Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011899.1 Kokia drynarioides strain JFW-HI SEQ_126896, 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: 143884
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:1277 original size:42 final size:42
Alignment explanation
Indices: 1225--1304 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
1215 GGAGATGGTG
* *
1225 AGGGAGAGGGAGAGGGAAAGGGAGAAATGGGAAGCGAGGGAA
1 AGGGACAGGGAAAGGGAAAGGGAGAAATGGGAAGCGAGGGAA
1267 AGGGACAGGGAAAGGGAAAGGGAGAAATGGGAAGCGAG
1 AGGGACAGGGAAAGGGAAAGGGAGAAATGGGAAGCGAG
1305 AGTGTAATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.41, C:0.04, G:0.53, T:0.03
Consensus pattern (42 bp):
AGGGACAGGGAAAGGGAAAGGGAGAAATGGGAAGCGAGGGAA
Found at i:1384 original size:23 final size:23
Alignment explanation
Indices: 1358--1402 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1348 GTAAATCGAA
1358 TTTAT-AAATATAAAATAAAAATG
1 TTTATAAAAT-TAAAATAAAAATG
*
1381 TTTATAAAATTAATATAAAAAT
1 TTTATAAAATTAAAATAAAAAT
1403 ATATTGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
TTTATAAAATTAAAATAAAAATG
Found at i:1611 original size:36 final size:36
Alignment explanation
Indices: 1564--1638 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
1554 TAACCATATT
*
1564 TTTCTTATAATTAATGGATGATGATGTTGATTTCAA
1 TTTCTTATAATTAATGGACGATGATGTTGATTTCAA
1600 TTTCTTATAATTAATGGACGATGATGTTGATTTCAA
1 TTTCTTATAATTAATGGACGATGATGTTGATTTCAA
1636 TTT
1 TTT
1639 AATTATTAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.48
Consensus pattern (36 bp):
TTTCTTATAATTAATGGACGATGATGTTGATTTCAA
Found at i:6792 original size:24 final size:25
Alignment explanation
Indices: 6752--6800 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
6742 ATTGAAAAAA
*
6752 AAAAAAGAAACTTAGGTATCAAGTT
1 AAAAAAGAAACTTAGGTACCAAGTT
6777 AAAAAA-AAA-TTCAGGTACCAAGTT
1 AAAAAAGAAACTT-AGGTACCAAGTT
6801 GAGCATTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 2 0.09
24 14 0.64
25 6 0.27
ACGTcount: A:0.53, C:0.10, G:0.14, T:0.22
Consensus pattern (25 bp):
AAAAAAGAAACTTAGGTACCAAGTT
Found at i:7561 original size:20 final size:20
Alignment explanation
Indices: 7504--7561 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
7494 TTATAATAGT
*
7504 TAAAATCTTATGCTTATTTA
1 TAAAATCTTATGCTTTTTTA
* *
7524 -AAACTTTGTATG-TATTTTTA
1 TAAAATCT-TATGCT-TTTTTA
7544 TAAAATCTTATGCTTTTT
1 TAAAATCTTATGCTTTTT
7562 GTCGAAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
19 6 0.21
20 17 0.59
21 6 0.21
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.53
Consensus pattern (20 bp):
TAAAATCTTATGCTTTTTTA
Found at i:18697 original size:2 final size:2
Alignment explanation
Indices: 18690--18714 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18680 GGTTGAAACA
18690 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 A
18715 AAATAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23930 original size:12 final size:13
Alignment explanation
Indices: 23913--23941 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
23903 TTATGCAGTT
23913 AAATTTAAAAA-A
1 AAATTTAAAAATA
23925 AAATTTAAAAATA
1 AAATTTAAAAATA
23938 AAAT
1 AAAT
23942 ATTGTCACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATTTAAAAATA
Found at i:32165 original size:49 final size:49
Alignment explanation
Indices: 32108--32205 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
32098 AATATATAAG
32108 TTAGAATTTTCAAAGTAAATAAAATAGGAATGATTAGTGTTGATAGAGA
1 TTAGAATTTTCAAAGTAAATAAAATAGGAATGATTAGTGTTGATAGAGA
*
32157 TTAGAATTTTCAAAGTAAATGAAATAGGAATGATTAGTGTTGATAGAGA
1 TTAGAATTTTCAAAGTAAATAAAATAGGAATGATTAGTGTTGATAGAGA
32206 AGATGGTTGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.44, C:0.02, G:0.21, T:0.33
Consensus pattern (49 bp):
TTAGAATTTTCAAAGTAAATAAAATAGGAATGATTAGTGTTGATAGAGA
Found at i:34284 original size:30 final size:30
Alignment explanation
Indices: 34200--34284 Score: 107
Period size: 30 Copynumber: 2.8 Consensus size: 30
34190 GTAAGCTCGA
* ** *
34200 TATAATGTCAGCTTATGTGAGCAAATTTGT
1 TATAATGTCAGCTTGTGTGAGCAACCTTGG
* *
34230 TATAATGTTAGCTTGTATGAGCAACCTTGG
1 TATAATGTCAGCTTGTGTGAGCAACCTTGG
*
34260 TATATTGTCAGCTTGTGTGAGCAAC
1 TATAATGTCAGCTTGTGTGAGCAAC
34285 TTATTATCGT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (30 bp):
TATAATGTCAGCTTGTGTGAGCAACCTTGG
Found at i:42667 original size:2 final size:2
Alignment explanation
Indices: 42660--42687 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42650 TTTGAAATTC
42660 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42688 TTTTTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49683 original size:23 final size:21
Alignment explanation
Indices: 49650--49698 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 21
49640 TATTATACAT
*
49650 TATTAAATTAATT-TATTTTAA
1 TATTAAATTAATTGT-TTATAA
49671 TATTAAACTTTAATTGTTTATAA
1 TATTAAA--TTAATTGTTTATAA
49694 TATTA
1 TATTA
49699 TATTTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 7 0.29
23 16 0.67
24 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
