Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1495
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: 36417
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:465 original size:41 final size:43
Alignment explanation
Indices: 368--475 Score: 163
Period size: 41 Copynumber: 2.6 Consensus size: 43
358 GTGGTTTTCA
*
368 GCACTAAGTGTGCGGCCAA-AAGTGTTCAGCGGTTGTGAGATT
1 GCACTAAGTGTGCGGGCAATAAGTGTTCAGCGGTTGTGAGATT
410 GCACTAAGTGTGCGGGCAATAAGTGTTCA-C-G-TGTGAGATT
1 GCACTAAGTGTGCGGGCAATAAGTGTTCAGCGGTTGTGAGATT
450 GGCACTAAGTGTGCGGGCAAT-AGTGT
1 -GCACTAAGTGTGCGGGCAATAAGTGT
476 GCGGGCGATA
Statistics
Matches: 63, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
40 14 0.22
41 21 0.33
42 19 0.30
43 9 0.14
ACGTcount: A:0.24, C:0.16, G:0.34, T:0.26
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCAGCGGTTGTGAGATT
Found at i:480 original size:55 final size:57
Alignment explanation
Indices: 416--524 Score: 195
Period size: 57 Copynumber: 1.9 Consensus size: 57
406 GATTGCACTA
416 AGTGTGCGGGCAATAAGTGTTCAC-G-TGTGAGATTGGCACTAAGTGTGCGGGCAAT
1 AGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTGGCACTAAGTGTGCGGGCAAT
*
471 AGTGTGCGGGCGATAAGTGTTCACGGTTGTGAGATTGGCACTAAGTGTGCGGGC
1 AGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTGGCACTAAGTGTGCGGGC
525 TTGAAATGTA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
55 23 0.45
56 1 0.02
57 27 0.53
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.26
Consensus pattern (57 bp):
AGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTGGCACTAAGTGTGCGGGCAAT
Found at i:2318 original size:47 final size:47
Alignment explanation
Indices: 2168--2497 Score: 504
Period size: 47 Copynumber: 7.1 Consensus size: 47
2158 CCCTTCGGGA
* * * * * * *
2168 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
2215 CCTGTCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2261 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
2308 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
2355 CTTATCAC-TATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
2401 CTTATCACATATATACACTTTCACATTCATCACATCGG-CATTTGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
2447 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
2494 CTTA
1 CTTA
2498 CTATCATTTC
Statistics
Matches: 261, Mismatches: 19, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
46 129 0.49
47 132 0.51
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:2327 original size:93 final size:94
Alignment explanation
Indices: 2168--2497 Score: 504
Period size: 93 Copynumber: 3.5 Consensus size: 94
2158 CCCTTCGGGA
* * * * * * * * *
2168 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
2233 TTTCACATTCA-CACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
*
2261 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATTACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
2326 TTTCACATTCATCACATCGGCTATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
*
2355 CTTATCAC-TATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
2419 TTTCACATTCATCACATCGG-CATTTGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
* *
2447 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
2498 CTATCATTTC
Statistics
Matches: 219, Mismatches: 16, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
92 14 0.06
93 181 0.83
94 24 0.11
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:2480 original size:23 final size:23
Alignment explanation
