Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014346.1 Kokia drynarioides strain JFW-HI SEQ_129383, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 106655
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5212 original size:53 final size:52
Alignment explanation
Indices: 5107--5344 Score: 280
Period size: 52 Copynumber: 4.6 Consensus size: 52
5097 ATAATTTAAT
* * ** *
5107 ACTCACAATGACACATAGTCATC-GAGCCTCTTGTTCCGTAAAGGAATCATAC
1 ACTCACGATGACACATAGTCATCGGA-CCTCATAATCCGTAAAGGATTCATAC
* * *
5159 ACTCATGATGACACATAGTTATCGGACCTTATAATCCCGTAAAGGATTCATAC
1 ACTCACGATGACACATAGTCATCGGACCTCATAAT-CCGTAAAGGATTCATAC
* * *
5212 ACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGTATTCATAT
1 ACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATAC
* * * * * *
5264 ACTCGCGGTGACACATATTCATCGAACCTCATAATCCTTAAAGGATTCATAT
1 ACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATAC
* *
5316 ACTCATGATGACACTTAGTCATCGGACCT
1 ACTCACGATGACACATAGTCATCGGACCT
5345 TTTTCATTTA
Statistics
Matches: 158, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
52 108 0.68
53 50 0.32
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.27
Consensus pattern (52 bp):
ACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATAC
Found at i:5254 original size:105 final size:104
Alignment explanation
Indices: 5107--5344 Score: 282
Period size: 105 Copynumber: 2.3 Consensus size: 104
5097 ATAATTTAAT
* * ** * *
5107 ACTCACAATGACACATAGTCATC-GAGCCTCTTGTTCCGTAAAGGAATCATACACTCATGATGAC
1 ACTCACGATGACACATAGTCATCGGA-CCTCATAATCCATAAAGGAATCATACACTCACGATGAC
* *
5171 ACATAGTT-ATCGGACCTTATAATCCCGTAAAGGATTCATAC
65 ACATA-TTCATCGAACCTCATAAT-CCGTAAAGGATTCATAC
* * * * *
5212 ACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGTATTCATATACTCGCGGTGACA
1 ACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGAATCATACACTCACGATGACA
* *
5277 CATATTCATCGAACCTCATAATCCTTAAAGGATTCATAT
66 CATATTCATCGAACCTCATAATCCGTAAAGGATTCATAC
* *
5316 ACTCATGATGACACTTAGTCATCGGACCT
1 ACTCACGATGACACATAGTCATCGGACCT
5345 TTTTCATTTA
Statistics
Matches: 114, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
104 44 0.39
105 68 0.60
106 2 0.02
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.27
Consensus pattern (104 bp):
ACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGAATCATACACTCACGATGACA
CATATTCATCGAACCTCATAATCCGTAAAGGATTCATAC
Found at i:11411 original size:14 final size:15
Alignment explanation
Indices: 11392--11421 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
11382 TCGGTGTTTT
11392 ACTGTTCAT-TTATC
1 ACTGTTCATCTTATC
11406 ACTGTTCATCTTATC
1 ACTGTTCATCTTATC
11421 A
1 A
11422 TTATATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.47
Consensus pattern (15 bp):
ACTGTTCATCTTATC
Found at i:12453 original size:52 final size:51
Alignment explanation
Indices: 12339--12472 Score: 162
Period size: 52 Copynumber: 2.6 Consensus size: 51
12329 ATTTCATTTA
* * **
12339 ATACTCACGATGAAATATAGTCATCGGACCTCTTGTCAGTAAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCTAATCAGTAAAGGAATCAT
* * *
12390 ACACTCACGATGACACATAGTCATCGGAGCTCATAATCCGTAAA-GAATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTC-TAATCAGTAAAGGAA-TCAT
* *
12442 ATACTCACGATGACACTTAGTCATTGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
12473 TTTTCATTTA
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
51 31 0.44
52 39 0.56
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.26
Consensus pattern (51 bp):
ATACTCACGATGACACATAGTCATCGGACCTCTAATCAGTAAAGGAATCAT
