Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold379
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: 429249
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 418 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:376719 original size:20 final size:22
Alignment explanation
Indices: 376679--376722 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
376669 TTTTTAACTG
*
376679 TTTATCAAGGGGGAGAAATTTT
1 TTTATCAAGAGGGAGAAATTTT
376701 TTTATCAA-AGGGA-AAATTTT
1 TTTATCAAGAGGGAGAAATTTT
376721 TT
1 TT
376723 AACGAGAGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.41
Consensus pattern (22 bp):
TTTATCAAGAGGGAGAAATTTT
Found at i:384642 original size:10 final size:9
Alignment explanation
Indices: 384616--384641 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
384606 TCGATAAATA
384616 AAATTTTTG
1 AAATTTTTG
384625 AAATTTTTG
1 AAATTTTTG
384634 AAATTTTT
1 AAATTTTT
384642 TTATAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (9 bp):
AAATTTTTG
Found at i:389946 original size:52 final size:52
Alignment explanation
Indices: 389801--389926 Score: 225
Period size: 52 Copynumber: 2.4 Consensus size: 52
389791 ATATGAAAAT
*
389801 TTTGCCTGCATGTATCGATACATTTCATAGTGCATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
*
389853 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTTGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
*
389905 TTTGCCTGCATATATCGATACA
1 TTTGCCTGCATGTATCGATACA
389927 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (52 bp):
TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
Found at i:389953 original size:13 final size:13
Alignment explanation
Indices: 389935--389959 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
389925 CAAAGATCAG
389935 TGTATCGATACAA
1 TGTATCGATACAA
389948 TGTATCGATACA
1 TGTATCGATACA
389960 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:390025 original size:19 final size:19
Alignment explanation
Indices: 390001--390066 Score: 90
Period size: 19 Copynumber: 3.8 Consensus size: 19
389991 AATAGCTTCG
390001 TATGTATCGATACAACACT
1 TATGTATCGATACAACACT
390020 TATGTATCGAT---ACA--
1 TATGTATCGATACAACACT
390034 T-TGTATCGATACAACACT
1 TATGTATCGATACAACACT
390052 TATGTATCGATACAA
1 TATGTATCGATACAA
390067 ATCGTTGACA
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 9 0.22
14 1 0.02
16 6 0.15
18 1 0.02
19 24 0.59
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (19 bp):
TATGTATCGATACAACACT
Found at i:390040 original size:13 final size:13
Alignment explanation
Indices: 390022--390046 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
390012 ACAACACTTA
390022 TGTATCGATACAT
1 TGTATCGATACAT
390035 TGTATCGATACA
1 TGTATCGATACA
390047 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:390042 original size:32 final size:32
Alignment explanation
Indices: 390003--390065 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
389993 TAGCTTCGTA
390003 TGTATCGATACAACACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
390035 TGTATCGATACAACACTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCGATACA
390066 AATCGTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:390785 original size:55 final size:55
Alignment explanation
Indices: 390716--390942 Score: 188
Period size: 55 Copynumber: 4.3 Consensus size: 55
390706 AGAAAGATAC
* *
390716 CAATATGCTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGT
1 CAATGTGCTGATTCACGGCCAACGACATTGGGCTTAAAGATGAGAAAAAGGATGT
** * * * * *
390771 CAATGTGCTGATTCACGATCAGCGGCATTAGACTT---G--GAG---AAGAATGT
1 CAATGTGCTGATTCACGGCCAACGACATTGGGCTTAAAGATGAGAAAAAGGATGT
** * * ** *
390818 CAATGTGCTGAGACAAGGCCAACGACATTGGGCTTAAGGAT--GTTAAA-GATGC
1 CAATGTGCTGATTCACGGCCAACGACATTGGGCTTAAAGATGAGAAAAAGGATGT
** * *
390870 CAATACGCTGATTCAAGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGT
