Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015301.1 Kokia drynarioides strain JFW-HI SEQ_130346, 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: 220244
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 329 characters in sequence are not A, C, G, or T
Found at i:3594 original size:28 final size:28
Alignment explanation
Indices: 3549--3628 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 28
3539 CCTTAATCAA
3549 TCTAGTGTTTAC-GATTTAGAGTTTTAAG
1 TCTAGTGTTTACAG-TTTAGAGTTTTAAG
*
3577 TCTAGTGTTTACAGTTTA-AGGTTTCAAG
1 TCTAGTGTTTACAGTTTAGA-GTTTTAAG
* * * *
3605 TTTAGGGTTTATAATTTAG-GTTTT
1 TCTAGTGTTTACAGTTTAGAGTTTT
3629 TGGGTTTAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
27 5 0.12
28 37 0.86
29 1 0.02
ACGTcount: A:0.24, C:0.06, G:0.21, T:0.49
Consensus pattern (28 bp):
TCTAGTGTTTACAGTTTAGAGTTTTAAG
Found at i:4026 original size:44 final size:45
Alignment explanation
Indices: 3902--4029 Score: 168
Period size: 45 Copynumber: 2.9 Consensus size: 45
3892 TAGAGTATCG
* *** ***
3902 CGGTGGCTCGTCAAACTCAACCTGATATCCTTCTTTTGAGTATTA
1 CGGTGGCTCGTCAAACTGAGGATGATATCCTTGGCTTGAGTATTA
* *
3947 CGGTGGCTCGTCAAATTGAGGCTGATATCCTTGGCTTGAGTATTA
1 CGGTGGCTCGTCAAACTGAGGATGATATCCTTGGCTTGAGTATTA
3992 CGGTGGCTCGTC-AACTGAGGATGATATCCTTGGCTTGA
1 CGGTGGCTCGTCAAACTGAGGATGATATCCTTGGCTTGA
4030 TGAGCTATGT
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
44 24 0.32
45 50 0.68
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (45 bp):
CGGTGGCTCGTCAAACTGAGGATGATATCCTTGGCTTGAGTATTA
Found at i:5946 original size:30 final size:30
Alignment explanation
Indices: 5852--5946 Score: 77
Period size: 30 Copynumber: 3.2 Consensus size: 30
5842 CAAAAATGTA
* *
5852 TTATTTACTAAAATGTTACAAAATATATAT
1 TTATTTACTAAAATGGTACAAAATAAATAT
* * * * * * **
5882 TTATATACCAAAATAGTATCCACA-CACCA-
1 TTATTTACTAAAATGGTA-CAAAATAAATAT
5911 TTATTTACTAAAATGGTACAAAATAAATAT
1 TTATTTACTAAAATGGTACAAAATAAATAT
5941 TTATTT
1 TTATTT
5947 TGTATCATTT
Statistics
Matches: 44, Mismatches: 18, Indels: 6
0.65 0.26 0.09
Matches are distributed among these distances:
28 3 0.07
29 17 0.39
30 21 0.48
31 3 0.07
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.38
Consensus pattern (30 bp):
TTATTTACTAAAATGGTACAAAATAAATAT
Found at i:6022 original size:14 final size:14
Alignment explanation
Indices: 5981--6022 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
5971 ATGAGGATAT
5981 TATTTTGATAATTA
1 TATTTTGATAATTA
**
5995 -ATTTTTTTATATTA
1 TATTTTGATA-ATTA
6009 TATTTTGATAATTA
1 TATTTTGATAATTA
6023 ATTAGTTAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
13 7 0.32
14 8 0.36
15 7 0.32
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (14 bp):
TATTTTGATAATTA
Found at i:6224 original size:21 final size:23
Alignment explanation
Indices: 6199--6273 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
6189 ATAAAAAATA
6199 TTTATAATTTTA-TAT-TAACTT
1 TTTATAATTTTATTATATAACTT
*
6220 TTTATAATTTTATTATATAACTAA
1 TTTATAATTTTATTATATAACT-T
* **
6244 TTT-TACTCGTATTATATAACTAT
1 TTTATAATTTTATTATATAACT-T
6267 TTTATAA
1 TTTATAA
6274 ATATACTCTA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
21 12 0.27
22 3 0.07
23 24 0.55
24 5 0.11
ACGTcount: A:0.36, C:0.07, G:0.01, T:0.56
Consensus pattern (23 bp):
TTTATAATTTTATTATATAACTT
Found at i:6528 original size:20 final size:21
Alignment explanation
Indices: 6503--6545 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
6493 TACTTACTAC
6503 TACTAA-TAACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
6523 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
6544 TA
1 TA
6546 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:6946 original size:63 final size:63
Alignment explanation
Indices: 6789--6935 Score: 258
Period size: 63 Copynumber: 2.3 Consensus size: 63
6779 CATATTAAAC
* * *
6789 AAATAAAATTATAATAACAAATCAATCACATTACTACTACTAACTAACAAATTAAAATATTCTA
1 AAATTAAATT-TAAAAATAAATCAATCACATTACTACTACTAACTAACAAATTAAAATATTCTA
6853 AAATTAAATTTAAAAATAAATCAATCACATTACTACTACTAACTAACAAATTAAAATATTCTA
1 AAATTAAATTTAAAAATAAATCAATCACATTACTACTACTAACTAACAAATTAAAATATTCTA
6916 AAATTAAATTTAAAAATAAA
1 AAATTAAATTTAAAAATAAA
6936 CACATTACAT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
63 71 0.89
64 9 0.11
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (63 bp):
AAATTAAATTTAAAAATAAATCAATCACATTACTACTACTAACTAACAAATTAAAATATTCTA
Found at i:6999 original size:13 final size:13
Alignment explanation
Indices: 6948--7008 Score: 56
Period size: 13 Copynumber: 4.7 Consensus size: 13
6938 CATTACATTT
6948 TTTTTCC-TTCTCC
1 TTTTTCCTTTCT-C
*
6961 TTCTTCCTTAT-TC
1 TTTTTCCTT-TCTC
*
6974 TTTCTTTCTTTCTC
1 TTT-TTCCTTTCTC
6988 TTTTTCCTTTCT-
1 TTTTTCCTTTCTC
7000 TTTTTCCTT
1 TTTTTCCTT
7009 CAATTTTCGT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
12 9 0.22
13 18 0.45
14 12 0.30
15 1 0.03
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTCCTTTCTC
Found at i:7002 original size:11 final size:12
Alignment explanation
Indices: 6947--7008 Score: 54