Found at i:15209 original size:23 final size:23
Alignment explanation
Indices: 15182--15225 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
15172 AATGAATTTT
*
15182 TTATTCTATTT-TTATTATTATCA
1 TTATTCT-TTTATCATTATTATCA
15205 TTATTCTTTTATCATTATTAT
1 TTATTCTTTTATCATTATTAT
15226 TTTAATTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (23 bp):
TTATTCTTTTATCATTATTATCA
Found at i:15216 original size:14 final size:14
Alignment explanation
Indices: 15193--15229 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
15183 TATTCTATTT
15193 TTATTATTATCATTA
1 TTATT-TTATCATTA
*
15208 TTCTTTTATCATTA
1 TTATTTTATCATTA
15222 TTATTTTA
1 TTATTTTA
15230 ATTTGTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTTATCATTA
Found at i:20015 original size:5 final size:5
Alignment explanation
Indices: 20001--20034 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
19991 AAAGATTATA
20001 AATA- AATAT AATAT AAATAT AATAT AATAT AATA
1 AATAT AATAT AATAT -AATAT AATAT AATAT AATA
20035 ATATTAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (5 bp):
AATAT
Found at i:20018 original size:11 final size:11
Alignment explanation
Indices: 19997--20034 Score: 62
Period size: 10 Copynumber: 3.6 Consensus size: 11
19987 ATTAAAAGAT
19997 TATAA-ATAAA
1 TATAATATAAA
20007 TATAATATAAA
1 TATAATATAAA
20018 TATAATAT-AA
1 TATAATATAAA
20028 TATAATA
1 TATAATA
20035 ATATTAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 14 0.52
11 13 0.48
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TATAATATAAA
Found at i:20026 original size:16 final size:15
Alignment explanation
Indices: 19997--20032 Score: 63
Period size: 16 Copynumber: 2.3 Consensus size: 15
19987 ATTAAAAGAT
19997 TATAAATAAATATAA
1 TATAAATAAATATAA
20012 TATAAATATAATATAA
1 TATAAATA-AATATAA
20028 TATAA
1 TATAA
20033 TAATATTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATAAATATAA
Found at i:21250 original size:22 final size:21
Alignment explanation
Indices: 21218--21268 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
21208 TTTGTCATAA
21218 TTTTAT-A-AAAT-TATAACTT
1 TTTTATAATAAATATATAA-TT
*
21237 TTTTATGAATAAATATATTATT
1 TTTTAT-AATAAATATATAATT
21259 TTTTATAATA
1 TTTTATAATA
21269 TATAGCATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 6 0.22
21 5 0.19
22 12 0.44
23 4 0.15
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTTATAATAAATATATAATT
Found at i:22861 original size:22 final size:25
Alignment explanation
Indices: 22817--22865 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
22807 ATCAACATAA
22817 TAATAACATATCTCAACAGCAACATT
1 TAATAACATA-CTCAACAGCAACATT
22843 TAATAACATA-T-AACA-CAACATT
1 TAATAACATACTCAACAGCAACATT
22865 T
1 T
22866 CGTGCAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.35
23 4 0.17
24 1 0.04
26 10 0.43
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.29
Consensus pattern (25 bp):
TAATAACATACTCAACAGCAACATT
Found at i:25038 original size:29 final size:29
Alignment explanation
Indices: 24996--25058 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
24986 TTAAATTGGT
24996 ACTAACCAGTCAGTTGGATCGTTAATGAC
1 ACTAACCAGTCAGTTGGATCGTTAATGAC
25025 ACTAACCAGTCAGTTGGATCGTTAATGAC
1 ACTAACCAGTCAGTTGGATCGTTAATGAC
25054 ACTAA
1 ACTAA
25059 GCAAGCTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (29 bp):
ACTAACCAGTCAGTTGGATCGTTAATGAC
Found at i:38545 original size:21 final size:21
Alignment explanation
Indices: 38511--38576 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
38501 AGAAGAGAGT
**
38511 TAACATTTACTGTTTAAAAAA