TATTAAATTAATTGTTTATAA
Found at i:60352 original size:25 final size:27
Alignment explanation
Indices: 60324--60382 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 27
60314 GAAGATGTAA
60324 AAATTTTT-AATA-ATTAATCGAATCG
1 AAATTTTTAAATACATTAATCGAATCG
60349 AAATTTTTTTCAAATACATTAATCGAATCG
1 AAA--TTTTT-AAATACATTAATCGAATCG
60379 AAAT
1 AAAT
60383 ATTTCAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
25 3 0.10
27 5 0.17
28 1 0.03
29 4 0.14
30 16 0.55
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (27 bp):
AAATTTTTAAATACATTAATCGAATCG
Found at i:61302 original size:31 final size:31
Alignment explanation
Indices: 61263--61335 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
61253 CCCAGCCTGA
61263 ATAT-TATGTTATAA-AATAATATTATACTA-
1 ATATATATGTTATAATAATAATATTATA-TAT
*
61292 ATTATATATGTTA-AATAATAATTTTATATAT
1 A-TATATATGTTATAATAATAATATTATATAT
61323 ATATATAT-TTATA
1 ATATATATGTTATA
61336 TTTATATAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
29 4 0.11
30 15 0.39
31 19 0.50
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (31 bp):
ATATATATGTTATAATAATAATATTATATAT
Found at i:63391 original size:22 final size:22
Alignment explanation
Indices: 63364--63406 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
63354 AAATTAAAGA
63364 TAAAATATAAAATATATATTTT
1 TAAAATATAAAATATATATTTT
* *
63386 TAAAATTTAAAATTTATATTT
1 TAAAATATAAAATATATATTT
63407 ATTCTAATTA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TAAAATATAAAATATATATTTT
Found at i:66808 original size:24 final size:24
Alignment explanation
Indices: 66777--66825 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
66767 ATTTATGAAG
66777 TTATAAATTTTATATT-TAAATATT
1 TTATAAA-TTTATATTATAAATATT
*
66801 TTATAAATTTATATTATATATATT
1 TTATAAATTTATATTATAAATATT
66825 T
1 T
66826 CAAAATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTATAAATTTATATTATAAATATT
Found at i:66831 original size:23 final size:23
Alignment explanation
Indices: 66779--66831 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
66769 TTATGAAGTT
*
66779 ATAAATTTTATATTTAAATATTTT
1 ATAAA-TTTATATTTAAATATTTC
*
66803 ATAAATTTATATTATATATATTTC
1 ATAAATTTATATT-TAAATATTTC
66827 A-AAAT
1 ATAAAT
66832 AATAATAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 12 0.46
24 14 0.54
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
ATAAATTTATATTTAAATATTTC
Found at i:81702 original size:9 final size:8
Alignment explanation
Indices: 81689--81730 Score: 57
Period size: 9 Copynumber: 5.0 Consensus size: 8
81679 CTTTTCTCAA
81689 TTTTTTCT
1 TTTTTTCT
*
81697 TCTTTTCT
1 TTTTTTCT
81705 TTATTTTCT
1 TT-TTTTCT
81714 TTATTTTCT
1 TT-TTTTCT
81723 TTTTTTCT
1 TTTTTTCT
81731 GTCTTTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
8 14 0.45
9 17 0.55
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTCT
Found at i:81713 original size:17 final size:16
Alignment explanation
Indices: 81689--81736 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 16
81679 CTTTTCTCAA
81689 TTTTTTCTTCTTTTCT
1 TTTTTTCTTCTTTTCT
*
81705 TTATTTTCTTTATTTTCT
1 TT-TTTTC-TTCTTTTCT
81723 TTTTTTCTGTCTTT
1 TTTTTTCT-TCTTT
81737 AAATACTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 3 0.11
17 14 0.52
18 10 0.37
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTTTTCTTCTTTTCT
Found at i:92166 original size:98 final size:98
Alignment explanation
Indices: 91997--92193 Score: 385
Period size: 98 Copynumber: 2.0 Consensus size: 98
91987 AGCCAAGACA
91997 AATTATCTCCCTCTTTAGAACTTTAGATAACATTGTAATCTTAACAATCTTTATGATGCAACATT
1 AATTATCTCCCTCTTTAGAACTTTAGATAACATTGTAATCTTAACAATCTTTATGATGCAACATT
92062 TTATTAATTTAACATAAGTAATCAATTGGCCAC
66 TTATTAATTTAACATAAGTAATCAATTGGCCAC
92095 AATTATCTCCCTCTTTAGAACTTTAGATAACATTGTAATCTTAACAATCTTTATGATGCAACATT
1 AATTATCTCCCTCTTTAGAACTTTAGATAACATTGTAATCTTAACAATCTTTATGATGCAACATT
*
92160 TTATTAATTTAATATAAGTAATCAATTGGCCAC
66 TTATTAATTTAACATAAGTAATCAATTGGCCAC
92193 A
1 A
92194 TTTACTTGTA
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (98 bp):
AATTATCTCCCTCTTTAGAACTTTAGATAACATTGTAATCTTAACAATCTTTATGATGCAACATT
TTATTAATTTAACATAAGTAATCAATTGGCCAC
Found at i:93573 original size:42 final size:42
Alignment explanation
Indices: 93494--93580 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 42
93484 CACTAATCTT
* * * *
93494 ACAACACATTCTGGTGTTAGATTGTATCAACAGTCTTATTTG
1 ACAACAAATTCTGGTATTAGATTGTATCAACACTCTTATTCG
* *
93536 ACAACAAATTCTGGTATTAGATTGTATCGATACTCTTATTCG
1 ACAACAAATTCTGGTATTAGATTGTATCAACACTCTTATTCG
93578 ACA
1 ACA
93581 GTCGATTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (42 bp):
ACAACAAATTCTGGTATTAGATTGTATCAACACTCTTATTCG
Found at i:100353 original size:115 final size:115
Alignment explanation
Indices: 100151--100367 Score: 434
Period size: 115 Copynumber: 1.9 Consensus size: 115
100141 AAAAATGCCG
100151 AAAGATTAATGTAGGATCCCCATTTCGTTCACAAGTGCATTGCTTGTTTTCACCTTCACCTCAGA
1 AAAGATTAATGTAGGATCCCCATTTCGTTCACAAGTGCATTGCTTGTTTTCACCTTCACCTCAGA
