Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011259.1 Kokia drynarioides strain JFW-HI SEQ_126238, 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: 24687
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:462 original size:13 final size:13
Alignment explanation
Indices: 444--472 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
434 TGATCTCTAG
444 ACCCGAACCTCAA
1 ACCCGAACCTCAA
457 ACCCGAACCTCAA
1 ACCCGAACCTCAA
470 ACC
1 ACC
473 GTAAACCCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.48, G:0.07, T:0.07
Consensus pattern (13 bp):
ACCCGAACCTCAA
Found at i:1679 original size:29 final size:29
Alignment explanation
Indices: 1647--1740 Score: 93
Period size: 29 Copynumber: 3.2 Consensus size: 29
1637 TTAAAAAAGA
*
1647 AATTTTTAGACATTCGAGGGTAAAAGGGT
1 AATTTTTAGACATTCGAGGGTAAAATGGT
* **
1676 AATTTTGAGAGTTTCGA-GGTCGAAAATGG-
1 AATTTTTAGACATTCGAGGGT--AAAATGGT
* * *
1705 AGTTTTTGGACATTCGGGGGTAAAATGGT
1 AATTTTTAGACATTCGAGGGTAAAATGGT
1734 AATTTTT
1 AATTTTT
1741 GAATGTTTTA
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
28 10 0.20
29 31 0.62
30 9 0.18
ACGTcount: A:0.30, C:0.06, G:0.29, T:0.35
Consensus pattern (29 bp):
AATTTTTAGACATTCGAGGGTAAAATGGT
Found at i:1742 original size:59 final size:59
Alignment explanation
Indices: 1647--2104 Score: 299
Period size: 58 Copynumber: 7.8 Consensus size: 59
1637 TTAAAAAAGA
* * * * *
1647 AATTTTTAGACATTCGAGGGT-AAAAGGGTAA-TTTT-GAGAGTTTCGAGGTCGAAAATGG
1 AATTTTTGGACATTCGGGGGTAAAAATGG-AATTTTTGGA-AGTTTTGAGGTCAAAAATGG
* * *
1705 AGTTTTTGGACATTCGGGGGT-AAAATGGTAATTTTT-GAATGTTTTAAGGTTAAAAATGG
1 AATTTTTGGACATTCGGGGGTAAAAATGG-AATTTTTGGAA-GTTTTGAGGTCAAAAATGG
* * * *
1764 AAAATTTT-GAGATTCGGGAGTAAAAATGGAATTTTTGGAAGTTTTGATGTCAAAAATGG
1 -AATTTTTGGACATTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGG
* *
1823 AATTTTTGGA-AGTTTGGGGGTAAAAATGGAATTTTTTGGAAGTTTTGGGGTCAAAAATGG
1 AATTTTTGGACA-TTCGGGGGTAAAAATGGAA-TTTTTGGAAGTTTTGAGGTCAAAAATGG
** * * *
1883 AATTTTTGGA-AGTTAC-TAGGTCAAAATGGAAATTTTGG-AGATTTGAGGGT-AAAAATGG
1 AATTTTTGGACA-TT-CGGGGGTAAAAATGGAATTTTTGGAAGTTTTGA-GGTCAAAAATGG
* **** * * *
1941 AAATTTTGGA-AGTTTTAAGGTCAAAATGGAATTTTTGGAAG-TTCGAGGGT-AAAAATAG
1 AATTTTTGGACA-TTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTGA-GGTCAAAAATGG
** * * *
1999 AATTTTTGGA-AGTTTTGGGGTCAAAATGCAATTTTTGGAAG-TTCGAGGGT--AAAATGG
1 AATTTTTGGACA-TTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTGA-GGTCAAAAATGG
* * * * *
2056 AATTTTTAGA-AGTTTTGGGGTTAAAAATGTAATTTTTGAAAG-TTTGAGG
1 AATTTTTGGACA--TTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTGAGG
2105 GTAAAATGGG
Statistics
Matches: 341, Mismatches: 46, Indels: 27
0.82 0.11 0.07
Matches are distributed among these distances:
57 18 0.05
58 171 0.50
59 85 0.25
60 67 0.20
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.35
Consensus pattern (59 bp):
AATTTTTGGACATTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGG
Found at i:1821 original size:30 final size:30
Alignment explanation
Indices: 1726--2104 Score: 333
Period size: 29 Copynumber: 12.9 Consensus size: 30
1716 ATTCGGGGGT
* *
1726 AAAATGGTAATTTTT-GAATGTTTTAAGGTTA
1 AAAATGG-AATTTTTGGAA-GTTTTGAGGTCA
* * * *
1757 AAAATGGAAAATTTT-G-AGATTCGGGAGT-A
1 AAAATGG-AATTTTTGGAAGTTTTGAG-GTCA
*
1786 AAAATGGAATTTTTGGAAGTTTTGATGTCA
1 AAAATGGAATTTTTGGAAGTTTTGAGGTCA
* *
1816 AAAATGGAATTTTTGGAAGTTTGGGGGT-A
1 AAAATGGAATTTTTGGAAGTTTTGAGGTCA
*
1845 AAAATGGAATTTTTTGGAAGTTTTGGGGTCA
1 AAAATGGAA-TTTTTGGAAGTTTTGAGGTCA
*
1876 AAAATGGAATTTTTGGAAGTTACT-AGGTC-
1 AAAATGGAATTTTTGGAAGTT-TTGAGGTCA
* *
1905 AAAATGGAAATTTTGG-AGATTTGAGGGT-A
1 AAAATGGAATTTTTGGAAGTTTTGA-GGTCA
* *
1934 AAAATGGAAATTTTGGAAGTTTTAAGGTC-
1 AAAATGGAATTTTTGGAAGTTTTGAGGTCA
*
1963 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
1 AAAATGGAATTTTTGGAAGTTTTGA-GGTCA
* *
1992 AAAATAGAATTTTTGGAAGTTTTGGGGTC-
1 AAAATGGAATTTTTGGAAGTTTTGAGGTCA
* *
2021 AAAATGCAATTTTTGGAAG-TTCGAGGGT--
1 AAAATGGAATTTTTGGAAGTTTTGA-GGTCA
* * *
2049 AAAATGGAATTTTTAGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTTGAGGTCA
* *
2079 AAAATGTAATTTTTGAAAG-TTTGAGG
1 AAAATGGAATTTTTGGAAGTTTTGAGG
2105 GTAAAATGGG
Statistics
Matches: 288, Mismatches: 40, Indels: 42
0.78 0.11 0.11
Matches are distributed among these distances:
27 1 0.00
28 36 0.12
29 133 0.46
30 93 0.32
31 25 0.09
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.36
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTTGAGGTCA
Found at i:3233 original size:3 final size:3
Alignment explanation
Indices: 3225--3277 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
3215 CTTTCGACCT
* * *
3225 TTA TTA TTA TTA ATA TATA TTA TTA TTA TTA -TA TTA TTA ATA ATA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3270 TTAA TTA T
1 TT-A TTA T
3278 AGTTTCCATT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:13498 original size:29 final size:28
Alignment explanation
Indices: 13465--13680 Score: 270
Period size: 29 Copynumber: 7.5 Consensus size: 28
13455 TTCGAGGTCG
* *
13465 AAAATGGAATTTTTAGAAGTTTGGGAGTA
1 AAAATGGAATTTTTGGAAGTTCGGG-GTA
13494 AAAATGGAATTTTTGGAAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAAG-TTCGGGGT-A
* * *
13524 AAAATGAAATTTTTGGAAGTTTGGGGGA
1 AAAATGGAATTTTTGGAAGTTCGGGGTA
*
13552 AAAATTGAATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTC-GGGGTA
* *
13581 AATATAGAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCG-GGGTA
*
13610 AATATGGAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCG-GGGTA
* *
13639 AATATGGAATTTTTGTAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTC-GGGGTA
13668 AAAATGGAATTTT
1 AAAATGGAATTTT
13681 CAAATAGTTT
Statistics
Matches: 168, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
28 21 0.12
29 122 0.73
30 25 0.15
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTCGGGGTA
Found at i:15451 original size:6 final size:6
Alignment explanation