1 TAACATTTGTTGTTTAAAAAA
* *
38532 TATCATTTGTTGTTTAGTAAAAT
1 TAACATTTGTTGTTTA--AAAAA
* *
38555 TAACATTTTTTGTATAAAAAA
1 TAACATTTGTTGTTTAAAAAA
38576 T
1 T
38577 GTCTTGAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.51
23 17 0.49
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (21 bp):
TAACATTTGTTGTTTAAAAAA
Found at i:54297 original size:25 final size:24
Alignment explanation
Indices: 54252--54298 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
54242 AGGGGGATTC
**
54252 TTATTTTATCTAATATTAATATAA
1 TTATTTTATCTAATACAAATATAA
*
54276 TTATATTTATTTAATACAAATAT
1 TTAT-TTTATCTAATACAAATAT
54299 TAATATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
TTATTTTATCTAATACAAATATAA
Found at i:55716 original size:32 final size:32
Alignment explanation
Indices: 55673--55736 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
55663 CCAGTTAACA
*
55673 AAATAATTTTTATTCATCCTTTTTAAAAGTAT
1 AAATAACTTTTATTCATCCTTTTTAAAAGTAT
55705 AAATAACTTTTATTCATCCTTTTTAAAAGTAT
1 AAATAACTTTTATTCATCCTTTTTAAAAGTAT
55737 TTTAGATCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.48
Consensus pattern (32 bp):
AAATAACTTTTATTCATCCTTTTTAAAAGTAT
Found at i:61150 original size:2 final size:2
Alignment explanation
Indices: 61145--61192 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
61135 CTCTCTCTCT
* *
61145 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA AA CA CA AA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
61187 CA CA CA
1 CA CA CA
61193 AGTGCAAGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.54, C:0.46, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:61493 original size:2 final size:2
Alignment explanation
Indices: 61486--61515 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
61476 TTCAAACACG
61486 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
61516 TGGTTACTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:62128 original size:15 final size:15
Alignment explanation
Indices: 62093--62140 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
62083 TAACAAAACG
*
62093 ATAAGTATTTAAAAT
1 ATAAATATTTAAAAT
*
62108 AT-AATATTTCAAAT
1 ATAAATATTTAAAAT
*
62122 ATAAATAATTAAAAT
1 ATAAATATTTAAAAT
62137 ATAA
1 ATAA
62141 TCTGAAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 12 0.43
15 16 0.57
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (15 bp):
ATAAATATTTAAAAT
Found at i:63304 original size:17 final size:15
Alignment explanation
Indices: 63282--63322 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 15
63272 AATTAGTCTT
63282 AAAAGTTTTTTGTACCA
1 AAAAGTTTTTTGTA--A
63299 AAAAGTATTTTTGTAA
1 AAAAGT-TTTTTGTAA
63315 AAAAGTTT
1 AAAAGTTT
63323 ATTCCAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 2 0.09
16 7 0.30
17 6 0.26
18 8 0.35
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.41
Consensus pattern (15 bp):
AAAAGTTTTTTGTAA
Found at i:63384 original size:18 final size:17
Alignment explanation
Indices: 63343--63385 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
63333 AAAATACATT
63343 TTATTTATTTTCAAAAAA
1 TTATTT-TTTTCAAAAAA
* *
63361 TAATTTTTTTCAAACAAC
1 TTATTTTTTTCAAA-AAA
63379 TTATTTT
1 TTATTTT
63386 GTAAAATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATTTTTTTCAAAAAA
Found at i:64783 original size:21 final size:21
Alignment explanation
Indices: 64759--64829 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
64749 ATCTAATGGA
64759 ATTTGTTTGGAATGTTAAATG
1 ATTTGTTTGGAATGTTAAATG
* * **
64780 ATTTATTTAGCCT-TTATCTAATGG