1 CAATGTGCTGATTCACGGCCAACGACATTGGGCTTAAAGATGAGAAAAAGGATGT
*
390925 TAATGTGCTGATTCACGG
1 CAATGTGCTGATTCACGG
390943 TCAGTGGCAT
Statistics
Matches: 128, Mismatches: 33, Indels: 22
0.70 0.18 0.12
Matches are distributed among these distances:
47 33 0.26
50 5 0.04
52 39 0.30
53 2 0.02
54 4 0.03
55 45 0.35
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (55 bp):
CAATGTGCTGATTCACGGCCAACGACATTGGGCTTAAAGATGAGAAAAAGGATGT
Found at i:390988 original size:154 final size:154
Alignment explanation
Indices: 390708--391002 Score: 527
Period size: 154 Copynumber: 1.9 Consensus size: 154
390698 GAAAAGTGAG
* *
390708 AAAGATACCAATATGCTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCA
1 AAAGATACCAATACGCTGATTCAAGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCA
390773 ATGTGCTGATTCACGATCAGCGGCATTAGACTTGGAGAAGAATGTCAATGTGCTGAGACAAGGCC
66 ATGTGCTGATTCACGATCAGCGGCATTAGACTTGGAGAAGAATGTCAATGTGCTGAGACAAGGCC
390838 AACGACATTGGGCTTAAGGATGTT
131 AACGACATTGGGCTTAAGGATGTT
* *
390862 AAAGATGCCAATACGCTGATTCAAGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTTA
1 AAAGATACCAATACGCTGATTCAAGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCA
* *
390927 ATGTGCTGATTCACGGTCAGTGGCATTAGACTTGGAGAAGAATGTCAATGTGCTGAGACAAGGCC
66 ATGTGCTGATTCACGATCAGCGGCATTAGACTTGGAGAAGAATGTCAATGTGCTGAGACAAGGCC
*
390992 AACGATATTGG
131 AACGACATTGG
391003 ACTTGTGCTA
Statistics
Matches: 134, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
154 134 1.00
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (154 bp):
AAAGATACCAATACGCTGATTCAAGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCA
ATGTGCTGATTCACGATCAGCGGCATTAGACTTGGAGAAGAATGTCAATGTGCTGAGACAAGGCC
AACGACATTGGGCTTAAGGATGTT
Found at i:391129 original size:49 final size:48
Alignment explanation
Indices: 391007--391288 Score: 191
Period size: 49 Copynumber: 5.8 Consensus size: 48
390997 TATTGGACTT
* * * * * *
391007 GTGCTAATGTGCTGATTCAAGACCAGCTACATTGGACTCAAGACGGAAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGC-GCATTGGACTTAA-A-GGTAAAG
*
391058 GTGCCAATATG-TCGATTCAAGGCCAGCGCTATTGGACTTAAAGGTGAAG
1 GTGCCAATATGCT-GATTCAAGGCCAGCGC-ATTGGACTTAAAGGTAAAG
* * * * * *
391107 ATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAGG
1 GTGCCAATATGCTGATTCAAGGCCAGC-GCATTGGACTTAAAGGTAAAG
* * * * *
391156 GTGCCAATGTGTTGATTTAAGGCCAGCGACATTGGTCTTCAAGGT----
1 GTGCCAATATGCTGATTCAAGGCCAGCG-CATTGGACTTAAAGGTAAAG
* ** *
391201 GT--CAATATGCTGATTCAAGGCCAGCGATATTGAGTTTTAAAGATAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCG-CATTG-GACTTAAAGGTAAAG
* * * *
391249 GTGCCAATATGATGGTTCAAGGCCAGTGATATTGGACTTA
1 GTGCCAATATGCTGATTCAAGGCCAGCG-CATTGGACTTA
391289 GAAGAAGACG
Statistics
Matches: 188, Mismatches: 31, Indels: 26
0.77 0.13 0.11
Matches are distributed among these distances:
43 26 0.14
44 8 0.04
45 2 0.01
48 2 0.01
49 86 0.46
50 32 0.17
51 32 0.17
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.27
Consensus pattern (48 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGCATTGGACTTAAAGGTAAAG
Found at i:391376 original size:28 final size:29
Alignment explanation
Indices: 391300--391376 Score: 70
Period size: 28 Copynumber: 2.6 Consensus size: 29
391290 AAGAAGACGC
391300 CATCAACTTGTGTGGGCTTTTGAAAGGGTTG
1 CATCAAC-T-TGTGGGCTTTTGAAAGGGTTG
**
391331 CATCAACTTGTGTACTTTTG-AA-GGTTG
1 CATCAACTTGTGGGCTTTTGAAAGGGTTG
*
391358 CCA-CTGACTTGTGGGCTTT
1 -CATC-AACTTGTGGGCTTT
391377 AAAAGGGGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
27 6 0.15
28 15 0.38
29 10 0.26
30 1 0.03
31 7 0.18
ACGTcount: A:0.18, C:0.17, G:0.27, T:0.38
Consensus pattern (29 bp):
CATCAACTTGTGGGCTTTTGAAAGGGTTG
Found at i:391437 original size:34 final size:34
Alignment explanation
Indices: 391397--391548 Score: 121
Period size: 34 Copynumber: 4.3 Consensus size: 34
391387 CCACTGCAAG
*
391397 GTTGTGGACTTAAAAGAAAAAAGAATGCCACGGA
