Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2239
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: 53194
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:217 original size:13 final size:13
Alignment explanation
Indices: 199--224 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
189 TACACCAAGT
199 ATGTATCGATACA
1 ATGTATCGATACA
212 ATGTATCGATACA
1 ATGTATCGATACA
225 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:222 original size:32 final size:33
Alignment explanation
Indices: 181--244 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
171 TAGCCAAACT
* **
181 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
213 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
245 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2476 original size:21 final size:21
Alignment explanation
Indices: 2443--2487 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2433 TTGCAAGATG
*
2443 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
2465 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
2485 AAA
1 AAA
2488 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:4311 original size:15 final size:15
Alignment explanation
Indices: 4291--4321 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4281 TAAAAATGTC
*
4291 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
4306 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
4321 C
1 C
4322 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:6421 original size:13 final size:13
Alignment explanation
Indices: 6403--6438 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
6393 TTTTTCTTTA
*
6403 TATCGATACATTG
1 TATCGATACAATG
6416 TATCGATACAATG
1 TATCGATACAATG
6429 TATCGATACA
1 TATCGATACA
6439 GGGTGATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:6602 original size:20 final size:20
Alignment explanation
Indices: 6559--6604 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
6549 AAATCTTTTG
6559 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
6580 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
6600 CAAAA
1 CAAAA
6605 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:8928 original size:2 final size:2
Alignment explanation
Indices: 8921--8951 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
8911 AATTGTGCTT
8921 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8952 TTGTATGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11072 original size:20 final size:19
Alignment explanation
Indices: 11049--11121 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
11039 CACATCCAGA
*
11049 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
11069 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
11088 TGTATCGATACATGCACAAT
1 TGTATCGATACATGTTC-AT
11108 TGTATCGATACATG
1 TGTATCGATACATG
11122 AAACTGGAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 17 0.35
20 30 0.62
21 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:11193 original size:33 final size:33
Alignment explanation
Indices: 11151--11213 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
11141 TACCACTGTT
* *
11151 TGTATCGATACATGGCACATTGTATCGATATAA
1 TGTATCGATACATGACAAATTGTATCGATATAA
*
11184 TGTATCGATACATGATAAATTGTATCGATA