Period size: 12 Copynumber: 4.8 Consensus size: 12
6937 ACATTACATT
6947 TTTTTTCCTTCTC
1 TTTTTTCCTT-TC
* *
6960 CTTCTTCCTTATTC
1 TTTTTTCC-T-TTC
6974 TTTCTTT-CTTTC
1 TTT-TTTCCTTTC
6986 TCTTTTTCCTTTC
1 T-TTTTTCCTTTC
6999 TTTTTTCCTT
1 TTTTTTCCTT
7009 CAATTTTCGT
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
12 16 0.40
13 15 0.38
14 6 0.15
15 3 0.08
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTTTCCTTTC
Found at i:7362 original size:14 final size:14
Alignment explanation
Indices: 7343--7369 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
7333 TTTTAAATAT
7343 ATAATAATAATAAA
1 ATAATAATAATAAA
7357 ATAATAATAATAA
1 ATAATAATAATAA
7370 CACGTGTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAATAATAATAAA
Found at i:8680 original size:17 final size:17
Alignment explanation
Indices: 8642--8696 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
8632 TTATACTATA
8642 TTAATATTTTTTAAATTAAT
1 TTAA-ATTTTTTAAA-T-AT
8662 TT-AATTTTTTAATATAT
1 TTAAATTTTTTAA-ATAT
*
8679 TTAAAATTTTTAAATAT
1 TTAAATTTTTTAAATAT
8696 T
1 T
8697 AAAAAATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
17 9 0.28
18 19 0.59
19 2 0.06
20 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTAAATTTTTTAAATAT
Found at i:8703 original size:18 final size:18
Alignment explanation
Indices: 8667--8701 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
8657 TTAATTTAAT
*
8667 TTTTTAATATATTTAAAA
1 TTTTTAATATATTAAAAA
8685 TTTTTAA-ATATTAAAAA
1 TTTTTAATATATTAAAAA
8702 ATAAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTTAATATATTAAAAA
Found at i:12829 original size:18 final size:17
Alignment explanation
Indices: 12808--12850 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
12798 GTAGGGTTAT
12808 AAATTATATAATATATAA
1 AAATTATATAATATA-AA
*
12826 AAATAATATAATATAAA
1 AAATTATATAATATAAA
*
12843 ACATTATA
1 AAATTATA
12851 ATTTTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATTATATAATATAAA
Found at i:14043 original size:24 final size:23
Alignment explanation
Indices: 14016--14071 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 23
14006 AAGAGATCGA
*
14016 AGATTTTAGAGATATGTATCGCAT
1 AGATTTTAGA-ATATATATCGCAT
*
14040 AGATTTTTTAGAATATATATTGCAT
1 AGA--TTTTAGAATATATATCGCAT
14065 AGATTTT
1 AGATTTT
14072 TTTAGAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 4 0.14
24 3 0.11
25 14 0.50
26 7 0.25
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (23 bp):
AGATTTTAGAATATATATCGCAT
Found at i:14055 original size:25 final size:26
Alignment explanation
Indices: 14019--14078 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
14009 AGATCGAAGA
*
14019 TTTTAGAGATATGTATCGCATAGA-TT
1 TTTTAGA-ATATATATCGCATAGATTT
*
14045 TTTTAGAATATATATTGCATAGATTT
1 TTTTAGAATATATATCGCATAGATTT
14071 TTTTAGAA
1 TTTTAGAA
14079 GAAAATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 14 0.45
26 17 0.55
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (26 bp):
TTTTAGAATATATATCGCATAGATTT
Found at i:21025 original size:23 final size:23
Alignment explanation
Indices: 20956--21025 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 23
20946 AAAATTCAAA
*
20956 AAAATTA-TAAATAT-TATTTTG
1 AAAATTATTAAAAATATATTTTG
* **
20977 AAAAATTATTAAATATATATAATG
1 -AAAATTATTAAAAATATATTTTG
* *
21001 AATATTTTTAAAAATATATTTTG
1 AAAATTATTAAAAATATATTTTG
21024 AA
1 AA
21026 CGACAAAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
22 7 0.18
23 27 0.69
24 5 0.13
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
AAAATTATTAAAAATATATTTTG
Found at i:21814 original size:1 final size:1
Alignment explanation
Indices: 21808--21834 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
21798 GATATATTTG
21808 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
21835 CTTTTCAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:27856 original size:20 final size:18
Alignment explanation
Indices: 27833--27869 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
27823 AATTATATCA
27833 TATTTTAAAGTTGTTTTTAT
1 TATTTTAAA-TT-TTTTTAT
27853 TATTTTAAATTTTTTTA
1 TATTTTAAATTTTTTTA
27870 AACATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
TATTTTAAATTTTTTTAT
Found at i:28092 original size:28 final size:29
Alignment explanation
Indices: 28034--28092 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
28024 CTCAAAAATT
* * *
28034 AAAATTAAATAATTTAGTGATTAAATCAA
1 AAAATTAAATAATTTAATAATAAAATCAA
28063 AAAATT-AATAATTTAATAATCAAAAT-AA
1 AAAATTAAATAATTTAATAAT-AAAATCAA
28091 AA
1 AA
28093 CTAATGCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (29 bp):
AAAATTAAATAATTTAATAATAAAATCAA
Found at i:29569 original size:21 final size:22
Alignment explanation
Indices: 29530--29575 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
29520 ATCTTTACAC
*
29530 TTTTATTTTTATGAATTTAATT
1 TTTTATTTTTATGAATTTAAAT
* *
29552 TTTTTTTTTTA-GATTTTAAAT
1 TTTTATTTTTATGAATTTAAAT
29573 TTT
1 TTT
29576 AAATTTAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (22 bp):
TTTTATTTTTATGAATTTAAAT