1 GTTGTGGACTTAAAAGAAAAAAGAATGCCACTGA
* * *
391431 GTTGTGGGCTTAAAAGGAAGAAAG-GTGCCA-TAGA
1 GTTGTGGACTTAAAA-GAAAAAAGAATGCCACT-GA
* * *
391465 GTTGTGGACTTAGAAG-GAAAAGAGTGCCACTGA
1 GTTGTGGACTTAAAAGAAAAAAGAATGCCACTGA
* * *
391498 GTTATGGGCTTTAAAAAGAAAAAAAAAAAGGTGCCACTGA
1 GTTGTGGAC-TT-AAAAG--AAAAAAGAA--TGCCACTGA
391538 GTTGTGGACTT
1 GTTGTGGACTT
391549 TAGAAGGTTG
Statistics
Matches: 91, Mismatches: 16, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
32 4 0.04
33 16 0.18
34 37 0.41
35 11 0.12
38 5 0.05
39 2 0.02
40 16 0.18
ACGTcount: A:0.38, C:0.11, G:0.30, T:0.22
Consensus pattern (34 bp):
GTTGTGGACTTAAAAGAAAAAAGAATGCCACTGA
Found at i:391598 original size:29 final size:29
Alignment explanation
Indices: 391523--391606 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 29
391513 AAGAAAAAAA
* * *
391523 AAAAGGTGCCACTGAGTTGTGGACTTTAG
1 AAAAGATGCCACTGACTTGTGGGCTTTAG
* * * *
391552 -AAGGTTGCCACTGGCTTGTGGGCTTTGG
1 AAAAGATGCCACTGACTTGTGGGCTTTAG
*
391580 AAAAGATGCCACTGACTTGGGGGCTTT
1 AAAAGATGCCACTGACTTGTGGGCTTT
391607 TGAAGGGCGA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
28 22 0.50
29 22 0.50
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (29 bp):
AAAAGATGCCACTGACTTGTGGGCTTTAG
Found at i:393058 original size:16 final size:16
Alignment explanation
Indices: 393039--393075 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
393029 TCCGGACCCT
393039 TTTTGTTGTTTTTTTG
1 TTTTGTTGTTTTTTTG
* *
393055 TTTTGTTTTTTTTTTT
1 TTTTGTTGTTTTTTTG
393071 TTTTG
1 TTTTG
393076 CGGAGGACGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (16 bp):
TTTTGTTGTTTTTTTG
Found at i:397316 original size:44 final size:44
Alignment explanation
Indices: 397229--397316 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
397219 AGTGTACTCC
* *
397229 ACAGTTTCCAGGACCAGAACTGCTGAGAGAAAGGCACCGAAACA
1 ACAGTTTCCAGGACCAGAACTGCAGAGAGAAAGGCACCAAAACA
*
397273 ACAGTTTCCAGGACCAGAACTGCAGAGAGAAAGGCACTAAAACA
1 ACAGTTTCCAGGACCAGAACTGCAGAGAGAAAGGCACCAAAACA
397317 CAGCATGACC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (44 bp):
ACAGTTTCCAGGACCAGAACTGCAGAGAGAAAGGCACCAAAACA
Found at i:397926 original size:2 final size:2
Alignment explanation
Indices: 397919--397955 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
397909 TGGCCTAAAT
397919 TA TA TA 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 TA TA TA T
397956 CTGTTAATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:398605 original size:13 final size:13
Alignment explanation
Indices: 398589--398616 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
398579 GCGATCAATT
398589 ATAATAAATATTA
1 ATAATAAATATTA
398602 ATAATAAATATTA
1 ATAATAAATATTA
398615 AT
1 AT
398617 GATGAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATAATAAATATTA
Found at i:403956 original size:2 final size:2
Alignment explanation
Indices: 403951--403986 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
403941 ACAGACACTC
403951 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
403987 TATGAAGTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:404759 original size:13 final size:13
Alignment explanation
Indices: 404741--404765 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
404731 TTCAACGATT
404741 TGTATCGATACAA
1 TGTATCGATACAA
404754 TGTATCGATACA
1 TGTATCGATACA
404766 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:404855 original size:13 final size:13
Alignment explanation
Indices: 404837--404861 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
404827 ATTACTCAAA
404837 TGTATCGATACAT
1 TGTATCGATACAT
404850 TGTATCGATACA
1 TGTATCGATACA
404862 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:404914 original size:52 final size:52
Alignment explanation
Indices: 404870--404998 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
404860 CACTGATCTT
404870 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* * * *