100216 AAATGATCATTCTAACTTAATTAAAAACAGGGGGTAAGACTAAACCAGGA
66 AAATGATCATTCTAACTTAATTAAAAACAGGGGGTAAGACTAAACCAGGA
100266 AAAGATTAATGTAGGATCCCCATTTCGTTCACAAGTGCATTGCTTGTTTTCACCTTCACCTCAGA
1 AAAGATTAATGTAGGATCCCCATTTCGTTCACAAGTGCATTGCTTGTTTTCACCTTCACCTCAGA
100331 AAATGATCATTCTAACTTAATTAAAAACAGGGGGTAA
66 AAATGATCATTCTAACTTAATTAAAAACAGGGGGTAA
100368 TAAGTTCTCT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 102 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (115 bp):
AAAGATTAATGTAGGATCCCCATTTCGTTCACAAGTGCATTGCTTGTTTTCACCTTCACCTCAGA
AAATGATCATTCTAACTTAATTAAAAACAGGGGGTAAGACTAAACCAGGA
Found at i:102729 original size:22 final size:19
Alignment explanation
Indices: 102684--102731 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 19
102674 TTTTTTTATC
102684 TAAAATTATTTATAATAAAA
1 TAAAA-TATTTATAATAAAA
*
102704 TAAAATATTATATTAATATAAT
1 TAAAATATT-TA-TAATA-AAA
102726 TAAAAT
1 TAAAAT
102732 TTAAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 4 0.17
20 7 0.29
21 5 0.21
22 8 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAAATATTTATAATAAAA
Found at i:104727 original size:88 final size:89
Alignment explanation
Indices: 104576--104751 Score: 230
Period size: 88 Copynumber: 2.0 Consensus size: 89
104566 GTATTTGAAT
* **
104576 TTGACACTTTTTCCTAATTTAGTACTTAAACTTTTTTTTGTCCAATTTGGTAATCAAACTTGACA
1 TTGACACTTTTTCCTAAGTTAGTACTTAAAC-TTTTTGAGTCCAATTTGGTAATCAAACTTGACA
104641 CTTTTTCCTAATATGGTACCTAAAC
65 CTTTTTCCTAATATGGTACCTAAAC
* * * ** *
104666 TTGACACTTTTT-TTAAGTTGGTACTTAAA-TTTTTGAGATCCAATTTGGTACTTGAACTTGACT
1 TTGACACTTTTTCCTAAGTTAGTACTTAAACTTTTTGAG-TCCAATTTGGTAATCAAACTTGACA
*
104729 CTTTTTCCTAATTTGGTACCTAA
65 CTTTTTCCTAATATGGTACCTAA
104752 TATTTTTTAA
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
87 6 0.08
88 43 0.57
89 14 0.19
90 12 0.16
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.45
Consensus pattern (89 bp):
TTGACACTTTTTCCTAAGTTAGTACTTAAACTTTTTGAGTCCAATTTGGTAATCAAACTTGACAC
TTTTTCCTAATATGGTACCTAAAC
Found at i:104990 original size:60 final size:59
Alignment explanation
Indices: 104908--105080 Score: 213
Period size: 60 Copynumber: 2.9 Consensus size: 59
104898 ATTGAATATT
* * *
104908 AAAAAAAGCTTAGGTACCAAATTAGAAAAAATTGTCAAGTTCAGGTACCAAATAGGGTCC
1 AAAAAAAGTTTAGGTACCAAATTAGAAAAAATTGTCAAGTTCAGGTATCAAATAGGGT-A
* * * * * *
104968 AAAAAAAGTTTAGATACCAAATTAGAAAAAAGTGTCAAATACGGGTATCAAATTGGGTA
1 AAAAAAAGTTTAGGTACCAAATTAGAAAAAATTGTCAAGTTCAGGTATCAAATAGGGTA
* *
105027 AAAAATAAATTTAGGTACCAAATTAG-AAAAATGTGTCAAGTTCAAGTATCAAAT
1 AAAAA-AAGTTTAGGTACCAAATTAGAAAAAAT-TGTCAAGTTCAGGTATCAAAT
105081 GTTATATTAG
Statistics
Matches: 95, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
59 10 0.11
60 85 0.89
ACGTcount: A:0.48, C:0.11, G:0.17, T:0.24
Consensus pattern (59 bp):
AAAAAAAGTTTAGGTACCAAATTAGAAAAAATTGTCAAGTTCAGGTATCAAATAGGGTA
Found at i:105170 original size:30 final size:30
Alignment explanation
Indices: 105134--105225 Score: 123
Period size: 30 Copynumber: 3.1 Consensus size: 30
105124 GATCTTTAGG
*
105134 AATTAATAGGAATATTTTAGGTACTACAAA
1 AATTAATAGGAATATTTTAGGTAATACAAA
*
105164 AATTAATAGGGAA-ATTTTAGGTAATATAAA
1 AATTAATA-GGAATATTTTAGGTAATACAAA
* * *
105194 AATTGATAGGATTATTTTAAGTAATACAAA
1 AATTAATAGGAATATTTTAGGTAATACAAA
105224 AA
1 AA
105226 AACAGTAGGA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
29 3 0.06
30 47 0.87
31 4 0.07
ACGTcount: A:0.49, C:0.03, G:0.14, T:0.34
Consensus pattern (30 bp):
AATTAATAGGAATATTTTAGGTAATACAAA
Found at i:111470 original size:5 final size:5
Alignment explanation
Indices: 111460--111499 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
111450 CCACAATCCG
* * *
111460 ACATC ACATC ACATC GCATC GCATC GCATC ACATC ACATC
1 ACATC ACATC ACATC ACATC ACATC ACATC ACATC ACATC
111500 CCCTTCTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.33, C:0.40, G:0.07, T:0.20
Consensus pattern (5 bp):
ACATC
Found at i:122140 original size:29 final size:29
Alignment explanation
Indices: 122079--122143 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
122069 TAGGGATTTT
***
122079 ATTAAATTAGTTAATTTATTATTAAATGG
1 ATTAAATTAGTTAATTTATTATTAAAAAA
* **
122108 ATTAATTTAGTTCTTTTATTATTAAAAAA
1 ATTAAATTAGTTAATTTATTATTAAAAAA
122137 ATTAAAT
1 ATTAAAT
122144 AAGATCAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (29 bp):
ATTAAATTAGTTAATTTATTATTAAAAAA
Found at i:126751 original size:2 final size:2
Alignment explanation
Indices: 126744--126769 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
126734 TATCATGTGA
126744 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
126770 TCCCCCCTTA
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:129901 original size:6 final size:6
Alignment explanation
Indices: 129892--129938 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
129882 TAAATTTGTT
* *
129892 TTTAAA TTTAAA TTT-AA TTTAAG TTTAAA TTT-AT TTTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
129939 ATTATTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
5 9 0.26
