAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (12 bp):
TTAAATCATATC
Found at i:684 original size:16 final size:16
Alignment explanation
Indices: 663--712 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
653 TGATGGAGAT
663 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
679 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
694 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
709 ATTA
1 ATTA
713 GTTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:997 original size:20 final size:21
Alignment explanation
Indices: 972--1014 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
962 TACTTACTAC
972 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
992 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
1013 TA
1 TA
1015 TAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:1399 original size:21 final size:21
Alignment explanation
Indices: 1370--1415 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1360 CTTTCTCCTT
1370 CTTCCTCTTCTTCCTTTTTTC
1 CTTCCTCTTCTTCCTTTTTTC
* *
1391 CTTCTTCTTCTTTCTTTTTTC
1 CTTCCTCTTCTTCCTTTTTTC
1412 CTTC
1 CTTC
1416 AATTTTCGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (21 bp):
CTTCCTCTTCTTCCTTTTTTC
Found at i:11034 original size:25 final size:25
Alignment explanation
Indices: 11006--11055 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
10996 ATCAGCTTTC
*
11006 TAAATAAATATAAATATATTTTTTT
1 TAAATAAATAAAAATATATTTTTTT
11031 TAAATAAATAAAAATATATTTTTTT
1 TAAATAAATAAAAATATATTTTTTT
11056 ATAAGTTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TAAATAAATAAAAATATATTTTTTT
Found at i:13215 original size:22 final size:22
Alignment explanation
Indices: 13189--13231 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
13179 CCAAATTTAG
* *
13189 GTGTTATATCATATAATTTCAA
1 GTGTTAAATAATATAATTTCAA
13211 GTGTTAAATAATATAATTTCA
1 GTGTTAAATAATATAATTTCA
13232 CTAAATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (22 bp):
GTGTTAAATAATATAATTTCAA
Found at i:16641 original size:20 final size:18
Alignment explanation
Indices: 16602--16637 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
16592 CCACCAAAAA
16602 TAAAATATATATTTAAAT
1 TAAAATATATATTTAAAT
*
16620 TAAACTATATATTTAAAT
1 TAAAATATATATTTAAAT
16638 ATTATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATATATATTTAAAT
Found at i:41505 original size:13 final size:13
Alignment explanation
Indices: 41466--41515 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
41456 TTTTATGAAC
41466 TTATATTTTTTTT
1 TTATATTTTTTTT
* *
41479 ATA-ATTTTCATTT
1 TTATATTTT-TTTT
*
41492 TT-CATTTTTTTT
1 TTATATTTTTTTT
41504 TTATATTTTTTT
1 TTATATTTTTTT
41516 GTAATTATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (13 bp):
TTATATTTTTTTT
Found at i:45050 original size:24 final size:24
Alignment explanation
Indices: 45018--45068 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
45008 AAAAATAATA
45018 TTTCAATTAAACTATGTTTATTTG
1 TTTCAATTAAACTATGTTTATTTG
45042 TTTCAATTAAACTATGTTTATTTG
1 TTTCAATTAAACTATGTTTATTTG
45066 TTT
1 TTT
45069 GAGTCAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTATGTTTATTTG
Found at i:45077 original size:24 final size:24
Alignment explanation
Indices: 45018--45080 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
45008 AAAAATAATA
*
45018 TTTCAATTAAACTATGTTTATTTG
1 TTTCAATCAAACTATGTTTATTTG
*
45042 TTTCAATTAAACTATGTTTATTTG
1 TTTCAATCAAACTATGTTTATTTG
* *
45066 TTTGAGTCAAACTAT
1 TTTCAATCAAACTAT
45081 TATTAGTCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.51
Consensus pattern (24 bp):
TTTCAATCAAACTATGTTTATTTG
Found at i:47031 original size:24 final size:24
Alignment explanation
Indices: 46963--47037 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
46953 AGAAATAATC
* *
46963 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
46987 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
47011 TTTCAATTAAACTATGTTTATATG
1 TTTCAATTAAACTCTGTTTATTTG
47035 TTT
1 TTT
47038 GAGTCGAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.53
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:49095 original size:2 final size:2
Alignment explanation
