Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012009.1 Kokia drynarioides strain JFW-HI SEQ_127007, 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: 99125
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6 characters in sequence are not A, C, G, or T
Found at i:790 original size:12 final size:12
Alignment explanation
Indices: 775--860 Score: 56
Period size: 12 Copynumber: 7.2 Consensus size: 12
765 ATTTTTTTTG
775 TTTATATTTTAA
1 TTTATATTTTAA
787 TTTA-ATTTCTAA
1 TTTATATTT-TAA
*
799 TTT-T-GTTTATA
1 TTTATATTTTA-A
*
810 TTT-TAATTTAA
1 TTTATATTTTAA
* * *
821 TTTCTAATTTCA
1 TTTATATTTTAA
833 TTTATATTTTAAA
1 TTTATATTTT-AA
846 TTTA-ATTTTTAA
1 TTTATA-TTTTAA
858 TTT
1 TTT
861 CGTTTATATT
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
10 2 0.03
11 15 0.25
12 35 0.57
13 9 0.15
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.65
Consensus pattern (12 bp):
TTTATATTTTAA
Found at i:803 original size:29 final size:30
Alignment explanation
Indices: 774--889 Score: 173
Period size: 30 Copynumber: 3.9 Consensus size: 30
764 GATTTTTTTT
*
774 GTTTATATTTT-AATTTAATTTCTAATTTT
1 GTTTATATTTTAAATTTAATTTCTAATTTC
803 GTTTATATTTT-AATTTAATTTCTAATTTC
1 GTTTATATTTTAAATTTAATTTCTAATTTC
* *
832 ATTTATATTTTAAATTTAATTTTTAATTTC
1 GTTTATATTTTAAATTTAATTTCTAATTTC
**
862 GTTTATATTTTAAATTTCTTTTCTAATT
1 GTTTATATTTTAAATTTAATTTCTAATT
890 ATTATTTTTT
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
29 38 0.48
30 41 0.52
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (30 bp):
GTTTATATTTTAAATTTAATTTCTAATTTC
Found at i:871 original size:18 final size:17
Alignment explanation
Indices: 846--879 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
836 ATATTTTAAA
*
846 TTTAATTTTTAATTTCG
1 TTTAATTTTAAATTTCG
863 TTTATATTTTAAATTTC
1 TTTA-ATTTTAAATTTC
880 TTTTCTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTAATTTTAAATTTCG
Found at i:908 original size:59 final size:59
Alignment explanation
Indices: 775--889 Score: 178
Period size: 59 Copynumber: 1.9 Consensus size: 59
765 ATTTTTTTTG
*
775 TTTATATTTT-AATTTAATTTCTAATTTTGTTTATATTTTAATTTAATTTCTAATTTCA
1 TTTATATTTTAAATTTAATTTCTAATTTCGTTTATATTTTAATTTAATTTCTAATTTCA
* **
833 TTTATATTTTAAATTTAATTTTTAATTTCGTTTATATTTTAAATTTCTTTTCTAATT
1 TTTATATTTTAAATTTAATTTCTAATTTCGTTTATATTTT-AATTTAATTTCTAATT
890 ATTATTTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
58 10 0.20
59 27 0.53
60 14 0.27
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (59 bp):
TTTATATTTTAAATTTAATTTCTAATTTCGTTTATATTTTAATTTAATTTCTAATTTCA
Found at i:1867 original size:61 final size:61
Alignment explanation
Indices: 1739--1918 Score: 171
Period size: 54 Copynumber: 3.0 Consensus size: 61
1729 ATACATGGCC
* * * *
1739 AACACCAAATAAATTTATTTATTTTATCAT-ATAAATAAGGTGGTGTCAGCCAA-ACATTAGCT
1 AACACCAAATAAATTT-TTT-TTTTATC-TGATAAATAAGGTAGTGTCGGCCAATGCATGAGCT
*
1801 AACACCAAATAAATTTGTTTTTTTATCTGATAAATAAGGTAGTGTCGGCCAATGCATGATC-
1 AACACCAAATAAATTT-TTTTTTTATCTGATAAATAAGGTAGTGTCGGCCAATGCATGAGCT
* * * * *
1862 CACACC-----AA-TTTTTTTTTATCTGATAAAAAAAGTTGTGTCGGCCAATGCATGACCT
1 AACACCAAATAAATTTTTTTTTTATCTGATAAATAAGGTAGTGTCGGCCAATGCATGAGCT
1917 AA
1 AA
1919 AGGTGGTGTC
Statistics
Matches: 103, Mismatches: 12, Indels: 13
0.80 0.09 0.10
Matches are distributed among these distances:
54 40 0.39
55 3 0.03
56 2 0.02
60 1 0.01
61 33 0.32
62 24 0.23
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (61 bp):
AACACCAAATAAATTTTTTTTTTATCTGATAAATAAGGTAGTGTCGGCCAATGCATGAGCT
Found at i:1973 original size:82 final size:84
Alignment explanation
Indices: 1836--1998 Score: 242
Period size: 82 Copynumber: 2.0 Consensus size: 84
1826 TCTGATAAAT
* * * *
1836 AAGGTAGTGTCGGCCAATGCATGATCCACACCAATTTTTTTTTATCTGATAAAAAAA-G-TTGTG
1 AAGGTAGTGTCGACCAATGCATGATCCACACCAAATTTTTTTCATCTGATAAAAAAATGCTGGTG
1899 TCGGCCAATGCATGACCTA
66 TCGGCCAATGCATGACCTA
*
1918 AAGGTGGTGTCGACCAATGCATGA-CCAACACCAAATTTTTTTCATCTGATAAAAAAATGCTGGT
1 AAGGTAGTGTCGACCAATGCATGATCC-ACACCAAATTTTTTTCATCTGATAAAAAAATGCTGGT
*
1982 GTCGGCTAATGCATGAC
65 GTCGGCCAATGCATGAC
1999 TAACACCAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
81 2 0.03
82 50 0.69
83 1 0.01
84 19 0.26
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (84 bp):
AAGGTAGTGTCGACCAATGCATGATCCACACCAAATTTTTTTCATCTGATAAAAAAATGCTGGTG
TCGGCCAATGCATGACCTA
Found at i:2124 original size:55 final size:56
Alignment explanation
Indices: 1931--2126 Score: 213
Period size: 55 Copynumber: 3.6 Consensus size: 56
1921 GTGGTGTCGA
* * **
1931 CCAATGCATGACCAACACC-AAATTTTTTTCATCTGATAAAAAAATGCTGGTGTCGG
1 CCAATGCATGACCAACACCAAAATTTTTTTTATCTGAT-AAAAAATACTGGTGTTTG
* * * * *