6 21 0.62
7 4 0.12
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:129902 original size:35 final size:35
Alignment explanation
Indices: 129863--129944 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 35
129853 CTAAACTCAT
* *
129863 TTTAAATTTATTTTAAGATTAAATTTGTTTTTAAA
1 TTTAAATTTATTTTAAGATTAAATTTATTTTCAAA
* *
129898 TTTAAATTTAATTTAAGTTTAAATTTATTTTCAAA
1 TTTAAATTTATTTTAAGATTAAATTTATTTTCAAA
*
129933 TTTAAAATTATT
1 TTTAAATTTATT
129945 ATAAATTTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (35 bp):
TTTAAATTTATTTTAAGATTAAATTTATTTTCAAA
Found at i:129907 original size:12 final size:12
Alignment explanation
Indices: 129892--129938 Score: 53
Period size: 11 Copynumber: 4.0 Consensus size: 12
129882 TAAATTTGTT
129892 TTTAAATTTAAA
1 TTTAAATTTAAA
*
129904 TTT-AATTTAAG
1 TTTAAATTTAAA
*
129915 TTTAAATTT-AT
1 TTTAAATTTAAA
129926 TTTCAAATTTAAA
1 TTT-AAATTTAAA
129939 ATTATTATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 14 0.48
12 14 0.48
13 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:129938 original size:18 final size:17
Alignment explanation
Indices: 129863--129957 Score: 102
Period size: 17 Copynumber: 5.4 Consensus size: 17
129853 CTAAACTCAT
129863 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
129881 -TTAAATTTGTTTTTAAA
1 TTTAAATTT-ATTTTAAA
* *
129898 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
129915 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* *
129933 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
129950 TTTGAAAT
1 TTT-AAAT
129958 AAATAAAGTT
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
17 33 0.52
18 31 0.48
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:130697 original size:3 final size:3
Alignment explanation
Indices: 130684--130724 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
130674 GTATTGAATG
* *
130684 AAT ATT AAT AAT AAT AAT ATT AAAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT A
130725 TTATTAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 31 0.94
4 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:130709 original size:22 final size:22
Alignment explanation
Indices: 130684--130727 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
130674 GTATTGAATG
*
130684 AATATTAATAATAATAATATTA
1 AATAATAATAATAATAATATTA
130706 AATAATAATAATAATAATATTA
1 AATAATAATAATAATAATATTA
130728 TTAAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AATAATAATAATAATAATATTA
Found at i:130711 original size:16 final size:15
Alignment explanation
Indices: 130684--130724 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
130674 GTATTGAATG
130684 AATATTAATAATAAT
1 AATATTAATAATAAT
130699 AATATTAAATAATAAT
1 AATATT-AATAATAAT
*
130715 AATAATAATA
1 AATATTAATA
130725 TTATTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATATTAATAATAAT
Found at i:130718 original size:25 final size:26
Alignment explanation
Indices: 130675--130732 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 26
130665 ATTAAGAATG
* *
130675 TATTGAATGAATATTAATAATAATAA
1 TATTAAATGAATAATAATAATAATAA
*
130701 TATTAAAT-AATAATAATAATAATAT
1 TATTAAATGAATAATAATAATAATAA
130726 TATTAAA
1 TATTAAA
130733 AAAAATCGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 22 0.76
26 7 0.24
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (26 bp):
TATTAAATGAATAATAATAATAATAA
Found at i:131867 original size:29 final size:28
Alignment explanation
Indices: 131816--132093 Score: 114
Period size: 30 Copynumber: 9.4 Consensus size: 28
131806 GAGACCCCTA
* *
131816 AACTATCCAAAATTTTCATTTTTA-CCTCCG
1 AACT-TCCAAAAATTCCA-TTTTACCCT-CG
* **
131846 AACTTTCAAAAAATTCCATTTTCGACCCTAA
1 AAC-TTCCAAAAATTCCATTTT--ACCCTCG
* * * **
131877 AACTTCTAAAAATTACTTTTTAACCCTAA
1 AACTTCCAAAAATTCCATTTT-ACCCTCG
* * *
131906 AACTTTCAAAAAATTCCAATTTTGCCAC-CAA
1 AAC-TTCCAAAAATTCC-ATTTTACC-CTC-G
*
131937 AACTTCCAAAAATTACATTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTACCCTCG
* ***
131965 AACTTCCAAAAATTCCTTTTTTGA-TAGCG
1 AACTTCCAAAAATTCC-ATTTT-ACCCTCG
* *
131994 AAACTTCCAAAAATTACATTTTTACCCTTG
1 -AACTTCCAAAAATTCCA-TTTTACCCTCG
* *
132024 AACTTTCAAAAATTCCATTTTTA-ACTCCG
1 AACTTCCAAAAATTCCA-TTTTACCCT-CG
* * * *
132053 AAACTTTCAAAAATTACTATTTTACCCCCA
1 -AACTTCCAAAAATT-CCATTTTACCCTCG
*
132083 AACCTCCAAAA
1 AACTTCCAAAA
132094 TCCTATTTTT
Statistics
Matches: 191, Mismatches: 39, Indels: 37
0.72 0.15 0.14
Matches are distributed among these distances:
28 18 0.09
29 60 0.31
30 93 0.49
31 17 0.09
32 3 0.02
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.34
Consensus pattern (28 bp):
AACTTCCAAAAATTCCATTTTACCCTCG
Found at i:131888 original size:30 final size:29
Alignment explanation
Indices: 131854--132125 Score: 146
Period size: 30 Copynumber: 9.2 Consensus size: 29
131844 CGAACTTTCA
*
131854 AAAAATTCCATTTTCGACCCTAAAACTTCT
1 AAAAATTCCATTTT-GACCCTAAAACTTCC
* * * *
131884 AAAAATTACTTTTTAACCCTAAAACTTTCA
1 AAAAATTCCATTTTGACCCTAAAAC-TTCC
*
131914 AAAAATTCCAATTTTG-CCACCAAAACTTCC
1 AAAAATTCC-ATTTTGACC-CTAAAACTTCC
