Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012054.1 Kokia drynarioides strain JFW-HI SEQ_127052, 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: 37829
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:631 original size:19 final size:19
Alignment explanation
Indices: 607--643 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
597 GCGCGTACGG
607 CCCTACGCAT-GCCGGACGA
1 CCCTACGC-TCGCCGGACGA
626 CCCTACGCTCGCCGGACG
1 CCCTACGCTCGCCGGACG
644 GCGACCAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.16, C:0.46, G:0.27, T:0.11
Consensus pattern (19 bp):
CCCTACGCTCGCCGGACGA
Found at i:1256 original size:30 final size:30
Alignment explanation
Indices: 1222--1607 Score: 175
Period size: 29 Copynumber: 13.1 Consensus size: 30
1212 AAAATCCTGT
* *
1222 TTTTAACCCCGAAACTTCTAAAAATTACTA
1 TTTTAACCCCGAAACTTCTAAAAATCACCA
* *
1252 TTTTACCCCCG-AACTTCCAAAAAATCA-CA
1 TTTTAACCCCGAAACTT-CTAAAAATCACCA
** * *
1281 TTTCTAACATCGAAAATT-TCGAAAATCACCA
1 TTT-TAACCCCGAAACTTCT-AAAAATCACCA
* * *
1312 TTTT-ACCCCCAAATTTCCAAAAATC-CCA
1 TTTTAACCCCGAAACTTCTAAAAATCACCA
*
1340 TTTTAACCCC-AAACCATCTAAAAATC-CCAA
1 TTTTAACCCCGAAA-CTTCTAAAAATCACC-A
* *
1370 TTTTAACCCCAAAACTTCCAAAAATC-CCA
1 TTTTAACCCCGAAACTTCTAAAAATCACCA
* ** *
1399 TTTTTGA-CCTTAAACCTTCTAAAAATTACCA
1 -TTTTAACCCCGAAA-CTTCTAAAAATCACCA
* *
1430 TTTT-ACCCCTAAA-TTCCCAAAAATC-CCA
1 TTTTAACCCCGAAACTT-CTAAAAATCACCA
* *** * * *
1458 TTTTTGACATTGAACCTTCTTAAAATTACCA
1 -TTTTAACCCCGAAACTTCTAAAAATCACCA
* *
1489 TTTTACCCCCG-AA-TTCCCAAAAATC-CCAA
1 TTTTAACCCCGAAACTT-CTAAAAATCACC-A
* * *
1518 TTTTAACCTCG-AA-TGTCCAAAAATC-CTA
1 TTTTAACCCCGAAACT-TCTAAAAATCACCA
* * *
1546 TTTTTGACCCCGAACCTTCT-AAAATTACCA
1 -TTTTAACCCCGAAACTTCTAAAAATCACCA
* *
1576 TTTT-ACCCCTAAACTTCCAAAAATC-CCA
1 TTTTAACCCCGAAACTTCTAAAAATCACCA
1604 TTTT
1 TTTT
1608 TGATTTCGAA
Statistics
Matches: 270, Mismatches: 59, Indels: 56
0.70 0.15 0.15
Matches are distributed among these distances:
28 38 0.14
29 110 0.41
30 101 0.37
31 21 0.08
ACGTcount: A:0.37, C:0.30, G:0.03, T:0.31
Consensus pattern (30 bp):
TTTTAACCCCGAAACTTCTAAAAATCACCA
Found at i:1333 original size:28 final size:28
Alignment explanation
Indices: 1208--1607 Score: 149
Period size: 30 Copynumber: 13.6 Consensus size: 28
1198 CCTTGGATTG
** *
1208 TCCAAAAATCCTGTTTTTAACCCCGAAACT
1 TCCAAAAATCC-CATTTTAACCCC-AAATT
* * * * * *
1238 TCTAAAAATTACTATTTTACCCCCGAACT
1 TCCAAAAA-TCCCATTTTAACCCCAAATT
* **
1267 TCCAAAAAATCACATTTCTAACATCGAAAATT
1 TCC-AAAAATCCCATTT-TAAC--CCCAAATT
* *
1299 T-CGAAAATCACCATTTTACCCCCAAATT
1 TCCAAAAATC-CCATTTTAACCCCAAATT
**
1327 TCCAAAAATCCCATTTTAACCCCAAACCA
1 TCCAAAAATCCCATTTTAACCCCAAA-TT
* *
1356 TCTAAAAATCCCAATTTTAACCCCAAAACT
1 TCCAAAAATCCC-ATTTTAACCCC-AAATT
* ** *
1386 TCCAAAAATCCCATTTTTGACCTTAAACCT
1 TCCAAAAATCCCA-TTTTAACCCCAAA-TT
* *
1416 TCTAAAAATTACCATTTT-ACCCCTAAATT
1 TCCAAAAA-TCCCATTTTAACCCC-AAATT