1987 CTAATGCATGACTAACACCAAAATTTTTTTTATCTAACAAAAAAGA-TGGTG-TTG
1 CCAATGCATGACCAACACCAAAATTTTTTTTATCTGATAAAAAATACTGGTGTTTG
* * **
2041 GCAAAGCATTGACCAACACCAAAATTTTTTTTATCTGATAAAAAATACTAATGTTTG
1 CCAATGCA-TGACCAACACCAAAATTTTTTTTATCTGATAAAAAATACTGGTGTTTG
*
2098 CCAATGTATGACCAACACC--AATTTTTTTT
1 CCAATGCATGACCAACACCAAAATTTTTTTT
2127 CTGACAAAAA
Statistics
Matches: 115, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
54 16 0.14
55 39 0.34
56 37 0.32
57 23 0.20
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (56 bp):
CCAATGCATGACCAACACCAAAATTTTTTTTATCTGATAAAAAATACTGGTGTTTG
Found at i:8898 original size:22 final size:22
Alignment explanation
Indices: 8873--8949 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
8863 ACTTTGTGAT
8873 TGTGTTTGGAGGGTATATTTGG
1 TGTGTTTGGAGGGTATATTTGG
*
8895 TGTGTTTGGAAGGTATATTTGG
1 TGTGTTTGGAGGGTATATTTGG
*
8917 TTGTGTTTGGAGAGTATATTTGG
1 -TGTGTTTGGAGGGTATATTTGG
* *
8940 GGCGTTTGGA
1 TGTGTTTGGA
8950 AAGTGTAAGC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
22 29 0.59
23 20 0.41
ACGTcount: A:0.16, C:0.01, G:0.39, T:0.44
Consensus pattern (22 bp):
TGTGTTTGGAGGGTATATTTGG
Found at i:9169 original size:80 final size:80
Alignment explanation
Indices: 9032--9431 Score: 489
Period size: 80 Copynumber: 5.0 Consensus size: 80
9022 TTTGCTCTTC
* * * * *
9032 CAATGTATATGTTTTCA-ACATGTTTCCTAGTCACAATATGGCAATATATTGTTATGAATTGCTA
1 CAATGCATATGTTTT-ATACATGTTTCCTAGTCACAATATGCCAATATATTATCATGAATTACTA
*
9096 GGAGTTATGATAGATG
65 TGAGTTATGATAGATG
* * **
9112 CAATGCATATGTTTTATAAATGTTTCCTAGTCACAATATGCTAATATATTATCATGAATTGTTAT
1 CAATGCATATGTTTTATACATGTTTCCTAGTCACAATATGCCAATATATTATCATGAATTACTAT
**
9177 GAGTTATTTTAGATG
66 GAGTTATGATAGATG
* * * * * *
9192 CAATGCATATGCTTCATAGATGTTTCCTAGTCATAATATGCCAATATATTATTAAGAAATT-CTA
1 CAATGCATATGTTTTATACATGTTTCCTAGTCACAATATGCCAATATATTATCATG-AATTACTA
*
9256 TGAGATATGATAGATG
65 TGAGTTATGATAGATG
* * * * * * * *
9272 AAATGTATGTATTTTTTATATGTTTCCTAGTCACAATATGCCAACATATTATCATGAACTACTAT
1 CAATGCATATGTTTTATACATGTTTCCTAGTCACAATATGCCAATATATTATCATGAATTACTAT
9337 GAGTTATGATAGATG
66 GAGTTATGATAGATG
* * *
9352 CAATGCATATGTGTTTATACATGTTTCTTAGTCACAATATGTCAATATATTATCATGAACTACTA
1 CAATGCATATGT-TTTATACATGTTTCCTAGTCACAATATGCCAATATATTATCATGAATTACTA
9417 TGAGTTATGATAGAT
65 TGAGTTATGATAGAT
9432 TCCAAGGCTA
Statistics
Matches: 272, Mismatches: 44, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
79 4 0.01
80 202 0.74
81 66 0.24
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.40
Consensus pattern (80 bp):
CAATGCATATGTTTTATACATGTTTCCTAGTCACAATATGCCAATATATTATCATGAATTACTAT
GAGTTATGATAGATG
Found at i:19744 original size:29 final size:29
Alignment explanation
Indices: 19702--19789 Score: 117
Period size: 29 Copynumber: 3.1 Consensus size: 29
19692 ATGTTTACAA
19702 GACACCT-TCACATTTTCAAGTGGTTGTAG
1 GACACCTCT-ACATTTTCAAGTGGTTGTAG
*
19731 GACACCTCTACATTTTCAAGTGGTTTTAG
1 GACACCTCTACATTTTCAAGTGGTTGTAG
* * *
19760 GAC-CCCCCATATTTTCAAGTGGTTGTAG
1 GACACCTCTACATTTTCAAGTGGTTGTAG
19788 GA
1 GA
19790 TGGTTTTCTA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
28 23 0.43
29 29 0.55
30 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (29 bp):
GACACCTCTACATTTTCAAGTGGTTGTAG
Found at i:19782 original size:28 final size:29
Alignment explanation
Indices: 19710--19789 Score: 117
Period size: 28 Copynumber: 2.8 Consensus size: 29
19700 AAGACACCTT
*
19710 CACATTTTCAAGTGGTTGTAGGACACCTC
1 CACATTTTCAAGTGGTTGTAGGACACCCC
* *
19739 TACATTTTCAAGTGGTTTTAGGAC-CCCC
1 CACATTTTCAAGTGGTTGTAGGACACCCC
*
19767 CATATTTTCAAGTGGTTGTAGGA
1 CACATTTTCAAGTGGTTGTAGGA
19790 TGGTTTTCTA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
28 23 0.51
29 22 0.49
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (29 bp):
CACATTTTCAAGTGGTTGTAGGACACCCC
Found at i:21738 original size:15 final size:15
Alignment explanation
Indices: 21701--21741 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
21691 TTTTCTTTGA
21701 TTTCACAATTTGAAGC
1 TTTCACAATTT-AAGC
21717 --T-ACAATTTAAGC
1 TTTCACAATTTAAGC
21729 TTTCACAATTTAA
1 TTTCACAATTTAA
21742 AACCACAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
12 4 0.18
13 7 0.32
14 2 0.09
15 9 0.41
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (15 bp):
TTTCACAATTTAAGC
Found at i:22340 original size:83 final size:82
Alignment explanation
Indices: 22065--22356 Score: 261
Period size: 83 Copynumber: 3.6 Consensus size: 82
22055 AACCCGAATG
* * * * * * * *
22065 TAGAATATAATCTATTAATCGGAGAGAATAAATCTCTG-AATAGATTTATTCCACTTA-TTTTAT
1 TAGAATAAAATCTGTTAAACGGCGAGAATAAATC-CCGAAACAAATTTATTCAACTTATTTTTAT
*
22128 TTGGAAAAAAAATCAAAC
