Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2191
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: 67951
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:8020 original size:28 final size:28
Alignment explanation
Indices: 7980--8051 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
7970 GGAATAAAGC
** *
7980 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
8008 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
8036 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
8052 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:8109 original size:52 final size:51
Alignment explanation
Indices: 8040--8373 Score: 216
Period size: 52 Copynumber: 6.4 Consensus size: 51
8030 AAATAACGAG
* *
8040 GTTGGAGTATCCTCGATTGTGAAAAATTGGTAGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGT-GTTTTGGAAATAAAATCGGA
* * ** * *
8092 GTTGGAGTATCCCCGATTAAAGGAAAATTGGCATTTTGAAAATAAAACCAGG-
1 GTTGGAGTATCCCCGATT-ATGAAAAATTGGTGTTTTGGAAATAAAATC-GGA
* * * * *
8144 GTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCAGG-
1 GTTGGAGTATCCCCGATTAT-GAAAAATTGGTGTTTTGGAAATAAAATC-GGA
* * *** * * *
8196 GTTGGAGTATCCCC--TCA-GAAATAACGGGGTTGGAGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTATGAAA-AA-----TTGGTGT-T-TTGGA-AATAAAATCGGA
8251 GTTGGAGTATCCCCGATTATGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAA-AAATTGGTG--TTTTGGAAATAAAATCGGA
* * * *
8305 GTTAGAGTATCCCTGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGA-AAAATTGGTGTTTTGGAAATAAAATCGGA
*
8356 GTTGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
8374 GTGGAGAATT
Statistics
Matches: 218, Mismatches: 42, Indels: 45
0.71 0.14 0.15
Matches are distributed among these distances:
48 4 0.02
49 2 0.01
50 1 0.00
51 33 0.15
52 89 0.41
53 29 0.13
54 30 0.14
55 17 0.08
56 3 0.01
57 4 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAATAAAATCGGA
Found at i:8255 original size:27 final size:28
Alignment explanation
Indices: 8194--8267 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 28
8184 AATAAAACCA
*
8194 GGGTTGGAGTATCCCCTCA-GAAATAACG
1 GGGTTGGAGTATCCCC-GATGAAATAACG
*
8222 GGGTTGGAGTATCCCCGATG-ATTAACG
1 GGGTTGGAGTATCCCCGATGAAATAACG
8249 GGGTTGGAGTATCCCCGAT
1 GGGTTGGAGTATCCCCGAT
8268 TATGAAGAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 26 0.60
28 17 0.40
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.24
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCGATGAAATAACG
Found at i:8285 original size:107 final size:104
Alignment explanation
Indices: 7926--8317 Score: 312
Period size: 107 Copynumber: 3.7 Consensus size: 104
7916 CCTTCGAAAA
* * * * * * *
7926 TAACGAGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAG
1 TAACGAGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACC-GGGTTGGAG
* *
7991 TATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAA
65 TATCCCCTC-GAAATAACGGGGTTGGAGTATCCCCGATG-AT
* * * *
8033 TAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTAGTTTTGGAAATAAAATCGGAGTTGGA
1 TAACGAGGTTGGAGTATCCCCGATTATGAAAAATTAGT-GTTTTGGAAATAAAACCGG-GTTGGA
* * ** ** **
8098 GTAT-CCC-CG-ATTAAAGGAAAATTGGCA-T-T--TTGAAAAT
64 GTATCCCCTCGAAATAACGG--GGTTGG-AGTATCCCCGATGAT
* * * * *
8135 AAAACCAGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCAGGGTTG
1 -TAACGA-GGTTGGAGTATCCCCGATTAT-GAAAAATTAGTGTTTTGGAAATAAAACC-GGGTTG
8200 GAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAT
62 GAGTATCCCCTC-GAAATAACGGGGTTGGAGTATCCCCGATGAT
* * * *
8244 TAACGGGGTTGGAGTATCCCCGATTATGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 TAACGAGGTTGGAGTATCCCCGATTATGAA-AAATTAGTG--TTTTGGAAATAAAACCGG-GTTG
8309 GAGTATCCC
62 GAGTATCCC
8318 TGATTATAGA
Statistics
Matches: 220, Mismatches: 44, Indels: 40
0.72 0.14 0.13
Matches are distributed among these distances:
102 1 0.00
103 6 0.03
104 50 0.23
105 18 0.08
106 15 0.07
107 67 0.30
108 34 0.15
109 29 0.13
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.27
Consensus pattern (104 bp):
TAACGAGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGGGTTGGAGT
ATCCCCTCGAAATAACGGGGTTGGAGTATCCCCGATGAT
Found at i:8332 original size:212 final size:211
Alignment explanation
Indices: 7932--8378 Score: 605
Period size: 212 Copynumber: 2.1 Consensus size: 211
7922 AAAATAACGA
* * * * * * *
7932 GGTTGGAGTATCCCCAATTAT-GAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTGTGGAAAAATCAATATTTTAGCAATAAAACCAGGGTTGGAGTATCC