Indices: 2411--2481 Score: 58
Period size: 23 Copynumber: 3.1 Consensus size: 23
2401 CTTATCACAT
2411 ATATACACTTTCACATTCATCAC
1 ATATACACTTTCACATTCATCAC
*** *
2434 ATCGGCA-TTTGGC-CTTATCA-CAC
1 ATATACACTTT--CACAT-TCATCAC
2457 ATATACACTTTCACATTCATCAC
1 ATATACACTTTCACATTCATCAC
2480 AT
1 AT
2482 CGGCTATTAG
Statistics
Matches: 34, Mismatches: 8, Indels: 12
0.63 0.15 0.22
Matches are distributed among these distances:
22 7 0.21
23 20 0.59
24 7 0.21
ACGTcount: A:0.31, C:0.30, G:0.06, T:0.34
Consensus pattern (23 bp):
ATATACACTTTCACATTCATCAC
Found at i:10160 original size:58 final size:59
Alignment explanation
Indices: 10060--10181 Score: 158
Period size: 58 Copynumber: 2.1 Consensus size: 59
10050 GGGAGGGACA
* * * *
10060 GGGACGATTCATTCATTGTTGGGTACCGAACATGCAACGGTATCTG-ATTTCTACC-TTT
1 GGGATGATTCATTCATTATTAGGTACCGAACATGCAACGGTATCCGAATTT-TACCTTTT
* * *
10118 GGGATGATTCATTCATTATTAGGTACTGAACATGTAATGGTATCCGAATTTTACCTTTT
1 GGGATGATTCATTCATTATTAGGTACCGAACATGCAACGGTATCCGAATTTTACCTTTT
10177 GGGAT
1 GGGAT
10182 TGGGGAGGGA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
58 43 0.78
59 12 0.22
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (59 bp):
GGGATGATTCATTCATTATTAGGTACCGAACATGCAACGGTATCCGAATTTTACCTTTT
Found at i:10953 original size:189 final size:186
Alignment explanation
Indices: 10624--10992 Score: 431
Period size: 189 Copynumber: 2.0 Consensus size: 186
10614 TTAACTAAAT
* * *
10624 TTTTTTTCTATTGGCCCAAAAGAAATACAATAATCCGAATAAAATATGGCATGATGGCACGGCAC
1 TTTTTTTCTATTGGCCCAAAACAAATACAAGAAGCCGAATAAAATATGGCATGATGGCACGGCAC
* * * * * * * **
10689 GATAGAAAATTGAACAAGTGCCCAGACCACCAGCAGTTGGGAGCTTGTACTCGTACCACCACGGC
66 GAAAGAAAATTAAACAAGTGACCAGACCACCAACAGTTGGGAGCTCGAACCCACACCACCACGGC
* *
10754 CCCCGTTGTGCCATGTTTC-CTGAGGGGGC-AGCACGGCCAAGTGTTTAACTTAGAAA
131 CCCCGTTGTGCCATGTTTCTC-AAGGGGGCGA-CACAGCCAAGTGTTTAACTTAGAAA
* * * * *
10810 TTTTTTT-TGTTGGCCCAAAACAAATACAAGAAGCTGAATGAAGTATGGCATGATGGCATGGCAC
1 TTTTTTTCTATTGGCCCAAAACAAATACAAGAAGCCGAATAAAATATGGCATGATGGCACGGCAC
* * *
10874 AGCACGGAAGAAAATTAAACAA-TTACCGGACCACCAACAGTTGGGAGCTCGAACCCACACCATC
66 -G-A---AAGAAAATTAAACAAGTGACCAGACCACCAACAGTTGGGAGCTCGAACCCACACCACC
* *
10938 GCGGCCCCTGTTGTGCCATGTTTCTCAAGGGGGCGACACAGCCAAGTGTTTAACT
126 ACGGCCCCCGTTGTGCCATGTTTCTCAAGGGGGCGACACAGCCAAGTGTTTAACT
10993 AACTCCTTAC
Statistics
Matches: 152, Mismatches: 24, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
185 49 0.32
186 8 0.05
187 1 0.01
189 79 0.52
190 15 0.10
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.22
Consensus pattern (186 bp):
TTTTTTTCTATTGGCCCAAAACAAATACAAGAAGCCGAATAAAATATGGCATGATGGCACGGCAC
GAAAGAAAATTAAACAAGTGACCAGACCACCAACAGTTGGGAGCTCGAACCCACACCACCACGGC
CCCCGTTGTGCCATGTTTCTCAAGGGGGCGACACAGCCAAGTGTTTAACTTAGAAA
Found at i:12079 original size:29 final size:29
Alignment explanation
Indices: 12016--12178 Score: 170
Period size: 29 Copynumber: 5.7 Consensus size: 29
12006 ACATACATGC
* *
12016 ATATGGCCCA-CAAGGCCCAA-TCTCATTT
1 ATATGGCCCATC-CGGCCCAATTCACATTT
*
12044 ATATGGCCTATCCGGCCCAATTCACATTT
1 ATATGGCCCATCCGGCCCAATTCACATTT
*
12073 ATATGGCCCATCCGGCCCAATTCACGTTT
1 ATATGGCCCATCCGGCCCAATTCACATTT
* *
12102 ATATGGCCCATCAGGCCCAATTCACATTC
1 ATATGGCCCATCCGGCCCAATTCACATTT
* * ** * * *
12131 ATATGACCCGTTAGGCCTAA-CCTCATTT
1 ATATGGCCCATCCGGCCCAATTCACATTT
*
12159 ATATGGCCCATCTGGCCCAA
1 ATATGGCCCATCCGGCCCAA
12179 ACCACATTAT
Statistics
Matches: 113, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