Found at i:30101 original size:15 final size:16
Alignment explanation
Indices: 30074--30103 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
30064 CAAAATATTT
30074 TTTATACATATTTATG
1 TTTATACATATTTATG
30090 TTTATA-ATATTTAT
1 TTTATACATATTTAT
30104 ATGTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (16 bp):
TTTATACATATTTATG
Found at i:34113 original size:39 final size:39
Alignment explanation
Indices: 33999--34171 Score: 157
Period size: 39 Copynumber: 4.4 Consensus size: 39
33989 GTGTCACCAT
* * * * *
33999 CAGTTTAGTATTGCATTGCAGTTTTTACAGTGTTACCGC
1 CAGTTCAGTATTGTATTACAGTATTTACAGTGTTACTGC
* * * * *
34038 CAGTTTAGTATTATACTACAGTACTTATAGTGTTACTGC
1 CAGTTCAGTATTGTATTACAGTATTTACAGTGTTACTGC
* * *
34077 CAGTCCAGTATTGTATTGCAGTATTTACAGTGTTACTGT
1 CAGTTCAGTATTGTATTACAGTATTTACAGTGTTACTGC
* * * * *
34116 CAATTCAGTTTTGTATTACAATATTTACAATGTTACTAC
1 CAGTTCAGTATTGTATTACAGTATTTACAGTGTTACTGC
* * *
34155 TAATTCGGTATTGTATT
1 CAGTTCAGTATTGTATT
34172 GCCCTTCAGT
Statistics
Matches: 107, Mismatches: 27, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 107 1.00
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (39 bp):
CAGTTCAGTATTGTATTACAGTATTTACAGTGTTACTGC
Found at i:34150 original size:78 final size:78
Alignment explanation
Indices: 34005--34152 Score: 179
Period size: 78 Copynumber: 1.9 Consensus size: 78
33995 CCATCAGTTT
* * * * * *
34005 AGTATTGCATTGCAGTTTTTACAGTGTTACCGCCAGTTTAGTATTATACTACAGTACTTATAGTG
1 AGTATTGCATTGCAGTATTTACAGTGTTACCGCCAATTCAGTATTATACTACAATACTTACAATG
34070 TTACTGCCAGTCC
66 TTACTGCCAGTCC
* * * * * * *
34083 AGTATTGTATTGCAGTATTTACAGTGTTACTGTCAATTCAGTTTTGTATTACAATATTTACAATG
1 AGTATTGCATTGCAGTATTTACAGTGTTACCGCCAATTCAGTATTATACTACAATACTTACAATG
34148 TTACT
66 TTACT
34153 ACTAATTCGG
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
78 57 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (78 bp):
AGTATTGCATTGCAGTATTTACAGTGTTACCGCCAATTCAGTATTATACTACAATACTTACAATG
TTACTGCCAGTCC
Found at i:34860 original size:25 final size:23
Alignment explanation
Indices: 34801--34949 Score: 133
Period size: 23 Copynumber: 6.5 Consensus size: 23
34791 TATACGGAAC
* * *
34801 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
34823 -AACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACACAGTGCT
* * *
34845 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
* * *
34868 AATCAGAGAGCACACAAAGTGTT
1 AAACAGAGAGCACACACAGTGCT
* *
34891 AATCAAAGAGCACACACAGTGCT
1 AAACAGAGAGCACACACAGTGCT
* *
34914 AATAACAAAGAGCACGAGAC-GTGCT
1 -A-AACAGAGAGCAC-ACACAGTGCT
34939 AAACAGAGAGC
1 AAACAGAGAGC
34950 GCGCTAGTGT
Statistics
Matches: 106, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
21 11 0.10
22 7 0.07
23 67 0.63
24 2 0.02
25 16 0.15
26 3 0.03
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACACAGTGCT
Found at i:38930 original size:95 final size:95
Alignment explanation
Indices: 38813--39000 Score: 324
Period size: 95 Copynumber: 2.0 Consensus size: 95
38803 TTGTTTCATT
38813 ACATTTTAATTTATATTATATAGAAATATAAAAGTAAAAAAAACTTTTTAATTTCTCTCAAATTC
1 ACATTTTAATTTATATTATATAGAAATATAAAAGTAAAAAAAACTTTTTAATTTCTCTCAAATTC
*
38878 GAAATTAAGCAAATTGATCTCTCTATAATC
66 GAAATTAAACAAATTGATCTCTCTATAATC
* *
38908 ACATTTTAATTTTTA-TATTATAGAAATATATAAGTAAAAAAAACTTTTTAATTTCTCTCAAATT
1 ACATTTTAATTTATATTA-TATAGAAATATAAAAGTAAAAAAAACTTTTTAATTTCTCTCAAATT
*
38972 CGAAATTAAACAAATTGATCTCTTTATAA
65 CGAAATTAAACAAATTGATCTCTCTATAA
39001 AAATTGGAGT
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
94 2 0.02
95 86 0.98
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (95 bp):
ACATTTTAATTTATATTATATAGAAATATAAAAGTAAAAAAAACTTTTTAATTTCTCTCAAATTC
GAAATTAAACAAATTGATCTCTCTATAATC
Found at i:42616 original size:15 final size:15
Alignment explanation
Indices: 42598--42631 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
42588 AAAAAAACCT
*
42598 TAAAGAAAAACATAA
1 TAAAAAAAAACATAA
*
42613 TAAAAAAAAATATAA
1 TAAAAAAAAACATAA
42628 TAAA
1 TAAA
42632 TTCCTGTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (15 bp):
TAAAAAAAAACATAA
Found at i:50394 original size:80 final size:79
Alignment explanation
Indices: 50259--50407 Score: 226
Period size: 80 Copynumber: 1.9 Consensus size: 79
50249 AAAAATTGAT
*
50259 TTTGATCACAGCCTTCTACTACTTGGGTCCCAGTTAGCATTGATATTGATACAACTTTTTAAGAT
1 TTTGATCACAGCCTTCAACTACTTGGGTCCCAGTTAGCATTGATATTGATACAAC-TTTTAAGAT
50324 TAAAAGTTGTGTTAA
65 TAAAAGTTGTGTTAA
* * * * * *
50339 TTTGATCACAGCCTTCAACTACTTGTGTCCCAGTTAGTATTGATTTTGGTGCAACTTTTGAGATT
1 TTTGATCACAGCCTTCAACTACTTGGGTCCCAGTTAGCATTGATATTGATACAACTTTTAAGATT
50404 AAAA
66 AAAA
50408 CAGTGCTAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
79 13 0.21
80 49 0.79
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (79 bp):
TTTGATCACAGCCTTCAACTACTTGGGTCCCAGTTAGCATTGATATTGATACAACTTTTAAGATT
AAAAGTTGTGTTAA
Found at i:58004 original size:38 final size:38
Alignment explanation
Indices: 57953--58030 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
57943 ACCTCCTATC
57953 TGATCACCCTAACATGAAGGTATAAGCTCTGTTAACTT