* **
131944 AAAAATTACATTTT-ACCCTCGAACTTCC
1 AAAAATTCCATTTTGACCCTAAAACTTCC
* ** *
131972 AAAAATTCCTTTTTTGATAGC-GAAACTTCC
1 AAAAATTCC-ATTTTGA-CCCTAAAACTTCC
* * ** *
132002 AAAAATTACATTTTTACCCTTGAACTTTC
1 AAAAATTCCATTTTGACCCTAAAACTTCC
* * *
132031 AAAAATTCCATTTTTAACTCC-GAAACTTTC
1 AAAAATTCCA-TTTTGAC-CCTAAAACTTCC
* ** *
132061 AAAAATTACTATTTT-ACCCCCAAACCTCC
1 AAAAATT-CCATTTTGACCCTAAAACTTCC
*
132090 -AAAA-TCCTATTTTTGA-CCTAAAAACTTTC
1 AAAAATTCC-A-TTTTGACCCT-AAAACTTCC
132119 AAAAATT
1 AAAAATT
132126 ACCCTTTTAC
Statistics
Matches: 184, Mismatches: 40, Indels: 35
0.71 0.15 0.14
Matches are distributed among these distances:
26 1 0.01
27 2 0.01
28 29 0.16
29 56 0.30
30 80 0.43
31 16 0.09
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAAATTCCATTTTGACCCTAAAACTTCC
Found at i:131975 original size:59 final size:59
Alignment explanation
Indices: 131815--132079 Score: 252
Period size: 59 Copynumber: 4.4 Consensus size: 59
131805 GGAGACCCCT
* *
131815 AAACTATCCAAAATTTTCATTTTTA-CCTCCGAACTTTCAAAAAATTCC-ATTTTCGAC-CCTA
1 AAACT-TCCAAAAATTACA-TTTTACCCT-CGAACTTTCAAAAAATTCCAATTTT-GACACC-A
* * ** *
131876 AAACTTCTAAAAATTACTTTTTAACCCTAAAACTTTCAAAAAATTCCAATTTTGCCACCA
1 AAACTTCCAAAAATTACATTTT-ACCCTCGAACTTTCAAAAAATTCCAATTTTGACACCA
* ** * * *
131936 AAACTTCCAAAAATTACATTTTACCCTCGAAC-TTCCAAAAATTCCTTTTTTGATAGCG
1 AAACTTCCAAAAATTACATTTTACCCTCGAACTTTCAAAAAATTCCAATTTTGACACCA
* * * * *
131994 AAACTTCCAAAAATTACATTTTTACCCTTGAACTTTC-AAAAATTCCATTTTTAACTCCG
1 AAACTTCCAAAAATTACA-TTTTACCCTCGAACTTTCAAAAAATTCCAATTTTGACACCA
*
132053 AAACTTTCAAAAATTACTATTTTACCC
1 AAACTTCCAAAAATTAC-ATTTTACCC
132080 CCAAACCTCC
Statistics
Matches: 172, Mismatches: 25, Indels: 16
0.81 0.12 0.08
Matches are distributed among these distances:
58 37 0.22
59 66 0.38
60 54 0.31
61 15 0.09
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.35
Consensus pattern (59 bp):
AAACTTCCAAAAATTACATTTTACCCTCGAACTTTCAAAAAATTCCAATTTTGACACCA
Found at i:132093 original size:59 final size:58
Alignment explanation
Indices: 131815--132154 Score: 242
Period size: 59 Copynumber: 5.7 Consensus size: 58
131805 GGAGACCCCT
* * * * * *
131815 AAACTATCCAAAATTTTCATTTTTACCTCCGAACTTTCAAAAAATTCCATTTTCGAC-CCTA
1 AAACT-TCCAAAAATTACA-TTTTACCCCCGAAC-TTCCAAAAATTCCATTTTTGACTCC-G
* * *** * * * * *
131876 AAACTTCTAAAAATTACTTTTTAACCCTAAAACTTTCAAAAAATTCCAATTTTGCCACCA
1 AAACTTCCAAAAATTACATTTT-ACCCCCGAAC-TTCCAAAAATTCCATTTTTGACTCCG
* * *
131936 AAACTTCCAAAAATTACATTTTACCCTCGAACTTCCAAAAATTCCTTTTTTGA-TAGCG
1 AAACTTCCAAAAATTACATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACT-CCG
** * *
131994 AAACTTCCAAAAATTACATTTTTACCCTTGAACTTTCAAAAATTCCATTTTTAACTCCG
1 AAACTTCCAAAAATTACA-TTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACTCCG
* * * **
132053 AAACTTTCAAAAATTACTATTTTACCCCCAAACCTCC-AAAA-TCCTATTTTTGAC-CTAA
1 AAACTTCCAAAAATTAC-ATTTTACCCCCGAACTTCCAAAAATTCC-ATTTTTGACTC-CG
* * *
132111 AAACTTTCAAAAATTACCCTTTTACCCCCGGA-TGTCCAAAAATT
1 AAACTTCCAAAAATTA-CATTTTACCCCCGAACT-TCCAAAAATT
132155 TTGTTTTTGA
Statistics
Matches: 227, Mismatches: 40, Indels: 25
0.78 0.14 0.09
Matches are distributed among these distances:
57 4 0.02
58 78 0.34
59 79 0.35
60 59 0.26
61 7 0.03
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (58 bp):
AAACTTCCAAAAATTACATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACTCCG
Found at i:137808 original size:1 final size:1
Alignment explanation
Indices: 137804--137867 Score: 56
Period size: 1 Copynumber: 64.0 Consensus size: 1
137794 AAAGAAGAAG
* * ** * * * *
137804 AAAAAGAAAAAACAAAAAGGAAAAAAAAATAAAAATAAAAAAATAAAAAAAAAATAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
137868 GGAGTGGTCA
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.88, C:0.02, G:0.05, T:0.06
Consensus pattern (1 bp):
A
Found at i:137827 original size:19 final size:19
Alignment explanation
Indices: 137788--137867 Score: 60
Period size: 19 Copynumber: 4.4 Consensus size: 19
137778 AATAAAAGAC
* *
137788 AAGAAAAAAGAAGAAGAAA
1 AAGAAAAAACAAAAAGAAA
*
137807 AAGAAAAAACAAAAAG-GA
1 AAGAAAAAACAAAAAGAAA
* *
137825 AA-AAAAAATAAAAATAAA
1 AAGAAAAAACAAAAAGAAA
* *
137843 AA-AATAAAAAAAAAATAAA
1 AAGAA-AAAACAAAAAGAAA
137862 AA-AAAA
1 AAGAAAA
137868 GGAGTGGTCA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
17 11 0.21
18 10 0.19
19 31 0.60
ACGTcount: A:0.85, C:0.01, G:0.09, T:0.05
Consensus pattern (19 bp):
AAGAAAAAACAAAAAGAAA
Found at i:137832 original size:25 final size:22
Alignment explanation
Indices: 137791--137867 Score: 73
Period size: 23 Copynumber: 3.4 Consensus size: 22
137781 AAAAGACAAG
* *
137791 AAAAAAGAAGAAGAAAAAGAAAA
1 AAAAAAAAAGAA-AAAAAAAAAA
* *
137814 AACAAAAAGGAAAAAAAAATAAA
1 AAAAAAAAAGAAAAAAAAA-AAA
* *
137837 AATAAAAAAATAAAAAAAAAATA
1 AA-AAAAAAAGAAAAAAAAAAAA
137860 AAAAAAAA
1 AAAAAAAA
137868 GGAGTGGTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
22 12 0.27
23 18 0.41
24 14 0.32
ACGTcount: A:0.86, C:0.01, G:0.08, T:0.05
Consensus pattern (22 bp):