Indices: 15435--15517 Score: 59
Period size: 6 Copynumber: 14.3 Consensus size: 6
15425 ATTTAAATAG
* *
15435 ATTTAAA ATTTAA ATTTATA A--TAA ATTTAA ATTTTA A-GTAA ATTTAA
1 ATTT-AA ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * * *
15482 ACTTAA A-ATAA ATTTAA TTTTAA A-ATAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT
15518 CCTGTTGGGC
Statistics
Matches: 59, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
4 2 0.03
5 13 0.22
6 38 0.64
7 6 0.10
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:15460 original size:17 final size:17
Alignment explanation
Indices: 15440--15517 Score: 111
Period size: 17 Copynumber: 4.6 Consensus size: 17
15430 AATAGATTTA
*
15440 AAATTTAAATTTATAAT
1 AAATTTAAATTTAAAAT
* *
15457 AAATTTAAATTTTAAGT
1 AAATTTAAATTTAAAAT
*
15474 AAATTTAAACTTAAAAT
1 AAATTTAAATTTAAAAT
*
15491 AAATTTAATTTTAAAAT
1 AAATTTAAATTTAAAAT
15508 AAATTTAAAT
1 AAATTTAAAT
15518 CCTGTTGGGC
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 52 1.00
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (17 bp):
AAATTTAAATTTAAAAT
Found at i:15462 original size:24 final size:23
Alignment explanation
Indices: 15425--15471 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
15415 TTGAGCTTTG
*
15425 ATTTAAATAGATTTAAAATTTAA
1 ATTTAAATAAATTTAAAATTTAA
*
15448 ATTTATAATAAATTTAAATTTTAA
1 ATTTA-AATAAATTTAAAATTTAA
15472 GTAAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTTAAATAAATTTAAAATTTAA
Found at i:16345 original size:14 final size:15
Alignment explanation
Indices: 16326--16354 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
16316 TTTTAAATAA
16326 ATTTAAATTT-TTTT
1 ATTTAAATTTATTTT
16340 ATTTAAATTTATTTT
1 ATTTAAATTTATTTT
16355 TCAATATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTAAATTTATTTT
Found at i:16662 original size:13 final size:11
Alignment explanation
Indices: 16643--16694 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
16633 TGGTATATAT
16643 TTAAATTATTA
1 TTAAATTATTA
16654 TGATAAATTA-TA
1 T--TAAATTATTA
*
16666 TTAAATTATTT
1 TTAAATTATTA
*
16677 TTAATTTATTA
1 TTAAATTATTA
16688 TTGAAAT
1 TT-AAAT
16695 GTTTATTCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
10 7 0.21
11 13 0.39
12 6 0.18
13 7 0.21
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (11 bp):
TTAAATTATTA
Found at i:18553 original size:3 final size:3
Alignment explanation
Indices: 18545--18573 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
18535 TATTAAAAAT
18545 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
18574 GCCCACTTGT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:19226 original size:16 final size:17
Alignment explanation
Indices: 19203--19241 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
19193 TTAAATAAAT
* *
19203 TATTAAAAATTATAAAA
1 TATTAAAAAATAAAAAA
19220 T-TTAAAAAATAAAAAA
1 TATTAAAAAATAAAAAA
19236 TATTAA
1 TATTAA
19242 TTTAATTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TATTAAAAAATAAAAAA