Indices: 49088--49126 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
49078 ACAAATAGCT
*
49088 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49127 GTATTTGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:49205 original size:3 final size:3
Alignment explanation
Indices: 49199--49223 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
49189 TCCTCCTCCC
49199 CCA CCA CCA CCA CCA CCA CCA CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA C
49224 TATCGCAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:50680 original size:31 final size:32
Alignment explanation
Indices: 50651--50711 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
50641 TTTTTTTTCC
* *
50651 CTTT-TTTTCTCT-GTTG-TTCTTTTCCTTTT
1 CTTTCTTTTCTCTCCTTGTTTCTTTCCCTTTT
50680 CTTTCTTTTCTCTCCTTGTTTCTTTCCCTTTT
1 CTTTCTTTTCTCTCCTTGTTTCTTTCCCTTTT
50712 ATTTTTGCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 4 0.15
30 8 0.30
31 3 0.11
32 12 0.44
ACGTcount: A:0.00, C:0.26, G:0.05, T:0.69
Consensus pattern (32 bp):
CTTTCTTTTCTCTCCTTGTTTCTTTCCCTTTT
Found at i:54370 original size:18 final size:19
Alignment explanation
Indices: 54336--54371 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
54326 TGATTCGAAC
*
54336 AAAAGAAGGAAATAAAATT
1 AAAAGAAGGAAAAAAAATT
54355 AAAAGAA-GAAAAAAAAT
1 AAAAGAAGGAAAAAAAAT
54372 ACTAGTAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (19 bp):
AAAAGAAGGAAAAAAAATT
Found at i:63428 original size:13 final size:13
Alignment explanation
Indices: 63399--63430 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
63389 ATATTTTTCC
63399 AAAA-CACTTTTT
1 AAAAGCACTTTTT
63411 AAAAGCACTTTTT
1 AAAAGCACTTTTT
63424 AAAAGCA
1 AAAAGCA
63431 ATGTTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (13 bp):
AAAAGCACTTTTT
Found at i:69633 original size:20 final size:21
Alignment explanation
Indices: 69608--69656 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
69598 ATTACATGTG
69608 AAAAATAATAAAATAAA-TAA
1 AAAAATAATAAAATAAATTAA
* * *
69628 ATAAATAATACATTAAATTAA
1 AAAAATAATAAAATAAATTAA
69649 AAAAATAA
1 AAAAATAA
69657 CTCTTAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAATAATAAAATAAATTAA
Found at i:74249 original size:30 final size:29
Alignment explanation
Indices: 74213--74635 Score: 295
Period size: 30 Copynumber: 14.2 Consensus size: 29
74203 GGTCATAACA
* *
74213 TAATTTTGAAAGAGTGTAGGGGTTAAAATG
1 TAATTTTGAAA-AGTTTAGGGGTCAAAATG
* * *
74243 TGATTTTAAAAAAGTTTAGGGGTTAAAATG
1 TAATTTT-GAAAAGTTTAGGGGTCAAAATG
* * *
74273 AAATTTTTGAAAAATTT-GGGTGTTAAAATG
1 TAA-TTTTGAAAAGTTTAGGG-GTCAAAATG
74303 TAATTTTGGAAAAGTTT-GGGTGTCAAAATG
1 TAATTTT-GAAAAGTTTAGGG-GTCAAAATG
** * *
74333 TGTTTTTGGTAAAGTTTAGAGGTCAAAATG
1 TAATTTT-GAAAAGTTTAGGGGTCAAAATG
* * *
74363 AAATTTTTGAAAAGTTTAAGGATCAAAATG
1 TAA-TTTTGAAAAGTTTAGGGGTCAAAATG
*
74393 TAATTTTAGGAAAGTTTAGGGGTCAAAATG
1 TAATTTT-GAAAAGTTTAGGGGTCAAAATG
* **
74423 TGATTTTGGAAAA-TGTTA-ATGTCAAAATG
1 TAATTTT-GAAAAGT-TTAGGGGTCAAAATG
* *
74452 TGATTTTGGAAAA-TTTTGGGGTCAAAATG
1 TAATTTT-GAAAAGTTTAGGGGTCAAAATG
* * **
74481 TGA-TTTAAGAAAGTTTAGAAGTCAAAATG
1 TAATTTTGA-AAAGTTTAGGGGTCAAAATG
* *
74510 TAAATTTTGAAAAGTTTAGGGGTTAAAATA
1 T-AATTTTGAAAAGTTTAGGGGTCAAAATG
** * *
74540 TAATTTTGGGAAGTTT-GGGGTTAAAATA
1 TAATTTTGAAAAGTTTAGGGGTCAAAATG
* * *
74568 TGATTTTGGAAAA-TTTTGAGGGTCAAAATA
1 TAATTTT-GAAAAGTTTAG-GGGTCAAAATG
* *
74598 TAATTTTTGAAAAGTTCAGGGGGCCAAAATG
1 TAA-TTTTGAAAAGTTTA-GGGGTCAAAATG
*
74629 TAGTTTT
1 TAATTTT
74636 TAAATAAAAA
Statistics
Matches: 319, Mismatches: 55, Indels: 38
0.77 0.13 0.09
Matches are distributed among these distances:
27 1 0.00
28 29 0.09
29 78 0.24
30 176 0.55
31 34 0.11
32 1 0.00
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (29 bp):
TAATTTTGAAAAGTTTAGGGGTCAAAATG
Found at i:74437 original size:15 final size:15
Alignment explanation
Indices: 74417--74465 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
74407 TTTAGGGGTC
74417 AAAATGTGATTTTGG
1 AAAATGTGATTTTGG
* * * *
74432 AAAATGTTAATGT-C
1 AAAATGTGATTTTGG
74446 AAAATGTGATTTTGG
1 AAAATGTGATTTTGG
74461 AAAAT
1 AAAAT
74466 TTTGGGGTCA
Statistics