AAAAAAAAAGAAAAAAAAAAAA
Found at i:139242 original size:100 final size:100
Alignment explanation
Indices: 139069--139340 Score: 323
Period size: 100 Copynumber: 2.7 Consensus size: 100
139059 GCACCATGAA
* * * * * * *
139069 ACATGACGGGAGAGAGCTAAGATCACAACGGCGGATCCAGTACTGCAAAGATACAAAAGGGAAGG
1 ACATGACGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCAAAGATACGAAAGGGAAAG
* *
139134 GTTTAAGTCGAAACGGCAAACCTTATACCTCAGAG
66 ATTTAAGTCGAAACAGCAAACCTTATACCTCAGAG
* *
139169 ACATGACGGGAAAGATTTAAGACCGCAATGGCGGATCCAGTACCGCAAAGATACGAAAGGGAAAG
1 ACATGACGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCAAAGATACGAAAGGGAAAG
* * *
139234 ATTTAAGTCGCAACAGCGAACCTTGTACCTCAGAG
66 ATTTAAGTCGAAACAGCAAACCTTATACCTCAGAG
* * * * * * * *
139269 ACATGACGGGAATGATCTAAG-CCGTAACGGCGAATCCAGTGCCGCGAAGACATG-AAGGGAAAT
1 ACATGACGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCAAAGATACGAAAGGGAAAG
*
139332 ATCTAAGTC
66 ATTTAAGTC
139341 ACAACGGAAG
Statistics
Matches: 147, Mismatches: 25, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
98 16 0.11
99 26 0.18
100 105 0.71
ACGTcount: A:0.37, C:0.21, G:0.27, T:0.16
Consensus pattern (100 bp):
ACATGACGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCAAAGATACGAAAGGGAAAG
ATTTAAGTCGAAACAGCAAACCTTATACCTCAGAG
Found at i:139367 original size:49 final size:48
Alignment explanation
Indices: 139283--139458 Score: 151
Period size: 49 Copynumber: 3.6 Consensus size: 48
139273 GACGGGAATG
* * * * ** *
139283 ATCTAAGCCGTAACGGCGAATCCAGTGCCGCGAAGACATGAAGGGAAA
1 ATCTAAGTCGCAACGGCGGATCCAGTACCATGAAGACATAAAGGGAAA
* ** *
139331 TATCTAAGTCACAACGGAAGATCCAGTACCATGAAGACA-CAAGGGAAA
1 -ATCTAAGTCGCAACGGCGGATCCAGTACCATGAAGACATAAAGGGAAA
* *
139379 AGTTTAAGTCGCAATGGCGGA-CCTAGTACC-TGAGAGACATAAAGGGAAA
1 A-TCTAAGTCGCAACGGCGGATCC-AGTACCATGA-AGACATAAAGGGAAA
**
139428 GATCTAAACCGCAACGGCGGATCCAGTACCA
1 -ATCTAAGTCGCAACGGCGGATCCAGTACCA
139459 CAAAGATACA
Statistics
Matches: 100, Mismatches: 20, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
47 6 0.06
48 33 0.33
49 58 0.58
50 3 0.03
ACGTcount: A:0.38, C:0.22, G:0.26, T:0.15
Consensus pattern (48 bp):
ATCTAAGTCGCAACGGCGGATCCAGTACCATGAAGACATAAAGGGAAA
Found at i:139433 original size:97 final size:99
Alignment explanation
Indices: 139314--139544 Score: 256
Period size: 97 Copynumber: 2.3 Consensus size: 99
139304 CCAGTGCCGC
* * * * ** *
139314 GAAGACATGAAGGGAAATATCTAAGTCACAACGGAAGATCCAGTACCATGAAG-ACACAAGGGAA
1 GAAGACATAAAGGGAAAGATCTAAGCCGCAACGGAAGATCCAGTACCACAAAGAACAAAAGGGAA
* *
139378 AAGTTTAAGTCGC-AATGGCGGACC-TAGTACCTGA
66 AAGTTTAAGTC-CAAATGGCGGACCGTA-AACCTCA
* **
139412 G-AGACATAAAGGGAAAGATCTAAACCGCAACGGCGGATCCAGTACCACAAAGATACAAAAGGGA
1 GAAGACATAAAGGGAAAGATCTAAGCCGCAACGGAAGATCCAGTACCACAAAGA-ACAAAAGGGA
**
139476 ACGGTTTAAGTCCAAATGGCGGACCGTAAACCTCA
65 AAAGTTTAAGTCCAAATGGCGGACCGTAAACCTCA
*
139511 GAAGACA-AGAAGGGAAAGATTTAAGCCGCAACGG
1 GAAGACATA-AAGGGAAAGATCTAAGCCGCAACGG
139545 CGAATCCAGT
Statistics
Matches: 111, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
97 42 0.38
98 2 0.02
99 37 0.33
100 30 0.27
ACGTcount: A:0.41, C:0.19, G:0.26, T:0.14
Consensus pattern (99 bp):
GAAGACATAAAGGGAAAGATCTAAGCCGCAACGGAAGATCCAGTACCACAAAGAACAAAAGGGAA
AAGTTTAAGTCCAAATGGCGGACCGTAAACCTCA
Found at i:139546 original size:100 final size:100
Alignment explanation
Indices: 139314--139596 Score: 290
Period size: 100 Copynumber: 2.9 Consensus size: 100
139304 CCAGTGCCGC
* * * * ** * *
139314 GAAGACATGAAGGGAAATATCTAAGTCACAACGGAAGATCCAGTACCATGAAG--ACACAAGGGA
1 GAAGACAAGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGATACAAAAGGGA
* *
139377 AAAGTTTAAGTCGCAATGGCGGACCTAGTACCTGA
66 AAAGTTTAAGTCGCAATGGCGGACCTAGAACCTCA
* *
139412 G-AGACATA-AAGGGAAAGATCTAAACCGCAACGGCGGATCCAGTACCACAAAGATACAAAAGGG
1 GAAGACA-AGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGATACAAAAGGG
**
139475 AACGGTTTAAGTC-CAAATGGCGGACCGTA-AACCTCA
65 AAAAGTTTAAGTCGC-AATGGCGGACC-TAGAACCTCA
* * * *** *
139511 GAAGACAAGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTATCACGAAGATTTGAAGGGGA
1 GAAGACAAGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGATACAAAAGGGA
* *
139576 AATGTTTAAGTCGCAAAGGCG
66 AAAGTTTAAGTCGCAATGGCG
139597 AACCCGATAC
Statistics
Matches: 151, Mismatches: 26, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
97 41 0.27
98 2 0.01
99 37 0.25
100 70 0.46
101 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.15
Consensus pattern (100 bp):
GAAGACAAGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGAAGATACAAAAGGGA
AAAGTTTAAGTCGCAATGGCGGACCTAGAACCTCA
Found at i:139862 original size:101 final size:101
Alignment explanation
Indices: 139686--139871 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 101
139676 GATCAAAACT
* *
139686 ACAATGGCAAGTCTTTATCTCTCTGAAGTTGCAGCAATGGCAAGATGAAGCTTTAACATCAATTC
1 ACAATGGCAAGTCTTTATCTCTCTGAAGTTGCAGCAATGGCAAGATGAAGCTTCAACATCAAATC
139751 CTACCCTCTTGAAGTTACAGTAAAGTCGGATTAAAA
66 CTACCCTCTTGAAGTTACAGTAAAGTCGGATTAAAA
* * *