1 ATTTGTTTGGAATGTTA---AAT-G
64804 AATTTGTTTGGAATGTTAAATG
1 -ATTTGTTTGGAATGTTAAATG
64826 ATTT
1 ATTT
64830 ATTTAGCCCT
Statistics
Matches: 36, Mismatches: 8, Indels: 12
0.64 0.14 0.21
Matches are distributed among these distances:
20 3 0.08
21 13 0.36
22 1 0.03
23 6 0.17
24 1 0.03
25 9 0.25
26 3 0.08
ACGTcount: A:0.28, C:0.04, G:0.18, T:0.49
Consensus pattern (21 bp):
ATTTGTTTGGAATGTTAAATG
Found at i:64795 original size:46 final size:46
Alignment explanation
Indices: 64745--64837 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
64735 AATGGGTGTT
64745 CTTTATCTAATGGAATTTGTTTGGAATGTTAAATGATTTATTTAGC
1 CTTTATCTAATGGAATTTGTTTGGAATGTTAAATGATTTATTTAGC
64791 CTTTATCTAATGGAATTTGTTTGGAATGTTAAATGATTTATTTAGC
1 CTTTATCTAATGGAATTTGTTTGGAATGTTAAATGATTTATTTAGC
64837 C
1 C
64838 CTTGTACGCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.47
Consensus pattern (46 bp):
CTTTATCTAATGGAATTTGTTTGGAATGTTAAATGATTTATTTAGC
Found at i:68437 original size:43 final size:43
Alignment explanation
Indices: 68383--68471 Score: 142
Period size: 43 Copynumber: 2.1 Consensus size: 43
68373 TTTGTTAATG
* * *
68383 TTAGTGGTGTTTGTGGGAAAAGCGTCGCTAAAGATCATGTTCT
1 TTAGCGGTGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
*
68426 TTAGCGGTGTTTGTGGGAAAAGCGCCGTTAAAGACCATGTTCT
1 TTAGCGGTGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
68469 TTA
1 TTA
68472 ACGGCTTAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.34
Consensus pattern (43 bp):
TTAGCGGTGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
Found at i:69515 original size:15 final size:15
Alignment explanation
Indices: 69495--69562 Score: 59
Period size: 15 Copynumber: 4.4 Consensus size: 15
69485 ATACTACAAA
69495 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
69510 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
69527 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
*
69544 ATA-TTAATATTAA-
1 ATATTTATTATTAAT
69557 ATATTT
1 ATATTT
69563 TCAATAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
13 3 0.07
14 11 0.25
15 12 0.27
16 1 0.02
17 7 0.16
18 1 0.02
19 9 0.20
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:69560 original size:49 final size:49
Alignment explanation
Indices: 69492--69606 Score: 132
Period size: 49 Copynumber: 2.3 Consensus size: 49
69482 TTTATACTAC
69492 AAAATATTTATTATT-AATATATTT-ATAAT-TGT-AATAAATATTTATTATT
1 AAAATA-TTATTATTAAATAT-TTTAATAATATGTGAA-AAATA-TTATTATT
* *
69541 AAAATATTAATATTAAATATTTTCAATAATATGTGAAAAATATTATTTTT
1 AAAATATTATTATTAAATATTTT-AATAATATGTGAAAAATATTATTATT
69591 AAAAT-TTATTATTAAA
1 AAAATATTATTATTAAA
69607 ATAAAATTGA
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
48 10 0.17
49 21 0.36
50 17 0.29
51 8 0.14
52 2 0.03
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.49
Consensus pattern (49 bp):
AAAATATTATTATTAAATATTTTAATAATATGTGAAAAATATTATTATT
Found at i:69605 original size:13 final size:14
Alignment explanation
Indices: 69577--69609 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
69567 TAATATGTGA
*
69577 AAAATATTATTTTT
1 AAAATATTATTATT
69591 AAAAT-TTATTATT
1 AAAATATTATTATT
69604 AAAATA
1 AAAATA
69610 AAATTGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAATATTATTATT
Found at i:85972 original size:16 final size:16
Alignment explanation
Indices: 85951--86008 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
85941 ACTCTTACTT
*
85951 TTTAATTAAGATGATA
1 TTTAATTAAAATGATA
*
85967 TTTAATAAAAAT-A-A
1 TTTAATTAAAATGATA
*
85981 GTTTAATTAATATGATA
1 -TTTAATTAAAATGATA