28 36 0.32
29 77 0.68
ACGTcount: A:0.25, C:0.33, G:0.15, T:0.27
Consensus pattern (29 bp):
ATATGGCCCATCCGGCCCAATTCACATTT
Found at i:14662 original size:40 final size:40
Alignment explanation
Indices: 14560--14781 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 40
14550 TTATTCGAAT
* * * *
14560 TATATCCGAGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGAC
1 TATATCCGGGCTAAGACCCGAAGGCATTTGTGC-GAGTGAC
* * *
14601 TATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTAC
1 TATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGAC
* * * * **
14641 TATATCTGGGCCAAAACCCGAAGGCATTTGTGCTAGCAAC
1 TATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGAC
* * *
14681 TATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGAC
1 TATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGAC
* * * **
14721 CATATCCGGGCTAAGACCCGAAGGC-CTTGTGCGAGGGGT
1 TATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGAC
14760 TATATCC-GGCTAA-ATCCCGAAG
1 TATATCCGGGCTAAGA-CCCGAAG
14782 ATACTTGGGT
Statistics
Matches: 149, Mismatches: 31, Indels: 5
0.81 0.17 0.03
Matches are distributed among these distances:
37 1 0.01
38 13 0.09
39 14 0.09
40 93 0.62
41 28 0.19
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGAC
Found at i:19184 original size:37 final size:37
Alignment explanation
Indices: 19134--19212 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
19124 TTATTACGAA
* *
19134 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTTATCGG
* *
19171 GTCTTACTCGGACAAAATCCCCACACGTAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTTATCGG
19208 GTCTT
1 GTCTT
19213 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTTATCGG
Found at i:19409 original size:47 final size:47
Alignment explanation
Indices: 19331--19743 Score: 657
Period size: 47 Copynumber: 8.7 Consensus size: 47
19321 CCCTTCGGGA
* * * * * *
19331 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
19378 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19425 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19472 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
19519 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
19566 CTTATCACATATATTCACTTTCACATTCATCACATAGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
19613 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
19662 CTTAACACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
19709 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
19744 AGAATCCTAA
Statistics
Matches: 342, Mismatches: 21, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
46 1 0.00
47 297 0.87
49 44 0.13
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:22710 original size:40 final size:40
Alignment explanation
Indices: 22676--22987 Score: 471
Period size: 40 Copynumber: 7.8 Consensus size: 40
22666 CCAGCATGAT
* * * *
22676 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
** *
22716 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * * *
22756 TGTTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * *
22796 TGCTCTTCGGGATTTAACCTGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* * *
22836 TGCTATTCGGAACTTAGTCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
22876 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
22916 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
22956 TGCTCTTCGGGACTTAGCCCGGATATATCACT
1 TGCTCTTCGGGACTTAGCCCGGATATATCACT
22988 CTCAATTCTC
Statistics