Matches: 25, Mismatches: 8, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (15 bp):
AAAATGTGATTTTGG
Found at i:74482 original size:58 final size:58
Alignment explanation
Indices: 74277--74610 Score: 248
Period size: 58 Copynumber: 5.7 Consensus size: 58
74267 AAAATGAAAT
* * ** *
74277 TTTTGAAAAATTT-GGGTGTTAAAATGTAATTTTGGAAAA-GTTTGGGTGTCAAAATGTGT
1 TTTTGGAAAATTTAGGG-GTCAAAATGTAATTTTGGAAAATG-TTAAG-GTCAAAATGTGA
* * * * *
74336 TTTTGGTAAAGTTTAGAGGTCAAAATGAAATTTTTGAAAA-GTTTAAGGATCAAAATGTAA
1 TTTTGG-AAAATTTAGGGGTCAAAATGTAATTTTGGAAAATG-TTAAGG-TCAAAATGTGA
* * *
74396 TTTTAGGAAAGTTTAGGGGTCAAAATGTGATTTTGGAAAATGTTAATGTCAAAATGTGA
1 TTTT-GGAAAATTTAGGGGTCAAAATGTAATTTTGGAAAATGTTAAGGTCAAAATGTGA
* * ** * * *
74455 TTTTGGAAAATTTTGGGGTCAAAATGTGATTTAAGAAAGT-TTAGAAGTCAAAATGTAAA
1 TTTTGGAAAATTTAGGGGTCAAAATGTAATTTTGGAAAATGTTA-AGGTCAAAATGT-GA
* * * * ** * *
74514 TTTT-GAAAAGTTTAGGGGTTAAAATATAATTTTGGGAAGT-TTGGGGTTAAAATATGA
1 TTTTGGAAAA-TTTAGGGGTCAAAATGTAATTTTGGAAAATGTTAAGGTCAAAATGTGA
* * *
74571 TTTTGGAAAATTTTGAGGGTCAAAATATAATTTTTGAAAA
1 TTTTGGAAAATTTAG-GGGTCAAAATGTAATTTTGGAAAA
74611 GTTCAGGGGG
Statistics
Matches: 224, Mismatches: 41, Indels: 21
0.78 0.14 0.07
Matches are distributed among these distances:
57 12 0.05
58 80 0.36
59 50 0.22
60 77 0.34
61 5 0.02
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.37
Consensus pattern (58 bp):
TTTTGGAAAATTTAGGGGTCAAAATGTAATTTTGGAAAATGTTAAGGTCAAAATGTGA
Found at i:75032 original size:30 final size:30
Alignment explanation
Indices: 74980--75038 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
74970 CCTAAAAATC
*
74980 TAAAAAAAAAATCATTTCTTCCTTTCTTTT
1 TAAAAAAAAAATCATTTCTTCCTCTCTTTT
* *
75010 TAAAAAAAAAA-CTTTTTTTTCCTCTCTTT
1 TAAAAAAAAAATC-ATTTCTTCCTCTCTTT
75039 CTCTTACGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.47
Consensus pattern (30 bp):
TAAAAAAAAAATCATTTCTTCCTCTCTTTT
Found at i:76593 original size:49 final size:49
Alignment explanation
Indices: 76539--77546 Score: 571
Period size: 49 Copynumber: 20.5 Consensus size: 49
76529 GACCTTAACT
*
76539 TTTCCCTTCATATCTTCATGGTATCGGATTCGCAGTTGCGGCCTTAATCC
1 TTTCCCTTCATATCTTCATGGTATCGGATTCGCAGTTGCGGCCTCAA-CC
* * *
76589 -TTCCCATTGC--ATCTACTAAGGTATCGGGTTCGCCA-TTGCGGCCTCAACC
1 TTTCCC-TT-CATATCTTC-ATGGTATCGGATTCG-CAGTTGCGGCCTCAACC
* * * * * * **
76638 TTTCCCTTTATATCTCCGTGGTACCGAATTTGCCA-TTATGGCCTCAACC
1 TTTCCCTTCATATCTTCATGGTATCGGATTCG-CAGTTGCGGCCTCAACC
* * * *
76687 TTTCCCTTCGTATCTTCATGGTA-CCGAGTTTGTCA-TTGTGGCCTCAACC
1 TTTCCCTTCATATCTTCATGGTATCGGA-TTCG-CAGTTGCGGCCTCAACC
** * * * * *
76736 TTTCCCTTCATATCTTTGTGGTA-CCGAGTTCACCGTTGCGGCCTAAACA
1 TTTCCCTTCATATCTTCATGGTATCGGA-TTCGCAGTTGCGGCCTCAACC
* * * *
76785 TTTCCCATCACATCTTCTTAGGTATCGGGTTCGTCA-TTGCGGCCTCAACC
1 TTTCCCTTCATATCTTCAT-GGTATCGGATTCG-CAGTTGCGGCCTCAACC
* * *
76835 TTTCCCTT-ATTATCTTCATGTTA-CCGAGTTCGCCGTTGCGGCCTCAACC
1 TTTCCCTTCA-TATCTTCATGGTATCGGA-TTCGCAGTTGCGGCCTCAACC
* * * *
76884 TTTCCCTTCATATC-TCTGTGGTACCAGG-TTCGCCGTTGCTGCCTCAACC
1 TTTCCCTTCATATCTTC-ATGGTATC-GGATTCGCAGTTGCGGCCTCAACC
* * * ** * *
76933 TTT-CCTTCGTATCTTTATGGTATCGAATTTACCGTTACGGCCTCAACC
1 TTTCCCTTCATATCTTCATGGTATCGGATTCGCAGTTGCGGCCTCAACC
* * * *** ** **
76981 TTTCCCTTCATATCTCCGTGGTA-CTGAGTTCATTGTTGTAGCCTCAATA
1 TTTCCCTTCATATCTTCATGGTATCGGA-TTCGCAGTTGCGGCCTCAACC
** * * * * * * * * * *
77030 TTTTTCATCACATCTTCTTAGGTATAGGGTTTGCCGTTGCGACTTTAACC
1 TTTCCCTTCATATCTTCAT-GGTATCGGATTCGCAGTTGCGGCCTCAACC
* * *
77080 TTTCCCTTCGTATCTTCATGGTACTAGG-TTGGCCA-TTGCGGCCTCAACC
1 TTTCCCTTCATATCTTCATGGTA-TCGGATTCG-CAGTTGCGGCCTCAACC
* * * *
77129 TTTCCCTTCATATCTCCGTGGTACCGGGTTCGCCA-TTGCGGCCTCAACC
1 TTTCCCTTCATATCTTCATGGTATCGGATTCG-CAGTTGCGGCCTCAACC
* * * * *
77178 TTTCCCATCACATCTTCTTAGGTATC-GAGTTCATCA-TTGCAGCCTCAACC
1 TTTCCCTTCATATCTTCAT-GGTATCGGA-TTC-GCAGTTGCGGCCTCAACC
* * *
77228 TTTCCCTTCGTATCTTTATGGTATCTGG-TTCGTCA-TTACGGCCTCAACC
1 TTTCCCTTCATATCTTCATGGTATC-GGATTCG-CAGTTGCGGCCTCAACC
* * *
77277 TTTCCCTTCGTATCTTCATGGTATC-GAGTTCG-TGTTGTGGCCTCAACC
1 TTTCCCTTCATATCTTCATGGTATCGGA-TTCGCAGTTGCGGCCTCAACC
* * * * * *
77325 TTTCCCATCACATCTTCTAAGGTACCGGATTCGTCA-TCGCGACCTCAATCC