Found at i:20906 original size:96 final size:96
Alignment explanation
Indices: 20735--20912 Score: 236
Period size: 96 Copynumber: 1.9 Consensus size: 96
20725 AAGGATGTTC
* * ** *
20735 GATTATCTCGATTTGAGGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAGA
1 GATTATCTCAATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCGCAAATTTTCAGAATCGAAGA
*
20800 TAAGGAAATATTGCCTCGATTAAGGGTATTT
66 TAAAGAAATATTGCCTCGATTAAGGGTATTT
* *
20831 GATTATTTCAATTTGAAGAAAAATTGCACCTAATAAGTTAAGGTGCAAATTTTC-GAAACTCGAA
1 GATTATCTCAATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCGCAAATTTTCAG-AA-TCGAA
20895 -ATAAA-AGAATATTGCCTC
64 GATAAAGA-AATATTGCCTC
20913 TATTTTAAAG
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
95 2 0.03
96 64 0.90
97 5 0.07
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (96 bp):
GATTATCTCAATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCGCAAATTTTCAGAATCGAAGA
TAAAGAAATATTGCCTCGATTAAGGGTATTT
Found at i:21162 original size:29 final size:29
Alignment explanation
Indices: 21130--21190 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
21120 AAAATGAGAC
*
21130 TTTTTGGATACCCGAGGGCAAAATGGTAA
1 TTTTTGAATACCCGAGGGCAAAATGGTAA
* *
21159 -TTTTGAATTCTCGAGGGCAAAATGGTAA
1 TTTTTGAATACCCGAGGGCAAAATGGTAA
21187 TTTT
1 TTTT
21191 GGGAAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (29 bp):
TTTTTGAATACCCGAGGGCAAAATGGTAA
Found at i:21246 original size:58 final size:57
Alignment explanation
Indices: 21172--21331 Score: 160
Period size: 58 Copynumber: 2.7 Consensus size: 57
21162 TGAATTCTCG
*
21172 AGGGCAAAATGGTAATTTTGGGAAAATTTAGGGTTAAAAATGGA-TTTTTAGACATTCA
1 AGGGTAAAATGGTAATTTT--GAAAATTTAGGGTTAAAAATGGAGTTTTTAGACATTCA
* * * * ** * *
21230 AGGGTAAAAGGGTAATTTTGAGAGTTTCAAGGTCGAAAATGGAGTTTTTGGACATTCG
1 AGGGTAAAATGGTAATTTTGAAAATTT-AGGGTTAAAAATGGAGTTTTTAGACATTCA
* * *
21288 GGGGTAAAATGGTAATTTTTGAAAGTTTTAGGATTAAAAATGGA
1 AGGGTAAAATGGTAA-TTTTGAAA-ATTTAGGGTTAAAAATGGA
21332 AATTTTGGAG
Statistics
Matches: 81, Mismatches: 17, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
56 6 0.07
57 12 0.15
58 42 0.52
59 18 0.22
60 3 0.04
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.33
Consensus pattern (57 bp):
AGGGTAAAATGGTAATTTTGAAAATTTAGGGTTAAAAATGGAGTTTTTAGACATTCA
Found at i:21247 original size:29 final size:29
Alignment explanation
Indices: 21208--21307 Score: 82
Period size: 29 Copynumber: 3.5 Consensus size: 29
21198 TTTAGGGTTA
21208 AAAATGG--ATTTTTAGACATTCAAGGGT
1 AAAATGGTAATTTTTAGACATTCAAGGGT
* * **
21235 AAAAGGGTAATTTTGAGAGTTTCAA-GGT
1 AAAATGGTAATTTTTAGACATTCAAGGGT
* * **
21263 CGAAAATGG-AGTTTTTGGACATTCGGGGGT
1 --AAAATGGTAATTTTTAGACATTCAAGGGT
21293 AAAATGGTAATTTTT
1 AAAATGGTAATTTTT
21308 GAAAGTTTTA
Statistics
Matches: 54, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
27 6 0.11
28 10 0.19
29 29 0.54
30 9 0.17
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (29 bp):