139787 ACAATGGCAAGTTTTTATCTCTCTGAAGTTGTAGTAA-GAGCAAGATGAAGCTTCAACATCAAAT
1 ACAATGGCAAGTCTTTATCTCTCTGAAGTTGCAGCAATG-GCAAGATGAAGCTTCAACATCAAAT
* *
139851 CCTATCTTCTTGAAGTTACAG
65 CCTACCCTCTTGAAGTTACAG
139872 CGAAGTTGAA
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
100 1 0.01
101 76 0.99
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (101 bp):
ACAATGGCAAGTCTTTATCTCTCTGAAGTTGCAGCAATGGCAAGATGAAGCTTCAACATCAAATC
CTACCCTCTTGAAGTTACAGTAAAGTCGGATTAAAA
Found at i:140003 original size:39 final size:39
Alignment explanation
Indices: 139949--140159 Score: 147
Period size: 39 Copynumber: 5.4 Consensus size: 39
139939 CTACATCGTT
139949 AACCAATCTCTTACCCCGAGCCTGAGGCAGATCATCATC
1 AACCAATCTCTTACCCCGAGCCTGAGGCAGATCATCATC
* * * * * *
139988 AACCAATCTCTTACCCCTAACCTGAGGCAAAGTGA-AACC
1 AACCAATCTCTTACCCCGAGCCTGAGGCAGA-TCATCATC
**** * *
140027 ATTTGATCTTTTACCCCGAGCTTGAGGCAGATCATCATC
1 AACCAATCTCTTACCCCGAGCCTGAGGCAGATCATCATC
* * * * * * *
140066 AACCAGTCTCTTACCCCAAGTCAGAGGTAGATTA-CAGCC
1 AACCAATCTCTTACCCCGAGCCTGAGGCAGATCATCA-TC
** * * * *
140105 ATTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCGTC
1 AACCAATCTCTTACCCCGAGCCTGAGGCAGATCATCATC
* *
140144 AACCAAACTCCTACCC
1 AACCAATCTCTTACCC
140160 TGATCACGAG
Statistics
Matches: 119, Mismatches: 49, Indels: 8
0.68 0.28 0.05
Matches are distributed among these distances:
38 4 0.03
39 112 0.94
40 3 0.03
ACGTcount: A:0.28, C:0.33, G:0.16, T:0.23
Consensus pattern (39 bp):
AACCAATCTCTTACCCCGAGCCTGAGGCAGATCATCATC
Found at i:140107 original size:78 final size:78
Alignment explanation
Indices: 139954--140159 Score: 254
Period size: 78 Copynumber: 2.6 Consensus size: 78
139944 TCGTTAACCA
* *
139954 ATCTCTTACCCCGAGCCTGAGGCAGATCATCATCAACCAATCTCTTACCCCTAACCTGAGGCAAA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCATCATCAACCAATCTCTTACCCCTAACCAGAGGCAAA
*
140019 GTGAAACCATTTG
66 GTGAAACCATTCG
* * * * *
140032 ATCTTTTACCCCGAGCTTGAGGCAGATCATCATCAACCAGTCTCTTACCCC-AAGTCAGAGGTAG
1 ATCTCTTACCCCGAGCTTGAGGCAGATCATCATCAACCAATCTCTTACCCCTAA-CCAGAGGCAA
* *
140096 A-TTACAGCCATTCG
65 AGTGA-AACCATTCG
* * * *
140110 ATCTCTTACCCCGAGCTTGGGGCAGATCATCGTCAACCAAACTCCTACCC
1 ATCTCTTACCCCGAGCTTGAGGCAGATCATCATCAACCAATCTCTTACCC
140160 TGATCACGAG
Statistics
Matches: 110, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
77 4 0.04
78 106 0.96
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.24
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCTTGAGGCAGATCATCATCAACCAATCTCTTACCCCTAACCAGAGGCAAA
GTGAAACCATTCG
Found at i:140603 original size:206 final size:206
Alignment explanation
Indices: 140245--141057 Score: 1171
Period size: 206 Copynumber: 3.9 Consensus size: 206
140235 CAACTCAAAG
* * *
140245 GTGAGCAAATCTTCGAATCCTAACTTTCTAATAAGATACTGAGAAGCGGGTCGAAGCAATAAAAT
1 GTGAGCAAATCTTCGAATCCTAACTTCCTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAAT
* *
140310 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAA
66 GGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAA
* * *
140375 GCAGATTGAAACAAATGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGATCAAATCAAAC
131 GCGGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAAC
140440 CCACGCTCGAT
196 CCACGCTCGAT
* * * * * *
140451 ATGAGCAAATCTTCGAATCATAGCTTCTTGATGAGATACTAAGAATCGGGTCGAAGCAATAAAAT
1 GTGAGCAAATCTTCGAATCCTAACTTCCTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAAT
* *
140516 GGTTAGCTTCTTGATGAGATACTGAGAAGCGAACCAAATTCGTCTTCCTGATGAGATACAGAGAA
66 GGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAA
140581 GCGGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAAC
131 GCGGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAAC
*
140646 CCATGCTCGAT
196 CCACGCTCGAT
* **
140657 GTGAGCAAATCTTTGAATCCTAACTTCCTGATGAGAGATACTGAGAAGCTAGTCGAAGCAATAAA
1 GTGAGCAAATCTTCGAATCCTAACTTCCTGAT--GAGATACTGAGAAGCGGGTCGAAGCAATAAA
* *
140722 ATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTGAT-ATGATACAGA
64 ATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGA-GATACAGA
* *
140786 GAAGCGGATTGAAACAATCGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAATACCAAATCA
128 GAAGCGGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCA
140851 AACCCACGCTCGAT
193 AACCCACGCTCGAT
* * * * * *
140865 GTGAGCAAATCTTCGAACCCTACCTTCCTGATGAGATACTGAGAAGCAGGTAGAAACAATAAAGT
1 GTGAGCAAATCTTCGAATCCTAACTTCCTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAAT
* * * * *
140930 GGTTAGC-TCCTTGATGATATACGGAGAAGTGAACCAAATCCGTCTTCCTGATGAAACACAGAGA
66 GGTTAGCTTCC-TGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGA
** ** ** * * * *
140994 AGTTGATCAAAACAAGTGATGCGGTCACCTTCCTGATGAGATACTGAGAAGAAGGCCAAGTCAA
130 AGCGGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
141058 TGAAACCAGA
Statistics
Matches: 543, Mismatches: 59, Indels: 10
0.89 0.10 0.02
Matches are distributed among these distances:
205 3 0.01
206 348 0.64
207 2 0.00
208 190 0.35
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.23
Consensus pattern (206 bp):