1 TGTATCGATACATGACAAATTGTATCGATA
11214 CATTGCTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (33 bp):
TGTATCGATACATGACAAATTGTATCGATATAA
Found at i:14447 original size:26 final size:26
Alignment explanation
Indices: 14411--14471 Score: 106
Period size: 26 Copynumber: 2.3 Consensus size: 26
14401 AAGGTTAAAT
14411 TTGATTAAGATAAAGTATGTGATGCA
1 TTGATTAAGATAAAGTATGTGATGCA
14437 TTGATTAAGATAAAGTATGTGATGCA
1 TTGATTAAGATAAAGTATGTGATGCA
14463 -TGTATTAAG
1 TTG-ATTAAG
14472 GGTAAGCATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 2 0.06
26 32 0.94
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (26 bp):
TTGATTAAGATAAAGTATGTGATGCA
Found at i:17427 original size:13 final size:13
Alignment explanation
Indices: 17409--17448 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
17399 ACAATGTTCT
*
17409 TTGTATTGATACA
1 TTGTATCGATACA
17422 TTGTATCGATACA
1 TTGTATCGATACA
*
17435 ATGTATCGATACA
1 TTGTATCGATACA
17448 T
1 T
17449 GGGTTACTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:21598 original size:20 final size:21
Alignment explanation
Indices: 21565--21603 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
21555 ATGTTACAGT
21565 TATTATTTTGCAAT-TTTAAC
1 TATTATTTTGCAATATTTAAC
21585 TATT-TTTTGTCAATATTTA
1 TATTATTTTG-CAATATTTA
21604 TCGAAGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.28, C:0.08, G:0.05, T:0.59
Consensus pattern (21 bp):
TATTATTTTGCAATATTTAAC
Found at i:22601 original size:20 final size:20
Alignment explanation
Indices: 22576--22625 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
22566 TTTTACAATT
* *
22576 TGTATCGATAAATTAGTGCA
1 TGTATCGATAAATAAGTGAA
*
22596 TGTATCGATAGATAAGTGAA
1 TGTATCGATAAATAAGTGAA
22616 TGTATCGATA
1 TGTATCGATA
22626 CATGTCTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (20 bp):
TGTATCGATAAATAAGTGAA
Found at i:22701 original size:20 final size:20
Alignment explanation
Indices: 22676--22729 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
22666 GGTGAAAAAT
22676 TGTATCGATATATAAGTAAA
1 TGTATCGATATATAAGTAAA
* *** *
22696 TGTATCGATACATTCTTCAA
1 TGTATCGATATATAAGTAAA
22716 TGTATCGATATATA
1 TGTATCGATATATA
22730 TAGGTTATTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (20 bp):
TGTATCGATATATAAGTAAA
Found at i:24580 original size:271 final size:271
Alignment explanation
Indices: 24097--24622 Score: 684
Period size: 271 Copynumber: 1.9 Consensus size: 271
24087 GTTTTTTTTT
* * *
24097 TTTTACAAATTCTCACATTGTGGAGAAGTCGACCATTGTGGTCCCATGCACCATTTTCGTCACTT
1 TTTTACAAATTCTCACATTGTGGAGAAATCGACCATTATGGTCCCATGCACCATTTTCGTCACTC
* *
24162 TTCCAAATGCAAGTATTATTAATAGAGAAGTCGACCGTTATGGTCTCCTATGCCACTCCCATCCC
66 TTCCAAATGCAAGTATTATTAATAGAGAAGTCGACCATTATGGTCTCCTATGCCACTCCCATCAC
* * *
24227 TCTTTCATTTACACAAACTCTTAATAGAGAAGTCAACCATTGTAGTCTCATGCGCCACTTCTATC
131 TCTCTCATTTACACAAACTCTTAATAGAAAAGTCAACCATTGTAGTCTCATGCGACACTTCTATC
* * * * *
24292 ACTCTCCCTATATACAAATTCTTTCAATGGAGAATTCTACCATTGTAGTC-CTATGCGCCATTTC
196 ACTCTCCCTATATACAAATTCTTCCAATGAAAAAGTCGACCATTGTAGTCTC-ATGCGCCATTTC
24356 CGTTACTTTCTC
260 CGTTACTTTCTC
** *
24368 TTTTACAAATTCTCACATTGTGGAGAAATCGACTGTTATGGTCCCATGCACCA-TTTCTTTCACT
1 TTTTACAAATTCTCACATTGTGGAGAAATCGACCATTATGGTCCCATGCACCATTTTC-GTCACT