AAAATGGTAATTTTTAGACATTCAAGGGT
Found at i:21338 original size:59 final size:58
Alignment explanation
Indices: 21198--21669 Score: 406
Period size: 59 Copynumber: 8.0 Consensus size: 58
21188 TTTGGGAAAA
* * * * *
21198 TTTAGGGTTAAAAATGG-ATTTTTAGACA-TTCAAGGGT-AAAAGGGTAA-TTTTGAGAGT
1 TTTA-GGTCAAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAATGG-AATTTTTGAAAGT
* * * *
21255 TTCAAGGTCGAAAATGGAGTTTTTGGACA-TTCGGGGGT-AAAATGGTAATTTTTGAAAGT
1 TT-TAGGTCAAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAATGG-AATTTTTGAAAGT
* * * * * *
21314 TTTAGGATTAAAAATGGAAATTTTGGAGGTTTGAGGGTAGAAATGGAATTTTTGGAAGT
1 TTTAGG-TCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGAAAGT
** ** *
21373 TTCGGGGTTGAAAATGGAATTTTTGGAAGTTCG-GAGGTAAAAATGGAATTTTTGGAAGT
1 TT-TAGGTCAAAAATGGAATTTTTGGAAGTTCGAG-GGTAAAAATGGAATTTTTGAAAGT
** *
21432 TTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAAT-GAATTTTTTAGAAGT
1 TT-TAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGA-AAGT
* * *
21491 TTTGAGGTCAAAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATGGAAATTTTGGAAGT
1 TTT-AGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGAAAGT
* * * * * *
21550 TTCAAGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGT
1 TT-TAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGAAAGT
* * * *
21609 TTCGAGGTCAAAAAT-GAGATTTTTGGAAGCTCGAGGGT-AAAATGTAATTTTCGAACAGT
1 TT-TAGGTCAAAAATGGA-ATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGAA-AGT
21668 TT
1 TT
21670 AGGGACCTCT
Statistics
Matches: 348, Mismatches: 52, Indels: 28
0.81 0.12 0.07
Matches are distributed among these distances:
57 12 0.03
58 53 0.15
59 267 0.77
60 16 0.05
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.34
Consensus pattern (58 bp):
TTTAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGAAAGT
Found at i:21361 original size:29 final size:29
Alignment explanation
Indices: 21265--21659 Score: 378
Period size: 29 Copynumber: 13.4 Consensus size: 29
21255 TTCAAGGTCG
* * *
21265 AAAATGGAGTTTTTGGACA-TTCGGGGGT-
1 AAAATGGAATTTTTGGA-AGTTTGAGGGTA
* * *
21293 AAAATGGTAATTTTTGAAAGTTTTAGGATTA
1 AAAATGG-AATTTTTGGAAGTTTGAGG-GTA
* *
21324 AAAATGGAAATTTTGGAGGTTTGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTA
* *
21353 GAAATGGAATTTTTGGAAGTTTCG-GGGTTG
1 AAAATGGAATTTTTGGAAGTTT-GAGGG-TA
*
21383 AAAATGGAATTTTTGGAAGTTCG-GAGGTA
1 AAAATGGAATTTTTGGAAGTTTGAG-GGTA
21412 AAAATGGAATTTTTGGAAGTTTCG-GGGTCA
1 AAAATGGAATTTTTGGAAGTTT-GAGGGT-A
*
21442 AAAATGGAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTA
*
21471 AAAAT-GAATTTTTTAGAAGTTTTGA-GGTCA
1 AAAATGGAA-TTTTTGGAAG-TTTGAGGGT-A
**
21501 AAAATGGAATTTTTGGAAGTTCAAGGGTA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTA
* * *
21530 AAAATGGAAATTTTGGAAGTTTCAAGGTTA
1 AAAATGGAATTTTTGGAAGTTT-GAGGGTA
* *
21560 AAAATGGGATTTTTGGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTA
21589 AAAATGGAATTTTTGGAAGTTTCGA-GGTCA
1 AAAATGGAATTTTTGGAAGTTT-GAGGGT-A