GTGAGCAAATCTTCGAATCCTAACTTCCTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAAT
GGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAA
GCGGATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAAC
CCACGCTCGAT
Found at i:141400 original size:11 final size:11
Alignment explanation
Indices: 141384--141441 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
141374 GCCCAAACTC
141384 ATTTTAAATTT
1 ATTTTAAATTT
141395 ATTTTAAATTT
1 ATTTTAAATTT
* *
141406 AAATTT-ATTTT
1 -ATTTTAAATTT
*
141417 AAGTTTAAATTT
1 -ATTTTAAATTT
141429 ATTTTCAAATTT
1 ATTTT-AAATTT
141441 A
1 A
141442 AAATTATTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 24 0.62
12 15 0.38
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (11 bp):
ATTTTAAATTT
Found at i:141406 original size:6 final size:6
Alignment explanation
Indices: 141386--141443 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
141376 CCAAACTCAT
* * * *
141386 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTAAG TTTAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
141431 TTTCAAA TTTAAA
1 TTT-AAA TTTAAA
141444 ATTATTATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
5 12 0.29
6 25 0.61
7 4 0.10
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:141408 original size:17 final size:17
Alignment explanation
Indices: 141386--141462 Score: 109
Period size: 17 Copynumber: 4.4 Consensus size: 17
141376 CCAAACTCAT
141386 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
141403 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAA
141420 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* *
141438 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
141455 TTTGAAAT
1 TTT-AAAT
141463 AAATAAAGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
17 36 0.68
18 17 0.32
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:142856 original size:24 final size:24
Alignment explanation
Indices: 142824--142889 Score: 114
Period size: 24 Copynumber: 2.8 Consensus size: 24
142814 AAAGGCCCTC
142824 AAAACGACATCGTTTTGAGGGCTT
1 AAAACGACATCGTTTTGAGGGCTT
*
142848 AAAATGACATCGTTTTGAGGGCTT
1 AAAACGACATCGTTTTGAGGGCTT
*
142872 AAAACGACGTCGTTTTGA
1 AAAACGACATCGTTTTGA
142890 TTAAAAAACC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (24 bp):
AAAACGACATCGTTTTGAGGGCTT
Found at i:143388 original size:29 final size:30
Alignment explanation
Indices: 143356--143563 Score: 123
Period size: 30 Copynumber: 7.0 Consensus size: 30
143346 TATATTTCTA
*
143356 ACCCCAAACTTTCCAAAAATTTCATTTTT-
1 ACCCCAAACTTTCCAAAAATTCCATTTTTG
* *
143385 ACCCCCGAACTTTCTAAAAATTCCATTTTTG
1 A-CCCCAAACTTTCCAAAAATTCCATTTTTG
* * *
143416 ACTCCGAAAC-TTCTAAAAATTCCATTTTTA
1 AC-CCCAAACTTTCCAAAAATTCCATTTTTG
* ** *
143446 ACCTCAAAACTTT-TGAAAATTAC-TATTTT-
1 ACC-CCAAACTTTCCAAAAATTCCAT-TTTTG
*
143475 ACCCCTAAAC-CTCC-AAAATTCCATTTTTG
1 ACCCC-AAACTTTCCAAAAATTCCATTTTTG
* *
143504 ACCCATAAACTTT-CAAAAATTACC-CTTTT-
1 ACCC-CAAACTTTCCAAAAATT-CCATTTTTG
* * *
143533 ACCCCTAAA-TGTCCAAAAATTTCGTTTTTG
1 ACCCC-AAACTTTCCAAAAATTCCATTTTTG
143563 A
1 A
143564 TCCCGATTTT
Statistics
Matches: 141, Mismatches: 20, Indels: 35
0.72 0.10 0.18
Matches are distributed among these distances:
28 16 0.11
29 39 0.28
30 76 0.54
31 10 0.07
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (30 bp):
ACCCCAAACTTTCCAAAAATTCCATTTTTG
Found at i:143465 original size:60 final size:57
Alignment explanation
Indices: 143341--143537 Score: 152
Period size: 58 Copynumber: 3.3 Consensus size: 57
143331 CGATTTCTCC
* **
143341 AAAATTA-TATTTCTAACCCC-AAACTTTCCAAAAATTTCATTTTTACCCCCGAACTTTCTA
1 AAAATTACTATTT-T-ACCCCGAAAC-TT-CAAAAATTCCATTTTTA-CCCAAAACTTTCTA
* * *
143401 AAAATT-CCATTTTTGACTCCGAAACTTCTAAAAATTCCATTTTTAACCTCAAAACTTT-TG
1 AAAATTACTA-TTTT-ACCCCGAAACTTC-AAAAATTCCATTTTT-ACC-CAAAACTTTCTA
* * *
143461 AAAATTACTATTTTACCCCTAAACCTCCAAAATTCCATTTTTGACCCATAAACTTTC-A
1 AAAATTACTATTTTACCCCGAAACTTCAAAAATTCCATTTTT-ACCCA-AAACTTTCTA
**
143519 AAAATTACCCTTTTACCCC
1 AAAATTACTATTTTACCCC
143538 TAAATGTCCA
Statistics
Matches: 112, Mismatches: 16, Indels: 20
0.76 0.11 0.14
Matches are distributed among these distances:
57 2 0.02
58 41 0.37
59 11 0.10
60 41 0.37
61 17 0.15
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (57 bp):
AAAATTACTATTTTACCCCGAAACTTCAAAAATTCCATTTTTACCCAAAACTTTCTA
Found at i:143502 original size:58 final size:58
Alignment explanation
Indices: 143431--143550 Score: 161
Period size: 58 Copynumber: 2.1 Consensus size: 58
143421 GAAACTTCTA
** *
143431 AAAATTCCATTTTTAACCTCA-AAACTTTTGAAAATTACTATTTTACCCCTAAACCTCC
1 AAAATTCCATTTTTAACC-CATAAACTTTCAAAAATTACCATTTTACCCCTAAACCTCC
* * **
143489 AAAATTCCATTTTTGACCCATAAACTTTCAAAAATTACCCTTTTACCCCTAAATGTCC
1 AAAATTCCATTTTTAACCCATAAACTTTCAAAAATTACCATTTTACCCCTAAACCTCC
143547 AAAA
1 AAAA
143551 ATTTCGTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
57 2 0.04
58 52 0.96
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.34
Consensus pattern (58 bp):
AAAATTCCATTTTTAACCCATAAACTTTCAAAAATTACCATTTTACCCCTAAACCTCC
Done.