* * * *
7996 CCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTG
66 CCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGATTATG
* *
8061 AAAAATTGGTAGTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGCAT
131 AAAAATTGGTAGTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAAAGGAAAATTAGCAT
8126 TTTGAAAATAAAACCAG
196 TTTGAAAATAAAACC-G
* * *
8143 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCAGGGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTGTGGAAAAATCAATATTTTAGCAATAAAACCAGGGTTGGAGTATCC
* *
8208 CCTCAGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGTATCCCCGATTATG
66 CCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGATTATG
* *
8272 AAGAAATTGGT-GTTTTTTGGAAATAAAATCGGAGTTAGAGTATCCCTGATTATA-GAAAATTAG
131 AA-AAATTGGTAG--TTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAAAGGAAAATTAG
** *
8335 TGTTTTGAAAATAAAATCG
193 CATTTTGAAAATAAAACCG
*
8354 GAGTTGGAATATCCCCGATTGTGGA
1 G-GTTGGAGTATCCCCGATTGTGGA
8379 GAATTAACGA
Statistics
Matches: 207, Mismatches: 24, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
211 50 0.24
212 120 0.58
213 37 0.18
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (211 bp):
GGTTGGAGTATCCCCGATTGTGGAAAAATCAATATTTTAGCAATAAAACCAGGGTTGGAGTATCC
CCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGATTATG
AAAAATTGGTAGTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAAAGGAAAATTAGCAT
TTTGAAAATAAAACCG
Found at i:8384 original size:51 final size:52
Alignment explanation
Indices: 8251--8384 Score: 162
Period size: 51 Copynumber: 2.6 Consensus size: 52
8241 GATTAACGGG
* * *
8251 GTTGGAGTATCCCCGATTATGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGGAG-AATTAGTG-TTTTTGAAAATAAAATCGGA
* * * *
8305 GTTAGAGTATCCCTGATTATAGAAAATTAGTG-TTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGGAGAATTAGTGTTTTTGAAAATAAAATCGGA
* *
8356 GTTGGAATATCCCCGATTGTGGAGAATTA
1 GTTGGAGTATCCCCGATTATGGAGAATTA
8385 ACGAACTCAA
Statistics
Matches: 67, Mismatches: 13, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
51 41 0.61
53 7 0.10
54 19 0.28
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.33
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATGGAGAATTAGTGTTTTTGAAAATAAAATCGGA
Found at i:13403 original size:13 final size:13
Alignment explanation
Indices: 13385--13422 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
13375 ATAAACCTTT
*
13385 TGTATCGATACAC
1 TGTATCGATACAA
13398 TGTATCGATACAA
1 TGTATCGATACAA
*
13411 TGTATTGATACA
1 TGTATCGATACA
13423 GAGAATGCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:13638 original size:8 final size:8
Alignment explanation
Indices: 13620--13650 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
13610 ATTTCAATAT
13620 CAAACATCA
1 CAAA-ATCA
13629 CAAAATCA
1 CAAAATCA
13637 CAAAATCA
1 CAAAATCA
13645 CAAAAT
1 CAAAAT
13651 TTAATCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (8 bp):
CAAAATCA
Found at i:14371 original size:20 final size:19
Alignment explanation
Indices: 14327--14379 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
14317 GTAGCCAAAC
* *
14327 TTGTATCGATACACCAAAG
1 TTGTATCGATACACAAAAA
14346 TATGTATCGATACACAAAAAA
1 T-TGTATCGATACAC-AAAAA
*
14367 TTGTATCTATACA
1 TTGTATCGATACA
14380 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 24 0.83
21 4 0.14
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (19 bp):
TTGTATCGATACACAAAAA
Found at i:20915 original size:13 final size:13
Alignment explanation
Indices: 20897--20922 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20887 TACAAAAAGT
20897 ATGTATCGATACA
1 ATGTATCGATACA
20910 ATGTATCGATACA
1 ATGTATCGATACA
20923 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:20920 original size:32 final size:33
Alignment explanation
Indices: 20879--20942 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
20869 TAGCCAAACT
*
20879 TGTATCGAT--ACAAAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAAT-TGTATCGATACAA
20911 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
20943 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 9 0.31
33 12 0.41
34 8 0.28
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:22683 original size:15 final size:15
Alignment explanation
Indices: 22663--22693 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
22653 TAAAAATGTC