** * * * * * *
24432 CTTCTTAATGTAAGTATTATTAATAGAGAAGTCGACCATTGTGGTCTTCTATTCCATTCCCGTCA
65 CTTCCAAATGCAAGTATTATTAATAGAGAAGTCGACCATTATGGTCTCCTATGCCACTCCCATCA
* * * * * * *
24497 CTCTCTCATTTATGA-ATACTTTTAATAGAAAAGTCAATCGTTGTGGT-TCAATGCGACACTTTT
130 CTCTCTCATTTA-CACAAACTCTTAATAGAAAAGTCAACCATTGTAGTCTC-ATGCGACACTTCT
*
24560 ATCACTCT-CCTCATATACAAATTCTTCCAATGAAAAAGTCGACCATTGTGGTCTCATGCGCCA
193 ATCACTCTCCCT-ATATACAAATTCTTCCAATGAAAAAGTCGACCATTGTAGTCTCATGCGCCA
24623 CTCCCGTCAC
Statistics
Matches: 218, Mismatches: 32, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
270 9 0.04
271 207 0.95
272 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.35
Consensus pattern (271 bp):
TTTTACAAATTCTCACATTGTGGAGAAATCGACCATTATGGTCCCATGCACCATTTTCGTCACTC
TTCCAAATGCAAGTATTATTAATAGAGAAGTCGACCATTATGGTCTCCTATGCCACTCCCATCAC
TCTCTCATTTACACAAACTCTTAATAGAAAAGTCAACCATTGTAGTCTCATGCGACACTTCTATC
ACTCTCCCTATATACAAATTCTTCCAATGAAAAAGTCGACCATTGTAGTCTCATGCGCCATTTCC
GTTACTTTCTC
Found at i:24633 original size:68 final size:66
Alignment explanation
Indices: 24254--24773 Score: 180
Period size: 68 Copynumber: 7.7 Consensus size: 66
24244 CTCTTAATAG
* * **
24254 AGAAGTCAACCATTGTAGTCTCATGCGCCACTTCTATCACTCTCCCTATATACAAATTCTTTCAA
1 AGAAGTCGACCATTGTGGTCTCATGCGCCACTTCCGTCACTCTCCC-ATATACAAATTC-TTCAA
*
24319 TGG
64 TGA
* * * * * * * * *
24322 AGAATTCTACCATTGTAGTC-CTATGCGCCATTTCCGTTACTTTCTCTTTTACAAATTC-TCACA
1 AGAAGTCGACCATTGTGGTCTC-ATGCGCCACTTCCGTCACTCTCCCATATACAAATTCTTCA-A
*
24385 TTGTGG
64 ---TGA
* ** * * * * ** ** * * *
24391 AGAAATCGACTGTTATGGTCCCATGCACCATTTCTTTCACTCTTCTTAATGTA-AGTATTATT-A
1 AGAAGTCGACCATTGTGGTCTCATGCGCCACTTCCGTCACTC-TC-CCATATACA-AATTCTTCA
24454 AT-A
63 ATGA
* * * ** *
24457 GAGAAGTCGACCATTGTGGTCTTCTAT--TCCA-TTCCCGTCACTCTCTCATTTATGAATACTTT
1 -AGAAGTCGACCATTGTGGTC-TC-ATGCGCCACTT-CCGTCACTCTCCCATATACAAATTC-TT
*
24519 TAATAGA
61 CAAT-GA
* * * * ***
24526 A-AAGTCAATCGTTGTGGT-TCAATGCGACACTTTTATCACTCTCCTCATATACAAATTCTTCCA
1 AGAAGTCGACCATTGTGGTCTC-ATGCGCCACTTCCGTCACTCTCC-CATATACAAATTCTT-CA
24589 ATGA
63 ATGA
* * * * * *
24593 AAAAGTCGACCATTGTGGTCTCATGCGCCACTCCCGTCACTTTTCCATTTACAAGTACTCTT-AA
1 AGAAGTCGACCATTGTGGTCTCATGCGCCACTTCCGTCACTCTCCCATATACAA--ATTCTTCAA
*
24657 TGG
64 TGA
* * ** * * *
24660 AGAAGTCGACCTTTGTGGTCTCATACGCCACTTCTATCATTCTCCACATATACAAGTTCTCTGAA
1 AGAAGTCGACCATTGTGGTCTCATGCGCCACTTCCGTCACTCTCC-CATATACAAATTCT-TCAA
*
24725 TGT
64 TGA
* * * * * *
24728 AGAAGTTGATCGTAGTGGTCTTATGCGCCACTTTCGTCACTCTCCC
1 AGAAGTCGACCATTGTGGTCTCATGCGCCACTTCCGTCACTCTCCC
24774 TAATATAAGT
Statistics
Matches: 329, Mismatches: 92, Indels: 63
0.68 0.19 0.13
Matches are distributed among these distances:
65 14 0.04
66 10 0.03
67 120 0.36
68 129 0.39
69 42 0.13
70 5 0.02
71 8 0.02
72 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.35
Consensus pattern (66 bp):
AGAAGTCGACCATTGTGGTCTCATGCGCCACTTCCGTCACTCTCCCATATACAAATTCTTCAATG
A
Found at i:25491 original size:14 final size:14
Alignment explanation
Indices: 25459--25871 Score: 196
Period size: 14 Copynumber: 29.5 Consensus size: 14
25449 ACCCGGCACC
* *
25459 TGGCACAGATAC-C
1 TGGCACAGGTACTT
*
25472 TGGCATAGGTACTT
1 TGGCACAGGTACTT
* *
25486 TGGCATAAGTACCTT
1 TGGCACAGGTA-CTT
* *