65 TTGGAAAAAAAATCAAAA
* * * * * * *
22146 TGGAATAAAAT-TGTTAAACAGCGAGAATAAATCTCAAAACAGATTTATT-TACTTAATTATTAT
1 TAGAATAAAATCTGTTAAACGGCGAGAATAAATCCCGAAACAAATTTATTCAACTT-ATTTTTAT
**
22209 TTGGAACCAAAATCCAAATA
65 TTGGAAAAAAAAT-CAAA-A
* ** * *
22229 TAAAATAAAATCTGTCGAACGACG-GAATAAATCCCGAAACAAATTTATTCAACTTATTCTTTTT
1 TAGAATAAAATCTGTTAAACGGCGAGAATAAATCCCGAAACAAATTTATTCAACTTATT-TTTAT
**
22293 TTGGAAATTAAATCAAAA
65 TTGGAAAAAAAATCAAAA
* *
22311 TAGAATAAAATCTGTTAAATGGCGAGAATAAATTCCGAAACAAATT
1 TAGAATAAAATCTGTTAAACGGCGAGAATAAATCCCGAAACAAATT
22357 ATTTTCCAAT
Statistics
Matches: 166, Mismatches: 36, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
79 4 0.02
80 30 0.18
81 25 0.15
82 24 0.14
83 58 0.35
84 25 0.15
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (82 bp):
TAGAATAAAATCTGTTAAACGGCGAGAATAAATCCCGAAACAAATTTATTCAACTTATTTTTATT
TGGAAAAAAAATCAAAA
Found at i:25496 original size:45 final size:45
Alignment explanation
Indices: 25426--25520 Score: 106
Period size: 45 Copynumber: 2.1 Consensus size: 45
25416 TTTCCATTTG
25426 CATTTTGAGAAAACTACATTCATTTTCAAATGATT-CCATTTCTC
1 CATTTTGAGAAAACTACATTCATTTTCAAATGATTCCCATTTCTC
** *
25470 CATTTTGGAGAAAACCATA-ATT-ATTTTTGAATGTTTCCCATTTCTC
1 CATTTT-GAGAAAA-C-TACATTCATTTTCAAATGATTCCCATTTCTC
*
25516 TATTT
1 CATTT
25521 CTATTCATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
44 6 0.14
45 18 0.42
46 17 0.40
47 2 0.05
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.44
Consensus pattern (45 bp):
CATTTTGAGAAAACTACATTCATTTTCAAATGATTCCCATTTCTC
Found at i:29468 original size:45 final size:45
Alignment explanation
Indices: 29404--29512 Score: 146
Period size: 45 Copynumber: 2.4 Consensus size: 45
29394 CCAATATATA
29404 TGTGGACAAAGCCACCAATATTCACAGACAAGCTACCATGTAGAT
1 TGTGGACAAAGCCACCAATATTCACAGACAAGCTACCATGTAGAT
* ** * * *
29449 TGTGGACAGAGCCACCAATATTCGTAGACAAGTTTCCATGTAGGT
1 TGTGGACAAAGCCACCAATATTCACAGACAAGCTACCATGTAGAT
* *
29494 TGTGGACGAAGCCATCAAT
1 TGTGGACAAAGCCACCAAT
29513 TCTTCCTCCT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (45 bp):
TGTGGACAAAGCCACCAATATTCACAGACAAGCTACCATGTAGAT
Found at i:30490 original size:17 final size:17
Alignment explanation
Indices: 30458--30491 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
30448 ACAAGGTCTT
30458 GAGTTAGAGAAGAAATC
1 GAGTTAGAGAAGAAATC
30475 GAGTCTAGAGAA-AAATC
1 GAGT-TAGAGAAGAAATC
30492 ATCATTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.47, C:0.09, G:0.26, T:0.18
Consensus pattern (17 bp):
GAGTTAGAGAAGAAATC
Found at i:32336 original size:30 final size:30
Alignment explanation
Indices: 32300--32359 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
32290 AGATGAAAGG
*
32300 TAGGTGGATTATTTCCTGGGTATTGTCTTA
1 TAGGTGGATTATTTCCTAGGTATTGTCTTA
32330 TAGGTGGATTATTTCCTAGGTATTGTCTTA
1 TAGGTGGATTATTTCCTAGGTATTGTCTTA
32360 CTTCTTGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.18, C:0.10, G:0.25, T:0.47
Consensus pattern (30 bp):
TAGGTGGATTATTTCCTAGGTATTGTCTTA
Found at i:33025 original size:19 final size:19
Alignment explanation
Indices: 32989--33026 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
32979 TTAGTGCAAG
*
32989 GTGGTGGGCACGGTGGTGA
1 GTGGTGGGCAAGGTGGTGA
33008 GTGGTGGTGCAAGG-GGTGA
1 GTGGTGG-GCAAGGTGGTGA
33027 CGTTGGAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.13, C:0.08, G:0.58, T:0.21
Consensus pattern (19 bp):
GTGGTGGGCAAGGTGGTGA
Found at i:35553 original size:20 final size:21
Alignment explanation
Indices: 35528--35567 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
35518 TGCATTGTTA
*
35528 GCATTTT-TAACTTAGTAATT
1 GCATTTTCTAACTCAGTAATT
35548 GCATTTTCTAACTCAGTAAT
1 GCATTTTCTAACTCAGTAAT
35568 GCTAGGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (21 bp):
GCATTTTCTAACTCAGTAATT
Found at i:35908 original size:11 final size:11
Alignment explanation
Indices: 35892--35917 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
35882 CAAGGGATCT
35892 TCTTGATGATA
1 TCTTGATGATA
35903 TCTTGATGATA
1 TCTTGATGATA
35914 TCTT
1 TCTT
35918 TGATATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (11 bp):
TCTTGATGATA
Found at i:48912 original size:23 final size:23
Alignment explanation
Indices: 48882--49121 Score: 295
Period size: 23 Copynumber: 10.4 Consensus size: 23
48872 TCCTTATATC
* *
48882 TATGCTTATATGTTAAT-TAGATT
1 TATGCTTAAATATTAATGT-GATT
48905 TATGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* * *
48928 TTTGCTTAAGTATTAATGTTATT
1 TATGCTTAAATATTAATGTGATT
*
48951 TATGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
*
48974 TTTGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* * *
