Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009651.1 Kokia drynarioides strain JFW-HI SEQ_124369, 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: 254301
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 179 characters in sequence are not A, C, G, or T
Found at i:874 original size:24 final size:23
Alignment explanation
Indices: 847--892 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
837 TTTTTTTTAC
847 AAAAAATTACTTATTTAATTTTTT
1 AAAAAA-TACTTATTTAATTTTTT
* *
871 AAAAAATATTTTTTTAATTTTT
1 AAAAAATACTTATTTAATTTTT
893 GTGTATCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
AAAAAATACTTATTTAATTTTTT
Found at i:1266 original size:22 final size:22
Alignment explanation
Indices: 1241--1287 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1231 ATATTTGGAA
*
1241 AGTCATCTAATAATGGGATTTG
1 AGTCATCTAATAATGAGATTTG
1263 AGTCATCTAATAATGAGATTTG
1 AGTCATCTAATAATGAGATTTG
1285 AGT
1 AGT
1288 ATAATTACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (22 bp):
AGTCATCTAATAATGAGATTTG
Found at i:11987 original size:392 final size:391
Alignment explanation
Indices: 11277--12029 Score: 1184
Period size: 392 Copynumber: 1.9 Consensus size: 391
11267 AAGGCACCTG
* * *
11277 CTTTTCTAGTGTGAACACTTCTCTTAATGTGAACATACCTTGTAGGTCACCATACCTTACCTAAA
1 CTTTTCTAGTGTGAACACTTCTCTTAATGTGAACATACCTTGTAGGCCACCAAACCCTACCTAAA
* ** *
11342 CATAACAACCCTACACCACAATTCAAAAAGAGTGATAGAATGAGTCTCATCATTTACATCCCCTA
66 CATAACAACCCTACACCACAATTCAAAAAGAATGATAGAATGAGTCTCATCACGTACATCCCCCA
** * * *
11407 TGCATTTTGCAATGATAGCTTATTGGTAGTAAGTTTACCATGTCAGCACTACCTACCATATGTAC
131 TGCATTTCACAATGATAGCTTATTGGTAGTAAGTTTACAATGTCAGAACTACCTACCATATATAC
* * *
11472 CCTTTAGTATGATAAAAAAGGGATCGACCCTTAAATACTCATAGTAATCCTATAGTCCTCAACAT
196 CCTTTAGCATGATAAAAAAGGGATAGACCCTTAAATACTCATAGTAACCCTATAGTCCTCAACAT
* *
11537 TTTCCTTCTCCTTTGAATTCTCAACCTTCTTAGTTTGCATACCTCTTCCAACTCTTCGCCTTGCT
261 TTTCCTTCTCCTTTGAATTCTCAACCTTCTTACTTTGCATACCTCCTCCAACTCTTCGCCTTGCT
*
11602 AGGGTGAATAGGCCTTCCTCAACACCATCACATCCTTGTGAACAAGCCACCCACTCAAGGTACCA
326 AGGATGAATAGGCCTTCCTCAACACCATCACATCCTTGTGAACAAGCCACCCACTCAAGGTACCA
11667 A
391 A
* *
11668 CTTTTCTAGTGTGAACAC-TCTTCTTAATGTGAACATACCTTTTAGGCCACCAAACCCTACTTAA
1 CTTTTCTAGTGTGAACACTTC-TCTTAATGTGAACATACCTTGTAGGCCACCAAACCCTACCTAA
*
11732 ACATAACAACCCTATACCACAATTCAAAAAGAATGATAGAATGAGTCTCATCACGTACATCCGCC
65 ACATAACAACCCTACACCACAATTCAAAAAGAATGATAGAATGAGTCTCATCACGTACATCC-CC
* *
11797 CATGCATTTCATAATGATGGCTTATTGGTAGTAAGTTTACAATGTCAGAACTACCTACCATATAT
129 CATGCATTTCACAATGATAGCTTATTGGTAGTAAGTTTACAATGTCAGAACTACCTACCATATAT
* *
11862 ACCCTTTAGCATGATGAAAACGGGATAGACCCTTAAATACTCATAGTAACCCTATAGTCCTCAAC
194 ACCCTTTAGCATGATAAAAAAGGGATAGACCCTTAAATACTCATAGTAACCCTATAGTCCTCAAC
* * * * **
11927 CTTTTCTTTCTCCTTTGAGTTCTCAGCCTTCTTACTTTGCATACCTCCTCCTGCTCTTCGCCTTG
259 ATTTTCCTTCTCCTTTGAATTCTCAACCTTCTTACTTTGCATACCTCCTCCAACTCTTCGCCTTG
* *
11992 CTAGGATGAATTGGTCTTCCTCAACACCATCACATCCT
324 CTAGGATGAATAGGCCTTCCTCAACACCATCACATCCT
12030 CTTCCTTGTC
Statistics
Matches: 327, Mismatches: 33, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
390 2 0.01
391 114 0.35
392 211 0.65
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (391 bp):
CTTTTCTAGTGTGAACACTTCTCTTAATGTGAACATACCTTGTAGGCCACCAAACCCTACCTAAA
CATAACAACCCTACACCACAATTCAAAAAGAATGATAGAATGAGTCTCATCACGTACATCCCCCA
TGCATTTCACAATGATAGCTTATTGGTAGTAAGTTTACAATGTCAGAACTACCTACCATATATAC
CCTTTAGCATGATAAAAAAGGGATAGACCCTTAAATACTCATAGTAACCCTATAGTCCTCAACAT
TTTCCTTCTCCTTTGAATTCTCAACCTTCTTACTTTGCATACCTCCTCCAACTCTTCGCCTTGCT
AGGATGAATAGGCCTTCCTCAACACCATCACATCCTTGTGAACAAGCCACCCACTCAAGGTACCA
A
Found at i:20482 original size:19 final size:20
Alignment explanation
Indices: 20430--20482 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
20420 TTATATTAGA
*
20430 AATTTTTTATAAATATTTTG
1 AATTTTTTATAATTATTTTG
* *
20450 AATTTTTAAAAATTATTTT-
1 AATTTTTTATAATTATTTTG
20469 AATTTTTTATAATT
1 AATTTTTTATAATT
20483 TTTGTTGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
AATTTTTTATAATTATTTTG
Found at i:37534 original size:3 final size:3
Alignment explanation
Indices: 37526--37559 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
37516 CATTTCTTTT
37526 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
37560 GTGACCTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:38348 original size:6 final size:6
Alignment explanation
Indices: 38334--38368 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
38324 CAAAGGAGGC
*
38334 TGCTCT TGCTGT TGCTGT TGCTGT TGCTGT TGCTG
1 TGCTGT TGCTGT TGCTGT TGCTGT TGCTGT TGCTG
38369 CTGATGGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.20, G:0.31, T:0.49
Consensus pattern (6 bp):
TGCTGT
Found at i:40603 original size:22 final size:22
Alignment explanation
Indices: 40578--40627 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
40568 TTTATATTGT
40578 TGTTTTGG-TGCTGTTTTTTTAC
1 TGTTTTGGTTGCTG-TTTTTTAC
* *
40600 TGTTTTGGTTGTTGTTTTTTGC
1 TGTTTTGGTTGCTGTTTTTTAC
40622 TGTTTT
1 TGTTTT
40628 AGTTTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.02, C:0.06, G:0.24, T:0.68
Consensus pattern (22 bp):
TGTTTTGGTTGCTGTTTTTTAC
Found at i:40700 original size:24 final size:24
Alignment explanation
Indices: 40673--40772 Score: 123
Period size: 24 Copynumber: 4.2 Consensus size: 24
40663 TTTTTAATTA
*
40673 TTTTGGTGTTGTTTTTGCTGTTAT
1 TTTTGTTGTTGTTTTTGCTGTTAT
** *
40697 TTTTGTTGCTACTTTTT-ATGTTAT
1 TTTTGTTG-TTGTTTTTGCTGTTAT
* *
40721 TTTTGTTGCTGTTTTTGTTGTTAT
1 TTTTGTTGTTGTTTTTGCTGTTAT
40745 TTTTGTTGTTG-TTTTGCTGTTAT
1 TTTTGTTGTTGTTTTTGCTGTTAT
40768 TTTTG
1 TTTTG
40773 CTACTGCTTT
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
23 21 0.33
24 37 0.58
25 6 0.09
ACGTcount: A:0.06, C:0.05, G:0.20, T:0.69
Consensus pattern (24 bp):
TTTTGTTGTTGTTTTTGCTGTTAT
Found at i:40712 original size:48 final size:48
Alignment explanation
Indices: 40663--40752 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 48
40653 TTTGGTGCTT
*
40663 TTTTTA-ATTA-TTTTGGTGTTGTTTTTGCTGTTATTTTTGTTGCTAC
1 TTTTTATATTATTTTTGGTGCTGTTTTTGCTGTTATTTTTGTTGCTAC
* * *
40709 TTTTTATGTTATTTTTGTTGCTGTTTTTGTTGTTATTTTTGTTG
1 TTTTTATATTATTTTTGGTGCTGTTTTTGCTGTTATTTTTGTTG
40753 TTGTTTTGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
46 6 0.16
47 3 0.08
48 29 0.76
ACGTcount: A:0.09, C:0.04, G:0.18, T:0.69
Consensus pattern (48 bp):
TTTTTATATTATTTTTGGTGCTGTTTTTGCTGTTATTTTTGTTGCTAC
Found at i:40767 original size:47 final size:47
Alignment explanation
Indices: 40673--40801 Score: 132
Period size: 47 Copynumber: 2.7 Consensus size: 47
40663 TTTTTAATTA
* * * * *
40673 TTTTGGTGTTGTTTTTGCTGTTATTTTTGTTGCTACTTTTTATGTTAT
1 TTTTGCTGCTGTTTTTGTTGTTATTTTTGTTG-TTCTTTTGATGTTAT