1 TTTCCCTTCATATCTTC-ATGGTATCGGATTCG-CAGTTGCGGCCTCAA-CC
* * * * * * * *
77376 -TTCTCTTCAAATTTTCATCGTACCAGATTCGCCGTTGCGACCTCAATCC
1 TTTCCCTTCATATCTTCATGGTATCGGATTCGCAGTTGCGGCCTCAA-CC
* * * * * *
77425 -TTCCTTTCAAATCTTCATGGTAGCGGGTTCGCCGTTGCGGTCTCAACC
1 TTTCCCTTCATATCTTCATGGTATCGGATTCGCAGTTGCGGCCTCAACC
* * *
77473 TTTCCCATCATATCTTCTAAGGTATC-AAGTTCGTC-GTTGCGGCCTCAACC
1 TTTCCCTTCATATCTTC-ATGGTATCGGA-TTCG-CAGTTGCGGCCTCAACC
*
77523 TTTCCCTTCATATCTTCAGGGTAT
1 TTTCCCTTCATATCTTCATGGTAT
77547 TATATTTGCC
Statistics
Matches: 742, Mismatches: 169, Indels: 95
0.74 0.17 0.09
Matches are distributed among these distances:
47 2 0.00
48 76 0.10
49 449 0.61
50 203 0.27
51 12 0.02
ACGTcount: A:0.17, C:0.30, G:0.17, T:0.36
Consensus pattern (49 bp):
TTTCCCTTCATATCTTCATGGTATCGGATTCGCAGTTGCGGCCTCAACC
Found at i:76642 original size:99 final size:98
Alignment explanation
Indices: 76516--77546 Score: 573
Period size: 99 Copynumber: 10.5 Consensus size: 98
76506 TAAGGTACAA
* * * *
76516 GGTTCGTCATTACGACCTTAACTTTTCCCTTCATATCTTCATGGTATCGGATTCGCAGTTGCGGC
1 GGTTCGTCATTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCGGATTCGCAGTTGCGGC
* * *
76581 CTTAATCC-TTCCCATTGCATCTACTAAGGTATCG
66 CTCAA-CCTTTCCC-TTGCATCTTCTATGGTATCG
* * * * * * * **
76615 GGTTCGCCATTGCGGCCTCAACCTTTCCCTTTATATCTCCGTGGTACCGAATTTGCCA-TTATGG
1 GGTTCGTCATTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCGGATTCG-CAGTTGCGG
* *
76679 CCTCAACCTTTCCCTTCGTATCTTC-ATGGTACCG
65 CCTCAACCTTTCCCTT-GCATCTTCTATGGTATCG
* * * ** * * *
76713 AGTTTGTCATTGTGGCCTCAACCTTTCCCTTCATATCTTTGTGGTA-CCGAGTTCACCGTTGCGG
1 GGTTCGTCATTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCGGA-TTCGCAGTTGCGG
* * **
76777 CCTAAACATTTCCCATCACATCTTCT-TAGGTATCG
65 CCTCAACCTTTCCC-TTGCATCTTCTAT-GGTATCG
* * *
76812 GGTTCGTCATTGCGGCCTCAACCTTTCCCTT-ATTATCTTCATGTTA-CCGAGTTCGCCGTTGCG
1 GGTTCGTCATTGCGGCCTCAACCTTTCCCTTCA-TATCTTCATGGTATCGGA-TTCGCAGTTGCG
* * * *
76875 GCCTCAACCTTTCCCTT-CATATCTCTGTGGTACCA
64 GCCTCAACCTTTCCCTTGCATCT-TCTATGGTATCG
* * * * * * ** * *
76910 GGTTCGCCGTTGCTGCCTCAACCTTT-CCTTCGTATCTTTATGGTATCGAATTTACCGTTACGGC
1 GGTTCGTCATTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCGGATTCGCAGTTGCGGC
* **
76974 CTCAACCTTTCCCTT-CATATCTCCGTGGTA-CTG
66 CTCAACCTTTCCCTTGCATCT-TCTATGGTATC-G
* * ** ** ** ** * * * * * * * *
77007 AGTTCATTGTTGTAGCCTCAATATTTTTCATCACATCTTCTTAGGTATAGGGTTTGCCGTTGCGA
1 GGTTCGTCATTGCGGCCTCAACCTTTCCCTTCATATCTTCAT-GGTATCGGATTCGCAGTTGCGG
* * * *
77072 CTTTAACCTTTCCCTTCGTATCTTC-ATGGTA-CTA
65 CCTCAACCTTTCCCTT-GCATCTTCTATGGTATC-G
* * * * * *
77106 GGTTGGCCATTGCGGCCTCAACCTTTCCCTTCATATCTCCGTGGTACCGGGTTCGCCA-TTGCGG
1 GGTTCGTCATTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCGGATTCG-CAGTTGCGG
**
77170 CCTCAACCTTTCCCATCACATCTTCT-TAGGTATCG
65 CCTCAACCTTTCCC-TTGCATCTTCTAT-GGTATCG
* * * * * *
77205 AGTTCATCATTGCAGCCTCAACCTTTCCCTTCGTATCTTTATGGTATCTGG-TTCGTCA-TTACG
1 GGTTCGTCATTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTATC-GGATTCG-CAGTTGCG
*
77268 GCCTCAACCTTTCCCTTCGTATCTTC-ATGGTATCG
64 GCCTCAACCTTTCCCTT-GCATCTTCTATGGTATCG
* * * * * * * *
77303 AGTTCGT-GTTGTGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGATTCGTCA-TCGCG
1 GGTTCGTCATTGCGGCCTCAACCTTTCCCTTCATATCTTC-ATGGTATCGGATTCG-CAGTTGCG
* * * * * *
77366 ACCTCAATCC-TTCTCTT-CAAATTTTC-ATCGTACCA
64 GCCTCAA-CCTTTCCCTTGC--ATCTTCTATGGTATCG
* * * * * * * * *
77401 GATTCGCCGTTGCGACCTCAATCC-TTCCTTTCAAATCTTCATGGTAGCGGGTTCGCCGTTGCGG
1 GGTTCGTCATTGCGGCCTCAA-CCTTTCCCTTCATATCTTCATGGTATCGGATTCGCAGTTGCGG
* * * *
77465 TCTCAACCTTTCCCAT-CATATCTTCTAAGGTATCA
65 CCTCAACCTTTCCCTTGC--ATCTTCTATGGTATCG
* * *
77500 AGTTCGTCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCAGGGTAT
1 GGTTCGTCATTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTAT
77547 TATATTTGCC
Statistics
Matches: 714, Mismatches: 181, Indels: 74
0.74 0.19 0.08
Matches are distributed among these distances:
96 1 0.00
97 110 0.15
98 245 0.34
99 346 0.48
100 9 0.01
101 3 0.00
ACGTcount: A:0.17, C:0.30, G:0.17, T:0.36
Consensus pattern (98 bp):
GGTTCGTCATTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCGGATTCGCAGTTGCGGC
CTCAACCTTTCCCTTGCATCTTCTATGGTATCG