* * *** **
1445 CCCAAAAATCCCATTTTTGACATTGAACCT
1 TCCAAAAATCCCA-TTTTAAC-CCCAAATT
* * * * *
1475 TCTTAAAATTACCATTTTACCCCCGAATT
1 TC-CAAAAATCCCATTTTAACCCCAAATT
* * * *
1504 CCCAAAAATCCCAATTTTAACCTCGAATG
1 TCCAAAAATCCC-ATTTTAACCCCAAATT
* * **
1533 TCCAAAAATCCTATTTTTGACCCCGAACCT
1 TCCAAAAATCCCA-TTTTAACCCC-AAATT
* * * *
1563 TCTAAAATTACCATTTT-ACCCCTAAACT
1 TCCAAAAATCCCATTTTAACCCC-AAATT
1591 TCCAAAAATCCCATTTT
1 TCCAAAAATCCCATTTT
1608 TGATTTCGAA
Statistics
Matches: 270, Mismatches: 79, Indels: 44
0.69 0.20 0.11
Matches are distributed among these distances:
28 57 0.21
29 85 0.31
30 100 0.37
31 23 0.09
32 5 0.02
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.31
Consensus pattern (28 bp):
TCCAAAAATCCCATTTTAACCCCAAATT
Found at i:1389 original size:59 final size:56
Alignment explanation
Indices: 1302--1525 Score: 187
Period size: 59 Copynumber: 3.8 Consensus size: 56
1292 GAAAATTTCG
*
1302 AAAATCACCATTTTACCCCCAAATTTCCAAAAATCCCATTTTAACCCCAAACCATCTA
1 AAAATC-CCATTTTA-CCCCAAAATTCCAAAAATCCCATTTTAACCCCAAACCATCTA
* ** *
1360 AAAATCCCAATTTTAACCCCAAAACTTCCAAAAATCCCATTTTTGACCTTAAACCTTCTA
1 AAAATCCC-ATTTT-ACCCCAAAA-TTCCAAAAATCCCA-TTTTAACCCCAAACCATCTA
* * * **** *
1420 AAAATTACCATTTTACCCCTAAATTCCCAAAAATCCCATTTTTGACATTGAACCTTCTTA
1 AAAA-TCCCATTTTACCCCAAAATT-CCAAAAATCCCA-TTTTAACCCCAAACCATC-TA
* * **
1480 AAATTACCATTTTACCCCCGAATTCCCAAAAATCCCAATTTTAACC
1 AAAATCCCATTTTACCCCAAAATT-CCAAAAATCCC-ATTTTAACC
1526 TCGAATGTCC
Statistics
Matches: 144, Mismatches: 14, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
57 2 0.01
58 20 0.14
59 88 0.61
60 31 0.22
61 3 0.02
ACGTcount: A:0.38, C:0.31, G:0.02, T:0.30
Consensus pattern (56 bp):
AAAATCCCATTTTACCCCAAAATTCCAAAAATCCCATTTTAACCCCAAACCATCTA
Found at i:1497 original size:118 final size:118
Alignment explanation
Indices: 1302--1526 Score: 267
Period size: 118 Copynumber: 1.9 Consensus size: 118
1292 GAAAATTTCG
* * *
1302 AAAATCACCATTTTACCCCCAAATTTCCAAAAATCCCATTTTAACCCCAAACCATCTAAAAATCC
1 AAAATCACCATTTTACCCCCAAATTCCCAAAAATCCCATTTTAACACCAAACCATCTAAAAATAC
* *
1367 CAATTTTAACCCCAAAACTT-CCAAAAATCCCATTTTTGACCTTAAACCTTCTA
66 CAATTTTAACCCCAAAA-TTCCCAAAAATCCCAATTTTAACCTTAAACCTTCTA
* * * *** * *
1420 AAAATTACCATTTTACCCCTAAATTCCCAAAAATCCCATTTTTGACATTGAACCTTCTTAAAATT
1 AAAATCACCATTTTACCCCCAAATTCCCAAAAATCCCA-TTTTAACACCAAACCATC-TAAAAAT
**
1485 ACC-ATTTT-ACCCCCGAATTCCCAAAAATCCCAATTTTAACCT
64 ACCAATTTTAACCCCAAAATTCCCAAAAATCCCAATTTTAACCT
1527 CGAATGTCCA
Statistics
Matches: 89, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
117 2 0.02
118 62 0.70
119 17 0.19
120 8 0.09
ACGTcount: A:0.37, C:0.31, G:0.02, T:0.30
Consensus pattern (118 bp):
AAAATCACCATTTTACCCCCAAATTCCCAAAAATCCCATTTTAACACCAAACCATCTAAAAATAC
CAATTTTAACCCCAAAATTCCCAAAAATCCCAATTTTAACCTTAAACCTTCTA
Found at i:1617 original size:87 final size:88
Alignment explanation
Indices: 1446--1608 Score: 240