* * *
40721 TTTTGTTGCTGTTTTTGTTGTTATTTTTGTTGTTGTTTTGCTGTTAT
1 TTTTGCTGCTGTTTTTGTTGTTATTTTTGTTGTTCTTTTGATGTTAT
* * ** *
40768 TTTTGCTACTGCTTTAATTGTTATTTTGGTTGTT
1 TTTTGCTGCTGTTTTTGTTGTTATTTTTGTTGTT
40802 TGTATGTTAT
Statistics
Matches: 68, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
47 39 0.57
48 29 0.43
ACGTcount: A:0.08, C:0.06, G:0.19, T:0.67
Consensus pattern (47 bp):
TTTTGCTGCTGTTTTTGTTGTTATTTTTGTTGTTCTTTTGATGTTAT
Found at i:40774 original size:12 final size:12
Alignment explanation
Indices: 40673--40772 Score: 96
Period size: 12 Copynumber: 8.4 Consensus size: 12
40663 TTTTTAATTA
* *
40673 TTTTGGTGTTGT
1 TTTTGTTGTTAT
*
40685 TTTTGCTGTTAT
1 TTTTGTTGTTAT
*
40697 TTTTGTTGCTACT
1 TTTTGTTGTTA-T
*
40710 TTTT-ATGTTAT
1 TTTTGTTGTTAT
* *
40721 TTTTGTTGCTGT
1 TTTTGTTGTTAT
40733 TTTTGTTGTTAT
1 TTTTGTTGTTAT
*
40745 TTTTGTTGTT-G
1 TTTTGTTGTTAT
*
40756 TTTTGCTGTTAT
1 TTTTGTTGTTAT
40768 TTTTG
1 TTTTG
40773 CTACTGCTTT
Statistics
Matches: 71, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
11 14 0.20
12 52 0.73
13 5 0.07
ACGTcount: A:0.06, C:0.05, G:0.20, T:0.69
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:45348 original size:23 final size:23
Alignment explanation
Indices: 45322--45398 Score: 82
Period size: 23 Copynumber: 3.2 Consensus size: 23
45312 TTGGATTATT
45322 AAATTAATTGATTCTAAATCATA
1 AAATTAATTGATTCTAAATCATA
* * * *
45345 AAATTATTTTTTATTTATAAATCACA
1 AAATTA--ATTGA-TTCTAAATCATA
*
45371 AAGTTAATTGATTCTAAATCATA
1 AAATTAATTGATTCTAAATCATA
45394 AAATT
1 AAATT
45399 CTCCAAATGC
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
23 20 0.49
24 3 0.07
25 3 0.07
26 15 0.37
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (23 bp):
AAATTAATTGATTCTAAATCATA
Found at i:60649 original size:30 final size:30
Alignment explanation
Indices: 60507--60739 Score: 103
Period size: 30 Copynumber: 7.8 Consensus size: 30
60497 AAATTGATAA
* *
60507 TTTTGG-GAAAGTTCAGGGTTAAAAGTAGAAT
1 TTTTGGAGAAA-TT-AGGGTTAAAAATGGAAT
* *
60538 TTTT--AGAAATTCGAGGG-CAAAAATGGTATT
1 TTTTGGAGAAATT--AGGGTTAAAAATGG-AAT
* **
60568 TTTTGGAAAAACCAGGGTTAAAAATGGAA-
1 TTTTGGAGAAATTAGGGTTAAAAATGGAAT
* * * *
60597 TTTTGG-GAAGTTTGGGGGTAAAAATGTAAT
1 TTTTGGAGAA-ATTAGGGTTAAAAATGGAAT
*
60627 TTTTGGAGAAATTAGGGTTAAAATTGGAA-
1 TTTTGGAGAAATTAGGGTTAAAAATGGAAT
* * *
60656 TTTT--AGAAAGGTTGGGGGT-AACATGGTAAT
1 TTTTGGAGAAA--TTAGGGTTAAAAATGG-AAT
* * * *
60686 ATTTGAAAAAATTAGGGTCAAAAATGGAA-
1 TTTTGGAGAAATTAGGGTTAAAAATGGAAT
60715 TTTTGGA-AAAGTTTAGGGGTTAAAA
1 TTTTGGAGAAA--TTA-GGGTTAAAA
60740 TATAATTTTG
Statistics
Matches: 148, Mismatches: 35, Indels: 38
0.67 0.16 0.17
Matches are distributed among these distances:
27 5 0.03
28 10 0.07
29 44 0.30
30 52 0.35
31 29 0.20
32 8 0.05
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.32
Consensus pattern (30 bp):
TTTTGGAGAAATTAGGGTTAAAAATGGAAT
Found at i:60655 original size:59 final size:60
Alignment explanation
Indices: 60507--60800 Score: 231
Period size: 59 Copynumber: 4.9 Consensus size: 60
60497 AAATTGATAA
* * * * * * * * *
60507 TTTTGGGAAAGTTCAGGGTTAAAAGTAGAATTTTTAGAAA-TTCGAGGGCAAAAATGGTATT
1 TTTTGGAAAAATT-AGGGTTAAAAATGGAA-TTTTGGAAAGTTTGGGGGTAAAAATGGTAAT
** *
60568 TTTTGGAAAAACCAGGGTTAAAAATGGAATTTTGGGAAGTTTGGGGGTAAAAAT-GTAAT
1 TTTTGGAAAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAAATGGTAAT
* * * * *
60627 TTTTGGAGAAATTAGGGTTAAAATTGGAATTTTAGAAAGGTTGGGGGT-AACATGGTAAT
1 TTTTGGAAAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAAATGGTAAT
* * * * * *
60686 ATTTGAAAAAATTAGGGTCAAAAATGGAATTTTGGAAAAGTTTAGGGGTTAAAAT-ATAA-
1 TTTTGGAAAAATTAGGGTTAAAAATGGAATTTTGG-AAAGTTTGGGGGTAAAAATGGTAAT
* ** * * *
60745 TTTTGGAAAAGTTTACTAG-TCAAAATGTAATTTTGGAAAAGTTTGGGGGTCAAAAT
1 TTTTGGAAAA-ATTA-GGGTTAAAAATGGAATTTTGG-AAAGTTTGGGGGTAAAAAT
60801 ATGATTTTTG
Statistics
Matches: 187, Mismatches: 40, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
58 4 0.02
59 94 0.50
60 75 0.40
61 14 0.07
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (60 bp):
TTTTGGAAAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAAATGGTAAT
Found at i:60740 original size:30 final size:30
Alignment explanation
Indices: 60582--60822 Score: 140
Period size: 30 Copynumber: 8.1 Consensus size: 30
60572 GGAAAAACCA
* *
60582 GGGTTAAAAATGGAATTTTGG-GAAGTTTGG
1 GGGTT-AAAATGGAATTTTGGAAAAGTTTAG
* *
60612 GGGTAAAAATGTAATTTTTGGAGAAA--TTA-
1 GGGTTAAAATGGAA-TTTTGGA-AAAGTTTAG
* *
60641 GGGTTAAAATTGGAATTTTAG-AAAGGTT-G
1 GGGTTAAAA-TGGAATTTTGGAAAAGTTTAG
* * **
60670 GGGGTAACATGGTAATATTT-GAAAAAATTA-
1 GGGTTAAAATGG-AAT-TTTGGAAAAGTTTAG
*
60700 GGGTCAAAAATGGAATTTTGGAAAAGTTTAG
1 GGGT-TAAAATGGAATTTTGGAAAAGTTTAG
** *
60731 GGGTTAAAATATAATTTTGGAAAAGTTTAC
1 GGGTTAAAATGGAATTTTGGAAAAGTTTAG
** * * *
60761 TAGTCAAAATGTAATTTTGGAAAAGTTTGG
1 GGGTTAAAATGGAATTTTGGAAAAGTTTAG
* * * *
60791 GGGTCAAAATATGATTTTTGG-ATAGTTTAG
1 GGGTTAAAAT-GGAATTTTGGAAAAGTTTAG
60821 GG
1 GG
60823 ACCTCAGAGC
Statistics
Matches: 163, Mismatches: 33, Indels: 30
0.72 0.15 0.13
Matches are distributed among these distances:
27 3 0.02
28 3 0.02
29 37 0.23
30 101 0.62
31 17 0.10
32 2 0.01
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (30 bp):
GGGTTAAAATGGAATTTTGGAAAAGTTTAG
Found at i:61861 original size:3 final size:3
Alignment explanation
Indices: 61848--61890 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
61838 CGGTTTTCTT
*
61848 TTA TT- TTA TTA TTA TTA TTA TTA TTAA TTA CTA -TA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TT
61891 TAATGTTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
2 4 0.11
3 29 0.81
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:61918 original size:12 final size:12
Alignment explanation
Indices: 61903--61928 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
61893 ATGTTATTGT
61903 TGCTATTATTAA
1 TGCTATTATTAA
61915 TGCTATTATTAA
1 TGCTATTATTAA
61927 TG
1 TG
61929 ACGGTGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.50
Consensus pattern (12 bp):
TGCTATTATTAA
Found at i:62605 original size:24 final size:23
Alignment explanation
Indices: 62564--62614 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
62554 GAATTTGGCC
* *
62564 TAATTGGATATTTATTTGGACTTG
1 TAATTGGACATTTATTT-GACATG
62588 TAATTGGACATTGT-TTTGACATG
1 TAATTGGACATT-TATTTGACATG
62611 TAAT
1 TAAT
62615 CTTTGGACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 9 0.38
24 14 0.58
25 1 0.04
ACGTcount: A:0.27, C:0.06, G:0.20, T:0.47
Consensus pattern (23 bp):
TAATTGGACATTTATTTGACATG
Found at i:62695 original size:18 final size:17
Alignment explanation
Indices: 62643--62748 Score: 113
Period size: 17 Copynumber: 6.2 Consensus size: 17