Found at i:76730 original size:148 final size:148
Alignment explanation
Indices: 76517--77545 Score: 797
Period size: 148 Copynumber: 7.0 Consensus size: 148
76507 AAGGTACAAG
* * * * *
76517 GTTCGTCATTACGACCTTAACTTTTCCCTTCATATCTTCATGGTATCG-GATTCG-CAGTTGCGG
1 GTTCGCCATTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGAG-TTCGTCA-TTGCGG
* ** * *
76580 CCTTAATCC-TTCCCATTGCATCTACTAAGGTATCGGGTTCGCCATTGCGGCCTCAACCTTTCCC
64 CCTCAA-CCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCATTGCGGCCTCAACCTTTCCC
** * *
76644 TTTATATCTCCGTGGTACCGA
128 TTCGTATCTTCATGGTACCGA
* * * * * *
76665 ATTTGCCATTATGGCCTCAACCTTTCCCTTCGTATCTTCATGGTACCGAGTTTGTCATTGTGGCC
1 GTTCGCCATTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGAGTTCGTCATTGCGGCC
* * ** * * * * * *
76730 TCAACCTTTCCCTTCATATCTT-TGTGGTACCGAGTTCACCGTTGCGGCCTAAACATTTCCCATC
66 TCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCATTGCGGCCTCAACCTTTCCCTTC
** * * *
76794 ACATCTTCTTAGGTATCGG
131 GTATCTTCAT-GGTACCGA
* * * * *
76813 GTTCGTCATTGCGGCCTCAACCTTTCCCTT-ATTATCTTCATGTTACCGAGTTCGCCGTTGCGGC
1 GTTCGCCATTACGGCCTCAACCTTTCCCTTCA-TATCTTCATGGTACCGAGTTCGTCATTGCGGC
* * ** * * *
76877 CTCAACCTTTCCCTTCATATC-TCTGTGGTACCAGGTTCGCCGTTGCTGCCTCAACCTTT-CCTT
65 CTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCATTGCGGCCTCAACCTTTCCCTT
* *
76940 CGTATCTTTATGGTATCGA
130 CGTATCTTCATGGTACCGA
* ** * * * * * ** **
76959 ATTTACCGTTACGGCCTCAACCTTTCCCTTCATATCTCCGTGGTACTGAGTTCATTGTTGTAGCC
1 GTTCGCCATTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGAGTTCGTCATTGCGGCC
** ** * ** * * * * *
77024 TCAATATTTTTCATCACATCTTCTTAGGTATAGGGTTTGCCGTTGCGACTTTAACCTTTCCCTTC
66 TCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCATTGCGGCCTCAACCTTTCCCTTC
*
77089 GTATCTTCATGGTA-CTA
131 GTATCTTCATGGTACCGA
* * * * * *
77106 GGTTGGCCATTGCGGCCTCAACCTTTCCCTTCATATCTCCGTGGTACCGGGTTCGCCATTGCGGC
1 -GTTCGCCATTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGAGTTCGTCATTGCGGC
* * * ** *
77171 CTCAACCTTTCCCATCACATCTTCTTAGGTATCGAGTTCATCATTGCAGCCTCAACCTTTCCCTT
65 CTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCATTGCGGCCTCAACCTTTCCCTT
* *
77236 CGTATCTTTATGGTATCTG-
130 CGTATCTTCATGGTA-CCGA
* * * * *
77255 GTTCGTCATTACGGCCTCAACCTTTCCCTTCGTATCTTCATGGTATCGAGTTCGT-GTTGTGGCC
1 GTTCGCCATTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGAGTTCGTCATTGCGGCC
* * * * *
77319 TCAACCTTTCCCATCACATCTTCTAAGGTACCGGATTCGTCATCGCGACCTCAATCC-TTCTCTT
66 TCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCATTGCGGCCTCAA-CCTTTCCCTT
** * *
77383 CAAATTTTCATCGTACC-A
130 CGTATCTTCATGGTACCGA
* * * * * * * * *
77401 GATTCGCCGTTGCGACCTCAATCC-TTCCTTTCAAATCTTCATGGTAGCGGGTTCGCCGTTGCGG
1 G-TTCGCCATTACGGCCTCAA-CCTTTCCCTTCATATCTTCATGGTACCGAGTTCGTCATTGCGG
* * * ** * *
77465 TCTCAACCTTTCCCATCATATCTTCTAAGGTATCAAGTTCGTCGTTGCGGCCTCAACCTTTCCCT
64 CCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCATTGCGGCCTCAACCTTTCCCT
* *
77530 TCATATCTTCAGGGTA
129 TCGTATCTTCATGGTA
77546 TTATATTTGC
Statistics
Matches: 694, Mismatches: 169, Indels: 36
0.77 0.19 0.04
Matches are distributed among these distances:
146 71 0.10
147 195 0.28
148 425 0.61
149 3 0.00
ACGTcount: A:0.17, C:0.30, G:0.17, T:0.36
Consensus pattern (148 bp):
GTTCGCCATTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGAGTTCGTCATTGCGGCC
TCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTCGCCATTGCGGCCTCAACCTTTCCCTTC
GTATCTTCATGGTACCGA
Found at i:77047 original size:245 final size:244
Alignment explanation
Indices: 76615--77242 Score: 720
Period size: 245 Copynumber: 2.5 Consensus size: 244
76605 TAAGGTATCG
* * * *
76615 GGTTCGCCATTGCGGCCTCAACCTTTCCCTTTATATCTCCGTGGTACCGAATTTGCCATT-ATGG
1 GGTTCGCCATTGCGGCCTCAACCTTTCCCTTCATATCTCCGTGGTACCG-GTTCGCCATTGCT-G
* ** **
76679 CCTCAACCTTTCCCTTCGTATCTTCATGGTACCGAGTTTGTCATTGTGGCCTCAACCTTTCCCTT
64 CCTCAACCTTT-CCTTCGTATCTTCATGGTACCGAATTTACCATTACGGCCTCAACCTTTCCCTT
** *
76744 CATATCTTTGTGGTACCGAGTTCACCGTTGCGGCCTAAACATTTCCCATCACATCTTCTTAGGTA
128 CATATCTCCGTGGTACCGAGTTCACCGTTGCAGCCTAAACATTTCCCATCACATCTTCTTAGGTA
* * * * *
76809 TCGGGTTCGTCATTGCGGCCTCAACCTTTCCCTTATTATCTTCATGTTACCGA