Period size: 87 Copynumber: 1.9 Consensus size: 88
1436 CCCTAAATTC
** *
1446 CCAAAAATCCCATTTTTGACATTGAACCTTCTTAAAATTACCATTTTACCCCCGAATTCCCAAAA
1 CCAAAAATCCCATTTTTGACACCGAACCTTCTTAAAATTACCATTTTACCCCCAAATTCCCAAAA
1511 ATCCCAATTTTAACCTCGAATGT
66 ATCCCAATTTTAACCTCGAATGT
* * *
1534 CCAAAAATCCTATTTTTGACCCCGAACCTTC-TAAAATTACCATTTTACCCCTAAACTT-CCAAA
1 CCAAAAATCCCATTTTTGACACCGAACCTTCTTAAAATTACCATTTTACCCCCAAA-TTCCCAAA
*
1597 AATCCCATTTTT
65 AATCCCAATTTT
1609 GATTTCGAAC
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
87 38 0.57
88 29 0.43
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (88 bp):
CCAAAAATCCCATTTTTGACACCGAACCTTCTTAAAATTACCATTTTACCCCCAAATTCCCAAAA
ATCCCAATTTTAACCTCGAATGT
Found at i:6536 original size:199 final size:199
Alignment explanation
Indices: 6215--7022 Score: 1325
Period size: 199 Copynumber: 4.1 Consensus size: 199
6205 TAGTAAGATG
*
6215 CTGAGAAGAAGACCAAAACGAGGCTC-AAGACGAGCAAATCTTCAAAACCCAGCTTCCTGATGAG
1 CTGAGAAGAAGACCCAAACGAGGCTCGAA-ACGAGCAAATCTTCAAAACCCAGCTTCCTGATGAG
* * *
6279 ACATTGAGAAGCAGGTGGAAGAAATAAATGGTTAGCTTCCAAATGAGGTACTGAGAAGTGAACCG
65 ACACTGAGAAGCAGGTGGAAGAAATAAATGGTTAGCTTCCAGATGAGGTACTGAGAAGTGAACCA
6344 AATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGTGATGGGATCATCTTCCTGATG
130 AATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGTGATGGGATCATCTTCCTGATG
*
6409 AGGCA
195 AGACA
* * * *
6414 CTGAGAAGAAGACCCAAATGAGGCTCGAAACGAGCAAGTCTTTAAAACCCAGCTTTCTGATGAGA
1 CTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAATCTTCAAAACCCAGCTTCCTGATGAGA
* *
6479 CACTGAGAAGCAGGTGGAAGAAATAAATAGTTAGATTCCAGATGAGGTACTGAGAAGTGAACCAA
66 CACTGAGAAGCAGGTGGAAGAAATAAATGGTTAGCTTCCAGATGAGGTACTGAGAAGTGAACCAA
* *
6544 ATTCGTCTTCTTGATGAGATACAGAGAAGCGGATTGAAATAGTGATGGGATCATCTTCCTGATGA
131 ATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGTGATGGGATCATCTTCCTGATGA
6609 -AGCA
196 GA-CA
*
6613 TTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAATCTTCAAAACCCAGCTTCCTGATGAGA
1 CTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAATCTTCAAAACCCAGCTTCCTGATGAGA
*
6678 CATTGAGAAGCAGGTGGAAGAAATAAATGGTTAGCTTCCAGATGAGGTACTGAGAAGTGAACCAA
66 CACTGAGAAGCAGGTGGAAGAAATAAATGGTTAGCTTCCAGATGAGGTACTGAGAAGTGAACCAA
*
6743 ATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGTGATAGGATCATCTTCCTGATGA
131 ATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGTGATGGGATCATCTTCCTGATGA
6808 GACA
196 GACA
*
6812 CTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAATCTTCAAAACTCAGCTTCCTGATGAGA
1 CTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAATCTTCAAAACCCAGCTTCCTGATGAGA
* *
6877 CACTGAGAAGCAGGTGGAAGCAATAAATGGTTAGCTTCCAGATAAGGTACTGAGAAGTGAACCAA
66 CACTGAGAAGCAGGTGGAAGAAATAAATGGTTAGCTTCCAGATGAGGTACTGAGAAGTGAACCAA
* * ** * *
6942 ATTCGCCTTCTTGATGAGATACAGAGAAGCGGATTGAAACAAACGACGCGG-TCATTTTCCTGAT
131 ATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAAC-AGTGATG-GGATCATCTTCCTGAT