62633 TATAATAAGT
* *
62643 TTTAAATATAATATAAA
1 TTTAAATTTAAAATAAA
* * *
62660 TATAAATTTATATTAAA
1 TTTAAATTTAAAATAAA
*
62677 TTTAAATTTTAAAACAAA
1 TTTAAA-TTTAAAATAAA
62695 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
62712 TTTATATTCAAAATAAA
1 TTTAAATTTAAAATAAA
**
62729 TTTAACCTTAAAATAAA
1 TTTAAATTTAAAATAAA
62746 TTT
1 TTT
62749 TAAAATGAGT
Statistics
Matches: 72, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
17 58 0.81
18 14 0.19
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:63415 original size:201 final size:194
Alignment explanation
Indices: 63060--63489 Score: 558
Period size: 201 Copynumber: 2.2 Consensus size: 194
63050 TGTCATTAAT
* * * * *
63060 TTGGTCTACTTCT-TAGTATCTTATCAGGAAGATGATCGAATCGCTTGTTTCAATCCGCTTCTCT
1 TTGGTATACTTCTCT-GTATCTTATCAGGAAGATAATCGAACCACTTGTTTCAATCCGCTTATCT
* * * *
63124 GTACCTCACCAGGAAGACGAATTTGGTCTACTTCTCTGTATTTCATTAGGAAGCTAACCATTTTA
65 GTACCTCACCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTA
* *
63189 TTGCTTCGACCTGCTTTTTAGTATCTCATCAAGAAGCTGGGATTCGAAGATTTACTCACATCAAG
130 TTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGATTCGAAGATTT-CT----TC--G
*
63254 CCTTGAG
188 CATTGAG
* *
63261 TTGGTATACTTCTCTGTATCTTATCAGGAAGATAATC-ACCCTATTTGTTTCAATCCGCTTATCT
1 TTGGTATACTTCTCTGTATCTTATCAGGAAGATAATCGAACC-ACTTGTTTCAATCCGCTTATCT
* * **
63325 GTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACTTTTTTA
65 GTACCTCACCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTA
* * * *
63390 TTGCTTCGCCCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCGCATTGAG
130 TTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGATTCGAAGATTTCTTCGCATTGAG
*
63455 TTGGTATACTTCTCTGTATCTCATCAGGAAGATAA
1 TTGGTATACTTCTCTGTATCTTATCAGGAAGATAA
63490 CTGCCTCACT
Statistics
Matches: 204, Mismatches: 23, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
194 41 0.20
196 2 0.01
200 3 0.01
201 157 0.77
202 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (194 bp):
TTGGTATACTTCTCTGTATCTTATCAGGAAGATAATCGAACCACTTGTTTCAATCCGCTTATCTG
TACCTCACCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
TGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGATTCGAAGATTTCTTCGCATTGAG
Found at i:74630 original size:60 final size:61
Alignment explanation
Indices: 74566--74737 Score: 208
Period size: 60 Copynumber: 2.9 Consensus size: 61
74556 AAAATTCGAA
**
74566 GGTAAAATGATTTTTTTTTGGAAAAATCAAGGTCAAAAATAGAATTTTGGAAAGTTCAGG-
1 GGTAAAATGATTAATTTTTGGAAAAATCAAGGTCAAAAATAGAATTTTGGAAAGTTCAGGT
* * * * *
74626 GGTAAAA--ATATAATTTTTAGAGAAATCAGGGTCAAAAATAGAATTTTGAAAAGTTCGGGT
1 GGTAAAATGAT-TAATTTTTGGAAAAATCAAGGTCAAAAATAGAATTTTGGAAAGTTCAGGT
* * * *
74686 GGTAAAATG-GTAATTTTTGGAAAAATCATGGTCAAAAATGGAATTTTAGAAA
1 GGTAAAATGATTAATTTTTGGAAAAATCAAGGTCAAAAATAGAATTTTGGAAA
74738 AAGGTTAGGG
Statistics
Matches: 94, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
58 2 0.02
59 42 0.45
60 50 0.53
ACGTcount: A:0.42, C:0.05, G:0.22, T:0.31
Consensus pattern (61 bp):
GGTAAAATGATTAATTTTTGGAAAAATCAAGGTCAAAAATAGAATTTTGGAAAGTTCAGGT
Found at i:74632 original size:29 final size:29
Alignment explanation
Indices: 74600--74692 Score: 93
Period size: 30 Copynumber: 3.1 Consensus size: 29
74590 AATCAAGGTC
74600 AAAAATAGAATTTTGGAAAGTTCAGGGGT
1 AAAAATAGAATTTTGGAAAGTTCAGGGGT
*
74629 AAAAATATAATTTTTAGAGAAA--TCA-GGGT
1 AAAAATAGAA-TTTT-G-GAAAGTTCAGGGGT
* *
74658 CAAAAATAGAATTTTGAAAAGTTCGGGTGGT
1 -AAAAATAGAATTTTGGAAAGTTCAGG-GGT
74689 AAAA
1 AAAA
74693 TGGTAATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
27 3 0.06
28 1 0.02
29 19 0.37
30 21 0.40
31 4 0.08
32 4 0.08
ACGTcount: A:0.45, C:0.04, G:0.23, T:0.28
Consensus pattern (29 bp):
AAAAATAGAATTTTGGAAAGTTCAGGGGT
Found at i:74640 original size:119 final size:121
Alignment explanation
Indices: 74517--74784 Score: 280
Period size: 119 Copynumber: 2.2 Consensus size: 121
74507 GGTAAAATGG
* * * * * **
74517 TAATTTTGAGAAAGTTTGGGGTTAAAAGTGGAATTTTTAAAAATTC-GAAGGTAAAATGATTTTT
1 TAATTTTGAGAAAGTTTGGGGTCAAAAATAGAATTTTGAAAAATTCGGAAGGTAAAATG-GTAAT
*
74581 TTTTGGAAAAATCAAGGTCAAAAATAGAATTTT-G-GAAA-GTTCAGGGGTAAAAATA
65 TTTTGGAAAAATCAAGGTCAAAAATAGAATTTTAGAAAAAGGTT-AGGGGTAAAAATA
** * **
74636 TAATTTTTAGAGAAA--TCAGGGTCAAAAATAGAATTTTGAAAAGTTCGGGTGGTAAAATGGTAA
1 TAA-TTTT-GAGAAAGTTTGGGGTCAAAAATAGAATTTTGAAAAATTCGGAAGGTAAAATGGTAA
* * * *
74699 TTTTTGGAAAAATCATGGTCAAAAATGGAATTTTAGAAAAAGGTTAGGGGTTAAAATG
64 TTTTTGGAAAAATCAAGGTCAAAAATAGAATTTTAGAAAAAGGTTAGGGGTAAAAATA
74757 TAATTTTG-GAAAAGTTTGAGGGTCAAAA
1 TAATTTTGAG-AAAGTTTG-GGGTCAAAA
74785 TATGATTTTT
Statistics
Matches: 120, Mismatches: 19, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
118 1 0.01
119 64 0.53
120 19 0.16
121 24 0.20
122 12 0.10
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.32
Consensus pattern (121 bp):
TAATTTTGAGAAAGTTTGGGGTCAAAAATAGAATTTTGAAAAATTCGGAAGGTAAAATGGTAATT
TTTGGAAAAATCAAGGTCAAAAATAGAATTTTAGAAAAAGGTTAGGGGTAAAAATA
Found at i:74662 original size:59 final size:58
Alignment explanation
Indices: 74580--74769 Score: 231
Period size: 59 Copynumber: 3.2 Consensus size: 58
74570 AAATGATTTT
* *
74580 TTTTTGGAAAAATCAAGGTCAAAAATAGAATTTTGGAAAGTTCAGGGGTAAAAATATAA
1 TTTTTGGAAAAATCAAGGTCAAAAATAGAATTTTGAAAAGTTCAGGGGT-AAAATGTAA
* * * *
74639 TTTTTAGAGAAATCAGGGTCAAAAATAGAATTTTGAAAAGTTCGGGTGGTAAAATGGTAA
1 TTTTTGGAAAAATCAAGGTCAAAAATAGAATTTTGAAAAGTTCAGG-GGTAAAAT-GTAA
* *
74699 TTTTTGGAAAAATCATGGTCAAAAATGGAATTTTAGAAAAAGGTT-AGGGGTTAAAATGTAA
1 TTTTTGGAAAAATCAAGGTCAAAAATAGAATTTT-G-AAAA-GTTCAGGGG-TAAAATGTAA
74760 -TTTTGGAAAA
1 TTTTTGGAAAA
74770 GTTTGAGGGT
Statistics
Matches: 114, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
59 46 0.40
60 46 0.40
61 7 0.06
62 12 0.11
63 3 0.03
ACGTcount: A:0.43, C:0.04, G:0.23, T:0.31
Consensus pattern (58 bp):
TTTTTGGAAAAATCAAGGTCAAAAATAGAATTTTGAAAAGTTCAGGGGTAAAATGTAA
Found at i:74737 original size:29 final size:29
Alignment explanation
Indices: 74581--74739 Score: 126
Period size: 29 Copynumber: 5.4 Consensus size: 29
74571 AATGATTTTT
*
74581 TTTTGGAAAAATCAAGGTCAAAAATAGAA
1 TTTTGGAAAAATCAGGGTCAAAAATAGAA
** *
74610 TTTTGGAAAGTTCAGGGGT-AAAAATATAA
1 TTTTGGAAAAATCA-GGGTCAAAAATAGAA
* *
74639 TTTTTAGAGAAATCAGGGTCAAAAATAGAA
1 -TTTTGGAAAAATCAGGGTCAAAAATAGAA
* ** *
74669 TTTT-GAAAAGTTC-GGGTGGTAAAATGGTAA
1 TTTTGGAAAA-ATCAGGGT-CAAAAATAG-AA
* *
74699 TTTTTGGAAAAATCATGGTCAAAAATGGAA
1 -TTTTGGAAAAATCAGGGTCAAAAATAGAA
*
74729 TTTTAGAAAAA
1 TTTTGGAAAAA
74740 GGTTAGGGGT
Statistics
Matches: 102, Mismatches: 19, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
28 8 0.08
29 47 0.46
30 26 0.25
31 13 0.13
32 8 0.08
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (29 bp):
TTTTGGAAAAATCAGGGTCAAAAATAGAA