193 TAGGGTTCGCCATTGCGACCTCAACCTTTCCCTTAGTATCTTCATGGTA-CGA
* * *
76862 -GTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTCTGTGGTACCAGGTTCGCCGTTGCTGC
1 GGTTCGCCATTGCGGCCTCAACCTTTCCCTTCATATCTCCGTGGTACC-GGTTCGCCATTGCTGC
* * *
76926 CTCAACCTTTCCTTCGTATCTTTATGGTATCGAATTTACCGTTACGGCCTCAACCTTTCCCTTCA
65 CTCAACCTTTCCTTCGTATCTTCATGGTACCGAATTTACCATTACGGCCTCAACCTTTCCCTTCA
* ** * * * **
76991 TATCTCCGTGGTACTGAGTTCATTGTTGTAGCCTCAATATTTTTCATCACATCTTCTTAGGTATA
130 TATCTCCGTGGTACCGAGTTCACCGTTGCAGCCTAAACATTTCCCATCACATCTTCTTAGGTATA
* * * * * *
77056 GGGTTTGCCGTTGCGACTTTAACCTTTCCCTTCGTATCTTCATGGTACTA
195 GGGTTCGCCATTGCGACCTCAACCTTTCCCTTAGTATCTTCATGGTACGA
* *
77106 GGTTGGCCATTGCGGCCTCAACCTTTCCCTTCATATCTCCGTGGTACCGGGTTCGCCATTGCGGC
1 GGTTCGCCATTGCGGCCTCAACCTTTCCCTTCATATCTCCGTGGTACC-GGTTCGCCATTGCTGC
* ** * * * * * * *
77171 CTCAACCTTTCCCATCACATCTTCTTAGGTATCGAGTTCATCATTGCAGCCTCAACCTTTCCCTT
65 CTCAACCTTT-CCTTCGTATCTTCAT-GGTACCGAATTTACCATTACGGCCTCAACCTTTCCCTT
*
77236 CGTATCT
128 CATATCT
77243 TTATGGTATC
Statistics
Matches: 321, Mismatches: 55, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
244 2 0.01
245 206 0.64
246 73 0.23
247 40 0.12
ACGTcount: A:0.16, C:0.30, G:0.17, T:0.36
Consensus pattern (244 bp):
GGTTCGCCATTGCGGCCTCAACCTTTCCCTTCATATCTCCGTGGTACCGGTTCGCCATTGCTGCC
TCAACCTTTCCTTCGTATCTTCATGGTACCGAATTTACCATTACGGCCTCAACCTTTCCCTTCAT
ATCTCCGTGGTACCGAGTTCACCGTTGCAGCCTAAACATTTCCCATCACATCTTCTTAGGTATAG
GGTTCGCCATTGCGACCTCAACCTTTCCCTTAGTATCTTCATGGTACGA
Found at i:85674 original size:30 final size:30
Alignment explanation
Indices: 85523--86009 Score: 356
Period size: 30 Copynumber: 16.4 Consensus size: 30
85513 ATAGGGTTGA
*
85523 AAAATG-AAGTTTTGGAGAA-TTTA-GGGTT
1 AAAATGTAA-TTTTGGAAAAGTTTAGGGGTT
*
85551 AAAATGTAATTTT-GATAGAGTTTAGGGGGTT
1 AAAATGTAATTTTGGA-AAAGTTTA-GGGGTT
* * * *
85582 AAAAGGTGATTTT-AAAAACTTTAGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
* * * ****
85611 AAAGTGAAATTTTGG-AAATTTTAGGCACC
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
*
85640 AAAATGCAATTTTGGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
* *
85670 AAAATGTGATTTTAGG-AAAGTTTAGGGGTC
1 AAAATGTAATTTT-GGAAAAGTTTAGGGGTT
* * *
85700 AAAATATAATTTTTGAAAAGTTTAAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
* * *
85730 AAAATGTAAATTTAGAAAAGTTTAGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
* * * **
85760 AAAATGTGATTCTGGAAAAGTTCA-ATGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
* * *
85789 AAAATGCAATTTTGAAAAAGTTT-GGATGTT
1 AAAATGTAATTTTGGAAAAGTTTAGG-GGTT
*
85819 AAAATGTGATTTTTGG-AAAGTTT-GAGGGTT
1 AAAATGT-AATTTTGGAAAAGTTTAG-GGGTT
* *
85849 AAAATGTAATTTTTGAAAAGTTTA-AGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
**
85878 AAAATGTAATTTTTAAAAAGTTTTA-GGGTT
1 AAAATGTAATTTTGGAAAAG-TTTAGGGGTT
* * *
85908 AAAATATAATTTTAGAAAAGTTTGGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
* * * * *
85938 ATAATATGATTTTAGAAAAGTTT-GAGAGTT
1 AAAATGTAATTTTGGAAAAGTTTAG-GGGTT
*** *
85968 AAAATGTAATTTTTTTAAAGTTTA-GGGCT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
*
85997 AAAATGTAGTTTT
1 AAAATGTAATTTT
86010 TAATAAAACA
Statistics
Matches: 364, Mismatches: 76, Indels: 37
0.76 0.16 0.08
Matches are distributed among these distances:
27 2 0.01
28 11 0.03
29 112 0.31
30 213 0.59
31 26 0.07
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGGTT
Found at i:85825 original size:89 final size:88
Alignment explanation
Indices: 85542--86009 Score: 410
Period size: 89 Copynumber: 5.2 Consensus size: 88
85532 TTTTGGAGAA
* * * *
85542 TTTAGGGTTAAAATGTAATTTT-GATAGAGTTTAGGGGGTTAAAAGGTGATTTT-AAAAACTTTA
1 TTTAGGGTTAAAATGTAATTTTAGA-AAAGTTTA-GGGGTTAAAATGTGATTTTGGAAAAGTTTA
* * * * *
85605 GGGGTTAAAGTGAAATTTTG-GAAAT
64 -AGGTTAAAATGTAATTTTGAAAAAG
*** * *
85630 TTTAGGCACCAAAATGCAATTTTGGAAAAGTTTAGGGGTTAAAATGTGATTTTAGG-AAAGTTTA
1 TTTAGG-GTTAAAATGTAATTTTAGAAAAGTTTAGGGGTTAAAATGTGATTTT-GGAAAAGTTTA
* * *
85694 GGGGTCAAAATATAATTTTTG-AAAAG
64 -AGGTTAAAATGTAA-TTTTGAAAAAG
* * * *
85720 TTTAAGGGTTAAAATGTAAATTTAGAAAAGTTTAGGGGTCAAAATGTGATTCTGGAAAAGTTCAA