25501 TGGTATAGGTATCTT
1 TGGCACAGGTA-CTT
*
25516 TGGCACAGGTA-TC
1 TGGCACAGGTACTT
* * * *
25529 TAGTATAGGTATTT
1 TGGCACAGGTACTT
25543 TGGCACAGGTAC-T
1 TGGCACAGGTACTT
* * * *
25556 TAGCACAAGCATTT
1 TGGCACAGGTACTT
*
25570 TGGCATAGGTATCTT
1 TGGCACAGGTA-CTT
* *
25585 TGGTACAAGTACTT
1 TGGCACAGGTACTT
* *
25599 TGGCACAAGTAC-C
1 TGGCACAGGTACTT
* *
25612 TAGCATAGGTATCTT
1 TGGCACAGGTA-CTT
* *
25627 TGGCACAAGTAC-C
1 TGGCACAGGTACTT
* *
25640 TGGTACAGGTATTT
1 TGGCACAGGTACTT
*
25654 TGGTACAGGTACTT
1 TGGCACAGGTACTT
*
25668 TGGCACAGGTAC-C
1 TGGCACAGGTACTT
* *
25681 TGGCACAAGCACTT
1 TGGCACAGGTACTT
*
25695 TGGCATAGGTATCTT
1 TGGCACAGGTA-CTT
* * **
25710 TAGCACATGTGGTT
1 TGGCACAGGTACTT
*
25724 TGGCATAGGTAGC--
1 TGGCACAGGTA-CTT
* *
25737 TGGCATAGGTATTT
1 TGGCACAGGTACTT
25751 TGGCACAGGTACTT
1 TGGCACAGGTACTT
* *
25765 GGGCATAGGTAC-T
1 TGGCACAGGTACTT
*
25778 TGGCACAGGCACTT
1 TGGCACAGGTACTT
*
25792 TGGCATAGGTATCTT
1 TGGCACAGGTA-CTT
* * * *
25807 TAGCATAAGAACTTT
1 TGGCACAGGTAC-TT
***
25822 TGGCACAAAAACTT
1 TGGCACAGGTACTT
* * *
25836 TGGTAGAAGTACTTT
1 TGGCACAGGTAC-TT
*
25851 TGGCACAAGTACTT
1 TGGCACAGGTACTT
25865 TGGCACA
1 TGGCACA
25872 CACAACTTTG
Statistics
Matches: 298, Mismatches: 85, Indels: 33
0.72 0.20 0.08
Matches are distributed among these distances:
13 76 0.26
14 136 0.46
15 86 0.29
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (14 bp):
TGGCACAGGTACTT
Found at i:25675 original size:28 final size:27
Alignment explanation
Indices: 25459--25802 Score: 145
Period size: 27 Copynumber: 12.4 Consensus size: 27
25449 ACCCGGCACC
* * * *
25459 TGGCACAGATACCTGGCATAGGTACTT
1 TGGCACAGGTACTTGGCACAGGTATTT
* * * *
25486 TGGCATAAGTACCTTTGGTATAGGTATCTT
1 TGGCACAGGTA-C-TTGGCACAGGTAT-TT
* * *
25516 TGGCACAGGTA-TCTAGTATAGGTATTT
1 TGGCACAGGTACT-TGGCACAGGTATTT
* * *
25543 TGGCACAGGTACTTAGCACAAGCATTT
1 TGGCACAGGTACTTGGCACAGGTATTT
* * * *
25570 TGGCATAGGTATCTTTGGTACAAGTACTT
1 TGGCACAGGTA-C-TTGGCACAGGTATTT
* * * *
25599 TGGCACAAGTACCTAGCATAGGTATCTT
1 TGGCACAGGTACTTGGCACAGGTAT-TT
* * *
25627 TGGCACAAGTACCTGGTACAGGTATTT
1 TGGCACAGGTACTTGGCACAGGTATTT
* **
25654 TGGTACAGGTACTTTGGCACAGGTA-CC
1 TGGCACAGGTAC-TTGGCACAGGTATTT
* * *
25681 TGGCACAAGCACTTTGGCATAGGTATCTT
1 TGGCACAGGTAC-TTGGCACAGGTAT-TT
* * ** * **
25710 TAGCACATGTGGTTTGGCATAGGTA-GC
1 TGGCACAGGT-ACTTGGCACAGGTATTT
* * *
25737 TGGCATAGGTATTTTGGCACAGGTACTT
1 TGGCACAGGTA-CTTGGCACAGGTATTT
* * * *
25765 GGGCATAGGTACTTGGCACAGGCACTT
1 TGGCACAGGTACTTGGCACAGGTATTT
*
25792 TGGCATAGGTA
1 TGGCACAGGTA
25803 TCTTTAGCAT
Statistics
Matches: 244, Mismatches: 59, Indels: 28
0.74 0.18 0.08
Matches are distributed among these distances:
27 125 0.51
28 59 0.24
29 49 0.20
30 11 0.05
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.31
Consensus pattern (27 bp):
TGGCACAGGTACTTGGCACAGGTATTT
Found at i:25770 original size:41 final size:39
Alignment explanation
Indices: 25515--25802 Score: 153
Period size: 41 Copynumber: 7.0 Consensus size: 39
25505 ATAGGTATCT
* * *
25515 TTGGCACAGGTATCTAGTATAGGTATTTTGGCACAGGTAC
1 TTGGCACAAGTA-CTGGCATAGGTATTTTGGCACAGGTAC
* ** * *
25555 TTAGCACAAGCATTTTGGCATAGGTATCTTTGGTACAAGTAC
1 TTGGCACAAG--TACTGGCATAGGTAT-TTTGGCACAGGTAC
* *
25597 TTTGGCACAAGTACCTAGCATAGGTATCTTTGGCACAAGTAC