Found at i:74785 original size:30 final size:31
Alignment explanation
Indices: 74715--74785 Score: 74
Period size: 30 Copynumber: 2.3 Consensus size: 31
74705 GAAAAATCAT
74715 GGTCAAAAATGGAATTTTAGAAAAAGGTTAGG
1 GGTC-AAAATGGAATTTTAGAAAAAGGTTAGG
* * * *
74747 GGTTAAAATGTAATTTT-GGAAAA-GTTTGAG
1 GGTCAAAATGGAATTTTAGAAAAAGGTTAG-G
74777 GGTCAAAAT
1 GGTCAAAAT
74786 ATGATTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
29 4 0.12
30 14 0.42
31 12 0.36
32 3 0.09
ACGTcount: A:0.41, C:0.03, G:0.27, T:0.30
Consensus pattern (31 bp):
GGTCAAAATGGAATTTTAGAAAAAGGTTAGG
Found at i:76578 original size:35 final size:34
Alignment explanation
Indices: 76537--76643 Score: 115
Period size: 35 Copynumber: 3.1 Consensus size: 34
76527 TATAATAAGT
* *
76537 TTTAAATTTAAATATAAATCTAAATTTATATTAAA
1 TTTAAATTTAAA-ATAAATCTAAATTTAAAATAAA
* *
76572 TTTAAATTTTAAAACAAATTTAAATTTAAAATAAA
1 TTTAAA-TTTAAAATAAATCTAAATTTAAAATAAA
* * * **
76607 TTTATATTCAAAATAAATTTAACCTTAAAATAAA
1 TTTAAATTTAAAATAAATCTAAATTTAAAATAAA
76641 TTT
1 TTT
76644 TAAAATGAGT
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
34 27 0.44
35 29 0.47
36 6 0.10
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (34 bp):
TTTAAATTTAAAATAAATCTAAATTTAAAATAAA
Found at i:76584 original size:7 final size:6
Alignment explanation
Indices: 76537--76628 Score: 66
Period size: 6 Copynumber: 15.8 Consensus size: 6
76527 TATAATAAGT
* * *
76537 TTTAAA TTTAAA TATAAA TCTAAA TTTATA -TTAAA TTTAAA TTTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA
** * * * *
76585 -ACAAA TTTAAA TTTAAA -ATAAA TTTATA TTCAAA -ATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
76629 CCTTAAAATA
Statistics
Matches: 64, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
5 14 0.22
6 44 0.69
7 6 0.09
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:76590 original size:29 final size:29
Alignment explanation
Indices: 76538--76593 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
76528 ATAATAAGTT
*
76538 TTAAATTTAAATATAAATCTAAATTTATA
1 TTAAATTTAAATATAAAACTAAATTTATA
*
76567 TTAAATTTAAATTTTAAAAC-AAATTTA
1 TTAAATTTAAA-TATAAAACTAAATTTA
76594 AATTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (29 bp):
TTAAATTTAAATATAAAACTAAATTTATA
Found at i:76619 original size:17 final size:17
Alignment explanation
Indices: 76537--76643 Score: 124
Period size: 17 Copynumber: 6.2 Consensus size: 17
76527 TATAATAAGT
76537 TTTAAATTTAAATATAAA
1 TTTAAATTTAAA-ATAAA
* * *
76555 TCTAAATTTATATTAAA
1 TTTAAATTTAAAATAAA
*
76572 TTTAAATTTTAAAACAAA
1 TTTAAA-TTTAAAATAAA
76590 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
76607 TTTATATTCAAAATAAA
1 TTTAAATTTAAAATAAA
**
76624 TTTAACCTTAAAATAAA
1 TTTAAATTTAAAATAAA
76641 TTT
1 TTT
76644 TAAAATGAGT
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
17 50 0.68
18 24 0.32
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:76979 original size:18 final size:17
Alignment explanation
Indices: 76946--76989 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
76936 AACAAAATAT
76946 ATATT-AAAATTATTAA
1 ATATTAAAAATTATTAA
*
76962 ATATTAAAAATATTTTAA
1 ATATTAAAAAT-TATTAA
*
76980 AAATTAAAAA
1 ATATTAAAAA
76990 ATATATGGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 5 0.21
17 5 0.21
18 14 0.58
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATTAAAAATTATTAA
Found at i:79550 original size:75 final size:75
Alignment explanation
Indices: 79426--79573 Score: 260
Period size: 75 Copynumber: 2.0 Consensus size: 75
79416 CTAGGGCTAT
* * *
79426 TTCTAGTTAGACTAGGAGTTCATTTTTCTATTGAAATAGACTTTCACAATTCAACAAGGTTTCTC
1 TTCTAATTAAACTAGGAGTTCATTTTTCTATTGAAATAGACTTTCACAATTCAACAAGATTTCTC
79491 CTCTTCTCAA
66 CTCTTCTCAA
*
79501 TTCTAATTAAACTAGGAGTTCATTTTTCTATTGAAATAGACTTTTACAATTCAACAAGATTTCTC
1 TTCTAATTAAACTAGGAGTTCATTTTTCTATTGAAATAGACTTTCACAATTCAACAAGATTTCTC
79566 CTCTTCTC
66 CTCTTCTC
79574 CCTATAAATA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (75 bp):
TTCTAATTAAACTAGGAGTTCATTTTTCTATTGAAATAGACTTTCACAATTCAACAAGATTTCTC
CTCTTCTCAA
Found at i:79819 original size:24 final size:24
Alignment explanation
Indices: 79790--79844 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
79780 GTCCACACTC
79790 GAAGCAGTTCGCGGTACAAGAATA
1 GAAGCAGTTCGCGGTACAAGAATA
* *
79814 GAAGCAATTCGCGGTACATGAATA
1 GAAGCAGTTCGCGGTACAAGAATA
79838 GAAGCAG
1 GAAGCAG
79845 CTCGAAAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.29, T:0.16
Consensus pattern (24 bp):
GAAGCAGTTCGCGGTACAAGAATA
Found at i:98901 original size:15 final size:16
Alignment explanation
Indices: 98881--98914 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
98871 CGAGCAAATA
98881 TATTCGATTCG-ATTC
1 TATTCGATTCGAATTC
*
98896 TATTCGATTTGAATTC
1 TATTCGATTCGAATTC
98912 TAT
1 TAT
98915 CTCACTCGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.50
Consensus pattern (16 bp):
TATTCGATTCGAATTC
Found at i:99566 original size:17 final size:17
Alignment explanation
Indices: 99528--99587 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
99518 TTAAGCTTAT
*
99528 TTTAAATTTAAATTGGAAA
1 TTTAAATTTAAAAT--AAA
**
99547 TTTAAATTTATCATAAA
1 TTTAAATTTAAAATAAA
*
99564 TTTAAATTTAAAATATA
1 TTTAAATTTAAAATAAA
99581 TTTAAAT
1 TTTAAAT
99588 AATGTCCAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 24 0.69
19 11 0.31
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:100301 original size:20 final size:20
Alignment explanation
Indices: 100276--100315 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
100266 AATATATTAA
100276 TAATAATAATAAATATTTTT
1 TAATAATAATAAATATTTTT
100296 TAATAATAATAAATATTTTT
1 TAATAATAATAAATATTTTT
100316 GGTAATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATAATAATAAATATTTTT
Found at i:101359 original size:29 final size:29
Alignment explanation
Indices: 101330--101454 Score: 117
Period size: 29 Copynumber: 4.3 Consensus size: 29
101320 TAATTTTTCT
* *
101330 AAAATTTACATTTTTACCCCCAAACTTCT
1 AAAAATTACATTTTTACCCCCAAACTTCC
* * * ***
101359 AAAAATTCCATTTTGACCCCGATTTTTCC
1 AAAAATTACATTTTTACCCCCAAACTTCC
*
101388 AAAAATTACATTTTTACTCCCAAACTTCC
1 AAAAATTACATTTTTACCCCCAAACTTCC
* * **
101417 AAAAAGTCCATTTTTGA-CCCCAATTTTCC
1 AAAAATTACATTTTT-ACCCCCAAACTTCC
101446 AAAAATTAC
1 AAAAATTAC
101455 CATCTACCCT
Statistics
Matches: 73, Mismatches: 22, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
29 72 0.99
30 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAAATTACATTTTTACCCCCAAACTTCC
Found at i:101384 original size:58 final size:59
Alignment explanation
Indices: 101322--101580 Score: 248
Period size: 58 Copynumber: 4.5 Consensus size: 59
101312 TTGACCCTTA
* * *
101322 ATTTTTCTAAAATTTA-CATTTTTACCCCCAAACTTCTAAAAATTCCA-TTTTGACCCCG