*
7006 GAGATA
194 GAGACA
7012 CTGAGAAGAAG
1 CTGAGAAGAAG
7023 GCGAAGCCAA
Statistics
Matches: 567, Mismatches: 37, Indels: 9
0.92 0.06 0.01
Matches are distributed among these distances:
199 531 0.94
200 34 0.06
201 2 0.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (199 bp):
CTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAATCTTCAAAACCCAGCTTCCTGATGAGA
CACTGAGAAGCAGGTGGAAGAAATAAATGGTTAGCTTCCAGATGAGGTACTGAGAAGTGAACCAA
ATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGTGATGGGATCATCTTCCTGATGA
GACA
Found at i:7370 original size:17 final size:17
Alignment explanation
Indices: 7333--7425 Score: 114
Period size: 17 Copynumber: 5.4 Consensus size: 17
7323 CCAAACTCCC
* *
7333 TTTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
*
7351 TTTAAACTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
7368 TTTAAATTTATTTTGAA
1 TTTAAATTTATTTTAAA
* *
7385 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
7402 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
7420 TTTAAA
1 TTTAAA
7426 ATTACTATAA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
17 45 0.70
18 19 0.30
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:7373 original size:6 final size:6
Alignment explanation
Indices: 7348--7425 Score: 65
Period size: 6 Copynumber: 13.5 Consensus size: 6
7338 ATTTGTTTAA
* * * *
7348 AAATTT AAACTT -ATTTT AAATTT AAATTT -ATTTT GAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* *
7394 -AATTT AAGTTT AAATTT -ATTTT CAAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT -AAATTT AAA
7426 ATTACTATAA
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
5 16 0.29
6 36 0.64
7 4 0.07
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:7409 original size:23 final size:23
Alignment explanation
Indices: 7362--7411 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
7352 TTAAACTTAT
* *
7362 TTTAAATTTAAATTTATTTTGAA
1 TTTAAATTTAAATTTAGTTTAAA
7385 TTTAAATTT-AATTTAAGTTTAAA
1 TTTAAATTTAAATTT-AGTTTAAA
7408 TTTA
1 TTTA
7412 TTTTCAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTAAATTTAAATTTAGTTTAAA
Found at i:9509 original size:17 final size:17
Alignment explanation
Indices: 9472--9564 Score: 114
Period size: 17 Copynumber: 5.4 Consensus size: 17
9462 CCAAACTCCC
* *
9472 TTTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
*
9490 TTTAAACTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
9507 TTTAAATTTATTTTGAA
1 TTTAAATTTATTTTAAA
* *
9524 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
9541 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
9559 TTTAAA
1 TTTAAA
9565 ATTACTATAA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
17 45 0.70
18 19 0.30
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:9512 original size:6 final size:6
Alignment explanation
Indices: 9487--9564 Score: 65
Period size: 6 Copynumber: 13.5 Consensus size: 6