1 -TTGGCACAAGTA-CTGGCATAGGTAT-TTTGGCACAGGTAC
* * * * * * *
25639 CTGGTACAGGTATTTTGGTACAGGTACTTTGGCACAGGTAC
1 TTGGCACAAGTA--CTGGCATAGGTATTTTGGCACAGGTAC
* * * * **
25680 CTGGCACAAGCACTTTGGCATAGGTATCTTTAGCACATGTGGT
1 TTGGCACAAGTAC--TGGCATAGGTAT-TTTGGCACAGGT-AC
* *
25723 TTGGCATAGGTAGCTGGCATAGGTATTTTGGCACAGGTAC
1 TTGGCACAAGTA-CTGGCATAGGTATTTTGGCACAGGTAC
* * * * * *
25763 TTGGGCATAGGTACTTGGCACAGGCACTTTGGCATAGGTA
1 TT-GGCACAAGTAC-TGGCATAGGTATTTTGGCACAGGTA
25803 TCTTTAGCAT
Statistics
Matches: 189, Mismatches: 46, Indels: 25
0.73 0.18 0.10
Matches are distributed among these distances:
40 11 0.06
41 92 0.49
42 68 0.36
43 17 0.09
44 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.31
Consensus pattern (39 bp):
TTGGCACAAGTACTGGCATAGGTATTTTGGCACAGGTAC
Found at i:25836 original size:15 final size:14
Alignment explanation
Indices: 25813--25899 Score: 66
Period size: 15 Copynumber: 5.9 Consensus size: 14
25803 TCTTTAGCAT
25813 AAGAACTTTTGGCAC
1 AAGAAC-TTTGGCAC
* * *
25828 AAAAACTTTGGTAG
1 AAGAACTTTGGCAC
*
25842 AAGTACTTTTGGCAC
1 AAGAAC-TTTGGCAC
*
25857 AAGTACTTTGGCAC
1 AAGAACTTTGGCAC
* *
25871 ACACAACTTTGGCAT
1 A-AGAACTTTGGCAC
*
25886 AAGTACTTTTGGCA
1 AAGAAC-TTTGGCA
25900 AGGGTGGCTT
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
14 22 0.39
15 35 0.61
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (14 bp):
AAGAACTTTGGCAC
Found at i:25895 original size:44 final size:44
Alignment explanation
Indices: 25788--25899 Score: 129
Period size: 44 Copynumber: 2.5 Consensus size: 44
25778 TGGCACAGGC
* * *
25788 ACTTTGGCATAGGTA-TCTTTAGCATAAGAACTTTTGGCACAAAA
1 ACTTTGGCATAAGTACT-TTTGGCACAAGAACTTTTGGCACAAAA
* * * *
25832 ACTTTGGTAGAAGTACTTTTGGCACAAGTAC-TTTGGCACACACA
1 ACTTTGGCATAAGTACTTTTGGCACAAGAACTTTTGGCACA-AAA
25876 ACTTTGGCATAAGTACTTTTGGCA
1 ACTTTGGCATAAGTACTTTTGGCA
25900 AGGGTGGCTT
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
43 9 0.16
44 47 0.82
45 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (44 bp):
ACTTTGGCATAAGTACTTTTGGCACAAGAACTTTTGGCACAAAA
Found at i:30416 original size:28 final size:28
Alignment explanation
Indices: 30268--30911 Score: 784
Period size: 28 Copynumber: 22.2 Consensus size: 28
30258 ACAGTAGTGA
30268 TTTGAAAAGGGTTGCCACTGACTTGCGTGGGC
1 TTTG-AAAGGG-TGCCACTGACTT--GTGGGC
* * *
30300 TTTTTTAAAAAGGTGCCACTAACTTGTGTAGGC
1 ---TTTGAAAGGGTGCCACTGACTTGTG--GGC
* * * *
30333 TTTGAAAAAAGTTGCCACCGACTCGTGGGC
1 TTTG--AAAGGGTGCCACTGACTTGTGGGC
* * *
30363 TTTGAAAGGAATTCCACTGACTTATGGGC
1 TTTGAAAGG-GTGCCACTGACTTGTGGGC
*
30392 TTTGAAAGGGTGCCACTGACTTATGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* *
30420 TTTGAAAGGAATGCCACTAACTTGTGGGC
1 TTTGAAAGG-GTGCCACTGACTTGTGGGC
**
30449 TTTGAAATTGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
*
30477 TTTGAAAGGGTGCCACTGACTTGTGGGT
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
*
30505 TTTGAAAGGATGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
30533 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* *
30561 TTTGAAAGGATGCCACTGACTTATGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* *
30589 TTTGAAAAGGATGCCACTGAGTTGTGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGC
* *