1 TGATCACCCTAACATGAAGGTATAAGCTCTGTTAACTT
57991 TGATCACCCTAACATGAAGGTATAAGCTCTGTTAACTT
1 TGATCACCCTAACATGAAGGTATAAGCTCTGTTAACTT
58029 TG
1 TG
58031 TGTTTTTAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (38 bp):
TGATCACCCTAACATGAAGGTATAAGCTCTGTTAACTT
Found at i:73269 original size:8 final size:8
Alignment explanation
Indices: 73256--73281 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
73246 ACCTTTGACC
73256 ACTCTCAA
1 ACTCTCAA
73264 ACTCTCAA
1 ACTCTCAA
73272 ACTCTCAA
1 ACTCTCAA
73280 AC
1 AC
73282 CATATCCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.23
Consensus pattern (8 bp):
ACTCTCAA
Found at i:73637 original size:2 final size:2
Alignment explanation
Indices: 73630--73655 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
73620 GTTATTTATT
73630 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
73656 CTCCTAACGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:78523 original size:33 final size:33
Alignment explanation
Indices: 78485--78591 Score: 187
Period size: 33 Copynumber: 3.2 Consensus size: 33
78475 ATAATATCTT
*
78485 ATAATATCCCATTAAAAATTAAATTACTAAGAG
1 ATAATATCCCATTAAAAATCAAATTACTAAGAG
*
78518 ATAATATCCCATTAAAAACCAAATTACTAAGAG
1 ATAATATCCCATTAAAAATCAAATTACTAAGAG
*
78551 ATAATATTCCATTAAAAATCAAATTACTAAGAG
1 ATAATATCCCATTAAAAATCAAATTACTAAGAG
78584 ATAATATC
1 ATAATATC
78592 TTATAATAAT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 69 1.00
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (33 bp):
ATAATATCCCATTAAAAATCAAATTACTAAGAG
Found at i:79190 original size:22 final size:21
Alignment explanation
Indices: 79144--79190 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
79134 TTGATGCTTA
* *
79144 AATTTTAAAGTATTTTAGTTT
1 AATTTTAAACTATTTTAGTTC
79165 AATTCTTAAACTATTTTA-TATC
1 AATT-TTAAACTATTTTAGT-TC
79187 AATT
1 AATT
79191 AAGTCGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.53
Consensus pattern (21 bp):
AATTTTAAACTATTTTAGTTC
Found at i:79822 original size:2 final size:2
Alignment explanation
Indices: 79809--79840 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
79799 TTTCCTTCCC
*
79809 CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
79841 GGTTCCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:81075 original size:7 final size:7
Alignment explanation
Indices: 81063--81090 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
81053 TGGAAAATCC
81063 TAGGTAT
1 TAGGTAT
81070 TAGGTAT
1 TAGGTAT
81077 TAGGTAT
1 TAGGTAT
81084 TAGGTAT
1 TAGGTAT
81091 ATTAGGATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (7 bp):
TAGGTAT
Found at i:81122 original size:3 final size:3
Alignment explanation
Indices: 81110--81159 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
81100 TAGACAAAAT
81110 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
81156 TAA T
1 TAA T
81160 TTGGGGATTG
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:84695 original size:2 final size:2
Alignment explanation
Indices: 84690--84725 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
84680 TGCTTGCCCC
84690 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
84726 TTGCCAAATT
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:89026 original size:2 final size:2
Alignment explanation
Indices: 89019--89056 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
89009 GAAATAAGGC
89019 AT 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 AT
89057 TAAGAATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:93174 original size:82 final size:82
Alignment explanation
Indices: 93070--93227 Score: 262
Period size: 82 Copynumber: 1.9 Consensus size: 82
93060 AAGAGAGTAG
* *
93070 GTAAAGAAGGTTAAACACGAGCAAATTATAGAGGCTTGGCCTTCTTCCCTAGGTGTCTTGAACTG
1 GTAAAGAAGGTTAAACACGAGCAAATTATAGAGGCTTGGCCTTCTGCCCTAGGTGCCTTGAACTG
93135 AAACACCTTGATTTAAA
66 AAACACCTTGATTTAAA
* * * *
93152 GTAAAGAAGGTTAAACATGAGCAATTTATAGAGGTTTGGCCTTCTGCCCTAGGTGCCTTGAACTT
1 GTAAAGAAGGTTAAACACGAGCAAATTATAGAGGCTTGGCCTTCTGCCCTAGGTGCCTTGAACTG
93217 AAACACCTTGA
66 AAACACCTTGA
93228 CTATGCTCCA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 70 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (82 bp):
GTAAAGAAGGTTAAACACGAGCAAATTATAGAGGCTTGGCCTTCTGCCCTAGGTGCCTTGAACTG
AAACACCTTGATTTAAA
Found at i:109446 original size:28 final size:29
Alignment explanation
Indices: 109406--109475 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
109396 ATACAATTGA
*
109406 ATAGTTGAGTGACCA-TTTGTAAGTTTTC
1 ATAGTTGAGTGACCATTTTGTAACTTTTC
* *
109434 ATAGTTGGGTGACCATTTTGTAACTTTTT
1 ATAGTTGAGTGACCATTTTGTAACTTTTC
*
109463 ATAATTGAGTGAC
1 ATAGTTGAGTGAC
109476 AAAAAAAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 14 0.39
29 22 0.61
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.43
Consensus pattern (29 bp):
ATAGTTGAGTGACCATTTTGTAACTTTTC
Found at i:114491 original size:14 final size:15
Alignment explanation
Indices: 114468--114505 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
114458 GGTTTAAAAT
*