48997 TGTGCTTAAATATTAATATTATT
1 TATGCTTAAATATTAATGTGATT
* *
49020 TGTGCTCAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
49043 TATGCTTAAATATTAAT-TAGATT
1 TATGCTTAAATATTAATGT-GATT
* * *
49066 TGTGCTTAAATATTATTATGATT
1 TATGCTTAAATATTAATGTGATT
*
49089 TATGATTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
49112 TGTGCTTAAA
1 TATGCTTAAA
49122 GAATTAAGAT
Statistics
Matches: 187, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
22 1 0.01
23 184 0.98
24 2 0.01
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (23 bp):
TATGCTTAAATATTAATGTGATT
Found at i:48993 original size:69 final size:69
Alignment explanation
Indices: 48882--49121 Score: 331
Period size: 69 Copynumber: 3.5 Consensus size: 69
48872 TCCTTATATC
* * * * *
48882 TATGCTTATATGTTAAT-TAGATTTATGCTTAAATATTAATGTGATTTTTGCTTAAGTATTAATG
1 TATGCTTAAATATTAATGT-GATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATA
48946 TTATT
65 TTATT
* *
48951 TATGCTTAAATATTAATATGATTTTTGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATAT
1 TATGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATAT
49016 TATT
66 TATT
* * *
49020 TGTGCTCAAATATTAATGTGATTTATGCTTAAATATTAAT-TAGATTTGTGCTTAAATATTATTA
1 TATGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGT-GATTTGTGCTTAAATATTAATA
*
49084 TGATT
65 TTATT
* *
49089 TATGATTAAATATTAATGTGATTTGTGCTTAAA
1 TATGCTTAAATATTAATGTGATTTATGCTTAAA
49122 GAATTAAGAT
Statistics
Matches: 153, Mismatches: 16, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
68 1 0.01
69 151 0.99
70 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (69 bp):
TATGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATAT
TATT
Found at i:49241 original size:36 final size:36
Alignment explanation
Indices: 49201--49300 Score: 137
Period size: 36 Copynumber: 2.8 Consensus size: 36
49191 TGTGAAAGTG
* * * *
49201 AATATGTGGGGATGTTCTTCACGCCATGCGACGGAA
1 AATATGTGGGTATGTTCTTCATGCCATGAGACAGAA
* *
49237 AATATGTGGGTATGTTTTTCATGCCATGAGATAGAA
1 AATATGTGGGTATGTTCTTCATGCCATGAGACAGAA
*
49273 AATATATGGGTATGTTCTTCATGCCATG
1 AATATGTGGGTATGTTCTTCATGCCATG
49301 TGACTGATTA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (36 bp):
AATATGTGGGTATGTTCTTCATGCCATGAGACAGAA
Found at i:52367 original size:926 final size:927
Alignment explanation
Indices: 49978--52390 Score: 4299
Period size: 927 Copynumber: 2.6 Consensus size: 927
49968 ACTATATGAG
49978 TCCAATGTGTGATGATAGTGCTCACTATATGTTTCATAGTCTCAACAGCCAAATTATCATAAATT
1 TCCAATGTGTGATGATAGTGCTCACTATATGTTTCATAGTCTCAACAGCCAAATTATCATAAATT
* *
50043 GTGCTTGATTATGATTATATATTTACATGACTGAATATACTTGTATGTGAATAAAGTATGCTGAA
66 GTGCTTGATTGTGATTATATATTTATATGACTGAATATACTTGTATGTGAATAAAGTATGCTGAA
50108 ACTTATGTAAAGAATGTGTAAATAAATACCAATGAGATGATATAAATGTGTTGTATGATTGTTGA
131 ACTTATGTAAAGAATGTGTAAATAAATACCAATGAGATGATATAAATGTGTTGTATGATTGTTGA
*
50173 ATAGATGCATGATGATTGTTTATGTAGTGGTTATTTTAGGCACTTACTGAGCTTGTTAAGCTCAC
196 ATAGATGCATGATGATTGTTTATGTAGTGGTTATTCTAGGCACTTACTGAGCTTGTTAAGCTCAC
50238 CCACCCCTTTTTAAACCATTGCAAATACTTAGTGTCGGTGTGAGTGGTGTGGTCTCGAGGGTGAT
261 CCACCCCTTTTTAAACCATTGCAAATACTTAGTGTCGGTGTGAGTGGTGTGGTCTCGAGGGTGAT
50303 CCAAGCCAAAATCGACACTTTATCCTTTATTAGTAGGTTGATAAGTTATTTATGTTTAGGAACCT
326 CCAAGCCAAAATCGACACTTTATCCTTTATTAGTAGGTTGATAAGTTATTTATGTTTAGGAACCT
50368 AAGGTAATGTGATAGGATTTATGATGGGTTTATATTGGTTTCTGTTATGTTCTTTTAGATATTTG
391 AAGGTAATGTGATAGGATTTATGATGGGTTTATATTGGTTTCTGTTATGTTCTTTTAGATATTTG
*
50433 CATGCCATTATTATAGACTTGAAAATATGATATTTGAGTCATTTTCTGGTTTGTTTTATATGATA
456 CATGCC---ATTATAGACTTGAAAATATGATATTTGAGACATTTTCTGGTTTGTTTTATATGATA
50498 AATGTTTGTTAGATGATAAATCGATGTAAGATGGAAAGATGATGATAGAGCTCACTATATGTTTC
518 AATGTTTGTTAGATGATAAATCGATGTAAGATGGAAAGATGATGATAGAGCTCACTATATGTTTC
* * *
50563 ATGGTCTTAACAGCTAAATTATTATAAATTGTGTTTGATTGTTATTATGAATATGTAGTGAATAT
583 ATAGTCTCAACAGCCAAATTATTATAAATTGTGTTTGATTGTTATTATGAATATGTAGTGAATAT
*
50628 ATGATAAAAATAAGTAACAATAATAATGTGGATATTTTTACTTTGTGATCTTATGAGACCTTTAG
648 ATGATAAAAATAAGTAACAATAATAATGTGAATATTTTTACTTTGTGATCTTATGAGACCTTTAG
* *
50693 GTATAGTTGGTATGTCATAAGATTGTGAGTACTCAGGTTTGTGTTATATGTAGGGCACTGATGAC
713 GTATAGTTGGCATGCCATAAGATTGTGAGTACTCAGGTTTGTGTTATATGTAGGGCACTGATGAC
50758 CAGGGACATGTTGGAGAGATAAGGAAATGCGAGCTATGCTCCATTCAACAGGATATGTTTGGTGT
778 CAGGGACATGTTGGAGAGATAAGGAAATGCGAGCTATGCTCCATTCAACAGGATATGTTTGGTGT
* *
50823 ATTGGAGAGTGCTAGTTATGTGCTTTACTTATAGGATATGTTTCGACTCTATGAGTCCAATTTTG
843 ATTGGAGAGTGCTAGCTATATGCTTTACTTATAGGATATGTTTCGACTCTATGAGTCCAATTTTG
50888 GTGTGTTGGAGATCTATGTA
908 GTGTGTTGGAGATCTATGTA
* *
50908 TCCAATATGTGATGATAGTGCTCACTGTATGTTTCATAGTCTCAACAGCCAAATTATCATAAATT
1 TCCAATGTGTGATGATAGTGCTCACTATATGTTTCATAGTCTCAACAGCCAAATTATCATAAATT