9477 ATTTGTTTAA
* * * *
9487 AAATTT AAACTT -ATTTT AAATTT AAATTT -ATTTT GAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* *
9533 -AATTT AAGTTT AAATTT -ATTTT CAAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT -AAATTT AAA
9565 ATTACTATAA
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
5 16 0.29
6 36 0.64
7 4 0.07
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:9548 original size:23 final size:23
Alignment explanation
Indices: 9501--9550 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
9491 TTAAACTTAT
* *
9501 TTTAAATTTAAATTTATTTTGAA
1 TTTAAATTTAAATTTAGTTTAAA
9524 TTTAAATTT-AATTTAAGTTTAAA
1 TTTAAATTTAAATTT-AGTTTAAA
9547 TTTA
1 TTTA
9551 TTTTCAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTAAATTTAAATTTAGTTTAAA
Found at i:11546 original size:60 final size:58
Alignment explanation
Indices: 11479--11798 Score: 197
Period size: 59 Copynumber: 5.4 Consensus size: 58
11469 CCCTGGATTG
* * *
11479 TCCAAAAATCCTGTTTTTAACCCCGAAACTTTTGAAAATTACTATTTTACCC-CTGAACT
1 TCCAAAAATCC-ATTTTTAACCCCGAAACTTTTGAAAATCACCATTTTACCCTC-GAACT
** * *
11538 TCCAAAAAATCACATTTCAAACCTCGAAACTTTTGAAAATCACCATTTTACCCTCGAATT
1 TCC-AAAAATC-CATTTTTAACCCCGAAACTTTTGAAAATCACCATTTTACCCTCGAACT
* * * * *
11598 TCCAAAAATCCCA-TTTTAACCCCGAACCATCTAAAAATC-CCAATTTTAACCC-CAAAACT
1 TCCAAAAAT-CCATTTTTAACCCCGAAACTTTTGAAAATCACC-ATTTT-ACCCTC-GAACT
* ** * ** * * *
11657 TCCAAAAATCCCATTTTTGACCTTGAACCTTCTAAAAAAT-ACCATTTTGCCC-CCAAAT
1 TCCAAAAAT-CCATTTTTAACCCCGAAACTT-TTGAAAATCACCATTTTACCCTCGAACT
* ** * * *
11715 TCCCAAAAATCTCATTTTTGA-CCTTAAACCTTCTAAAAATTACCATTTTACCCTCGAA-T
1 T-CCAAAAATC-CATTTTTAACCCCGAAA-CTTTTGAAAATCACCATTTTACCCTCGAACT
*
11774 TCCCAAAAATCCAAATTTTAACCCC
1 T-CCAAAAATCC-ATTTTTAACCCC
11799 AAATGTCCAA
Statistics
Matches: 209, Mismatches: 35, Indels: 33
0.75 0.13 0.12
Matches are distributed among these distances:
57 2 0.01
58 41 0.20
59 84 0.40
60 72 0.34
61 10 0.05
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (58 bp):
TCCAAAAATCCATTTTTAACCCCGAAACTTTTGAAAATCACCATTTTACCCTCGAACT
Found at i:11593 original size:30 final size:29
Alignment explanation
Indices: 11493--11595 Score: 75
Period size: 30 Copynumber: 3.4 Consensus size: 29
11483 AAAATCCTGT
* *
11493 TTTTAACCCCGAAACTTTTGAAAATTACTA
1 TTTT-ACCCCGAAACTTTTGAAAATCACCA
***
11523 TTTTACCCCTG-AACTTCCAAAAAATCA-CA
1 TTTTACCCC-GAAACTT-TTGAAAATCACCA
* *
11552 TTTCAAACCTCGAAACTTTTGAAAATCACCA
1 TTT--TACCCCGAAACTTTTGAAAATCACCA
11583 TTTTACCCTCGAA
1 TTTTACCC-CGAA
11596 TTTCCAAAAA
Statistics
Matches: 54, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
29 17 0.31
30 23 0.43
31 14 0.26
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.32
Consensus pattern (29 bp):
TTTTACCCCGAAACTTTTGAAAATCACCA
Found at i:11619 original size:29 final size:27
Alignment explanation
Indices: 11522--11878 Score: 178
Period size: 29 Copynumber: 12.2 Consensus size: 27