114468 TTTTAATTAATT-AA
1 TTTTATTTAATTAAA
114482 TTTTATTTAATTAAA
1 TTTTATTTAATTAAA
114497 TATTTATTT
1 T-TTTATTT
114506 TCATTCTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.52
15 3 0.14
16 7 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTATTTAATTAAA
Found at i:122137 original size:29 final size:29
Alignment explanation
Indices: 122081--122138 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
122071 CGTAGAAATG
*
122081 GGTTTAGAGTTTTTTTTAGTTAAGATTTA
1 GGTTTAGAGTTTTTTTTAATTAAGATTTA
122110 GGTTTAGA-TTTTTTAATTAATTAA-ATTTA
1 GGTTTAGAGTTTTTT--TTAATTAAGATTTA
122139 TTTAATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 6 0.23
29 13 0.50
30 7 0.27
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (29 bp):
GGTTTAGAGTTTTTTTTAATTAAGATTTA
Found at i:129357 original size:21 final size:21
Alignment explanation
Indices: 129315--129357 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
129305 AAAATTATTT
*
129315 AATAATTTTACTATTTCAAAA
1 AATAATTTTAATATTTCAAAA
*
129336 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAAT-ATTTCAAAA
129358 TCATTTGCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
AATAATTTTAATATTTCAAAA
Found at i:134654 original size:27 final size:26
Alignment explanation
Indices: 134623--134682 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 26
134613 ACAAATTTCA
* *
134623 TAATTATATATAATTTTATATGAATTT
1 TAATTATATACAATTATATAT-AATTT
*
134650 TAATTTTATACAATTATATATAATTT
1 TAATTATATACAATTATATATAATTT
134676 TAATTAT
1 TAATTAT
134683 GATTCAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 11 0.38
27 18 0.62
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (26 bp):
TAATTATATACAATTATATATAATTT
Found at i:134695 original size:37 final size:37
Alignment explanation
Indices: 134624--134698 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 37
134614 CAAATTTCAT
* *
134624 AATTATATATAATTTTATATGAATTTTAATTTTATAC
1 AATTATATATAATTTTATATGAATTTCAAATTTATAC
134661 AATTATATATAATTTTAATTATG-A-TTCAAATTTATAC
1 AATTATATATAATTTT-A-TATGAATTTCAAATTTATAC
134698 A
1 A
134699 TGAAATTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 28 0.82
38 2 0.06
39 4 0.12
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.51
Consensus pattern (37 bp):
AATTATATATAATTTTATATGAATTTCAAATTTATAC
Found at i:134696 original size:27 final size:26
Alignment explanation
Indices: 134637--134712 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 26
134627 TATATATAAT
*
134637 TTTATATGAATTTTAATTTTATACAA
1 TTTATATGAATTTTAATTTGATACAA
*
134663 TTATATAT-AATTTTAATTATGATTCAAA
1 TT-TATATGAATTTTAATT-TGATAC-AA
134691 TTTATACATGAAATTTTAATTT
1 TTTAT--ATG-AATTTTAATTT
134713 TGATTTAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
26 12 0.29
27 12 0.29
28 4 0.10
29 2 0.05
30 1 0.02
31 10 0.24
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (26 bp):
TTTATATGAATTTTAATTTGATACAA
Found at i:134731 original size:31 final size:31
Alignment explanation
Indices: 134671--134731 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
134661 AATTATATAT
*
134671 AATTTTAATTATGATTCAAATTTATACATGA
1 AATTTTAATTATGATTCAAATTTACACATGA
* *
134702 AATTTTAATTTTGATT-TAATTATACACATG
1 AATTTTAATTATGATTCAAATT-TACACATG
134732 TAAAAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (31 bp):
AATTTTAATTATGATTCAAATTTACACATGA
Found at i:135242 original size:31 final size:29
Alignment explanation
Indices: 135202--135270 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 29
135192 AATGAAATTC
135202 TTTACATGTGTAAAATTGAATCAAAATCAAA
1 TTTA-ATGTGTAAAATTGAAT-AAAATCAAA
** *
135233 GTTTAATGTGTGTAATTGCATAAAATCAAA
1 -TTTAATGTGTAAAATTGAATAAAATCAAA
*
135263 TTTCATGT
1 TTTAATGT
135271 ATCAAAATGC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 7 0.21
30 9 0.27
31 13 0.39
32 4 0.12
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.38
Consensus pattern (29 bp):
TTTAATGTGTAAAATTGAATAAAATCAAA
Found at i:136890 original size:30 final size:30
Alignment explanation
Indices: 136854--136939 Score: 136
Period size: 30 Copynumber: 2.9 Consensus size: 30
136844 ACTTATTTTA
* * *
136854 TTGTTAATTTTATTATTATTTTTGAGGCGT
1 TTGTTAATTTTGTTATTATTTTAGAGGCAT
*
136884 TTGTTAATTTTGCTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAGAGGCAT
136914 TTGTTAATTTTGTTATTATTTTAGAG
1 TTGTTAATTTTGTTATTATTTTAGAG
136940 ATATTTATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.22, C:0.03, G:0.16, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAGAGGCAT
Found at i:141526 original size:60 final size:60
Alignment explanation
Indices: 141433--141554 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
141423 TTCTCCTAAA
141433 TTATTGTTGCTCGTCAGTTCAAGTTGCTATCGAAGATAGTTTTATCATCCAATGTGTTTG
1 TTATTGTTGCTCGTCAGTTCAAGTTGCTATCGAAGATAGTTTTATCATCCAATGTGTTTG
141493 TTATTGTTGCTCGTCAGTTCAAGTTGCTATCGAAGATAGTTTTATCATCCAATGTGTTTG
1 TTATTGTTGCTCGTCAGTTCAAGTTGCTATCGAAGATAGTTTTATCATCCAATGTGTTTG
141553 TT
1 TT
141555 TATGCATGCA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.21, C:0.15, G:0.20, T:0.44