Matches: 242, Mismatches: 30, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 242 1.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:24247 original size:37 final size:37
Alignment explanation
Indices: 24197--24275 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
24187 TTATTACGAA
* *
24197 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTTATCGG
*
24234 GTCTTACCCGGACAAAATCCCCACACGTAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTTATCGG
24271 GTCTT
1 GTCTT
24276 TAGAGCTCGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTTATCGG
Found at i:24472 original size:47 final size:47
Alignment explanation
Indices: 24394--24663 Score: 407
Period size: 47 Copynumber: 5.7 Consensus size: 47
24384 CCCTTCGGGA
* * * * * *
24394 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
24441 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24488 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
24535 CTTATCATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
24582 CTTATCACATATATACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
24629 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
24664 AGAATCCTAA
Statistics
Matches: 206, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
46 1 0.00
47 205 1.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:30632 original size:26 final size:26
Alignment explanation
Indices: 30603--30652 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
30593 AGTTAGTAAT
*
30603 AAAGAAATGGA-GAAAGAAAAAAAAGG
1 AAAGAAA-GGATGAAACAAAAAAAAGG
30629 AAAGAAAGGATGAAACAAAAAAAA
1 AAAGAAAGGATGAAACAAAAAAAA
30653 AAATGTGTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.72, C:0.02, G:0.22, T:0.04
Consensus pattern (26 bp):
AAAGAAAGGATGAAACAAAAAAAAGG
Found at i:32649 original size:89 final size:85
Alignment explanation
Indices: 32535--32728 Score: 232
Period size: 88 Copynumber: 2.2 Consensus size: 85
32525 TTAGGATTCT
* * *
32535 ATGTGATGGATGTGAACATGCATATATGAGATAAGGCCTAATGGCT-CG-ATGTGATGAATGTGA
1 ATGTGATGAATGTGAAGAT--ATATAT--GATAAGGCCT-AT-GCTGCGCATGT-ATGAATGTAA
*
32598 AAGTGTATATATGTGATAAGGCTAATGGCCG
59 AAGTGTATATAT-TGATAAGGCT--T-GACG
32629 AT-TGATGAATGTGAAGATATATATGATAAGGCCTATGCTGCGCATGTATGAATGTAAAAGTGTA
1 ATGTGATGAATGTGAAGATATATATGATAAGGCCTATGCTGCGCATGTATGAATGTAAAAGTGTA
32693 TATATTGATAAGGCTTGACG
66 TATATTGATAAGGCTTGACG
32713 ATGTGATGAATGTGAA
1 ATGTGATGAATGTGAA
32729 AGTGTATATA
Statistics
Matches: 93, Mismatches: 4, Indels: 15
0.83 0.04 0.13
Matches are distributed among these distances:
84 5 0.05
85 14 0.15
87 13 0.14
88 25 0.27
89 14 0.15
91 6 0.06
93 14 0.15
94 2 0.02
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (85 bp):
ATGTGATGAATGTGAAGATATATATGATAAGGCCTATGCTGCGCATGTATGAATGTAAAAGTGTA
TATATTGATAAGGCTTGACG
Found at i:32731 original size:42 final size:44
Alignment explanation
Indices: 32535--32747 Score: 192
Period size: 48 Copynumber: 4.8 Consensus size: 44
32525 TTAGGATTCT
* * * *
32535 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCTCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGG-CT-AT-G-ACG
*
32583 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCT-AT-GACG
* *
32629 AT-TGATGAATGTG-AA--G-ATATATATGATAAGGCCTATGCTGCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGG-CTATG--ACG
*
32671 CATGT-ATGAATGTAAAAGTGTATATAT-TGATAAGGCT-TGACG
1 -ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCTATGACG
32713 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