1 TTT-AGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGGTTAAAATGTGATTTTGGAAAAGTTTAA
* *
85785 TGTTAAAATGCAATTTTGAAAAAG
65 GGTTAAAATGTAATTTTGAAAAAG
* * * * *
85809 TTT-GGATGTTAAAATGTGATTTTTGGAAAGTTT-GAGGGTTAAAATGTAATTTTTGAAAAGTTT
1 TTTAGG--GTTAAAATGTAATTTTAGAAAAGTTTAG-GGGTTAAAATGTGATTTTGGAAAAGTTT
*
85872 AAGGTTAAAATGTAATTTTTAAAAAG
63 AAGGTTAAAATGTAATTTTGAAAAAG
* * * * * *
85898 TTTTAGGGTTAAAATATAATTTTAGAAAAGTTTGGGGGTTATAATATGATTTTAGAAAAGTTTGA
1 -TTTAGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGGTTAAAATGTGATTTTGGAAAAGTTTAA
***
85963 GAGTTAAAATGTAATTTTTTTAAAG
65 G-GTTAAAATGTAATTTTGAAAAAG
* *
85988 TTTAGGGCTAAAATGTAGTTTT
1 TTTAGGGTTAAAATGTAATTTT
86010 TAATAAAACA
Statistics
Matches: 311, Mismatches: 54, Indels: 29
0.79 0.14 0.07
Matches are distributed among these distances:
87 2 0.01
88 30 0.10
89 191 0.61
90 83 0.27
91 5 0.02
ACGTcount: A:0.37, C:0.02, G:0.22, T:0.38
Consensus pattern (88 bp):
TTTAGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGGTTAAAATGTGATTTTGGAAAAGTTTAAG
GTTAAAATGTAATTTTGAAAAAG
Found at i:86012 original size:119 final size:117
Alignment explanation
Indices: 85542--86009 Score: 438
Period size: 119 Copynumber: 3.9 Consensus size: 117
85532 TTTTGGAGAA
* ** *
85542 TTTAGGGTTAAAATGTAATTTTGATAGAGTTTAGGGGGTTAAAAGGTGATTTTA-AAAACTTT-A
1 TTTAGGGTTAAAATGTAATTTTGA-AAAGTTT-GGGGGTTAAAATATGATTTTAGAAAAGTTTGA
* * * * * * *
85605 GGGGTTAAAGTG-AAATTTTGGAAATTTTAGGCACCAAAATGCAATTTTGGAAAAG
64 -GGGTTAAAATGTAAATTTTGAAAAGTTTAGG-GCTAAAATGTAATTTTGAAAAAG
* * * * * * *
85660 TTTAGGGGTTAAAATGTGATTTTAGGAAAGTTTAGGGGTCAAAATATAATTTTTGAAAAGTTTAA
1 TTTA-GGGTTAAAATGTAATTTT-GAAAAGTTTGGGGGTTAAAATATGATTTTAGAAAAGTTTGA
* * * * *
85725 GGGTTAAAATGTAAATTTAGAAAAGTTTAGGGGTCAAAATGTGATTCTGGAAAAG
64 GGGTTAAAATGTAAATTTTGAAAAGTTTAGGGCT-AAAATGTAATTTTGAAAAAG
* ** * ** * * *
85780 TTCAATGTTAAAATGCAATTTTGAAAAAGTTTGGATGTTAAAATGTGATTTTTGGAAAGTTTGAG
1 TTTAGGGTTAAAATGTAATTTTG-AAAAGTTTGGGGGTTAAAATATGATTTTAGAAAAGTTTGAG
* * * *
85845 GGTTAAAATGTAATTTTTGAAAAGTTTAAGGTTAAAATGTAATTTTTAAAAAG
65 GGTTAAAATGTAAATTTTGAAAAGTTTAGGGCTAAAATGTAATTTTGAAAAAG
* *
85898 TTTTAGGGTTAAAATATAATTTTAGAAAAGTTTGGGGGTTATAATATGATTTTAGAAAAGTTTGA
1 -TTTAGGGTTAAAATGTAATTTT-GAAAAGTTTGGGGGTTAAAATATGATTTTAGAAAAGTTTGA
* * ** *
85963 GAGTTAAAATGTAATTTTTTTAAAGTTTAGGGCTAAAATGTAGTTTT
64 GGGTTAAAATGTAAATTTTGAAAAGTTTAGGGCTAAAATGTAATTTT
86010 TAATAAAACA
Statistics
Matches: 282, Mismatches: 59, Indels: 17
0.79 0.16 0.05
Matches are distributed among these distances:
118 36 0.13
119 207 0.73
120 39 0.14
ACGTcount: A:0.37, C:0.02, G:0.22, T:0.38
Consensus pattern (117 bp):
TTTAGGGTTAAAATGTAATTTTGAAAAGTTTGGGGGTTAAAATATGATTTTAGAAAAGTTTGAGG
GTTAAAATGTAAATTTTGAAAAGTTTAGGGCTAAAATGTAATTTTGAAAAAG
Found at i:86898 original size:14 final size:14
Alignment explanation
Indices: 86879--86925 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
86869 AAACGTTTTA
86879 AAATTAATAA-TAAT
1 AAATT-ATAATTAAT
86893 AAATTATAATTAAT
1 AAATTATAATTAAT
* *
86907 AATAATAAAATTAAT
1 AA-ATTATAATTAAT
86922 AAAT
1 AAAT
86926 ATATTGATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 4 0.14
14 12 0.43
15 12 0.43
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATTATAATTAAT
Found at i:97539 original size:2 final size:2
Alignment explanation
Indices: 97532--97566 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
97522 AATTCCATAA
97532 AT 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 AT A
97567 AAAGAAGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:98307 original size:29 final size:30
Alignment explanation
Indices: 98251--98309 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
98241 TTTTAGATCA
*
98251 TTTTTATTTTGGCCACTTACGTTTTAAATG
1 TTTTTATTTTGGCCACTTACGTGTTAAATG
*
98281 TTTTTATTTTGGTCACTCT-C-TGTTAAATG
1 TTTTTATTTTGGCCACT-TACGTGTTAAATG
98310 GTTAACAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 8 0.31
30 17 0.65
31 1 0.04
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.54
Consensus pattern (30 bp):
TTTTTATTTTGGCCACTTACGTGTTAAATG
Found at i:109214 original size:18 final size:18
Alignment explanation
Indices: 109174--109216 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