Consensus pattern (60 bp):
TTATTGTTGCTCGTCAGTTCAAGTTGCTATCGAAGATAGTTTTATCATCCAATGTGTTTG
Found at i:144491 original size:87 final size:87
Alignment explanation
Indices: 144345--144524 Score: 351
Period size: 87 Copynumber: 2.1 Consensus size: 87
144335 ATTTGGATCA
144345 ATCTTTGGATCTAATTTTTCTTTCAATGGAAGAACCCAAACAAGGTTCTTGTTTTGATACATTGA
1 ATCTTTGGATCTAATTTTTCTTTCAATGGAAGAACCCAAACAAGGTTCTTGTTTTGATACATTGA
144410 AGCTTGATTAACACTTATAATG
66 AGCTTGATTAACACTTATAATG
144432 ATCTTTGGATCTAATTTTTCTTTCAATGGAAGAACCCAAACAAGGTTCTTGTTTTGATACATTGA
1 ATCTTTGGATCTAATTTTTCTTTCAATGGAAGAACCCAAACAAGGTTCTTGTTTTGATACATTGA
*
144497 AGCTTGATTAACACTTGTAATG
66 AGCTTGATTAACACTTATAATG
144519 ATCTTT
1 ATCTTT
144525 AAACATTTGA
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 92 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (87 bp):
ATCTTTGGATCTAATTTTTCTTTCAATGGAAGAACCCAAACAAGGTTCTTGTTTTGATACATTGA
AGCTTGATTAACACTTATAATG
Found at i:145755 original size:8 final size:8
Alignment explanation
Indices: 145742--145774 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
145732 TTCTTAGCAA
145742 ATAAAAAT
1 ATAAAAAT
*
145750 ATAAAACT
1 ATAAAAAT
145758 ATAAAAAT
1 ATAAAAAT
145766 A-AAAAAT
1 ATAAAAAT
145773 AT
1 AT
145775 TTAAAAGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (8 bp):
ATAAAAAT
Found at i:146113 original size:48 final size:49
Alignment explanation
Indices: 146035--146132 Score: 180
Period size: 48 Copynumber: 2.0 Consensus size: 49
146025 TGAAAGTGAA
146035 AAAAATTGATGTCTTTTTAGATTGATGCCTCAAATGAATTTGTTGCGTTT
1 AAAAATTGATGTC-TTTTAGATTGATGCCTCAAATGAATTTGTTGCGTTT
146085 AAAAATTGATGTC-TTTAGATTGATGCCTCAAATGAATTTGTTGCGTTT
1 AAAAATTGATGTCTTTTAGATTGATGCCTCAAATGAATTTGTTGCGTTT
146133 GAGGACATGT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 35 0.73
50 13 0.27
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.43
Consensus pattern (49 bp):
AAAAATTGATGTCTTTTAGATTGATGCCTCAAATGAATTTGTTGCGTTT
Found at i:150700 original size:2 final size:2
Alignment explanation
Indices: 150693--150717 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
150683 TGTAAAAACT
150693 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 T
150718 TTTGGGTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:151229 original size:18 final size:18
Alignment explanation
Indices: 151203--151243 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
151193 TTTTTTTACT
*
151203 AATTTAAATTTTTAAA-A
1 AATTTAAATATTTAAATA
151220 AATTTCAAATATTTAAATA
1 AATTT-AAATATTTAAATA
151239 AATTT
1 AATTT
151244 TTTTCCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 10 0.48
19 6 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
AATTTAAATATTTAAATA
Found at i:168576 original size:20 final size:20
Alignment explanation
Indices: 168553--168638 Score: 70
Period size: 19 Copynumber: 4.3 Consensus size: 20
168543 TAATTTTATG
*
168553 TTTAAATTATTTAATAATAT
1 TTTAAATTTTTTAATAATAT
**
168573 TTTATAATTTTTTTGTAATA-
1 TTTA-AATTTTTTAATAATAT
* *
168593 -TTAATAATTTTTAATAA-AA
1 TTTAA-ATTTTTTAATAATAT
*
168612 TTTAAATTTTTTGAATAATTT
1 TTTAAATTTTTT-AATAATAT
168633 TTTAAA
1 TTTAAA
168639 AATTATTAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
18 2 0.04
19 18 0.35
20 13 0.25
21 18 0.35
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTAAATTTTTTAATAATAT
Found at i:168581 original size:21 final size:21
Alignment explanation
Indices: 168526--168662 Score: 63
Period size: 21 Copynumber: 6.6 Consensus size: 21
168516 GTTTTTCTAT
** *
168526 ATATTTTATTAAAAATTTAATT
1 ATATTTTA-TAATTATTTAATA
*
168548 TTATGTTTA-AATTATTTAATA
1 ATAT-TTTATAATTATTTAATA
* **
168569 ATATTTTATAATTTTTTTGTA
1 ATATTTTATAATTATTTAATA
*
168590 ATA-TTAATAATT-TTTAATA
1 ATATTTTATAATTATTTAATA
* *
168609 A-AATTTA-AATTTTTTGAATA
1 ATATTTTATAATTATTT-AATA
* * *
168629 ATTTTTTAAAAATTATTAAAT-
1 ATATTTT-ATAATTATTTAATA
168650 AT-TTTTAATAATT
1 ATATTTT-ATAATT
168663 TTATATTCTT
Statistics
Matches: 90, Mismatches: 17, Indels: 18
0.72 0.14 0.14
Matches are distributed among these distances:
18 5 0.06
19 12 0.13
20 27 0.30
21 29 0.32
22 7 0.08
23 10 0.11
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATATTTTATAATTATTTAATA
Found at i:168648 original size:31 final size:31
Alignment explanation
Indices: 168593--168664 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
168583 TTTTGTAATA
168593 TTAATAA-TTTTTAATAAAATTTAAAT-TTT
1 TTAATAATTTTTTAATAAAATTTAAATATTT
*
168622 TTGAATAATTTTTTAA-AAATTATTAAATATTT
1 TT-AATAATTTTTTAATAAAAT-TTAAATATTT
168654 TTAATAATTTT
1 TTAATAATTTT
168665 ATATTCTTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
29 2 0.05
30 9 0.24
31 22 0.58
32 5 0.13
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (31 bp):
TTAATAATTTTTTAATAAAATTTAAATATTT
Found at i:168788 original size:13 final size:13
Alignment explanation
Indices: 168765--168798 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
168755 CAATTATCCT
168765 ATTTTTTTTTA-A
1 ATTTTTTTTTATA
168777 ATTTTGTTTTTATA
1 ATTTT-TTTTTATA