* * *
50973 GTGCTTGATTGTCATTATATATTAATATGACTGAATATACTTGTATGTGAATAAAGTATGATGAA
66 GTGCTTGATTGTGATTATATATTTATATGACTGAATATACTTGTATGTGAATAAAGTATGCTGAA
*
51038 ACTTATGTAAAGAATGTGTAAATGAATACCAATGAGATGATATAAATGTGTTGTATGATTGTTGA
131 ACTTATGTAAAGAATGTGTAAATAAATACCAATGAGATGATATAAATGTGTTGTATGATTGTTGA
51103 ATAGATGCATGATGATTGTTTATGTAGTGGTTATTCTAGGCACTTACTGAGCTTGTTAAGCTCAC
196 ATAGATGCATGATGATTGTTTATGTAGTGGTTATTCTAGGCACTTACTGAGCTTGTTAAGCTCAC
*
51168 CCACCCCTTTTTAAACCATTGCAGATACTTAGTGTCGGTGTGAGTGGTGTGGTCTCGAGGGTGAT
261 CCACCCCTTTTTAAACCATTGCAAATACTTAGTGTCGGTGTGAGTGGTGTGGTCTCGAGGGTGAT
51233 CCAAGCCAAAATCGACACTTTATCCTTTATTAGTAGGTTGATAAGTTATTTATGTTTAGGAACCT
326 CCAAGCCAAAATCGACACTTTATCCTTTATTAGTAGGTTGATAAGTTATTTATGTTTAGGAACCT
* *
51298 AAGGTAATGTGATATGATTTATGATGAGTTTATATTGGTTTCTGTTATGTTCTTTTAGATATTTG
391 AAGGTAATGTGATAGGATTTATGATGGGTTTATATTGGTTTCTGTTATGTTCTTTTAGATATTTG
* *
51363 CATGCCATTATAAACTTGAAAATATGATATTTGAGACATCTTCTGGTTTGTTTTATATGATAAAT
456 CATGCCATTATAGACTTGAAAATATGATATTTGAGACATTTTCTGGTTTGTTTTATATGATAAAT
51428 GTTTGTTAGATGATAAATCGATGTAAGATGGAAAGATGATGATAGAGCTCACTATATGTTTCATA
521 GTTTGTTAGATGATAAATCGATGTAAGATGGAAAGATGATGATAGAGCTCACTATATGTTTCATA
51493 GTCTCAACAGCCAAATTATTATAAATTGTGTTTGATTGTTATTATGAATATGTAGTGAATATATG
586 GTCTCAACAGCCAAATTATTATAAATTGTGTTTGATTGTTATTATGAATATGTAGTGAATATATG
* *
51558 ATAAAAATAAGTAACAATAGTAATGTGAATATTTTTGCTTTGTGATCTTATGAGACCTTT-GGAT
651 ATAAAAATAAGTAACAATAATAATGTGAATATTTTTACTTTGTGATCTTATGAGACCTTTAGG-T
* *
51622 ATTGTTGGCATGCCATAAGATTGTGAGTACTTAGGTTTGTGTTATATGTAGGGCACTGATGACCA
715 ATAGTTGGCATGCCATAAGATTGTGAGTACTCAGGTTTGTGTTATATGTAGGGCACTGATGACCA
* *
51687 GGGACATGTTGGAGAGATAAGGGAATGCGAGCTATGCTCCATTCAACATGATATGTTTGGTGTAT
780 GGGACATGTTGGAGAGATAAGGAAATGCGAGCTATGCTCCATTCAACAGGATATGTTTGGTGTAT
* *
51752 TGGAGAGTGCTAGCTATATGCTTTACTTATGGGATATGTTTTGACTCTATGAGTCCAATTTTGGT
845 TGGAGAGTGCTAGCTATATGCTTTACTTATAGGATATGTTTCGACTCTATGAGTCCAATTTTGGT
51817 GTGTTGGAGATCTATGTA
910 GTGTTGGAGATCTATGTA
*
51835 TCCAATGTGTGATGATAGTGCTCACTATATGTTTCATAGTCTCAACAACC-AATTATCATAAATT
1 TCCAATGTGTGATGATAGTGCTCACTATATGTTTCATAGTCTCAACAGCCAAATTATCATAAATT
* * *
51899 TTTCTTGATTGTGATTATTTATTTATATGACTGAATATACTTGTATGTGAATAAAGTATGCTGAA
66 GTGCTTGATTGTGATTATATATTTATATGACTGAATATACTTGTATGTGAATAAAGTATGCTGAA
*
51964 ACTTATGTAAAGAATGTGTAAATAAATACCAATGAGATGATATAAATGTGTTGTATGATTGTTTA
131 ACTTATGTAAAGAATGTGTAAATAAATACCAATGAGATGATATAAATGTGTTGTATGATTGTTGA
** * * * *
52029 ATAGATAAATGACGATTGTTTACGTAGTGGTTATTCTAGGCGCTCACTGAGCTTGTTAAGCTCAC
196 ATAGATGCATGATGATTGTTTATGTAGTGGTTATTCTAGGCACTTACTGAGCTTGTTAAGCTCAC
* * * * * *
52094 CTACTCTTTTTTAAACCATTGCAAATACTTAGTGTCAGTGTGAGCGGTGTGGTCTTGAGGGTGAT
261 CCACCCCTTTTTAAACCATTGCAAATACTTAGTGTCGGTGTGAGTGGTGTGGTCTCGAGGGTGAT
*
52159 CCAAGCCAAAGTCGACACTTTATCCTTTATTAGTAGGTTGATAAGTTATTTATGTTTAGGAACCT
326 CCAAGCCAAAATCGACACTTTATCCTTTATTAGTAGGTTGATAAGTTATTTATGTTTAGGAACCT
52224 AAGGTAATGTGATAGGATTTATGATGGGTTTATATTGGTTTCTGTTATGTTCTTTTAGATATTTG
391 AAGGTAATGTGATAGGATTTATGATGGGTTTATATTGGTTTCTGTTATGTTCTTTTAGATATTTG
* *
52289 CATGCCATTATAGACTTGAAAATATGATATTTGAGACATTTTTTGGTTTGTCTTATATGATAAAT
456 CATGCCATTATAGACTTGAAAATATGATATTTGAGACATTTTCTGGTTTGTTTTATATGATAAAT
* *
52354 GTTTGTTAGATGATAAATCGATGCAAGATGGGAAGAT
521 GTTTGTTAGATGATAAATCGATGTAAGATGGAAAGAT
52391 TTAACATTAA
Statistics
Matches: 1418, Mismatches: 64, Indels: 6
0.95 0.04 0.00
Matches are distributed among these distances:
926 478 0.34
927 491 0.35
930 449 0.32
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (927 bp):
TCCAATGTGTGATGATAGTGCTCACTATATGTTTCATAGTCTCAACAGCCAAATTATCATAAATT
GTGCTTGATTGTGATTATATATTTATATGACTGAATATACTTGTATGTGAATAAAGTATGCTGAA
ACTTATGTAAAGAATGTGTAAATAAATACCAATGAGATGATATAAATGTGTTGTATGATTGTTGA
ATAGATGCATGATGATTGTTTATGTAGTGGTTATTCTAGGCACTTACTGAGCTTGTTAAGCTCAC
CCACCCCTTTTTAAACCATTGCAAATACTTAGTGTCGGTGTGAGTGGTGTGGTCTCGAGGGTGAT
CCAAGCCAAAATCGACACTTTATCCTTTATTAGTAGGTTGATAAGTTATTTATGTTTAGGAACCT
AAGGTAATGTGATAGGATTTATGATGGGTTTATATTGGTTTCTGTTATGTTCTTTTAGATATTTG
CATGCCATTATAGACTTGAAAATATGATATTTGAGACATTTTCTGGTTTGTTTTATATGATAAAT
GTTTGTTAGATGATAAATCGATGTAAGATGGAAAGATGATGATAGAGCTCACTATATGTTTCATA
GTCTCAACAGCCAAATTATTATAAATTGTGTTTGATTGTTATTATGAATATGTAGTGAATATATG
ATAAAAATAAGTAACAATAATAATGTGAATATTTTTACTTTGTGATCTTATGAGACCTTTAGGTA
TAGTTGGCATGCCATAAGATTGTGAGTACTCAGGTTTGTGTTATATGTAGGGCACTGATGACCAG
GGACATGTTGGAGAGATAAGGAAATGCGAGCTATGCTCCATTCAACAGGATATGTTTGGTGTATT
GGAGAGTGCTAGCTATATGCTTTACTTATAGGATATGTTTCGACTCTATGAGTCCAATTTTGGTG
TGTTGGAGATCTATGTA
Found at i:54450 original size:23 final size:23
Alignment explanation
Indices: 54419--54539 Score: 143