404922 TGTATCGATACATACAGGCAAATTTGCCTAGATGTATCAATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
404974 GGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
404999 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:408717 original size:21 final size:21
Alignment explanation
Indices: 408691--408734 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
408681 CAGCCTTTCT
408691 TGCAAATTGGTGGAAGGAAAA
1 TGCAAATTGGTGGAAGGAAAA
*
408712 TGCAAATTGTTGGAAGGAAAA
1 TGCAAATTGGTGGAAGGAAAA
408733 TG
1 TG
408735 AACAAAACAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.05, G:0.32, T:0.23
Consensus pattern (21 bp):
TGCAAATTGGTGGAAGGAAAA
Found at i:409380 original size:20 final size:20
Alignment explanation
Indices: 409355--409397 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
409345 CACTCTATGG
409355 TCAATGTTTAAGCTAGCATC
1 TCAATGTTTAAGCTAGCATC
409375 TCAATGTTTAAGCTAGCATC
1 TCAATGTTTAAGCTAGCATC
409395 TCA
1 TCA
409398 TAAGCATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (20 bp):
TCAATGTTTAAGCTAGCATC
Found at i:413307 original size:32 final size:34
Alignment explanation
Indices: 413264--413332 Score: 97
Period size: 32 Copynumber: 2.1 Consensus size: 34
413254 ACAAGAGGGG
*
413264 AAAGAAAGGAAAAGAAAAATAGAG-AAA-AAAAT
1 AAAGAAAGGAAAAGAAAAAAAGAGAAAAGAAAAT
* *
413296 AAAGGAAGGAAAAGAAAAAAAGGGAAAAGAAAAT
1 AAAGAAAGGAAAAGAAAAAAAGAGAAAAGAAAAT
413330 AAA
1 AAA
413333 AAAAATTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 21 0.66
33 3 0.09
34 8 0.25
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (34 bp):
AAAGAAAGGAAAAGAAAAAAAGAGAAAAGAAAAT
Found at i:413321 original size:15 final size:15
Alignment explanation
Indices: 413271--413328 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
413261 GGGAAAGAAA
*
413271 GGAAAAGAAAAATAG
1 GGAAAAGAAAAAAAG
* *
413286 AGAAAA-AAATAAAGGAA
1 GGAAAAGAAA-AAA--AG
413303 GGAAAAGAAAAAAAG
1 GGAAAAGAAAAAAAG
413318 GGAAAAGAAAA
1 GGAAAAGAAAA
413329 TAAAAAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
14 3 0.09
15 19 0.56
17 9 0.26
18 3 0.09
ACGTcount: A:0.72, C:0.00, G:0.24, T:0.03
Consensus pattern (15 bp):
GGAAAAGAAAAAAAG
Found at i:415142 original size:16 final size:16
Alignment explanation
Indices: 415121--415153 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
415111 TTTTTTTTTT
415121 AAATTTCAAGGATTTC
1 AAATTTCAAGGATTTC
415137 AAATTTCAAGGATTTC
1 AAATTTCAAGGATTTC
415153 A
1 A
415154 TGTACCATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (16 bp):
AAATTTCAAGGATTTC
Found at i:417163 original size:32 final size:30
Alignment explanation
Indices: 417127--417185 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
417117 GAAATCAAAT
417127 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
417159 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
417186 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:417552 original size:20 final size:21
Alignment explanation
Indices: 417504--417559 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
417494 AAATTCCAAT
**
417504 AACATGTATCGATACATCTTT
1 AACATGTATCGATACATCTGC
**
417525 TTCATGTATCGATACAT-TGC
1 AACATGTATCGATACATCTGC
417545 AACATGTATCGATAC
1 AACATGTATCGATAC
417560 TTTGAATTGT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (21 bp):
AACATGTATCGATACATCTGC
Found at i:420026 original size:13 final size:13
Alignment explanation
Indices: 420008--420045 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
419998 ATAATCCCCC
420008 TGTATCGATACAG
1 TGTATCGATACAG
*
420021 TGTATCGATACAT
1 TGTATCGATACAG
420034 TGTATCGATACA
1 TGTATCGATACA
420046 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:422146 original size:15 final size:15
Alignment explanation
Indices: 422126--422155 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
422116 ATTTCGTTTG
*