85998 -TTACATTAAAA
1 TTTA-ATTAAAA
86009 AGAATAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
14 1 0.03
15 14 0.42
16 17 0.52
17 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (16 bp):
TTTAATTAAAATGATA
Found at i:88853 original size:24 final size:24
Alignment explanation
Indices: 88813--88862 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
88803 ATAGATGTTC
*
88813 AACCTTTCATTTCCTTTAACCTTT
1 AACCTTCCATTTCCTTTAACCTTT
88837 AACCTTCCATCTT-CTTTAACCTTT
1 AACCTTCCAT-TTCCTTTAACCTTT
88861 AA
1 AA
88863 TATTCTTGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.24, C:0.30, G:0.00, T:0.46
Consensus pattern (24 bp):
AACCTTCCATTTCCTTTAACCTTT
Found at i:94284 original size:35 final size:33
Alignment explanation
Indices: 94243--94309 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 33
94233 GTGAAATGAT
*
94243 AGCAAAATAGTGAGAAAACAATA-AAAAAAAATAGC
1 AGCAAAACAGT-A-AAAA-AATACAAAAAAAATAGC
94278 AGCAAAACAGTAAAAAAATAGCAAAAAAAATA
1 AGCAAAACAGTAAAAAAATA-CAAAAAAAATA
94310 TTTTTTTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
32 4 0.14
33 4 0.14
34 11 0.38
35 10 0.34
ACGTcount: A:0.69, C:0.09, G:0.12, T:0.10
Consensus pattern (33 bp):
AGCAAAACAGTAAAAAAATACAAAAAAAATAGC
Found at i:95630 original size:90 final size:90
Alignment explanation
Indices: 95466--95644 Score: 204
Period size: 90 Copynumber: 2.0 Consensus size: 90
95456 TTTTTTTTTT
* *
95466 CTTTTTTTTTTACATTCAATTAAGCACTTGAACTTTCAAAATAGATCAAAAAAGCCCTCAAACTC
1 CTTTTTTTTTTACACTCAATTAAGCACTTGAACTTTCAAAATAGATCAAAAAAGCACTCAAACTC
*
95531 CTTCAAAAAAAGTAATTAAGTCCCTA
66 CTTCAAAAAAAGCAATTAAG-CCCTA
* * * *
95557 CTTTTTTTTTTA-ACTCAATTGAGTACTTGAACTTTCAAAAT-GCAT-AAAAAAGATACTCAATT
1 CTTTTTTTTTTACACTCAATTAAGCACTTGAACTTTCAAAATAG-ATCAAAAAAG-CACTCAA-A
* **
95619 TTTTTTC-AAAAAAGCAATTAAGCCCT
63 CTCCTTCAAAAAAAGCAATTAAGCCCT
95645 TGCTCTTATT
Statistics
Matches: 75, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
89 12 0.16
90 47 0.63
91 16 0.21
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (90 bp):
CTTTTTTTTTTACACTCAATTAAGCACTTGAACTTTCAAAATAGATCAAAAAAGCACTCAAACTC
CTTCAAAAAAAGCAATTAAGCCCTA
Found at i:95734 original size:19 final size:18
Alignment explanation
Indices: 95665--95733 Score: 70
Period size: 18 Copynumber: 3.8 Consensus size: 18
95655 AAAAATTAGA
**
95665 AAAAATATAAATAATAAT
1 AAAAATATAAATTTTAAT
*
95683 AAATA-ATAAATTTTAGA-
1 AAAAATATAAATTTTA-AT
*
95700 AAAATTATTAAATTTTAAT
1 AAAAATA-TAAATTTTAAT
95719 AAAAATATAAATTTT
1 AAAAATATAAATTTT
95734 TTAGAATTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
17 11 0.27
18 15 0.37
19 15 0.37
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (18 bp):
AAAAATATAAATTTTAAT
Found at i:95809 original size:20 final size:20
Alignment explanation
Indices: 95786--95831 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
95776 AAAAAATTGT
95786 AAAATTTTATAGAAATCAT-A
1 AAAATTTTATA-AAATCATCA
* *
95806 AAAAATTTATAAAATTATCA
1 AAAATTTTATAAAATCATCA
95826 AAAATT
1 AAAATT
95832 CCCTTTAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAATTTTATAAAATCATCA
Found at i:95820 original size:19 final size:20
Alignment explanation
Indices: 95786--95831 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
95776 AAAAAATTGT
*
95786 AAAATTTTATAGAAATCATA
1 AAAAATTTATAGAAATCATA
* *
95806 AAAAATTTATA-AAATTATC
1 AAAAATTTATAGAAATCATA
95825 AAAAATT
1 AAAAATT
95832 CCCTTTAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAAATTTATAGAAATCATA
Found at i:96037 original size:21 final size:21
Alignment explanation