32748 CAACAGGTGA
Statistics
Matches: 144, Mismatches: 9, Indels: 29
0.79 0.05 0.16
Matches are distributed among these distances:
40 1 0.01
41 20 0.14
42 28 0.19
43 17 0.12
44 7 0.05
45 13 0.09
46 13 0.09
47 14 0.10
48 31 0.22
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.31
Consensus pattern (44 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCTATGACG
Found at i:32738 original size:89 final size:91
Alignment explanation
Indices: 32535--32747 Score: 248
Period size: 89 Copynumber: 2.4 Consensus size: 91
32525 TTAGGATTCT
* *
32535 ATGTGATGGATGTGAACATGCATATATGA-GATAAGGCCTAATGGCTCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAA-ATG-ATATAT-ATGATAAGGCCTAATGGCTCGATGTGATGAATGTAAA
*
32599 AGTGTATATATGTGATAAGGCTAATGGCCG
63 AGTGTATATATGTGATAAGGCT-ATGGACG
32629 AT-TGATGAATGTG-AA-GATATATATGATAAGGCCT-AT-GCTGCGCATGT-ATGAATGTAAAA
1 ATGTGATGAATGTGAAATGATATATATGATAAGGCCTAATGGCT-CG-ATGTGATGAATGTAAAA
32688 GTGTATATAT-TGATAAGGCT-T-GACG
64 GTGTATATATGTGATAAGGCTATGGACG
*
32713 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
1 ATGTGATGAATGTGAAA-TG-ATATATATGATAAG
32748 CAACAGGTGA
Statistics
Matches: 107, Mismatches: 4, Indels: 21
0.81 0.03 0.16
Matches are distributed among these distances:
84 5 0.05
85 12 0.11
86 2 0.02
87 13 0.12
88 27 0.25
89 33 0.31
90 1 0.01
91 1 0.01
92 1 0.01
93 10 0.09
94 2 0.02
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.31
Consensus pattern (91 bp):
ATGTGATGAATGTGAAATGATATATATGATAAGGCCTAATGGCTCGATGTGATGAATGTAAAAGT
GTATATATGTGATAAGGCTATGGACG
Found at i:33123 original size:34 final size:38
Alignment explanation
Indices: 33070--33147 Score: 94
Period size: 35 Copynumber: 2.2 Consensus size: 38
33060 CGTACTATAT
*
33070 TCCGGTCTAAAGACCCGATAA-TACGTGTGG-GATTTTG
1 TCCGGTCTAAAGACCCGATAACTACGTGTGGAGA-TTAG
*
33107 TCCGGT-T-AAGA-CCGATAACTTCGTGTGGAGATTAG
1 TCCGGTCTAAAGACCCGATAACTACGTGTGGAGATTAG
33142 TCCGGT
1 TCCGGT
33148 AAACTTCGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
34 7 0.19
35 21 0.57
36 3 0.08
37 6 0.16
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.29
Consensus pattern (38 bp):
TCCGGTCTAAAGACCCGATAACTACGTGTGGAGATTAG
Found at i:34573 original size:40 final size:40
Alignment explanation
Indices: 34322--34632 Score: 313
Period size: 40 Copynumber: 7.8 Consensus size: 40
34312 GAGAATTGAG
34322 AGTGATATAT-CGGGCTAAGTCCCGAAGAGCATTCGTGGGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGT--GCT
34363 AGTGATATATCCGGGGGCTAAGTCCCGAAGAGCA-TCGTGCT
1 AGTGATATATCC--GGGCTAAGTCCCGAAGAGCATTCGTGCT
34404 AGTAGA-ATAT-CGTGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGT-GATATATCCG-GGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
34444 AGTGA-ATATCCGGACT-AGT-TCGAATAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
34481 CAGTGATATAT-C-GGTTAA-TCCCGAAGAAGGCATTTCGTGCT
1 -AGTGATATATCCGGGCTAAGTCCCGAAG-A-GCA-TTCGTGCT
* * * *
34522 AGTGATGTATCCGGACTAAGTTCCGAAGAACATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
34562 AGTGATATATCCGTGCTAA-ACCCGAAAGAGCATTCATGCT
1 AGTGATATATCCGGGCTAAGTCCCG-AAGAGCATTCGTGCT
* * *
34602 GGTGTTATATCCGGGCTAGGT-CCGAAGAGCA
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCA
34633 ATCATGCTGG
Statistics
Matches: 227, Mismatches: 24, Indels: 40
0.78 0.08 0.14
Matches are distributed among these distances:
37 19 0.08
38 15 0.07
39 43 0.19
40 80 0.35
41 31 0.14
42 8 0.04
43 11 0.05
44 20 0.09
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
Done.