Period size: 23 Copynumber: 5.3 Consensus size: 23
54409 AGGTTAAAGA
54419 TTAAATATTAATGTGATTTGTGC
1 TTAAATATTAATGTGATTTGTGC
* *
54442 TTAAGTATTAATGTGATTTATGC
1 TTAAATATTAATGTGATTTGTGC
*
54465 TTAAATATTACTGTGATTTGTGC
1 TTAAATATTAATGTGATTTGTGC
* * **
54488 TTAAATATTAATATAATTTGCAC
1 TTAAATATTAATGTGATTTGTGC
* * * *
54511 TAAAATATTAATGAGATTTATGA
1 TTAAATATTAATGTGATTTGTGC
54534 TTAAAT
1 TTAAAT
54540 GTTTTTTACT
Statistics
Matches: 79, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 79 1.00
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.45
Consensus pattern (23 bp):
TTAAATATTAATGTGATTTGTGC
Found at i:54469 original size:46 final size:46
Alignment explanation
Indices: 54419--54771 Score: 398
Period size: 46 Copynumber: 7.8 Consensus size: 46
54409 AGGTTAAAGA
*
54419 TTAAATATTAATGTGATTTGTGCTTAAGTATTAATGTGATTTATGC
1 TTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATTTATGC
* * * ***
54465 TTAAATATTACTGTGATTTGTGCTTAAATATTAATATAATTTGCAC
1 TTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATTTATGC
* * * * *
54511 TAAAATATTAATGAGATTTATGATTAAAT-GT--T-T--TTTA--C
1 TTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATTTATGC
* * * * * *
54549 TTAAATATTAACGTGATTTATGCTTAAATATGAATGTGTTTTCTAC
1 TTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATTTATGC
* *
54595 TTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATTTGTGT
1 TTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATTTATGC
* *
54641 TTAAATATTAATGTGATTTATGCTTAAATATTAAGGTGATTTATGC
1 TTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATTTATGC
* * **
54687 TTAAATATTATTGTGATTTGTGCTTAAATATTAATATGATTTATTA
1 TTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATTTATGC
*
54733 TTAAATATTAATGTGATTTGTGCTTAAAGAATTAATGTG
1 TTAAATATTAATGTGATTTGTGCTTAAA-TATTAATGTG
54772 TGATATTGTG
Statistics
Matches: 257, Mismatches: 41, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
38 26 0.10
40 3 0.01
41 1 0.00
42 2 0.01
43 1 0.00
44 3 0.01
45 1 0.00
46 212 0.82
47 8 0.03
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (46 bp):
TTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATTTATGC
Found at i:54507 original size:69 final size:69
Alignment explanation
Indices: 54419--54771 Score: 416
Period size: 69 Copynumber: 5.2 Consensus size: 69
54409 AGGTTAAAGA
* *
54419 TTAAATATTAATGTGATTTGTGCTTAAGTATTAATGTGATTTATGCTTAAATATTACTGTGATTT
1 TTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTT
54484 GTGC
66 GTGC
* * ** * * *
54488 TTAAATATTAATATAATTTGCACTAAAATATTAATGAGATTTATG-----AT-TAAATGT--TTT
1 TTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTT
* *
54545 TTAC
66 GTGC
* * * * * *
54549 TTAAATATTAACGTGATTTATGCTTAAATATGAATGTGTTTTCTACTTAAATATTAATGTGATTT
1 TTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTT
54614 GTGC
66 GTGC
* *
54618 TTAAATATTAATGTGATTTGTGTTTAAATATTAATGTGATTTATGCTTAAATATTAAGGTGATTT
1 TTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTT
*
54683 ATGC
66 GTGC
* * **
54687 TTAAATATTATTGTGATTTGTGCTTAAATATTAATATGATTTATTATTAAATATTAATGTGATTT
1 TTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTT
54752 GTGC
66 GTGC
*
54756 TTAAAGAATTAATGTG
1 TTAAA-TATTAATGTG
54772 TGATATTGTG
Statistics
Matches: 231, Mismatches: 44, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
61 38 0.16
63 5 0.02
64 2 0.01
66 2 0.01
67 6 0.03
69 170 0.74
70 8 0.03
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (69 bp):
TTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTT
GTGC
Found at i:54558 original size:84 final size:84
Alignment explanation
Indices: 54464--54623 Score: 207
Period size: 84 Copynumber: 1.9 Consensus size: 84
54454 GTGATTTATG
* *
54464 CTTAAATATT-ACTGTGATTTGTGCTTAAATATTAATATAATTTGC-ACTAAAATATTAATGAGA
1 CTTAAATATTAAC-GTGATTTATGCTTAAATATGAATAT-ATTTGCTACTAAAATATTAATGAGA
54527 TTTATGATTAAATGTTTTTTA
64 TTTATGATTAAATGTTTTTTA
* * * * *
54548 CTTAAATATTAACGTGATTTATGCTTAAATATGAATGTGTTTTCTACTTAAATATTAATGTGATT
1 CTTAAATATTAACGTGATTTATGCTTAAATATGAATATATTTGCTACTAAAATATTAATGAGATT
* *
54613 TGTGCTTAAAT
66 TATGATTAAAT
54624 ATTAATGTGA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
83 4 0.06
84 59 0.91
85 2 0.03
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (84 bp):
CTTAAATATTAACGTGATTTATGCTTAAATATGAATATATTTGCTACTAAAATATTAATGAGATT
TATGATTAAATGTTTTTTA
Found at i:54575 original size:23 final size:23
Alignment explanation
Indices: 54548--54771 Score: 295
Period size: 23 Copynumber: 9.7 Consensus size: 23
54538 ATGTTTTTTA
*
54548 CTTAAATATTAACGTGATTTATG
1 CTTAAATATTAATGTGATTTATG
* * * *
54571 CTTAAATATGAATGTGTTTTCTA
1 CTTAAATATTAATGTGATTTATG
*