30618 TTTGAAAAGAGTTGCCACCGACTCGTGTGGGC
1 TTTG-AAAG-GGTGCCACTGACT--TGTGGGC
*
30650 TTTGAAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
30678 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
*
30706 TTTGAAAGGATGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* * * *
30734 TTTAAAAAGAGTTTCCACCGACTCGTGTGGGC
1 TTT-GAAAG-GGTGCCACTGACT--TGTGGGC
*
30766 TTTGAAAGGGTGCCACTGACTTGTGGGT
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
30794 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
*
30822 TTTGAAAGGATGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* * *
30850 TTTGAGAGGGTTCCACTAACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
30878 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
30906 TTTGAA
1 TTTGAA
30912 GAGATAAACG
Statistics
Matches: 536, Mismatches: 59, Indels: 35
0.85 0.09 0.06
Matches are distributed among these distances:
28 334 0.62
29 81 0.15
30 50 0.09
31 11 0.02
32 38 0.07
33 14 0.03
34 5 0.01
35 3 0.01
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.30
Consensus pattern (28 bp):
TTTGAAAGGGTGCCACTGACTTGTGGGC
Found at i:32169 original size:9 final size:9
Alignment explanation
Indices: 32155--32196 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
32145 TTTCCTTGGC
32155 TTTTTTATT
1 TTTTTTATT
32164 TTTTTTAGTT
1 TTTTTTA-TT
*
32174 TTTTCT-TT
1 TTTTTTATT
*
32182 TTTTTTGTT
1 TTTTTTATT
32191 TTTTTT
1 TTTTTT
32197 TGGGGTATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 7 0.24
9 15 0.52
10 7 0.24
ACGTcount: A:0.05, C:0.02, G:0.05, T:0.88
Consensus pattern (9 bp):
TTTTTTATT
Found at i:32177 original size:17 final size:17
Alignment explanation
Indices: 32155--32194 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
32145 TTTCCTTGGC
32155 TTTTTTATTTTTTTTAG
1 TTTTTTATTTTTTTTAG
* *
32172 TTTTTTCTTTTTTTTTG
1 TTTTTTATTTTTTTTAG
32189 TTTTTT
1 TTTTTT
32195 TTTGGGGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.05, C:0.03, G:0.05, T:0.88
Consensus pattern (17 bp):
TTTTTTATTTTTTTTAG
Found at i:46074 original size:51 final size:51
Alignment explanation
Indices: 46008--46140 Score: 185
Period size: 51 Copynumber: 2.6 Consensus size: 51
45998 TAACTAGATA
* *
46008 TATCGATACATTGAAAAATGTATTGATACATCTAAGTAAAAAGACAGAATG
1 TATCGATACACTGAAAAATGTATCGATACATCTAAGTAAAAAGACAGAATG
* * *
46059 TATCAATACACTGAAAAATGTATCGATACATCTGAGTAAAAAGACAGATTG
1 TATCGATACACTGAAAAATGTATCGATACATCTAAGTAAAAAGACAGAATG
* * * *
46110 TATCGATACATTCATACATGTATCGATACAT
1 TATCGATACACTGAAAAATGTATCGATACAT
46141 TAAAGAATGT
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 72 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.29
Consensus pattern (51 bp):
TATCGATACACTGAAAAATGTATCGATACATCTAAGTAAAAAGACAGAATG
Found at i:46080 original size:20 final size:21
Alignment explanation
Indices: 46055--46093 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
46045 AAAAAGACAG
46055 AATGTATCAATACA-CTGAAA
1 AATGTATCAATACATCTGAAA
*
46075 AATGTATCGATACATCTGA
1 AATGTATCAATACATCTGA
46094 GTAAAAAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (21 bp):
AATGTATCAATACATCTGAAA
Found at i:46133 original size:20 final size:20
Alignment explanation
Indices: 46108--46160 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