1 ATTTTTCCAAAAATTACCA-TTTTACCCCCAAACTTCTAAAAATTCCATTTTTAACCCCG
* * * *
101380 ATTTTTCCAAAAATTA-CATTTTTACTCCCAAACTTCCAAAAAGTCCATTTTTGACCCC-
1 ATTTTTCCAAAAATTACCA-TTTTACCCCCAAACTTCTAAAAATTCCATTTTTAACCCCG
* * * * * *
101438 AATTTTCCAAAAATTACCA-TCTACCCTCGAACTT-TCAAAA-TCCAATTTTAACCCCG
1 ATTTTTCCAAAAATTACCATTTTACCCCCAAACTTCTAAAAATTCCATTTTTAACCCCG
* *
101494 ATTCTTTCCAAAAATTACCATTTTACCCTCAAA-TGTCT-AAAATTTCATTTTTAACCCCG
1 ATT-TTTCCAAAAATTACCATTTTACCCCCAAACT-TCTAAAAATTCCATTTTTAACCCCG
** * *
101553 AACTTTCCCAAAATTACCATTTCACCCC
1 ATTTTTCCAAAAATTACCATTTTACCCC
101581 ATGTGTCCAG
Statistics
Matches: 169, Mismatches: 24, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
55 13 0.08
56 6 0.04
57 28 0.17
58 94 0.56
59 28 0.17
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.36
Consensus pattern (59 bp):
ATTTTTCCAAAAATTACCATTTTACCCCCAAACTTCTAAAAATTCCATTTTTAACCCCG
Found at i:101506 original size:115 final size:114
Alignment explanation
Indices: 101360--101572 Score: 274
Period size: 115 Copynumber: 1.9 Consensus size: 114
101350 CAAACTTCTA
*
101360 AAAATTCCATTTTGACCCCGATTTTTCCAAAAATTA-CATTTTTACTCC-CAAACT-TCCAAAAA
1 AAAATTCCATTTTAACCCCGATTTTTCCAAAAATTACCA-TTTTAC-CCTCAAA-TGT-CAAAAA
* *
101422 GTCCATTTTTGACCCC-AATTTTCCAAAAATTACCATCTACCCTCGAACTTTC
62 GTCCATTTTTAACCCCGAACTTTCCAAAAATTACCATCTACCCTCGAACTTTC
* *
101474 AAAA-TCCAATTTTAACCCCGATTCTTTCCAAAAATTACCATTTTACCCTCAAATGTCTAAAATT
1 AAAATTCC-ATTTTAACCCCGATT-TTTCCAAAAATTACCATTTTACCCTCAAATGTCAAAAAGT
* *
101538 TCATTTTTAACCCCGAACTTTCCCAAAATTACCAT
64 CCATTTTTAACCCCGAACTTTCCAAAAATTACCAT
101573 TTCACCCCAT
Statistics
Matches: 86, Mismatches: 7, Indels: 11
0.83 0.07 0.11
Matches are distributed among these distances:
113 3 0.03
114 39 0.45
115 42 0.49
116 2 0.02
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (114 bp):
AAAATTCCATTTTAACCCCGATTTTTCCAAAAATTACCATTTTACCCTCAAATGTCAAAAAGTCC
ATTTTTAACCCCGAACTTTCCAAAAATTACCATCTACCCTCGAACTTTC
Found at i:102490 original size:3 final size:3
Alignment explanation
Indices: 102482--102510 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
102472 GGTTTCGACA
102482 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
102511 CGTTTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:102842 original size:3 final size:3
Alignment explanation
Indices: 102829--102866 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
102819 GCAGTAGAAT
*
102829 AGA AGA A-A AGA AGA AGA AGA AGA AGA AAA AG- AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
102867 ATGGAGATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:102854 original size:20 final size:20
Alignment explanation
Indices: 102829--102866 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
102819 GCAGTAGAAT
102829 AGAAG-AAAAGAAGAAGAAGA
1 AGAAGAAAAAG-AGAAGAAGA
102849 AGAAGAAAAAGAGAAGAA
1 AGAAGAAAAAGAGAAGAA
102867 ATGGAGATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (20 bp):
AGAAGAAAAAGAGAAGAAGA
Found at i:103410 original size:18 final size:18
Alignment explanation
Indices: 103376--103414 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
103366 TGCTTGCTAT
103376 TTGGTATTTTTGTTTTTG
1 TTGGTATTTTTGTTTTTG
*
103394 TTGGTTTTTGTTG-TTTTG
1 TTGGTATTT-TTGTTTTTG
103412 TTG
1 TTG
103415 TCGATTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.03, C:0.00, G:0.26, T:0.72
Consensus pattern (18 bp):
TTGGTATTTTTGTTTTTG
Found at i:107855 original size:23 final size:23
Alignment explanation
Indices: 107788--107855 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
107778 TTGTTTATTA
*
107788 TTCGTGAACATGTTCAATTATATG
1 TTCGTGAACATGTTCGATTA-ATG
** * *
107812 TTTATGAACATGTTTGTTTAATG
1 TTCGTGAACATGTTCGATTAATG
107835 TTCGTGAACATGTTCGATTAA
1 TTCGTGAACATGTTCGATTAA
107856 GTTAAATGAA
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 20 0.57
24 15 0.43
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.44
Consensus pattern (23 bp):
TTCGTGAACATGTTCGATTAATG
Found at i:109375 original size:24 final size:25
Alignment explanation
Indices: 109331--109385 Score: 85
Period size: 24 Copynumber: 2.2 Consensus size: 25
109321 TATATATATA
*
109331 AATATTTACAAAATATTAAATAAAT
1 AATATTTACAAAATATCAAATAAAT
*
109356 AATATTTA-TAAATATCAAATAAAT
1 AATATTTACAAAATATCAAATAAAT
109380 AATATT
1 AATATT
109386 AAAAACTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 20 0.71
25 8 0.29
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (25 bp):
AATATTTACAAAATATCAAATAAAT
Found at i:127170 original size:39 final size:39
Alignment explanation
Indices: 127107--127189 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 39
127097 GATTGAATTG
127107 AGCAAAGTTTGTACACCAAATCACTAATGTAAAGGTAAA
1 AGCAAAGTTTGTACACCAAATCACTAATGTAAAGGTAAA
* * * * *
127146 AGCAAAGTTTGTACATCAAGTCACTATTGTGATGGTAAA
1 AGCAAAGTTTGTACACCAAATCACTAATGTAAAGGTAAA
127185 AGCAA
1 AGCAA
127190 GCTTGTGGGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.25
Consensus pattern (39 bp):
AGCAAAGTTTGTACACCAAATCACTAATGTAAAGGTAAA
Found at i:128606 original size:3 final size:3
Alignment explanation
Indices: 128598--128623 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
128588 ATGAAGATAA
128598 CAG CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CA
128624 ATGACAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.31, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:130082 original size:2 final size:2
Alignment explanation
Indices: 130075--130103 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
130065 CCCTATTAGG
130075 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 A
130104 ATGTCAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:139723 original size:18 final size:18
Alignment explanation
Indices: 139661--139727 Score: 64
Period size: 18 Copynumber: 3.6 Consensus size: 18
139651 TTCTCTCTCT
*
139661 CCTCTCTCTCTCCCTTTC
1 CCTCTCTCTCTCCTTTTC
* *
139679 CTTCTC-CTTCTCCCTTTCCC
1 CCTCTCTC-TCT-CCTTT-TC
139699 TCCTCTCTCTCTCCTTTTC
1 -CCTCTCTCTCTCCTTTTC
139718 CCTCTCTCTC
1 CCTCTCTCTC
139728 CTCTCCTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
17 1 0.03
18 18 0.46
19 5 0.13
20 6 0.15
21 8 0.21
22 1 0.03
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (18 bp):
CCTCTCTCTCTCCTTTTC
Found at i:139734 original size:21 final size:21
Alignment explanation
Indices: 139653--139745 Score: 82
Period size: 21 Copynumber: 4.3 Consensus size: 21
139643 ACTGCTGCTT
*
139653 CTCTCTCTCCTCT-CTCTCTCC
1 CTCTCTCTCCTCTCCT-TTTCC
* *
139674 CTTTCCTTCTCCTTCTCCCTTTCC
1 CTCT-C-TCTCC-TCTCCTTTTCC
139698 CTC-CTCTCTCTCTCCTTTTCC
1 CTCTCTCTC-CTCTCCTTTTCC
* *
139719 CTCTCTCTCCTCTCCTTATCT
1 CTCTCTCTCCTCTCCTTTTCC