11512 GAAAATTACT
*
11522 ATTTTACCCCTGAACTTCCAAAAAATCAC
1 ATTTTACCCC-GAACTTCC-AAAAATCCC
* * ***
11551 ATTTCAAACCTCGAAACTTTTGAAAATCACC
1 ATTT--TACCCCG-AACTTCCAAAAATC-CC
*
11582 ATTTTACCCTCGAATTTCCAAAAATCCC
1 ATTTTACCC-CGAACTTCCAAAAATCCC
* *
11610 ATTTTAACCCCGAACCATCTAAAAATCCC
1 ATTTT-ACCCCGAA-CTTCCAAAAATCCC
*
11639 AATTTTAACCCCAAAACTTCCAAAAATCCC
1 -ATTTT-ACCCC-GAACTTCCAAAAATCCC
** * *
11669 ATTTTTGACCTTGAACCTTCTAAAAAATACC
1 A-TTTT-ACCCCGAA-CTTC-CAAAAATCCC
* * * *
11700 ATTTTGCCCCCAAATTCCCAAAAATCTC
1 ATTTTACCCCGAACTT-CCAAAAATCCC
*** * *
11728 ATTTTTGACCTTAAACCTTCTAAAAATTACC
1 A-TTTT-ACCCCGAA-CTTCCAAAAA-TCCC
*
11759 ATTTTACCCTCGAA-TTCCCAAAAATCCAA
1 ATTTTACCC-CGAACTT-CCAAAAATCC-C
*
11788 ATTTTAACCCC-AAATGTCCAAAAATCCC
1 ATTTT-ACCCCGAACT-TCCAAAAATCCC
* * *
11816 ATTTTTGACCCCGAACCTTCTAAAATTACC
1 A-TTTT-ACCCCGAA-CTTCCAAAAATCCC
11846 ATTTTACCCCCGAACTTCCAAAAATCCC
1 ATTTTA-CCCCGAACTTCCAAAAATCCC
11874 ATTTT
1 ATTTT
11879 TTATTTCGAA
Statistics
Matches: 246, Mismatches: 55, Indels: 55
0.69 0.15 0.15
Matches are distributed among these distances:
28 45 0.18
29 90 0.37
30 80 0.33
31 31 0.13
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.30
Consensus pattern (27 bp):
ATTTTACCCCGAACTTCCAAAAATCCC
Found at i:11646 original size:30 final size:30
Alignment explanation
Indices: 11601--11879 Score: 141
Period size: 30 Copynumber: 9.5 Consensus size: 30
11591 TCGAATTTCC
*
11601 AAAAATCCC-ATTTTAACCCCGAACCATCT
1 AAAAATCCCAATTTTAACCCCGAACCTTCT
* * *
11630 AAAAATCCCAATTTTAACCCCAAAACTTCC
1 AAAAATCCCAATTTTAACCCCGAACCTTCT
* * **
11660 AAAAATCCCATTTTTGACCTTGAACCTTCT
1 AAAAATCCCAATTTTAACCCCGAACCTTCT
* * * * *
11690 AAAAAATACC-ATTTT-GCCCCCAA-ATTCCC
1 -AAAAATCCCAATTTTAACCCCGAACCTT-CT
* * * ***
11719 AAAAATCTCATTTTTGACCTTAAACCTTCT
1 AAAAATCCCAATTTTAACCCCGAACCTTCT
* *
11749 AAAAATTACC-ATTTT-ACCCTCGAA--TTCCC
1 AAAAA-TCCCAATTTTAACCC-CGAACCTT-CT
* * *
11778 AAAAATCCAAATTTTAACCCC-AA-ATGTCC
1 AAAAATCCCAATTTTAACCCCGAACCT-TCT
* *
11807 AAAAATCCCATTTTTGACCCCGAACCTTCT
1 AAAAATCCCAATTTTAACCCCGAACCTTCT
* * * *
11837 AAAATTACC-ATTTTACCCCCGAA-CTTCC
1 AAAAATCCCAATTTTAACCCCGAACCTTCT
*
11865 AAAAATCCCATTTTT
1 AAAAATCCCAATTTT
11880 TATTTCGAAC
Statistics
Matches: 183, Mismatches: 51, Indels: 32
0.69 0.19 0.12
Matches are distributed among these distances:
28 26 0.14
29 69 0.38
30 75 0.41
31 13 0.07
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.30
Consensus pattern (30 bp):
AAAAATCCCAATTTTAACCCCGAACCTTCT
Found at i:11656 original size:88 final size:85
Alignment explanation
Indices: 11564--11878 Score: 287
Period size: 88 Copynumber: 3.6 Consensus size: 85
11554 TCAAACCTCG
* * *
11564 AAACTTTTGAAAATCACCATTTTACCCTCGAATTTCCAAAAATCCCATTTTAACCCCGAACCATC
1 AAACTTCTAAAAATCACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTAACCCC-AA--ATC
* * *
11629 TAAAAATCCCAATTTTAACCCCA
63 CAAAAATCCCATTTTTGACCCCA
* * * * **