46098 AAAGACAGAT
* *
46108 TGTATCGATACATTCATA-CA
1 TGTATCGATACATT-AAAGAA
46128 TGTATCGATACATTAAAGAA
1 TGTATCGATACATTAAAGAA
46148 TGTATCGATACAT
1 TGTATCGATACAT
46161 CTGGGTGCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATTAAAGAA
Found at i:47104 original size:23 final size:21
Alignment explanation
Indices: 47055--47104 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
47045 TACAACCTAT
* *
47055 TTTTTAATTTTTTATAAAAAA
1 TTTTAAATATTTTATAAAAAA
47076 TATTTAAATATTTTATCAAACAAA
1 T-TTTAAATATTTTAT-AAA-AAA
47100 TTTTA
1 TTTTA
47105 TTGAATATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 1 0.04
22 12 0.50
23 7 0.29
24 4 0.17
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTAAATATTTTATAAAAAA
Found at i:47975 original size:23 final size:23
Alignment explanation
Indices: 47949--48017 Score: 59
Period size: 27 Copynumber: 2.8 Consensus size: 23
47939 CTTAATTTTA
47949 TTTTTTTTAAATAAATTTTA-TT
1 TTTTTTTTAAATAAATTTTATTT
* * *
47971 TTTTTATTAAGATAACTCTTATTTT
1 TTTTTTTTAA-ATAAATTTTA-TTT
47996 TATATTTATTTAAATAAATTTT
1 T-T-TTT-TTTAAATAAATTTT
48018 TATATTAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
22 9 0.26
23 8 0.23
25 3 0.09
26 1 0.03
27 10 0.29
28 4 0.11
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (23 bp):
TTTTTTTTAAATAAATTTTATTT
Found at i:48032 original size:18 final size:17
Alignment explanation
Indices: 48000--48069 Score: 79
Period size: 18 Copynumber: 4.0 Consensus size: 17
47990 TATTTTTATA
48000 TTTATTTAAAT-AAATT
1 TTTATTTAAATAAAATT
*
48016 TTTATATTAAATAAAATA
1 TTTAT-TTAAATAAAATT
* *
48034 TTAATTTATATTAAAATT
1 TTTATTTA-AATAAAATT
48052 TTTATTTAAATATAAATT
1 TTTATTTAAATA-AAATT
48070 ACTAATTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
16 5 0.11
17 12 0.27
18 27 0.61
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTATTTAAATAAAATT
Found at i:48032 original size:22 final size:22
Alignment explanation
Indices: 47991--48033 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
47981 GATAACTCTT
* * *
47991 ATTTTTATATTTATTTAAATAA
1 ATTTTTATATTAAATAAAATAA
48013 ATTTTTATATTAAATAAAATA
1 ATTTTTATATTAAATAAAATA
48034 TTAATTTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTTTTATATTAAATAAAATAA
Found at i:48335 original size:29 final size:28
Alignment explanation
Indices: 48282--48374 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 28
48272 CAAAACCAAA
*
48282 TTTTAACTTTT-AATTTACCGTTAAATAAT
1 TTTTAA-TTTTAAATTTA-TGTTAAATAAT
48311 TTTTAATTTTAAATTTATGTATAAATAAGT
1 TTTTAATTTTAAATTTATGT-TAAATAA-T
* * *
48341 ATTTAATTATAAAGTTATAT-TTAAATAAA
1 TTTTAATTTTAAA-TT-TATGTTAAATAAT
48370 TTTTA
1 TTTTA
48375 TTTATTTAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
28 6 0.11
29 23 0.43
30 19 0.35
31 3 0.06
32 3 0.06
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (28 bp):
TTTTAATTTTAAATTTATGTTAAATAAT
Found at i:48348 original size:30 final size:29
Alignment explanation
Indices: 48303--48372 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
48293 AATTTACCGT
* * * *
48303 TAAATAATTTTTAATTTTAAATTTATGTA
1 TAAATAATATTTAATTATAAAGTTATATA
*
48332 TAAATAAGTATTTAATTATAAAGTTATATT
1 TAAATAA-TATTTAATTATAAAGTTATATA
48362 TAAATAA-ATTT
1 TAAATAATATTT