109164 ATTCAAGGTG
109174 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
109192 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
109210 TAATTAA
1 TAATTAA
109217 AAACCTAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:115635 original size:23 final size:22
Alignment explanation
Indices: 115592--115640 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
115582 GACTTCTTAT
* *
115592 TAAAATAAAATTCAATGGTAAAA
1 TAAAATAAAAGTAAATGGT-AAA
115615 TAAAATAAAAGTAAA-GTGTAAA
1 TAAAATAAAAGTAAATG-GTAAA
115637 TAAA
1 TAAA
115641 CTAGACTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.63, C:0.02, G:0.10, T:0.24
Consensus pattern (22 bp):
TAAAATAAAAGTAAATGGTAAA
Found at i:122232 original size:12 final size:12
Alignment explanation
Indices: 122215--122250 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
122205 AGAAAAACTT
*
122215 ATTGATGCTTTA
1 ATTGATGTTTTA
122227 ATTGATGTTTTA
1 ATTGATGTTTTA
*
122239 AGTGATGTTTTA
1 ATTGATGTTTTA
122251 TTTACACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.53
Consensus pattern (12 bp):
ATTGATGTTTTA
Found at i:126528 original size:6 final size:6
Alignment explanation
Indices: 126517--126543 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
126507 GAAGGAAGGG
126517 AAGGAA AAGGAA AAGGAA AAGGAA AAG
1 AAGGAA AAGGAA AAGGAA AAGGAA AAG
126544 AAAGGGGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (6 bp):
AAGGAA
Found at i:133573 original size:29 final size:29
Alignment explanation
Indices: 133532--133605 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 29
133522 GAAACTTTGG
* *
133532 AAAGGTAAGCCTTTGTGGCGAACCTC-AT-
1 AAAGG-AAGCCTTTGTGGCAAAACTCTATA
133560 AAAGGAACGTCC-TTGTGGCAAAACTCTATA
1 AAAGGAA-G-CCTTTGTGGCAAAACTCTATA
133590 AAAGGAAGCCTTTGTG
1 AAAGGAAGCCTTTGTG
133606 ACGTTCTCTG
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
27 2 0.05
28 20 0.51
29 10 0.26
30 7 0.18
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.24
Consensus pattern (29 bp):
AAAGGAAGCCTTTGTGGCAAAACTCTATA
Found at i:137087 original size:19 final size:20
Alignment explanation
Indices: 137051--137088 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
137041 AATTGTAAAT
* *
137051 AATACATTTTAATTATATTC
1 AATACATTTGAATAATATTC
137071 AATA-ATTTGAATAATATT
1 AATACATTTGAATAATATT
137089 ATTTTAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (20 bp):
AATACATTTGAATAATATTC
Found at i:137282 original size:4 final size:4
Alignment explanation
Indices: 137275--137309 Score: 52
Period size: 4 Copynumber: 8.2 Consensus size: 4
137265 TTTTTAAAAA
137275 AAAT AAATT AAAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAA-T -AAAT AAAT AAAT AAAT AAAT AAAT A
137310 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 24 0.83
5 2 0.07
6 3 0.10
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:137287 original size:12 final size:14
Alignment explanation
Indices: 137268--137308 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
137258 AAAATATTTT
*
137268 TTAAAAAAAATAAA
1 TTAAAATAAATAAA
137282 TTAAAATAAATAAA
1 TTAAAATAAATAAA
137296 -T-AAATAAATAAA
1 TTAAAATAAATAAA
137308 T
1 T
137309 ATATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 11 0.44
13 1 0.04
14 13 0.52
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
TTAAAATAAATAAA
Found at i:138216 original size:16 final size:17
Alignment explanation
Indices: 138195--138228 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
138185 ATTAGGTTTA
138195 TTTTGGTACTTG-TATT
1 TTTTGGTACTTGATATT
138211 TTTTGGTACTTGATATT
1 TTTTGGTACTTGATATT
138228 T
1 T
138229 GAACTTGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.15, C:0.06, G:0.18, T:0.62
Consensus pattern (17 bp):
TTTTGGTACTTGATATT
Found at i:141507 original size:23 final size:24
Alignment explanation
Indices: 141464--141508 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
141454 ACATATTTAA
*
141464 TGTTTTAATTTATTTTAAATAATG
1 TGTTTTAATTTAATTTAAATAATG
141488 TGTTTTAA-TTAATTTAAATAA
1 TGTTTTAATTTAATTTAAATAA
141509 CTTTTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (24 bp):
TGTTTTAATTTAATTTAAATAATG
Done.