*
22663 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
22678 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
22693 C
1 C
22694 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:27311 original size:13 final size:13
Alignment explanation
Indices: 27293--27318 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27283 TACACAAAGT
27293 ATGTATCGATACA
1 ATGTATCGATACA
27306 ATGTATCGATACA
1 ATGTATCGATACA
27319 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:28130 original size:13 final size:13
Alignment explanation
Indices: 28108--28146 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
28098 ACATTATTCT
28108 TTGTATCGATACA
1 TTGTATCGATACA
*
28121 TTGTACCGATACA
1 TTGTATCGATACA
*
28134 CTGTATCGATACA
1 TTGTATCGATACA
28147 GGGGGATTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:30639 original size:20 final size:21
Alignment explanation
Indices: 30616--30670 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
30606 ACAATTTAAA
* *
30616 GTATCGATACATGTTGCA-AT
1 GTATCGATACATGTAGAAGAT
*
30636 GTATCGATACATGAAGAAGAT
1 GTATCGATACATGTAGAAGAT
30657 GTATCGATACATGT
1 GTATCGATACATGT
30671 CATTGAGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.31
Consensus pattern (21 bp):
GTATCGATACATGTAGAAGAT
Found at i:30736 original size:13 final size:13
Alignment explanation
Indices: 30718--30743 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30708 TACACAAAGT
30718 ATGTATCGATACA
1 ATGTATCGATACA
30731 ATGTATCGATACA
1 ATGTATCGATACA
30744 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:30741 original size:32 final size:33
Alignment explanation
Indices: 30700--30763 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
30690 TAGCCAAACT
**
30700 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
30732 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
30764 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:31555 original size:20 final size:20
Alignment explanation
Indices: 31527--31566 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
31517 ACATCTAAAA
31527 ATTCATTGTATCGATACATT
1 ATTCATTGTATCGATACATT
*
31547 ATTCTTTGTATCGATACATT
1 ATTCATTGTATCGATACATT
31567 GTATCGATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (20 bp):
ATTCATTGTATCGATACATT
Found at i:31570 original size:13 final size:13
Alignment explanation
Indices: 31552--31590 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
31542 ACATTATTCT
31552 TTGTATCGATACA
1 TTGTATCGATACA
31565 TTGTATCGATACA
1 TTGTATCGATACA
*
31578 CTGTATCGATACA
1 TTGTATCGATACA
31591 AGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:37710 original size:13 final size:13
Alignment explanation
Indices: 37692--37717 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37682 CAACATTTTG
37692 TGTATCGATACAT
1 TGTATCGATACAT
37705 TGTATCGATACAT
1 TGTATCGATACAT
37718 ACTTTGGTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:37714 original size:33 final size:33
Alignment explanation
Indices: 37672--37736 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
37662 TACAAGCCAA
*
37672 TGTATCGATACA-ACATTTTGTGTATCGATACAT
1 TGTATCGATACATAC-TTTGGTGTATCGATACAT
37705 TGTATCGATACATACTTTGGTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
37737 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.38
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:40322 original size:13 final size:13
Alignment explanation
Indices: 40304--40342 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
40294 ATAATCCCTT
*
40304 TGTATCGATACAG
1 TGTATCGATACAA
40317 TGTATCGATACAA
1 TGTATCGATACAA
40330 TGTATCGATACAA
1 TGTATCGATACAA
40343 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:40353 original size:20 final size:20
Alignment explanation
Indices: 40328--40406 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
40318 GTATCGATAC
40328 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
**
40348 AATGTATCGATACATTGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
40373 AATGTATCGATACAGAGAAA
1 AATGTATCGATACAAAGAAA
*
40393 CATGTATCGATACA
1 AATGTATCGATACA
40407 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
20 31 0.63
25 18 0.37
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:48822 original size:8 final size:8
Alignment explanation
Indices: 48804--48834 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