422126 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
422141 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
422156 AGACATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.13, T:0.50
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:423989 original size:21 final size:21
Alignment explanation
Indices: 423960--424004 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
423950 AAGTTTTTAT
*
423960 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
423980 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
424002 TTT
1 TTT
424005 CAACTTCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:425921 original size:32 final size:30
Alignment explanation
Indices: 425885--425943 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
425875 GAAATCAAAT
425885 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
425917 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
425944 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:427360 original size:22 final size:21
Alignment explanation
Indices: 427332--427376 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
427322 ATATCTTGCT
427332 CACCT-AACGCATTACCCTAACA
1 CACCTAAACGC-TTA-CCTAACA
*
427354 CACCTAAATGCTTACCTAACA
1 CACCTAAACGCTTACCTAACA
427375 CA
1 CA
427377 TCACCTAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 9 0.43
22 8 0.38
23 4 0.19
ACGTcount: A:0.38, C:0.38, G:0.04, T:0.20
Consensus pattern (21 bp):
CACCTAAACGCTTACCTAACA
Found at i:427402 original size:34 final size:34
Alignment explanation
Indices: 427333--427444 Score: 163
Period size: 34 Copynumber: 3.3 Consensus size: 34
427323 TATCTTGCTC
* * *
427333 ACCTAACGCATTACCCTAACACACCTAA-ATGCTT
1 ACCTAACACATCA-CCTAACACACCTAATATACTT
427367 ACCTAACACATCACCTAACACACCTAATATACTT
1 ACCTAACACATCACCTAACACACCTAATATACTT
* *
427401 ACCTAACACACCACCTAACACACCTAATATACTC
1 ACCTAACACATCACCTAACACACCTAATATACTT
427435 ACCTAACACA
1 ACCTAACACA
427445 CCTAATATGT
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
33 14 0.19
34 58 0.81
ACGTcount: A:0.40, C:0.38, G:0.02, T:0.21
Consensus pattern (34 bp):
ACCTAACACATCACCTAACACACCTAATATACTT
Found at i:427423 original size:12 final size:12
Alignment explanation
Indices: 427367--427424 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
427357 CTAAATGCTT
*
427367 ACCTAACACATC
1 ACCTAACACACC
427379 ACCT-A-ACA-C
1 ACCTAACACACC
* * *
427388 ACCTAATATACTT
1 ACCTAACACAC-C
427401 ACCTAACACACC
1 ACCTAACACACC
427413 ACCTAACACACC
1 ACCTAACACACC
427425 TAATATACTC
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
9 5 0.14
10 4 0.11
11 3 0.08
12 16 0.43
13 9 0.24
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.17
Consensus pattern (12 bp):
ACCTAACACACC
Found at i:427440 original size:22 final size:21
Alignment explanation
Indices: 427412--427466 Score: 83
Period size: 22 Copynumber: 2.6 Consensus size: 21
427402 CCTAACACAC
427412 CACCTAACACACCTAATATACT
1 CACCTAACACACCTAATAT-CT
*
427434 CACCTAACACACCTAATATGT
1 CACCTAACACACCTAATATCT
*
427455 TACCTAACACAC
1 CACCTAACACAC
427467 TTAACAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 12 0.39
22 19 0.61
ACGTcount: A:0.40, C:0.36, G:0.02, T:0.22
Consensus pattern (21 bp):
CACCTAACACACCTAATATCT
Found at i:427445 original size:34 final size:34
Alignment explanation
Indices: 427347--427446 Score: 166
Period size: 34 Copynumber: 3.0 Consensus size: 34
427337 AACGCATTAC
* *
427347 CCTAACACACCTAA-ATGCTTACCTAACACATCA
1 CCTAACACACCTAATATACTTACCTAACACACCA
427380 CCTAACACACCTAATATACTTACCTAACACACCA
1 CCTAACACACCTAATATACTTACCTAACACACCA
*
427414 CCTAACACACCTAATATACTCACCTAACACACC
1 CCTAACACACCTAATATACTTACCTAACACACC
427447 TAATATGTTA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
33 14 0.22
34 49 0.78
ACGTcount: A:0.40, C:0.39, G:0.01, T:0.20
Consensus pattern (34 bp):
CCTAACACACCTAATATACTTACCTAACACACCA
Done.