139740 CTCTCT
1 CTCTCT
139746 TTCTCCTTAT
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
21 36 0.61
22 8 0.14
23 5 0.08
24 9 0.15
25 1 0.02
ACGTcount: A:0.01, C:0.52, G:0.00, T:0.47
Consensus pattern (21 bp):
CTCTCTCTCCTCTCCTTTTCC
Found at i:139744 original size:39 final size:39
Alignment explanation
Indices: 139659--139768 Score: 118
Period size: 39 Copynumber: 2.8 Consensus size: 39
139649 GCTTCTCTCT
* *
139659 CTCCTCTCTCTCTCCCTTTCCTTCTC-CTTCTCCCTTTCC
1 CTCCTCTCTCTCTCCTTTTCCTTCTCTCTCCTCCCTTT-C
*
139698 CTCCTCTCTCTCTCCTTTTCCCTCTCTCTCCTCTCCTTAT-
1 CTCCTCTCTCTCTCCTTTTCCTTCTCTCTCCTC-CCTT-TC
* * *
139738 CT-CTCTCTTTCTCCTTATCCTTATCTCTCCT
1 CTCCTCTCTCTCTCCTTTTCCTTCTCTCTCCT
139769 TTCTCTTTCC
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
39 49 0.80
40 7 0.11
41 4 0.07
42 1 0.02
ACGTcount: A:0.03, C:0.49, G:0.00, T:0.48
Consensus pattern (39 bp):
CTCCTCTCTCTCTCCTTTTCCTTCTCTCTCCTCCCTTTC
Found at i:139752 original size:18 final size:19
Alignment explanation
Indices: 139701--139756 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 19
139691 CCTTTCCCTC
*
139701 CTCTCT-CTCTCCTTTTCCCT
1 CTCTCTCCTCTCCTTAT--CT
139721 CTCTCTCCTCTCCTTATCT
1 CTCTCTCCTCTCCTTATCT
*
139740 CTCTCT-TTCTCCTTATC
1 CTCTCTCCTCTCCTTATC
139757 CTTATCTCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 10 0.30
19 8 0.24
20 6 0.18
21 9 0.27
ACGTcount: A:0.04, C:0.46, G:0.00, T:0.50
Consensus pattern (19 bp):
CTCTCTCCTCTCCTTATCT
Found at i:139768 original size:66 final size:66
Alignment explanation
Indices: 139653--139792 Score: 149
Period size: 66 Copynumber: 2.1 Consensus size: 66
139643 ACTGCTGCTT
* * * * *
139653 CTCTCTCTCCTCTCTCTCTCCCTTTCCTTCTCCTTCTCCCTTTCCCTCCTCTCTCTCTCCTTTTC
1 CTCTCTCTCCTCTCTCTATCCCTCTCCTTCTCCTTATCCCTTTCCCTCCTCTCTCTCTCCCTATC
139718 C
66 C
* * * * *
139719 CTCTCTCTCCTCTC-CTTATCTCTCTCTTTCTCCTTAT-CCTTATCTCTCCTTTCTCTTTCCCTA
1 CTCTCTCTCCTCTCTC-TATCCCTCTCCTTCTCCTTATCCCTT-TCCCTCCTCTCTCTCTCCCTA
139782 TCC
64 TCC
*
139785 CTTTCTCT
1 CTCTCTCT
139793 ATCTTTTTCC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
65 5 0.08
66 56 0.92
ACGTcount: A:0.03, C:0.48, G:0.00, T:0.49
Consensus pattern (66 bp):
CTCTCTCTCCTCTCTCTATCCCTCTCCTTCTCCTTATCCCTTTCCCTCCTCTCTCTCTCCCTATC
C
Found at i:139864 original size:6 final size:6
Alignment explanation
Indices: 139855--139879 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
139845 CTATCTCTCC
139855 CCTTTT CCTTTT CCTTTT CCTTTT C
1 CCTTTT CCTTTT CCTTTT CCTTTT C
139880 TCTATCGCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (6 bp):
CCTTTT
Found at i:147284 original size:24 final size:22
Alignment explanation
Indices: 147252--147295 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
147242 TTGGTTTCTT
*
147252 ATTTTATTTTAAAGGTTTAATTTG
1 ATTTGATTTTAAA--TTTAATTTG
147276 ATTTGATTTTAAATTTAATT
1 ATTTGATTTTAAATTTAATT
147296 CATCATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
24 12 0.63
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (22 bp):
ATTTGATTTTAAATTTAATTTG
Found at i:149875 original size:31 final size:31
Alignment explanation
Indices: 149834--149998 Score: 94
Period size: 31 Copynumber: 5.4 Consensus size: 31
149824 AAAAAAACTT
* *
149834 AGGTACCAAATTAGGAAAAAATATCAAGTTC
1 AGGTATCAAATTAGAAAAAAATATCAAGTTC
* *** *
149865 AGGTATCAAATT-GGATCCAA-A-CAAGTTT
1 AGGTATCAAATTAGAAAAAAATATCAAGTTC
149893 AGGTATCAAATTTA-AAAAATATATATCAAGTTC
1 AGGTATCAAA-TTAGAAAAA-A-ATATCAAGTTC
** *
149926 AAATATCAAATTGAGTCAAAAAAA-A--AAGTTT
1 AGGTATCAAATT-AG--AAAAAAATATCAAGTTC
* *
149957 AAGTACCAAA-TAGAAAAAAAGTATCAAGTTC
1 AGGTATCAAATTAGAAAAAAA-TATCAAGTTC
*
149988 AGGTAACAAAT
1 AGGTATCAAAT
149999 ATTATATTAA
Statistics
Matches: 101, Mismatches: 18, Indels: 29
0.68 0.12 0.20
Matches are distributed among these distances:
27 7 0.07
28 16 0.16
29 7 0.07
30 7 0.07
31 38 0.38
32 3 0.03
33 16 0.16
34 1 0.01
35 1 0.01
36 5 0.05
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.25
Consensus pattern (31 bp):
AGGTATCAAATTAGAAAAAAATATCAAGTTC
Found at i:161404 original size:23 final size:23
Alignment explanation
Indices: 161372--161444 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
161362 CGTTAGCGCA
*
161372 CTTACTGTTCAGCACTGTGTGTG
1 CTTACGGTTCAGCACTGTGTGTG
161395 CTTACGGTTCAGCACTGTGTGTG
1 CTTACGGTTCAGCACTGTGTGTG
* * * *
161418 TTTACTGATTC-GCACTATATGTG
1 CTTAC-GGTTCAGCACTGTGTGTG
161441 CTTA
1 CTTA
161445 TTTATTTGCA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 39 0.91
24 4 0.09
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (23 bp):
CTTACGGTTCAGCACTGTGTGTG
Found at i:161455 original size:23 final size:23
Alignment explanation
Indices: 161383--161493 Score: 125
Period size: 23 Copynumber: 4.8 Consensus size: 23
161373 TTACTGTTCA
* *
161383 GCACTGTGTGTGCTTAC-GGTTCA
1 GCACTGTGTGTGCTTACTGATT-T
* *
161406 GCACTGTGTGTGTTTACTGATTC
1 GCACTGTGTGTGCTTACTGATTT
* * * *
161429 GCACTATATGTGCTTATTTATTT
1 GCACTGTGTGTGCTTACTGATTT
*
161452 GCACTGTGTGTGCCTACTGATTT
1 GCACTGTGTGTGCTTACTGATTT
161475 GCACTGTGTGTGCTTACTG
1 GCACTGTGTGTGCTTACTG
161494 TTTCCCCAGC
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
23 69 0.96
24 3 0.04
ACGTcount: A:0.14, C:0.19, G:0.25, T:0.41
Consensus pattern (23 bp):
GCACTGTGTGTGCTTACTGATTT
Found at i:169566 original size:20 final size:20
Alignment explanation
Indices: 169543--169580 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
169533 TTTTAATTCA
* *
169543 TTTAAATTAATTTAAAATTT
1 TTTAAATCAAATTAAAATTT
169563 TTTAAATCAAATTAAAAT
1 TTTAAATCAAATTAAAAT
169581 AATAAAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAAATCAAATTAAAATTT
Found at i:171008 original size:282 final size:282
Alignment explanation
Indices: 170379--171345 Score: 1516
Period size: 282 Copynumber: 3.4 Consensus size: 282
170369 GATAAGTTGT
* *
170379 AAGGCTTGTTTCTCAAAACATTCGCAGTGGCCGTCTAAGACCTTTCGCCTTTCGCCGGGCTTGAG
1 AAGGCTTGTTTCTCAAAACATTCGCAGTGGCCGCCTAAGAGCTTTCGCCTTTCGCCGGGCTTGAG
* * * **
170444 AGCTTGTGCTGCTTCATTCCTTCCTTGGATGTCTGAGACCTTTCATGA-CT-TCTATACGATTGT
66 AGCTTGTGCTGCTTCATTCCTTCCTTGGATGTCTGAGACCTTTTATGATTTGTATATATAATTGT
* * * *
170507 T-GTTTTCATTATTTGTGCTTGAAAATCCAGTTACTTTCTCAGAAATCTGGTTTTATATTTTTTT
131 TATTTTTTATTATTTGTGCTTGAAAATTCAGTTACTTTCTCAG-AATCTGGTTGTATA-TTTTTT
*
170571 CCTTTTTTAACAGTTCCATTGATAAACGATATTCTTAAAATTCAGTCAAAGTGAAATGTATTTCT
194 CCTTGTTTAACAGTTCCATTGATAAACGATATTCTTAAAATTCAGTCAAAG-GAAA--TATTTCT
* *
170636 TGTGTATAGGTTTATGATGATAATCCA
256 TATGTATGGGTTTATGATGATAATCCA
170663 AAGGCTTGTTTCTCAAAACATTCGCAGTGGCCGCCTAAGAGCTTTCGCCTTTCGCCGGGCTTGAG
1 AAGGCTTGTTTCTCAAAACATTCGCAGTGGCCGCCTAAGAGCTTTCGCCTTTCGCCGGGCTTGAG
170728 AGCTTGTGCTGCTTCATTCCTTCCTTGGATGTCTGAGACCTTTTATGATTTGTATATATAATTGT