168791 ATTTTTTT
1 ATTTTTTT
168799 ATAATTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 9 0.45
14 6 0.30
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (13 bp):
ATTTTTTTTTATA
Found at i:171001 original size:18 final size:17
Alignment explanation
Indices: 170978--171020 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
170968 TTTATATTTT
* *
170978 TAAAAATATTAATTATTA
1 TAAAAATATT-AGTATGA
*
170996 TAAAAAAATTAGTATGA
1 TAAAAATATTAGTATGA
171013 TAAAAATA
1 TAAAAATA
171021 ATTTCTAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (17 bp):
TAAAAATATTAGTATGA
Found at i:176689 original size:917 final size:907
Alignment explanation
Indices: 174915--176700 Score: 3473
Period size: 917 Copynumber: 2.0 Consensus size: 907
174905 NNNNNNNNNN
174915 TACAACCAACATTACGAGCATATACATGTAACCTATACAACACCTAGTACATGTCACTTTTACCA
1 TACAACCAACATTACGAGCATATACATGTAACCTATACAACACCTAGTACATGTCACTTTTACCA
174980 AAAGAGGAGAATTATATCATCGAGTTTATATTGAGGTCGGGATCGATCTGGATGCTGATCAAGAC
66 AAAGAGGAGAATTATATCATCGAGTTTATATTGAGGTCGGGATCGATCTGGATGCTGATCAAGAC
175045 CTTAATTTCTACTAACCTGCGCACGGAAACTACCGTATGTTGAGTATTTCATACTCAGTGGTATT
131 CTTAATTTCTACTAACCTGCGCACGGAAACTACCGTATGTTGAGTATTTCATACTCAGTGGTATT
175110 ACTATAATTCAAATTATAAATAACCAAATAAATTTCACATAATCAATCATATAATACATGAACAC
196 ACTATAATTCAAATTATAAATAACCAAATAAATTTCACATAATCAATCATATAATACATGAACAC
175175 ATATTATCTTAATTTATACACCACTTTCATTCCATATCAATATCAAATCAATTTAACCATTTCAT
261 ATATTATCTTAATTTATACACCACTTTCATTCCATATCAATATCAAATCAATTTAACCATTTCAT
175240 TCTCATTTCTCAATTTCATCACATATCACTTTATATGCCTCAATTTTTCATTTTTATTCAATTTT
326 TCTCATTTCTCAATTTCATCACATATCACTTTATATGCCTCAATTTTTCATTTTTATTCAATTTT
175305 TCTTTTTCACATTGTTTACCCCTATTAACAAGACTCGGACCTTGGCGGATACACGGATCCAACCA
391 TCTTTTTCACATTGTTTACCCCTATTAACAAGACTCGGACCTTGGCGGATACACGGATCCAACCA
175370 AACACACCAGAATGGCACCCAGTGCCCATCGGATAGTTCGAAGCAATAAAGTGACACCCAGTGTC
456 AACACACCAGAATGGCACCCAGTGCCCATCGGATAGTTCGAAGCAATAAAGTGACACCCAGTGTC
175435 TCATCCGCCTAGCCGAAGTAAAGTGGTACCCAATACCTCATCGAATCTGTCCGAAGTAAAATAAT
521 TCATCCGCCTAGCCGAAGTAAAGTGGTACCCAATACCTCATCGAATCTGTCCGAAGTAAAATAAT
175500 GACACCCAATGTCTCATCGACTCAAGGTCGAAGTATCCTTGAACTCTTCCAATCCTATGGGATGC
586 GACACCCAATGTCTCATCGACTCAAGGTCGAAGTATCCTTGAACTCTTCCAATCCTATGGGATGC
175565 CAATTATATCCGACTCAGCCCGACTAGTTAAGAGGGACTTTCAATTTCAATTCATATCACTTTCA
651 CAATTATATCCGACTCAGCCCGACTAGTTAAGAGGGACTTTCAATTTCAATTCATATCACTTTCA
175630 ATTTTAATTTCACTTATTAAATTTAAATATCAAAATAAACATTAAATAATTAATAATTTAAATTA
716 ATTTTAATTTCACTTATTAAATTTAAATATCAAAATAAACATTAAATAATTAATAATTTAAATTA
175695 TAGTAATACAAACCCAGATTTCGCGATTACTCCTCGATAACTTTCTCCTTTCCTTTTTGTGCCGA
781 TAGTAATACAAACCCAGATTTCGCGATTACTCCTCGATAACTTTCTCCTTTCCTTTTTGTGCCGA
*
175760 TGCTTCGGGTTCTTTTCTAGCTACAAAAAAAAAAAAAAAATTTACANNNNNNNNNNTATTTTTTT
846 TGCTTCGGGTTCTTTGCTAGCTACAAAAAAAAAAAAAAAATTTACA----------TATTTTTTT
175825 TTTTTTT
901 TTTTTTT
175832 TACAACCAACATTACGAGCATATACATGTAACCTATACAACACCTAGTACATGTCACTTTTACCA
1 TACAACCAACATTACGAGCATATACATGTAACCTATACAACACCTAGTACATGTCACTTTTACCA
175897 AAAGAGGAGAATTATATCATCGAGTTTATATTGAGGTCGGGATCGATCTGGATGCTGATCAAGAC
66 AAAGAGGAGAATTATATCATCGAGTTTATATTGAGGTCGGGATCGATCTGGATGCTGATCAAGAC
175962 CTTAATTTCTACTAACCTGCGCACGGAAACTACCGTATGTTGAGTATTTCATACTCAGTGGTATT
131 CTTAATTTCTACTAACCTGCGCACGGAAACTACCGTATGTTGAGTATTTCATACTCAGTGGTATT
176027 ACTATAATTCAAATTATAAATAACCAAATAAATTTCACATAATCAATCATATAATACATGAACAC
196 ACTATAATTCAAATTATAAATAACCAAATAAATTTCACATAATCAATCATATAATACATGAACAC
176092 ATATTATCTTAATTTATACACCACTTTCATTCCATATCAATATCAAATCAATTTAACCATTTCAT
261 ATATTATCTTAATTTATACACCACTTTCATTCCATATCAATATCAAATCAATTTAACCATTTCAT
176157 TCTCATTTCTCAATTTCATCACATATCACTTTATATGCCTCAATTTTTCATTTTTATTCAATTTT
326 TCTCATTTCTCAATTTCATCACATATCACTTTATATGCCTCAATTTTTCATTTTTATTCAATTTT
176222 TCTTTTTCACATTGTTTACCCCTATTAACAAGACTCGGACCTTGGCGGATACACGGATCCAACCA
391 TCTTTTTCACATTGTTTACCCCTATTAACAAGACTCGGACCTTGGCGGATACACGGATCCAACCA
176287 AACACACCAGAATGGCACCCAGTGCCCATCGGATAGTTCGAAGCAATAAAGTGACACCCAGTGTC
456 AACACACCAGAATGGCACCCAGTGCCCATCGGATAGTTCGAAGCAATAAAGTGACACCCAGTGTC
176352 TCATCCGCCTAGCCGAAGTAAAGTGGTACCCAATACCTCATCGAATCTGTCCGAAGTAAAATAAT
521 TCATCCGCCTAGCCGAAGTAAAGTGGTACCCAATACCTCATCGAATCTGTCCGAAGTAAAATAAT
176417 GACACCCAATGTCTCATCGACTCAAGGTCGAAGTATCCTTGAACTCTTCCAATCCTATGGGATGC
586 GACACCCAATGTCTCATCGACTCAAGGTCGAAGTATCCTTGAACTCTTCCAATCCTATGGGATGC
176482 CAATTATATCCGACTCAGCCCGACTAGTTAAGAGGGACTTTCAATTTCAATTCATATCACTTTCA
651 CAATTATATCCGACTCAGCCCGACTAGTTAAGAGGGACTTTCAATTTCAATTCATATCACTTTCA
176547 ATTTTAATTTCACTTATTAAATTTAAATATCAAAATAAACATTAAATAATTAATAATTTAAATTA
716 ATTTTAATTTCACTTATTAAATTTAAATATCAAAATAAACATTAAATAATTAATAATTTAAATTA
176612 TAGTAATACAAACCCAGATTTCGCGATTACTCCTCGATAACTTTCTCCTTTCCTTTTTGTGCCGA
781 TAGTAATACAAACCCAGATTTCGCGATTACTCCTCGATAACTTTCTCCTTTCCTTTTTGTGCCGA
176677 TGCTTCGGGTTCTTTGCTAGCTAC
846 TGCTTCGGGTTCTTTGCTAGCTAC
176701 RMAAATRAWA
Statistics
Matches: 868, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
917 868 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (907 bp):