* *
21619 AAAAT-GAGATTTTTGGAAGCTCGAGGGT-
1 AAAATGGA-ATTTTTGGAAGTTTGAGGGTA
*
21647 AAAATGTAATTTT
1 AAAATGGAATTTT
21660 CGAACAGTTT
Statistics
Matches: 308, Mismatches: 38, Indels: 42
0.79 0.10 0.11
Matches are distributed among these distances:
28 21 0.07
29 139 0.45
30 138 0.45
31 10 0.03
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTGAGGGTA
Found at i:21397 original size:118 final size:117
Alignment explanation
Indices: 21169--21670 Score: 488
Period size: 118 Copynumber: 4.3 Consensus size: 117
21159 TTTTGAATTC
* * * * * **
21169 TCGAGGG-CAAAATGGTAATTTTGGGAAAATTTAGGGTTAAAAATGG-ATTTTTAGACA-TTCAA
1 TCGAGGGTAAAAATGG-AATTTT-TGAAAGTTTAAGGTTAAAAATGGAATTTTTGGA-AGTTTGA
* * * *
21231 GGGT-AAAAGGGTAA-TTTT-GAGAGTTTCAAGGTCGAAAATGGAGTTTTTGGACA-T
63 GGGTAAAAATGG-AATTTTTGGA-AGTTTCGAGGTCAAAAATGGAATTTTTGGA-AGT
* * * *
21285 TCGGGGGT-AAAATGGTAATTTTTGAAAGTTTTAGGATTAAAAATGGAAATTTTGGAGGTTTGAG
1 TCGAGGGTAAAAATGG-AATTTTTGAAAGTTTAAGG-TTAAAAATGGAATTTTTGGAAGTTTGAG
* * **
21349 GGTAGAAATGGAATTTTTGGAAGTTTCGGGGTTGAAAATGGAATTTTTGGAAGT
64 GGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGT
* ** * *
21403 TCG-GAGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGAG
1 TCGAG-GGTAAAAATGGAATTTTTGAAAGTTT-AAGGTTAAAAATGGAATTTTTGGAAGTTTGAG
* *
21467 GGTAAAAAT-GAATTTTTTAGAAGTTTTGAGGTCAAAAATGGAATTTTTGGAAGT
64 GGTAAAAATGGAA-TTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGT
* * * * *
21521 TCAAGGGTAAAAATGGAAATTTTGGAAGTTTCAAGGTTAAAAATGGGATTTTTGGAAGTTTGGGG
1 TCGAGGGTAAAAATGGAATTTTTGAAAGTTT-AAGGTTAAAAATGGAATTTTTGGAAGTTTGAGG
*
21586 GTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAAT-GAGATTTTTGGAAGC
65 GTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGA-ATTTTTGGAAGT
* *
21639 TCGAGGGT-AAAATGTAATTTTCGAACAGTTTA
1 TCGAGGGTAAAAATGGAATTTTTGAA-AGTTTA
21671 GGGACCTCTA
Statistics
Matches: 325, Mismatches: 45, Indels: 31
0.81 0.11 0.08
Matches are distributed among these distances:
115 9 0.03
116 30 0.09
117 37 0.11
118 234 0.72
119 15 0.05
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.33
Consensus pattern (117 bp):
TCGAGGGTAAAAATGGAATTTTTGAAAGTTTAAGGTTAAAAATGGAATTTTTGGAAGTTTGAGGG
TAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGT
Found at i:21472 original size:177 final size:176
Alignment explanation
Indices: 21252--21669 Score: 556
Period size: 177 Copynumber: 2.4 Consensus size: 176
21242 TAATTTTGAG
* * * *
21252 AGTTTCAAGGTCGAAAATGGAGTTTTTGGACA-TTCGGGGGTAAAATGGTAATTTTTGAAAGTTT
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAT-GTAATTTTTGAAAGTTT
* * ** * * **
21316 T-AGGATTAAAAATGGAAATTTTGGAGGTTTGAGGGTAGAAATGGAATTTTTGGAAGTTTCGGGG
64 TGAGG-TCAAAAATGGAAATTTTGGAAGTTCAAGGGTAAAAATGGAAATTTTGGAAGTTTCAAGG
*
21380 TTGAAAATGGAATTTTTGGAAGTTCGGAGGTAAAAATGGAATTTTTGGA
128 TTAAAAATGGAATTTTTGGAAGTTCGGAGGTAAAAATGGAATTTTTGGA
* *
21429 AGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATG-AATTTTTTAGAAGTTT