48373 TATTTATTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 4 0.11
29 7 0.20
30 24 0.69
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (29 bp):
TAAATAATATTTAATTATAAAGTTATATA
Found at i:48395 original size:26 final size:26
Alignment explanation
Indices: 48362--48445 Score: 82
Period size: 26 Copynumber: 3.1 Consensus size: 26
48352 AAGTTATATT
*
48362 TAAATAAATTTTATTTATTTAAAATA
1 TAAATAAATTTAATTTATTTAAAATA
48388 TAAATAAAAATTTAAAATTTATTT-AAATA
1 TAAAT--AAATTT--AATTTATTTAAAATA
* *
48417 TAATAAAAATATAATTTATTTAAAA-A
1 TAA-ATAAATTTAATTTATTTAAAATA
48443 TAA
1 TAA
48446 TAATTAATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
26 18 0.37
27 3 0.06
28 11 0.22
29 8 0.16
30 9 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
TAAATAAATTTAATTTATTTAAAATA
Found at i:48446 original size:26 final size:27
Alignment explanation
Indices: 48374--48448 Score: 98
Period size: 26 Copynumber: 2.7 Consensus size: 27
48364 AATAAATTTT
48374 ATTTATTTAAAATATAAATAAAAATTTAAA
1 ATTTATTTAAAA-AT-AATAAAAA-TTAAA
* *
48404 ATTTATTTAAATATAATAAAAA-TATA
1 ATTTATTTAAAAATAATAAAAATTAAA
48430 ATTTATTTAAAAATAATAA
1 ATTTATTTAAAAATAATAA
48449 TTAATTTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 21 0.50
28 8 0.19
29 2 0.05
30 11 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
ATTTATTTAAAAATAATAAAAATTAAA
Found at i:48448 original size:18 final size:17
Alignment explanation
Indices: 48420--48455 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
48410 TTAAATATAA
*
48420 TAAAAATATAATTTATT
1 TAAAAATATAATTAATT
48437 TAAAAATAATAATTAATT
1 TAAAAAT-ATAATTAATT
48455 T
1 T
48456 TTATATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAAATATAATTAATT
Found at i:51341 original size:19 final size:20
Alignment explanation
Indices: 51303--51354 Score: 88
Period size: 19 Copynumber: 2.6 Consensus size: 20
51293 TTACACACTC
51303 TTATGTATCGATATAATTCA
1 TTATGTATCGATATAATTCA
51323 TTATGTATCGATA-AATTCA
1 TTATGTATCGATATAATTCA
*
51342 TAATGTATCGATA
1 TTATGTATCGATA
51355 CATGCATTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.42
Consensus pattern (20 bp):
TTATGTATCGATATAATTCA
Found at i:51420 original size:20 final size:20
Alignment explanation
Indices: 51395--51469 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
51385 CGTTGGACTC
51395 AATGTATCGATACTATTCAT
1 AATGTATCGATACTATTCAT
*
51415 AATGTATCGATAC-ATGAACAGT
1 AATGTATCGATACTAT--TCA-T
* * * *
51437 TATATATCGATATTATTCAG
1 AATGTATCGATACTATTCAT
51457 AATGTATCGATAC
1 AATGTATCGATAC
51470 ATGAATAGTG
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
19 2 0.05
20 23 0.55
21 4 0.10
22 11 0.26
23 2 0.05
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACTATTCAT
Found at i:53105 original size:33 final size:34
Alignment explanation
Indices: 53044--53107 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
53034 TACCACTGTT
* * *
53044 TGTATTGATACATGGTTACATTGTATCGATATAA
1 TGTATCGATACATGATGACATTGTATCGATATAA
53078 TGTATCGATACATGATGA-ATTGTATCGATA
1 TGTATCGATACATGATGACATTGTATCGATA
53108 CATTGCTTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 12 0.44
34 15 0.56
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (34 bp):
TGTATCGATACATGATGACATTGTATCGATATAA
Done.