54594 CTTAAATATTAATGTGATTTGTG
1 CTTAAATATTAATGTGATTTATG
*
54617 CTTAAATATTAATGTGATTTGTG
1 CTTAAATATTAATGTGATTTATG
*
54640 TTTAAATATTAATGTGATTTATG
1 CTTAAATATTAATGTGATTTATG
*
54663 CTTAAATATTAAGGTGATTTATG
1 CTTAAATATTAATGTGATTTATG
* *
54686 CTTAAATATTATTGTGATTTGTG
1 CTTAAATATTAATGTGATTTATG
* *
54709 CTTAAATATTAATATGATTTATT
1 CTTAAATATTAATGTGATTTATG
* *
54732 ATTAAATATTAATGTGATTTGTG
1 CTTAAATATTAATGTGATTTATG
*
54755 CTTAAAGAATTAATGTG
1 CTTAAA-TATTAATGTG
54772 TGATATTGTG
Statistics
Matches: 174, Mismatches: 26, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
23 165 0.95
24 9 0.05
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.47
Consensus pattern (23 bp):
CTTAAATATTAATGTGATTTATG
Found at i:61914 original size:40 final size:40
Alignment explanation
Indices: 61867--61946 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
61857 CTGAAGAAAG
*
61867 AAAAGAAAAAGAATACTCATAGGCTAGCTAAAGGAATTGC
1 AAAAGAAAAAGAATACTCATAGGATAGCTAAAGGAATTGC
61907 AAAAGAAAAAGAATACTCATAGGATAGCTAAAGGAATTGC
1 AAAAGAAAAAGAATACTCATAGGATAGCTAAAGGAATTGC
61947 TTTATATTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.51, C:0.11, G:0.20, T:0.17
Consensus pattern (40 bp):
AAAAGAAAAAGAATACTCATAGGATAGCTAAAGGAATTGC
Found at i:64502 original size:18 final size:19
Alignment explanation
Indices: 64469--64504 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
64459 ACATTTTTAG
*
64469 GTTTGTTTATATGATAAAT
1 GTTTGTTTAGATGATAAAT
64488 GTTTG-TTAGATGATAAA
1 GTTTGTTTAGATGATAAA
64505 ACGATGTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.47
Consensus pattern (19 bp):
GTTTGTTTAGATGATAAAT
Found at i:67898 original size:46 final size:46
Alignment explanation
Indices: 67847--68322 Score: 403
Period size: 46 Copynumber: 10.3 Consensus size: 46
67837 TGATAATTAA
* *
67847 ATTTATGCTTAAATATTAATGTGATCTGTGCTTAAGTATTAATGTG
1 ATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTG
* * *
67893 ATTTATGCTTTAATAGTGCTTAAATATTAATTTGATTTGTGCTTAAATATTAATATA
1 ----A----TT--TA-TGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTG
* * * * * *
67950 ATTTGTACTCAAATATTAATGAGATTTATG-GT---TA--AAT-T-
1 ATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTG
* * * * *
67988 ATTTGTGCTTAAATATTAACGTGATTTATGGTTAAATATGAATGTG
1 ATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTG
* * * *
68034 ATTTCTACTTAAATATTAATGTGGTTTATGCTTAAATATTAATGTG
1 ATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTG
* * *
68080 ATTTGTGCTTAAATATTAA-GTTGATTTATACTTAAATATTAATGTG
1 ATTTATGCTTAAATATTAATG-TGATTTGTGCTTAAATATTAATGTG
* * * *
68126 ATTTGTGCTTAAATATTAATTTGATTTGTGGTTAAATATTAATATG
1 ATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTG
* *
68172 ATTTGTGCTCAAATATTAATGTGATTTGTGCTTAAATATTAATGTG
1 ATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTG
* * * * * *
68218 ATTTGTGCTTAAATATTAATATGACTTATGATTAAATATTAATATG
1 ATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTG
* * * * * *
68264 ATTTGTGCTTAAATATTAATATGACTTATGATTAAATAGTAATGTG
1 ATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTG
*
68310 ATTTGTGCTTAAA
1 ATTTATGCTTAAA
68323 GAATTAAGAT
Statistics
Matches: 365, Mismatches: 44, Indels: 38
0.82 0.10 0.09
Matches are distributed among these distances:
38 26 0.07
39 2 0.01
40 3 0.01
42 4 0.01
44 3 0.01
45 3 0.01
46 279 0.76
47 1 0.00
49 2 0.01
50 1 0.00
53 1 0.00
54 2 0.01
56 2 0.01
57 36 0.10
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.46
Consensus pattern (46 bp):
ATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTG
Found at i:67901 original size:23 final size:23
Alignment explanation
Indices: 67847--67907 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
67837 TGATAATTAA
67847 ATTTATGCTTAAATATTAATGTG
1 ATTTATGCTTAAATATTAATGTG
* * *
67870 ATCTGTGCTTAAGTATTAATGTG
1 ATTTATGCTTAAATATTAATGTG
*
67893 ATTTATGCTTTAATA
1 ATTTATGCTTAAATA
67908 GTGCTTAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.48
Consensus pattern (23 bp):
ATTTATGCTTAAATATTAATGTG
Found at i:67921 original size:34 final size:34
Alignment explanation
Indices: 67874--67941 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
67864 AATGTGATCT
* *
67874 GTGCTTAAGTATTAATGTGATTTATGCTTTAATA
1 GTGCTTAAATATTAATGTGATTTATGCTTAAATA
* *
67908 GTGCTTAAATATTAATTTGATTTGTGCTTAAATA
1 GTGCTTAAATATTAATGTGATTTATGCTTAAATA
67942 TTAATATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (34 bp):
GTGCTTAAATATTAATGTGATTTATGCTTAAATA
Found at i:67938 original size:23 final size:23
Alignment explanation
Indices: 67908--67969 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
67898 TGCTTTAATA
* *
67908 GTGCTTAAATATTAATTTGATTT