48794 ATTTCAACAT
48804 CAAACATCA
1 CAAA-ATCA
48813 CAAAATCA
1 CAAAATCA
48821 CAAAATCA
1 CAAAATCA
48829 CAAAAT
1 CAAAAT
48835 TTAATCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (8 bp):
CAAAATCA
Found at i:53133 original size:3 final size:3
Alignment explanation
Indices: 53125--53155 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
53115 TCTGATTCAC
*
53125 CAT CAT CAT CAT CAT CAT CAT CAT CTT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
53156 GTCCTTGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:55373 original size:19 final size:18
Alignment explanation
Indices: 55348--55412 Score: 59
Period size: 19 Copynumber: 3.8 Consensus size: 18
55338 ATTTCAACAA
55348 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
* *
55366 TGTTGTATCCATTC--AA-
1 T-TTGTATCGATACATAAG
55382 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
55398 TTTTGTATCGATACA
1 -TTTGTATCGATACA
55413 ATGTATCGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 13
0.68 0.08 0.25
Matches are distributed among these distances:
13 9 0.25
15 2 0.06
17 2 0.06
18 1 0.03
19 22 0.61
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:55391 original size:32 final size:32
Alignment explanation
Indices: 55350--55420 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
55340 TTCAACAATT
*
55350 TGTATCGATACATAAGTGTTGTATCCATTCAA
1 TGTATCGATACATAAGTGTTGTATCCATACAA
* *
55382 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCCATACAA
55414 TGTATCG
1 TGTATCG
55421 CTATGAAGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCCATACAA
Found at i:55483 original size:13 final size:13
Alignment explanation
Indices: 55465--55489 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55455 ATTACTCAAA
55465 TGTATCGATACAT
1 TGTATCGATACAT
55478 TGTATCGATACA
1 TGTATCGATACA
55490 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:55534 original size:32 final size:31
Alignment explanation
Indices: 55443--55542 Score: 92
Period size: 32 Copynumber: 3.1 Consensus size: 31
55433 TGCCAAGAAA
**
55443 ATGTATCGATACATTACTCAAATGTATCGATAC
1 ATGTATCGATACACCA-T-AAATGTATCGATAC
* *** *
55476 ATTGTATCGATACACTGATCTTTGTATCAATAC
1 A-TGTATCGATACAC-CATAAATGTATCGATAC
55509 ATGTATCGATACACCATAAAATGTATCGATAC
1 ATGTATCGATACACCAT-AAATGTATCGATAC
55541 AT
1 AT
55543 ACAGGCAAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
31 2 0.04
32 25 0.47
33 12 0.23
34 13 0.25
35 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (31 bp):
ATGTATCGATACACCATAAATGTATCGATAC
Found at i:55565 original size:52 final size:52
Alignment explanation
Indices: 55509--55658 Score: 264
Period size: 52 Copynumber: 2.9 Consensus size: 52
55499 GTATCAATAC
55509 ATGTATCGATACACCATAAAATGTATCGATACATACAGGCAAATTTGCCCAG
1 ATGTATCGATACACCATAAAATGTATCGATACATACAGGCAAATTTGCCCAG
55561 ATGTATCGATACACCATAAAATGTATCGATACATACAGGCAAATTTGCCCAG
1 ATGTATCGATACACCATAAAATGTATCGATACATACAGGCAAATTTGCCCAG
* * * *
55613 ATGTATCGATACACTATGAAATGTATCGATACATGCAGGTAAATTT
1 ATGTATCGATACACCATAAAATGTATCGATACATACAGGCAAATTT
55659 TCATATTTCG
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 94 1.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (52 bp):
ATGTATCGATACACCATAAAATGTATCGATACATACAGGCAAATTTGCCCAG
Found at i:55849 original size:19 final size:18
Alignment explanation
Indices: 55824--55920 Score: 79
Period size: 19 Copynumber: 5.8 Consensus size: 18
55814 ATTTGAACGA
55824 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
55842 TGTTGTATCGAT--AGAA-
1 T-TTGTATCGATACATAAG
55858 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
55874 TGTTGTATCAATAC--AA-
1 T-TTGTATCGATACATAAG
55890 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
55906 TTTTGTATCGATACA
1 -TTTGTATCGATACA
55921 ATGTATCGCT
Statistics
Matches: 62, Mismatches: 4, Indels: 25
0.68 0.04 0.27
Matches are distributed among these distances:
13 19 0.31
15 5 0.08
17 5 0.08
18 1 0.02
19 32 0.52
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:55862 original size:32 final size:32
Alignment explanation
Indices: 55826--55928 Score: 179
Period size: 32 Copynumber: 3.2 Consensus size: 32
55816 TTGAACGATT
*
55826 TGTATCGATACATAAGTGTTGTATCGATAGAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
55858 TGTATCGATACATAAGTGTTGTATCAATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
55890 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