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGT-AAAATGTAATTTTTGA-AAGTTT
*
21493 TGAGGTCAAAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATGGAAATTTTGGAAGTTTCAAGGT
64 TGAGGTCAAAAATGGAAATTTTGGAAGTTCAAGGGTAAAAATGGAAATTTTGGAAGTTTCAAGGT
* * *
21558 TAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGA
129 TAAAAATGGAATTTTTGGAAGTTCGGAGGTAAAAATGGAATTTTTGGA
* *
21606 AGTTTCGAGGTCAAAAAT-GAGATTTTTGGAAGCTCGAGGGTAAAATGTAATTTTCGAACAGTTT
1 AGTTTCGAGGTCAAAAATGGA-ATTTTTGGAAGTTCGAGGGTAAAATGTAATTTTTGAA-AGTTT
21670 AGGGACCTCT
Statistics
Matches: 211, Mismatches: 23, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
176 18 0.09
177 185 0.88
178 8 0.04
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (176 bp):
AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGTAATTTTTGAAAGTTTTG
AGGTCAAAAATGGAAATTTTGGAAGTTCAAGGGTAAAAATGGAAATTTTGGAAGTTTCAAGGTTA
AAAATGGAATTTTTGGAAGTTCGGAGGTAAAAATGGAATTTTTGGA
Found at i:23474 original size:6 final size:6
Alignment explanation
Indices: 23463--23505 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
23453 TATAATAAGT
* *
23463 TTTAAA TTTAAA TATAAA TATAAA TTTAAA -TTAAA -TTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
23506 TAAAACAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 10 0.29
6 24 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:23480 original size:12 final size:12
Alignment explanation
Indices: 23465--23521 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
23455 TAATAAGTTT
23465 TAAATTTAAATA
1 TAAATTTAAATA
* *
23477 TAAATATAAATT
1 TAAATTTAAATA
23489 TAAA-TTAAAT-
1 TAAATTTAAATA
23499 TAAATTTTAAA-A
1 TAAA-TTTAAATA
*
23511 CAAATTTAAAT
1 TAAATTTAAAT
23522 TCAAAATCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 4 0.11
11 11 0.30
12 22 0.59
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (12 bp):
TAAATTTAAATA
Found at i:23486 original size:18 final size:16
Alignment explanation
Indices: 23464--23505 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 16
23454 ATAATAAGTT
23464 TTAAATTTAAATATAAA
1 TTAAATTTAAAT-TAAA
23481 TATAAATTTAAATTAAA
1 T-TAAATTTAAATTAAA
23498 TTAAATTT
1 TTAAATTT
23506 TAAAACAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.29
17 6 0.25
18 11 0.46
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAATTTAAATTAAA
Found at i:23521 original size:18 final size:17
Alignment explanation
Indices: 23463--23555 Score: 91
Period size: 17 Copynumber: 5.4 Consensus size: 17
23453 TATAATAAGT
23463 TTTAAATTTAAATATAAA
1 TTTAAATTTAAA-ATAAA
* *
23481 TATAAATTTAAATTAAA
1 TTTAAATTTAAAATAAA
*
23498 -TTAAATTTTAAAACAAA
1 TTTAAA-TTTAAAATAAA
* *
23515 TTTAAATTCAAAATCAA
1 TTTAAATTTAAAATAAA
23532 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
23549 TCTTAAA
1 T-TTAAA
23556 ATGGGTTTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
16 7 0.12
17 33 0.55
18 18 0.30
19 2 0.03
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Done.