66 AGCTTGTGCTGCTTCATTCCTTCCTTGGATGTCTGAGACCTTTTATGATTTGTATATATAATTGT
*
170793 TATTTTTTATTATTTGTGCTTGAAAATTCAATTACTTTCTCAGAAGTCTGGTTGTATATTTTTTC
131 TATTTTTTATTATTTGTGCTTGAAAATTCAGTTACTTTCTCAGAA-TCTGGTTGTATATTTTTTC
* * *
170858 CTTGTTTACCAGTTCAATTGATAAACGATATTCTTAAAATTCAGTCAAAGG-AA-ATTTCTTCTG
195 CTTGTTTAACAGTTCCATTGATAAACGATATTCTTAAAATTCAGTCAAAGGAAATATTTCTTATG
170921 TATGGGTTTATGATGATAAGTCCA
260 TATGGGTTTATGATGATAA-TCCA
*
170945 AAGGCTTGTTTCTCAAAACATTCGCAGTGGCCGCCTAAGAGCATTCGCCTTTCGCCGGGCTTGAG
1 AAGGCTTGTTTCTCAAAACATTCGCAGTGGCCGCCTAAGAGCTTTCGCCTTTCGCCGGGCTTGAG
* *
171010 AGCTTGTGCTGCTTCATTCTTTCCTCGGATGTCTGAGACCTTTTATGATTTGTATATATAATTGT
66 AGCTTGTGCTGCTTCATTCCTTCCTTGGATGTCTGAGACCTTTTATGATTTGTATATATAATTGT
* *
171075 TATTTTTTATTTTTTGTGCTTGAAAATTCAGTTACTTTCTCAGATATCTGGTTGTATATGTTTTC
131 TATTTTTTATTATTTGTGCTTGAAAATTCAGTTACTTTCTCAGA-ATCTGGTTGTATATTTTTTC
* *
171140 CTTG-TTAATCAGTTCCATTGATAAAAGATATTCTTAAAATTCAGTCAAAGGGAAATATATTTTT
195 CTTGTTTAA-CAGTTCCATTGATAAACGATATTCTTAAAATTCAGTCAAA-GGAAATAT-TTCTT
*
171204 ATGAATGGGTTTATGATGATAATCCA
257 ATGTATGGGTTTATGATGATAATCCA
*
171230 AAGGCTTGTTTCTCAAAACATTCGCAGTGGCTGCCTAAGAGCTTTCGCCTTTCGCCGGGCTTGAG
1 AAGGCTTGTTTCTCAAAACATTCGCAGTGGCCGCCTAAGAGCTTTCGCCTTTCGCCGGGCTTGAG
* *
171295 AGCTTGTGCTGCTT-TTATCCTTCCTTGGATGTCTGAGACCTTTTATTATTT
66 AGCTTGTGCTGCTTCAT-TCCTTCCTTGGATGTCTGAGACCTTTTATGATTT
171346 CATTATAAAT
Statistics
Matches: 636, Mismatches: 35, Indels: 23
0.92 0.05 0.03
Matches are distributed among these distances:
281 30 0.05
282 233 0.37
283 3 0.00
284 115 0.18
285 116 0.18
286 91 0.14
287 48 0.08
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (282 bp):
AAGGCTTGTTTCTCAAAACATTCGCAGTGGCCGCCTAAGAGCTTTCGCCTTTCGCCGGGCTTGAG
AGCTTGTGCTGCTTCATTCCTTCCTTGGATGTCTGAGACCTTTTATGATTTGTATATATAATTGT
TATTTTTTATTATTTGTGCTTGAAAATTCAGTTACTTTCTCAGAATCTGGTTGTATATTTTTTCC
TTGTTTAACAGTTCCATTGATAAACGATATTCTTAAAATTCAGTCAAAGGAAATATTTCTTATGT
ATGGGTTTATGATGATAATCCA
Found at i:176695 original size:41 final size:41
Alignment explanation
Indices: 176638--176733 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
176628 GAATTTTATT
176638 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
* *
176679 TTAACAATAATTCTAGTCATCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
176720 TTAACAAGAATTCT
1 TTAACAAGAATTCT
176734 CTACGAACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.38, C:0.28, G:0.04, T:0.30
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
Found at i:176758 original size:17 final size:17
Alignment explanation
Indices: 176722--176760 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
176712 TCTCCACCTT
* *
176722 AACAAGAATTCTCTACG
1 AACAAGAACTCTCAACG
*
176739 AACAAGAACTCTCAATG
1 AACAAGAACTCTCAACG
176756 AACAA
1 AACAA
176761 ATTCTCCACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.23, G:0.10, T:0.18
Consensus pattern (17 bp):
AACAAGAACTCTCAACG
Found at i:180222 original size:18 final size:18
Alignment explanation
Indices: 180199--180238 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
180189 TTCATCTTGT
180199 CATACGAGGCTAAGGAAG
1 CATACGAGGCTAAGGAAG
180217 CATACGAGGCTAAGGAAG
1 CATACGAGGCTAAGGAAG
180235 CATA
1 CATA
180239 AACTTCATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.30, T:0.12
Consensus pattern (18 bp):
CATACGAGGCTAAGGAAG
Found at i:196934 original size:37 final size:36
Alignment explanation
Indices: 196888--196957 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
196878 TACTTTAATA
*
196888 TTAAATTAATA-AAATACTATTAAAATAAGTATTAAAT
1 TTAAATTAATATAAATA-TATTAAAAGAA-TATTAAAT
* *
196925 TTAATTTAATATTAATATATTAAAAGAATATTA
1 TTAAATTAATATAAATATATTAAAAGAATATTA
196958 TTTTTGAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 5 0.17
37 20 0.69
38 4 0.14
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (36 bp):
TTAAATTAATATAAATATATTAAAAGAATATTAAAT
Found at i:197756 original size:18 final size:18
Alignment explanation
Indices: 197735--197778 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
197725 TTTTAAAAAA
*
197735 TATAAATTTTGAAATTTT
1 TATAAATTTTGAAAATTT
*
197753 TATAAATATTTTAAAATTT
1 TATAAAT-TTTGAAAATTT
197772 TA-AAATT
1 TATAAATT
197779 ATTTTGCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 11 0.48
19 11 0.48
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TATAAATTTTGAAAATTT
Found at i:197781 original size:19 final size:20
Alignment explanation
Indices: 197740--197784 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
197730 AAAAATATAA
*
197740 ATTTTGAAATTTTTATAAAT
1 ATTTTGAAAATTTTATAAAT
197760 ATTTT-AAAATTTTA-AAATT
1 ATTTTGAAAATTTTATAAA-T
197779 ATTTTG
1 ATTTTG
197785 CATTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 3 0.14
19 14 0.64
20 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (20 bp):
ATTTTGAAAATTTTATAAAT
Found at i:197810 original size:19 final size:20
Alignment explanation
Indices: 197773--197810 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
197763 TTAAAATTTT
* *
197773 AAAATTATTTTGCATTTTAA
1 AAAATGATTTTGCAATTTAA
197793 AAAATGATTTTG-AATTTA
1 AAAATGATTTTGCAATTTA
197811 TTTTTTTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (20 bp):
AAAATGATTTTGCAATTTAA
Found at i:201082 original size:16 final size:16
Alignment explanation
Indices: 201061--201117 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 16
201051 AGCAAAATGC
201061 TAATCAACATGCATGT
1 TAATCAACATGCATGT
201077 TAATCAAACA--CATGT
1 TAATC-AACATGCATGT
201092 AGCTAATCAACATGCATGT
1 ---TAATCAACATGCATGT
201111 TAATCAA
1 TAATCAA
201118 ACACATGTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
15 5 0.14
16 12 0.34
17 8 0.23
18 5 0.14
19 5 0.14
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (16 bp):
TAATCAACATGCATGT
Found at i:201102 original size:34 final size:34
Alignment explanation
Indices: 201059--201129 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
201049 TCAGCAAAAT
201059 GCTAATCAACATGCATGTTAATCAAACACATGTA
1 GCTAATCAACATGCATGTTAATCAAACACATGTA
201093 GCTAATCAACATGCATGTTAATCAAACACATGTA
1 GCTAATCAACATGCATGTTAATCAAACACATGTA
201127 GCT
1 GCT
201130 CAAAAATAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (34 bp):
GCTAATCAACATGCATGTTAATCAAACACATGTA
Found at i:201109 original size:19 final size:18
Alignment explanation
Indices: 201058--201110 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 18
201048 TTCAGCAAAA
201058 TGCTAATCAACATGCATG
1 TGCTAATCAACATGCATG
201076 T--TAATCAAACA--CATG
1 TGCTAATC-AACATGCATG
201091 TAGCTAATCAACATGCATG
1 T-GCTAATCAACATGCATG
201110 T
1 T
201111 TAATCAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
15 5 0.17
16 5 0.17
17 8 0.28