1 GTGCTTAAATATTAATATAATTT
67931 GTGCTTAAATATTAATATAATTT
1 GTGCTTAAATATTAATATAATTT
* *
67954 GTACTCAAATATTAAT
1 GTGCTTAAATATTAAT
67970 GAGATTTATG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (23 bp):
GTGCTTAAATATTAATATAATTT
Found at i:67976 original size:23 final size:22
Alignment explanation
Indices: 67914--67976 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
67904 AATAGTGCTT
* * *
67914 AAATATTAATTTGATTTGTGCTT
1 AAATATTAA-TAGATTTGTACTC
*
67937 AAATATTAATATAATTTGTACTC
1 AAATATTAATA-GATTTGTACTC
67960 AAATATTAATGAGATTT
1 AAATATTAAT-AGATTT
67977 ATGGTTAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 1 0.03
23 31 0.94
24 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.46
Consensus pattern (22 bp):
AAATATTAATAGATTTGTACTC
Found at i:68002 original size:38 final size:38
Alignment explanation
Indices: 67950--68024 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
67940 TATTAATATA
*
67950 ATTTGTACTCAAATATTAATGAGATTTATGGTTAAATT
1 ATTTGTACTCAAATATTAACGAGATTTATGGTTAAATT
* * *
67988 ATTTGTGCTTAAATATTAACGTGATTTATGGTTAAAT
1 ATTTGTACTCAAATATTAACGAGATTTATGGTTAAAT
68025 ATGAATGTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (38 bp):
ATTTGTACTCAAATATTAACGAGATTTATGGTTAAATT
Found at i:68014 original size:23 final size:23
Alignment explanation
Indices: 67988--68322 Score: 438
Period size: 23 Copynumber: 14.6 Consensus size: 23
67978 TGGTTAAATT
*
67988 ATTTGTGCTTAAATATTAACGTG
1 ATTTGTGCTTAAATATTAATGTG
* * *
68011 ATTTATGGTTAAATATGAATGTG
1 ATTTGTGCTTAAATATTAATGTG
* *
68034 ATTTCTACTTAAATATTAATGTG
1 ATTTGTGCTTAAATATTAATGTG
* *
68057 GTTTATGCTTAAATATTAATGTG
1 ATTTGTGCTTAAATATTAATGTG
68080 ATTTGTGCTTAAATATTAA-GTTG
1 ATTTGTGCTTAAATATTAATG-TG
* *
68103 ATTTATACTTAAATATTAATGTG
1 ATTTGTGCTTAAATATTAATGTG
*
68126 ATTTGTGCTTAAATATTAATTTG
1 ATTTGTGCTTAAATATTAATGTG
* *
68149 ATTTGTGGTTAAATATTAATATG
1 ATTTGTGCTTAAATATTAATGTG
*
68172 ATTTGTGCTCAAATATTAATGTG
1 ATTTGTGCTTAAATATTAATGTG
68195 ATTTGTGCTTAAATATTAATGTG
1 ATTTGTGCTTAAATATTAATGTG
*
68218 ATTTGTGCTTAAATATTAATATG
1 ATTTGTGCTTAAATATTAATGTG
* * * *
68241 ACTTATGATTAAATATTAATATG
1 ATTTGTGCTTAAATATTAATGTG
*
68264 ATTTGTGCTTAAATATTAATATG
1 ATTTGTGCTTAAATATTAATGTG
* * * *
68287 ACTTATGATTAAATAGTAATGTG
1 ATTTGTGCTTAAATATTAATGTG
68310 ATTTGTGCTTAAA
1 ATTTGTGCTTAAA
68323 GAATTAAGAT
Statistics
Matches: 271, Mismatches: 39, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
22 1 0.00
23 269 0.99
24 1 0.00
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (23 bp):
ATTTGTGCTTAAATATTAATGTG
Found at i:68046 original size:61 final size:61
Alignment explanation
Indices: 67927--68047 Score: 134
Period size: 61 Copynumber: 2.0 Consensus size: 61
67917 TATTAATTTG
* * * **
67927 ATTTGTGCTTAAATATTAATATAATTTGTACTCAAATATTAATGAGATTTATGGTTAAATT
1 ATTTGTGCTTAAATATTAACATAATTTATACTCAAATATGAATGAGATTTATACTTAAATT
* * ** * * *
67988 ATTTGTGCTTAAATATTAACGTGATTTATGGTTAAATATGAATGTGATTTCTACTTAAAT
1 ATTTGTGCTTAAATATTAACATAATTTATACTCAAATATGAATGAGATTTATACTTAAAT
68048 ATTAATGTGG
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (61 bp):
ATTTGTGCTTAAATATTAACATAATTTATACTCAAATATGAATGAGATTTATACTTAAATT
Found at i:70465 original size:38 final size:38
Alignment explanation
Indices: 70414--70491 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
70404 GTACAATATA
70414 GACAACCATAATGATCTCATGCAATTTCCATATCTATT
1 GACAACCATAATGATCTCATGCAATTTCCATATCTATT
*
70452 GACAACCATAATGATCTCATGCAATTTTCATATCTATT
1 GACAACCATAATGATCTCATGCAATTTCCATATCTATT
70490 GA
1 GA
70492 TGCATAGAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.35
Consensus pattern (38 bp):
GACAACCATAATGATCTCATGCAATTTCCATATCTATT
Found at i:70836 original size:21 final size:22
Alignment explanation
Indices: 70805--70846 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
70795 ATTCACATGT
70805 TTTCTTACTCATGATTCTTTTG
1 TTTCTTACTCATGATTCTTTTG
**
70827 TTTC-TACTCATTTTTCTTTT
1 TTTCTTACTCATGATTCTTTT
70847 CCTTTTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.12, C:0.19, G:0.05, T:0.64
Consensus pattern (22 bp):
TTTCTTACTCATGATTCTTTTG
Found at i:77932 original size:27 final size:27
Alignment explanation
Indices: 77900--77965 Score: 82
Period size: 25 Copynumber: 2.5 Consensus size: 27
77890 GCTATATGTG
* *
77900 AGCCCTTGTGGTAGAATCTACTATACA
1 AGCCCTTGTGGCAGAATCTAATATACA
* *
77927 AGCCC-T-TGGCAGAATCTAATGTACG
1 AGCCCTTGTGGCAGAATCTAATATACA
77952 AGCCCTTGTGGCAG
1 AGCCCTTGTGGCAG
77966 GAACTTGTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 20 0.61
26 2 0.06
27 11 0.33
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (27 bp):
AGCCCTTGTGGCAGAATCTAATATACA
Done.