TACAACCAACATTACGAGCATATACATGTAACCTATACAACACCTAGTACATGTCACTTTTACCA
AAAGAGGAGAATTATATCATCGAGTTTATATTGAGGTCGGGATCGATCTGGATGCTGATCAAGAC
CTTAATTTCTACTAACCTGCGCACGGAAACTACCGTATGTTGAGTATTTCATACTCAGTGGTATT
ACTATAATTCAAATTATAAATAACCAAATAAATTTCACATAATCAATCATATAATACATGAACAC
ATATTATCTTAATTTATACACCACTTTCATTCCATATCAATATCAAATCAATTTAACCATTTCAT
TCTCATTTCTCAATTTCATCACATATCACTTTATATGCCTCAATTTTTCATTTTTATTCAATTTT
TCTTTTTCACATTGTTTACCCCTATTAACAAGACTCGGACCTTGGCGGATACACGGATCCAACCA
AACACACCAGAATGGCACCCAGTGCCCATCGGATAGTTCGAAGCAATAAAGTGACACCCAGTGTC
TCATCCGCCTAGCCGAAGTAAAGTGGTACCCAATACCTCATCGAATCTGTCCGAAGTAAAATAAT
GACACCCAATGTCTCATCGACTCAAGGTCGAAGTATCCTTGAACTCTTCCAATCCTATGGGATGC
CAATTATATCCGACTCAGCCCGACTAGTTAAGAGGGACTTTCAATTTCAATTCATATCACTTTCA
ATTTTAATTTCACTTATTAAATTTAAATATCAAAATAAACATTAAATAATTAATAATTTAAATTA
TAGTAATACAAACCCAGATTTCGCGATTACTCCTCGATAACTTTCTCCTTTCCTTTTTGTGCCGA
TGCTTCGGGTTCTTTGCTAGCTACAAAAAAAAAAAAAAAATTTACATATTTTTTTTTTTTTT
Found at i:177265 original size:20 final size:20
Alignment explanation
Indices: 177240--177280 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
177230 CTGTTCTTCC
* * *
177240 TTCTTTTTTTTTTTTTTTCT
1 TTCTTTATTCTTTTATTTCT
177260 TTCTTTATTCTTTTATTTCT
1 TTCTTTATTCTTTTATTTCT
177280 T
1 T
177281 ATATATCATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (20 bp):
TTCTTTATTCTTTTATTTCT
Found at i:186034 original size:19 final size:17
Alignment explanation
Indices: 185996--186028 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
185986 ATTTTTAGAG
185996 ATTCTAATTAAGAGATT
1 ATTCTAATTAAGAGATT
186013 ATTCTAATTAAGAGAT
1 ATTCTAATTAAGAGAT
186029 ATTATTTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (17 bp):
ATTCTAATTAAGAGATT
Found at i:198946 original size:14 final size:14
Alignment explanation
Indices: 198927--198969 Score: 86
Period size: 14 Copynumber: 3.1 Consensus size: 14
198917 GTTGGAATGA
198927 AGGTTTGAACAAAT
1 AGGTTTGAACAAAT
198941 AGGTTTGAACAAAT
1 AGGTTTGAACAAAT
198955 AGGTTTGAACAAAT
1 AGGTTTGAACAAAT
198969 A
1 A
198970 ATGTTATATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.28
Consensus pattern (14 bp):
AGGTTTGAACAAAT
Found at i:201826 original size:17 final size:17
Alignment explanation
Indices: 201804--201839 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
201794 GTACAAATGA
201804 TAGTTTAATATCGAGTG
1 TAGTTTAATATCGAGTG
*
201821 TAGTTTAATATTGAGTG
1 TAGTTTAATATCGAGTG
201838 TA
1 TA
201840 CAGTTGACCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.22, T:0.44
Consensus pattern (17 bp):
TAGTTTAATATCGAGTG
Found at i:205012 original size:12 final size:13
Alignment explanation
Indices: 204992--205024 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
204982 ATCTTTTCTT
*
204992 AAAAGAAACAA-A
1 AAAAAAAACAAGA
205004 AAAAAAAACAAGA
1 AAAAAAAACAAGA
205017 AAAAAAAA
1 AAAAAAAA
205025 ACCAAATTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (13 bp):
AAAAAAAACAAGA
Found at i:213588 original size:38 final size:38
Alignment explanation
Indices: 213537--213613 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
213527 TCATTCTCTA
*
213537 ATCATAAAGTTTGAAGTTTAATACTTATTAATGGGAAT
1 ATCATAAAATTTGAAGTTTAATACTTATTAATGGGAAT
213575 ATCATAAAATTTGAAGTTTAATACTTATTAATGGGAAT
1 ATCATAAAATTTGAAGTTTAATACTTATTAATGGGAAT
213613 A
1 A
213614 GAGCATGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (38 bp):
ATCATAAAATTTGAAGTTTAATACTTATTAATGGGAAT
Found at i:218974 original size:23 final size:23
Alignment explanation
Indices: 218891--219064 Score: 149
Period size: 23 Copynumber: 7.5 Consensus size: 23
218881 TATACGGAAC
* * *
218891 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
*
218913 -AACAGAGAGCACATA-AGTGCT
1 AAACAGAGAGCACACACAGTGCT
* * *
218934 GGGCAACATAGAACACACACAGTGCT
1 ---AAACAGAGAGCACACACAGTGCT
* *
218960 AAACAGAGAGTACACAAAGTGCT
1 AAACAGAGAGCACACACAGTGCT
* *
218983 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACACAGTGCT
*
219006 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACACAGTGCT
*
219029 AATAACAGAGAGCACGAAAC-GTGCT
1 -A-AACAGAGAGCAC-ACACAGTGCT
219054 AAACAGAGAGC
1 AAACAGAGAGC
219065 GCGCTAGTGT
Statistics
Matches: 127, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
21 16 0.13
22 1 0.01
23 71 0.56
24 2 0.02
25 28 0.22
26 9 0.07
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACACAGTGCT
Found at i:218998 original size:48 final size:48
Alignment explanation
Indices: 218946--219064 Score: 156
Period size: 48 Copynumber: 2.5 Consensus size: 48
218936 GCAACATAGA
*
218946 ACACACACAGTGCTAAACAGAGAGTACACAAAGTGCTAAT-CAGAGAGC
1 ACACA-ACAGTGCTAAACAGAGAGCACACAAAGTGCTAATACAGAGAGC
* *
218994 ACACAA-AGTGCTAATCAGAGAGCACACACAGTGCTAATAACAGAGAGC
1 ACACAACAGTGCTAAACAGAGAGCACACAAAGTGCTAAT-ACAGAGAGC
219042 ACGA-AAC-GTGCTAAACAGAGAGC
1 AC-ACAACAGTGCTAAACAGAGAGC
219065 GCGCTAGTGT
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
46 29 0.46
47 1 0.02
48 32 0.51
49 1 0.02
ACGTcount: A:0.44, C:0.23, G:0.22, T:0.12
Consensus pattern (48 bp):
ACACAACAGTGCTAAACAGAGAGCACACAAAGTGCTAATACAGAGAGC
Done.