11652 AAACTTCCAAAAATC-CCATTTTTGA-CCTTGAACCTTCTAAAAAATACCATTTTGCCCCCAAAT
1 AAACTTCTAAAAATCACCA-TTTT-ACCCTCGAA-CTTC-CAAAAATCCCATTTTAACCCCAAA-
* **
11715 TCCCAAAAATCTCATTTTTGACCTTA
61 T-CCAAAAATCCCATTTTTGACCCCA
* * *
11741 AACCTTCTAAAAATTACCATTTTACCCTCGAA-TTCCCAAAAATCCAAATTTTAACCCCAAATGT
1 AAACTTCTAAAAATCACCATTTTACCCTCGAACTT-CCAAAAATCC-CATTTTAACCCCAAA--T
*
11805 CCAAAAATCCCATTTTTGACCCCG
62 CCAAAAATCCCATTTTTGACCCCA
* * *
11829 AACCTTCT-AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTT
1 AAACTTCTAAAAATCACCATTTTACCCTCGAACTTCCAAAAATCCCATTTT
11879 TTATTTCGAA
Statistics
Matches: 184, Mismatches: 31, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
86 5 0.03
87 45 0.24
88 67 0.36
89 47 0.26
90 20 0.11
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.30
Consensus pattern (85 bp):
AAACTTCTAAAAATCACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTAACCCCAAATCCAA
AAATCCCATTTTTGACCCCA
Found at i:11702 original size:31 final size:31
Alignment explanation
Indices: 11660--11763 Score: 99
Period size: 31 Copynumber: 3.5 Consensus size: 31
11650 CAAAACTTCC
* *
11660 AAAAATCCCATTTTTGACCTTGAACCTTCTA
1 AAAAATACCATTTTTGACCTTAAACCTTCTA
* ** **
11691 AAAAATACCA-TTTTGCCCCCAAA--TTCCC
1 AAAAATACCATTTTTGACCTTAAACCTTCTA
11719 AAAAAT-CTCATTTTTGACCTTAAACCTTCTA
1 AAAAATAC-CATTTTTGACCTTAAACCTTCTA
*
11750 AAAATTACCATTTT
1 AAAAATACCATTTT
11764 ACCCTCGAAT
Statistics
Matches: 55, Mismatches: 13, Indels: 10
0.71 0.17 0.13
Matches are distributed among these distances:
27 1 0.02
28 11 0.20
29 10 0.18
30 9 0.16
31 23 0.42
32 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.35
Consensus pattern (31 bp):
AAAAATACCATTTTTGACCTTAAACCTTCTA
Found at i:11721 original size:59 final size:59
Alignment explanation
Indices: 11573--11785 Score: 234
Period size: 59 Copynumber: 3.6 Consensus size: 59
11563 GAAACTTTTG
* * * * ** *
11573 AAAATCACCATTTTACCCTCGAATTTCCAAAAATCCCA-TTTTAACCCCGAACCATCT-A
1 AAAAT-ACCATTTTACCCCCAAATTCCCAAAAATCCCATTTTTGACCTTGAACCTTCTAA
* *
11631 AAAATCCCAATTTTAACCCCAAAACTT-CCAAAAATCCCATTTTTGACCTTGAACCTTCTAA
1 AAAATACC-ATTTT-ACCCCCAAA-TTCCCAAAAATCCCATTTTTGACCTTGAACCTTCTAA
* * *
11692 AAAATACCATTTTGCCCCCAAATTCCCAAAAATCTCATTTTTGACCTTAAACCTTCTAA
1 AAAATACCATTTTACCCCCAAATTCCCAAAAATCCCATTTTTGACCTTGAACCTTCTAA
* * *
11751 AAATTACCATTTTACCCTCGAATTCCCAAAAATCC
1 AAAATACCATTTTACCCCCAAATTCCCAAAAATCC
11786 AAATTTTAAC
Statistics
Matches: 131, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
57 2 0.02
58 12 0.09
59 87 0.66
60 22 0.17
61 8 0.06
ACGTcount: A:0.37, C:0.31, G:0.03, T:0.30
Consensus pattern (59 bp):
AAAATACCATTTTACCCCCAAATTCCCAAAAATCCCATTTTTGACCTTGAACCTTCTAA
Found at i:11850 original size:58 final size:58
Alignment explanation
Indices: 11788--11907 Score: 152
Period size: 58 Copynumber: 2.1 Consensus size: 58
11778 AAAAATCCAA
* *
11788 ATTTTAACCCC-AAATGTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAATTACC
1 ATTTTAACCCCGAAAT-TCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAACTACC
* * * ***
11846 ATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTATTTCGAACCTTCCAAAACTACC
1 ATTTTAACCCCGAAATTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAACTACC
11904 ATTT
1 ATTT
11908 GGCCCCTGTG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 50 0.94
59 3 0.06
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.33
Consensus pattern (58 bp):
ATTTTAACCCCGAAATTCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAACTACC
Found at i:16547 original size:40 final size:40
Alignment explanation
Indices: 16502--16579 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
16492 ATTTATCAAA
* * * *
16502 TATTTATATATATTAAATTTTTTGGTTTATCTTGTTTTTT
1 TATTTATATATATTAAAATTTATGCTTTATCTTATTTTTT
* *
16542 TATTTATATTTTTTAAAATTTATGCTTTATCTTATTTT
1 TATTTATATATATTAAAATTTATGCTTTATCTTATTTT
16580 ATACTAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.24, C:0.04, G:0.05, T:0.67
Consensus pattern (40 bp):
TATTTATATATATTAAAATTTATGCTTTATCTTATTTTTT
Found at i:16709 original size:12 final size:12
Alignment explanation
Indices: 16689--16719 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
16679 AAGCCTTGTA
16689 ATATATATTTAT
1 ATATATATTTAT
*
16701 ATTTATATTTAT
1 ATATATATTTAT
16713 ATATATA
1 ATATATA
16720 AAATAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATATATATTTAT
Found at i:19375 original size:26 final size:26
Alignment explanation
Indices: 19338--19388 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
19328 AATCATCCTC
*
19338 TTTTTCTAACAAATATTAAAATAAATA
1 TTTTTCTAACAAA-ATGAAAATAAATA
19365 TTTTT-TAACAAAATGAAAATAAAT
1 TTTTTCTAACAAAATGAAAATAAAT
19389 TTTCAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.48
26 7 0.30
27 5 0.22
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (26 bp):
TTTTTCTAACAAAATGAAAATAAATA
Found at i:19538 original size:18 final size:17
Alignment explanation
Indices: 19506--19540 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
19496 ATCCAAACAT
19506 TAACAATAAAATAGTAA
1 TAACAATAAAATAGTAA
*
19523 TAACATATATAATAGTAA
1 TAACA-ATAAAATAGTAA
19541 AATAATAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.29
Consensus pattern (17 bp):
TAACAATAAAATAGTAA
Found at i:32221 original size:41 final size:41
Alignment explanation
Indices: 32169--32250 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
32159 ACATTTGAAA
32169 ATTTTGATTATTCTTTT-AAATTTTATGTTGATGATAAAAAT
1 ATTTTGATTATT-TTTTAAAATTTTATGTTGATGATAAAAAT
*
32210 ATTTTGATTATTTTTTAAAATTTTATGTTGATGTTAAAAAT
1 ATTTTGATTATTTTTTAAAATTTTATGTTGATGATAAAAAT
32251 GTAGAGTTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 4 0.10
41 35 0.90
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.55
Consensus pattern (41 bp):
ATTTTGATTATTTTTTAAAATTTTATGTTGATGATAAAAAT
Done.