55922 TGTATCG
1 TGTATCG
55929 CTATGAAGCT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 67 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:55991 original size:13 final size:13
Alignment explanation
Indices: 55973--55997 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55963 ATTACTCAAA
55973 TGTATCGATACAT
1 TGTATCGATACAT
55986 TGTATCGATACA
1 TGTATCGATACA
55998 CTTATCTTTG
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:55995 original size:34 final size:33
Alignment explanation
Indices: 55952--56018 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
55942 ACCAAGAAAA
55952 TGTATCGATACA-TTACTCAAATGTATCGATACAT
1 TGTATCGATACACTTA-TC-AATGTATCGATACAT
**
55986 TGTATCGATACACTTATCTTTGTATCGATACAT
1 TGTATCGATACACTTATCAATGTATCGATACAT
56019 GCAGGCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 13 0.43
34 14 0.47
35 3 0.10
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (33 bp):
TGTATCGATACACTTATCAATGTATCGATACAT
Found at i:56050 original size:52 final size:52
Alignment explanation
Indices: 56006--56134 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
55996 CACTTATCTT
*
56006 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACCATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
56058 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
56110 TGTATCGATACATGCAGGTAAATTT
1 TGTATCGATACATGCAGGCAAATTT
56135 TCATATTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:62396 original size:13 final size:13
Alignment explanation
Indices: 62378--62403 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
62368 TACAAGCCAA
62378 TGTATCGATACAT
1 TGTATCGATACAT
62391 TGTATCGATACAT
1 TGTATCGATACAT
62404 ACTTTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:62501 original size:20 final size:20
Alignment explanation
Indices: 62476--62541 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
62466 TCTTTTTCAA
62476 GTATCGATACAATGCAACAT
1 GTATCGATACAATGCAACAT
62496 GTATCGATAC-A-G-----T
1 GTATCGATACAATGCAACAT
**
62509 GTATCGATACTGTGCAACAT
1 GTATCGATACAATGCAACAT
62529 GTATCGATACAAT
1 GTATCGATACAAT
62542 TAAATGTGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 14
0.68 0.06 0.26
Matches are distributed among these distances:
13 11 0.31
15 1 0.03
18 1 0.03
19 1 0.03
20 22 0.61
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (20 bp):
GTATCGATACAATGCAACAT
Found at i:62515 original size:33 final size:33
Alignment explanation
Indices: 62476--62539 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
62466 TCTTTTTCAA
62476 GTATCGATACAATGCAACATGTATCGATACAGT
1 GTATCGATACAATGCAACATGTATCGATACAGT
**
62509 GTATCGATACTGTGCAACATGTATCGATACA
1 GTATCGATACAATGCAACATGTATCGATACA
62540 ATTAAATGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (33 bp):
GTATCGATACAATGCAACATGTATCGATACAGT
Found at i:65010 original size:20 final size:21
Alignment explanation
Indices: 64967--65050 Score: 64
Period size: 20 Copynumber: 3.9 Consensus size: 21
64957 CCCTGTATCG
* *
64967 ATACAATGTATTGATACAAAGA
1 ATAC-ATGTATCGATACATAGA
*
64989 ATA-ATGTATCGATACATTGA
1 ATACATGTATCGATACATAGA
* *
65009 ATTTCCAGATGTATTGATACATAGA
1 A--T--ACATGTATCGATACATAGA
65034 A-ACATGTATCGATACAT
1 ATACATGTATCGATACAT
65051 TTTGGAAATT
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
20 29 0.58
22 4 0.08
24 1 0.02
25 16 0.32
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (21 bp):
ATACATGTATCGATACATAGA
Found at i:65405 original size:23 final size:22
Alignment explanation
Indices: 65376--65440 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 22
65366 GGGAGTATGA
65376 GATACATCATTCTTTGTATCATT
1 GATACATCATTCTTTGTATCA-T
65399 G-TCACATCATTCTTTGTATC--
1 GAT-ACATCATTCTTTGTATCAT
65419 GATACATCATTCTTTGTATCAT
1 GATACATCATTCTTTGTATCAT
65441 CCCTAGCCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
20 18 0.47
21 1 0.03
22 1 0.03
23 18 0.47
ACGTcount: A:0.25, C:0.20, G:0.09, T:0.46
Consensus pattern (22 bp):
GATACATCATTCTTTGTATCAT
Found at i:66937 original size:15 final size:15
Alignment explanation
Indices: 66917--66957 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
66907 ATTCATCAAT
66917 TTCATTTGGAGCTTC
1 TTCATTTGGAGCTTC
*
66932 TTCATTTTGAGCTTC
1 TTCATTTGGAGCTTC
*
66947 CTCAATTTGGA
1 TTC-ATTTGGA
66958 CATTTTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (15 bp):
TTCATTTGGAGCTTC
Done.