18 6 0.21
19 5 0.17
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (18 bp):
TGCTAATCAACATGCATG
Found at i:201123 original size:19 final size:19
Alignment explanation
Indices: 201067--201124 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 19
201057 ATGCTAATCA
201067 ACATGCATGTTAATCAAAC
1 ACATGCATGTTAATCAAAC
* *
201086 ACATGTA-GCTAATC--A-
1 ACATGCATGTTAATCAAAC
201101 ACATGCATGTTAATCAAAC
1 ACATGCATGTTAATCAAAC
201120 ACATG
1 ACATG
201125 TAGCTCAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
15 6 0.19
16 7 0.23
18 7 0.23
19 11 0.35
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (19 bp):
ACATGCATGTTAATCAAAC
Found at i:201124 original size:15 final size:15
Alignment explanation
Indices: 201072--201125 Score: 56
Period size: 15 Copynumber: 3.3 Consensus size: 15
201062 AATCAACATG
201072 CATGTTAATCAAACA
1 CATGTTAATCAAACA
201087 CATGTAGCTAATC-AACA
1 CATGT---TAATCAAACA
201104 TGCATGTTAATCAAACA
1 --CATGTTAATCAAACA
201121 CATGT
1 CATGT
201126 AGCTCAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
15 10 0.30
16 5 0.15
17 8 0.24
18 5 0.15
19 5 0.15
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (15 bp):
CATGTTAATCAAACA
Found at i:204228 original size:24 final size:24
Alignment explanation
Indices: 204185--204231 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
204175 TTAAACTTTA
*
204185 TTTATTTGTTTCAATTAAACTCTG
1 TTTATTTGTTTCAATCAAACTCTG
* *
204209 TTTATTTGTTTGAGTCAAACTCT
1 TTTATTTGTTTCAATCAAACTCT
204232 TGTTAGTCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.13, G:0.11, T:0.53
Consensus pattern (24 bp):
TTTATTTGTTTCAATCAAACTCTG
Found at i:208912 original size:22 final size:22
Alignment explanation
Indices: 208887--208932 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
208877 CAAATTTATG
208887 GAAAT-GTTAGAATGAAAGTTTA
1 GAAATAGTTA-AATGAAAGTTTA
*
208909 GAAATAGTTAAATGAATGTTTA
1 GAAATAGTTAAATGAAAGTTTA
208931 GA
1 GA
208933 CATGCTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.33
Consensus pattern (22 bp):
GAAATAGTTAAATGAAAGTTTA
Found at i:211448 original size:135 final size:134
Alignment explanation
Indices: 211207--211453 Score: 361
Period size: 135 Copynumber: 1.8 Consensus size: 134
211197 TCCTTAGCTG
* * *
211207 TTTCTACATCTCTAGTGGCCTACTCGGATCTCCAGTAAGAGATCTCGATAGGTTTTGTTTATTTA
1 TTTCTACATCTCTAGTGGCCTACTCAGATCTCCAGTAAGAGATCTCAATAGGTTTTGTTAATTTA
* *
211272 ATCTTTAGTTTAGTAGTTTGTTAGGGTAACCAGTTGTTTGGTTGTGGCATAGCAAGCTGCCATTA
66 ATCTTTAGTTCAATAGTTTGTTAGGGTAACCAGTTGTTTGGTTGTGGCATAGCAAGCTGCCATTA
211337 GTTA
131 GTTA
* ** *
211341 TTTCTACATCT-TTGATGGCCTACTCAGATCTCTGGTAGGAGATCTCAAGTAGGTTTTGTTAATT
1 TTTCTACATCTCTAG-TGGCCTACTCAGATCTCCAGTAAGAGATCTCAA-TAGGTTTTGTTAATT
* **
211405 TAGTCTTTAGTTCAATAGTTTGTTAGGGTGGCCAGTTGTTTGGTTGTGG
64 TAATCTTTAGTTCAATAGTTTGTTAGGGTAACCAGTTGTTTGGTTGTGG
211454 AACAATTGGT
Statistics
Matches: 99, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
133 2 0.02
134 39 0.39
135 58 0.59
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (134 bp):
TTTCTACATCTCTAGTGGCCTACTCAGATCTCCAGTAAGAGATCTCAATAGGTTTTGTTAATTTA
ATCTTTAGTTCAATAGTTTGTTAGGGTAACCAGTTGTTTGGTTGTGGCATAGCAAGCTGCCATTA
GTTA
Found at i:224243 original size:16 final size:16
Alignment explanation
Indices: 224222--224270 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
224212 GACTTCAACA
224222 AATATTTTTAAAAATT
1 AATATTTTTAAAAATT
*
224238 AATATTTTCTCAAAAAAT
1 AATATTTT-T-AAAAATT
224256 AAT-TATTTTAAAAAT
1 AATAT-TTTTAAAAAT
224271 CACCTCTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 13 0.46
17 3 0.11
18 12 0.43
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (16 bp):
AATATTTTTAAAAATT
Found at i:224669 original size:28 final size:30
Alignment explanation
Indices: 224603--224671 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 30
224593 AATTTTTATA
224603 ATTTATTATAATTATTAAAAAAATTTAAAAT
1 ATTTATTATAATTATT-AAAAAATTTAAAAT
* *
224634 -TTTATTATAATTATT-AATATTTTAAAAT
1 ATTTATTATAATTATTAAAAAATTTAAAAT
224662 ATTT-TTATAA
1 ATTTATTATAA
224672 CCATTTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 17 0.49
29 3 0.09
30 15 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
ATTTATTATAATTATTAAAAAATTTAAAAT
Found at i:229974 original size:25 final size:25
Alignment explanation
Indices: 229925--229974 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
229915 ATTTAAAAAA
* *
229925 ATTAAATTTAAAATTAATTATAAAT
1 ATTAAATTGAAAATTAATTACAAAT
229950 ATTAAATTGAATAATTAATT-CAAAT
1 ATTAAATTGAA-AATTAATTACAAAT
229975 TAAACAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
ATTAAATTGAAAATTAATTACAAAT
Found at i:242157 original size:6 final size:6
Alignment explanation
Indices: 242135--242177 Score: 68
Period size: 6 Copynumber: 7.0 Consensus size: 6
242125 ACATATAATG
*
242135 AAATAA AATAGAA AAATAA AAATAA AAATAA AAATAA AAATAA
1 AAATAA AA-ATAA AAATAA AAATAA AAATAA AAATAA AAATAA
242178 TTGGGTTGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:243344 original size:21 final size:21
Alignment explanation
Indices: 243318--243368 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
243308 ATAGATGCCT
*
243318 CAGTTTTCTTTTGAAAATCTA
1 CAGTTTGCTTTTGAAAATCTA
243339 CAGTTTGCTTTTGAAAATCTA
1 CAGTTTGCTTTTGAAAATCTA
* *
243360 TAGATTGCT
1 CAGTTTGCT
243369 GCTGAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (21 bp):
CAGTTTGCTTTTGAAAATCTA
Found at i:243374 original size:21 final size:21
Alignment explanation
Indices: 243329--243375 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
243319 AGTTTTCTTT
* **
243329 TGAAAATCTACAGTTTGCTTT
1 TGAAAATCTACAGATTGCTGC
*
243350 TGAAAATCTATAGATTGCTGC
1 TGAAAATCTACAGATTGCTGC
243371 TGAAA
1 TGAAA
243376 TTTAAGAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (21 bp):
TGAAAATCTACAGATTGCTGC
Found at i:248459 original size:22 final size:23
Alignment explanation
Indices: 248409--248459 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
248399 TGGGGAAAAT
* *
248409 AGTAAGCACACACAATGTAATCC
1 AGTAGGCACACACAATGCAATCC
248432 AGTAGGCACACACAATGCAAT-C
1 AGTAGGCACACACAATGCAATCC
248454 AGTAGG
1 AGTAGG
248460 TGTACATAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.16
Consensus pattern (23 bp):
AGTAGGCACACACAATGCAATCC
Found at i:248502 original size:23 final size:23
Alignment explanation
Indices: 248476--248529 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
248466 TAGCGCAAAT
*
248476 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACAAAGTGCGAAA
*
248499 CAGTATGCACACAAAGTGCGAAA
1 CAGTAAGCACACAAAGTGCGAAA
248522 CAGTAAGC
1 CAGTAAGC
248530 GTGCTAGCGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (23 bp):
CAGTAAGCACACAAAGTGCGAAA
Done.