Indices: 95981--96037 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
95971 TTGGTATGAT
*
95981 AAATTTATAATTTTTTTTACA
1 AAATTTATAATTTTCTTTACA
96002 AAATTTAT-A-TTTCTTTACA
1 AAATTTATAATTTTCTTTACA
***
96021 TTTTTTATAATTTTCTT
1 AAATTTATAATTTTCTT
96038 AGGACTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 14 0.47
20 2 0.07
21 14 0.47
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (21 bp):
AAATTTATAATTTTCTTTACA
Found at i:96095 original size:18 final size:18
Alignment explanation
Indices: 96074--96118 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
96064 TTTCTATATA
* *
96074 TTTTATAATTTTTACGAT
1 TTTTATAAATTTTACAAT
96092 TTTTATAAAATTTTACAAT
1 TTTTAT-AAATTTTACAAT
96111 TTTATATA
1 TTT-TATA
96119 TTTATTCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 6 0.26
19 14 0.61
20 3 0.13
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTTATAAATTTTACAAT
Found at i:96385 original size:89 final size:89
Alignment explanation
Indices: 96208--96389 Score: 242
Period size: 89 Copynumber: 2.1 Consensus size: 89
96198 AATTTTTAAT
*
96208 AAAAGCAAGGACTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTTTTTTGATGCATTTTAAAAGTT
1 AAAAGCAAGGACTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTTTTTTAATGCATTTTAAAAGTT
* * *
96273 CAAGTACCCAATTGAACGCAAAAA
66 CAAATACCCAAATGAACGAAAAAA
* * * * *
96297 AAAAGTAAGGGCTTAATTGCTTTTTTTGAAAAGGTTTGTGGGTCTTTTTAATGCATTTTGAAAGT
1 AAAAGCAAGGACTTAATTGCTTTTTTTGAAAAAGTTTGAGGGT-TTTTTAATGCATTTTAAAAGT
* *
96362 TCAAATATCCAAATG-A-GTAAAAA
65 TCAAATACCCAAATGAACGAAAAAA
96385 AAAAG
1 AAAAG
96390 ATGAACTTAT
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
88 11 0.13
89 40 0.49
90 31 0.38
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (89 bp):
AAAAGCAAGGACTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTTTTTTAATGCATTTTAAAAGTT
CAAATACCCAAATGAACGAAAAAA
Found at i:96862 original size:23 final size:23
Alignment explanation
Indices: 96836--96882 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
96826 TAATTATGTA
96836 CCTGTTAAGATACATGAGACCTC
1 CCTGTTAAGATACATGAGACCTC
96859 CCTGTTAAGATACATGAGACCTC
1 CCTGTTAAGATACATGAGACCTC
96882 C
1 C
96883 TATAAATAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (23 bp):
CCTGTTAAGATACATGAGACCTC
Found at i:98956 original size:28 final size:29
Alignment explanation
Indices: 98920--98976 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
98910 AAACTAGACT
*
98920 TCATTTATTTTA-TATTAATTAGAATAAG
1 TCATCTATTTTATTATTAATTAGAATAAG
*
98948 TCATCTATTTTATTTTTAATTAGAATAAG
1 TCATCTATTTTATTATTAATTAGAATAAG
98977 GTGTTTCAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 11 0.42
29 15 0.58
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (29 bp):
TCATCTATTTTATTATTAATTAGAATAAG
Found at i:102946 original size:17 final size:17
Alignment explanation
Indices: 102911--102949 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
102901 AGGTGGAGAA
** *
102911 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAAAGAATT
102928 CTTGTTCGTAAAGAATT
1 CTTGTTCGTAAAGAATT
102945 CTTGT
1 CTTGT
102950 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAAAGAATT
Found at i:106106 original size:22 final size:22
Alignment explanation
Indices: 106085--106125 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
106075 AACATTTTTA
*
106085 AAAAAT-TATAATAATAAATTT
1 AAAAATATATAAAAATAAATTT
106106 AAAAATATATAAAAATAAAT
1 AAAAATATATAAAAATAAAT
106126 AAATGTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
AAAAATATATAAAAATAAATTT
Done.