Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012645.1 Kokia drynarioides strain JFW-HI SEQ_127655, 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: 165910
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:5189 original size:12 final size:10
Alignment explanation
Indices: 5153--5194 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
5143 TTTCTTGAAA
*
5153 AAGAAAAATG
1 AAGAAAAAGG
5163 -AGAAAAAGG
1 AAGAAAAAGG
5172 AAGAAAAAGAG
1 AAGAAAAAG-G
5183 AAAGAAAAAGG
1 -AAGAAAAAGG
5194 A
1 A
5195 TTCAATGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
9 8 0.29
10 9 0.32
11 2 0.07
12 9 0.32
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.02
Consensus pattern (10 bp):
AAGAAAAAGG
Found at i:8596 original size:19 final size:19
Alignment explanation
Indices: 8572--8611 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
8562 ATCGTAAAAA
8572 ATTAGGAAATGAATAACTG
1 ATTAGGAAATGAATAACTG
*
8591 ATTAGGAACTGAATAACTG
1 ATTAGGAAATGAATAACTG
8610 AT
1 AT
8612 ATAGAAAGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.28
Consensus pattern (19 bp):
ATTAGGAAATGAATAACTG
Found at i:9912 original size:21 final size:21
Alignment explanation
Indices: 9865--9914 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
9855 GTCGAGGCAC
**
9865 TGGTAGGGGTAGTATTGTTCT
1 TGGTAGGGGTAGTACCGTTCT
*
9886 TAGTAGGGGTAGTACCGCTT-T
1 TGGTAGGGGTAGTACCG-TTCT
9907 TGGTAGGG
1 TGGTAGGG
9915 ATCGTGGGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.16, C:0.08, G:0.40, T:0.36
Consensus pattern (21 bp):
TGGTAGGGGTAGTACCGTTCT
Found at i:11840 original size:10 final size:10
Alignment explanation
Indices: 11805--11847 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
11795 TGGCAATGTA
*
11805 TTTCTTTTCT
1 TTTCTTTTTT
*
11815 TTTCTCTTTT
1 TTTCTTTTTT
*
11825 CTTCTTTTTT
1 TTTCTTTTTT
11835 TTTCTTTATTT
1 TTTCTTT-TTT
11846 TT
1 TT
11848 GTGATGATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
10 22 0.81
11 5 0.19
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:12452 original size:17 final size:18
Alignment explanation
Indices: 12432--12473 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
12422 ACTATAATGC
12432 AAATGCACTAACAAAT-A
1 AAATGCACTAACAAATAA
* *
12449 AAATGCAGTGACAAATAA
1 AAATGCACTAACAAATAA
12467 AAATGCA
1 AAATGCA
12474 ATGAGAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.57, C:0.14, G:0.12, T:0.17
Consensus pattern (18 bp):
AAATGCACTAACAAATAA
Found at i:26384 original size:61 final size:61
Alignment explanation
Indices: 26284--26402 Score: 195
Period size: 61 Copynumber: 2.0 Consensus size: 61
26274 AAATGACCAA
*
26284 ATATTATGTATGCGATAGGTTTACTATTGATCTGCCGTAATTTAACCTAGTAGATTAAGCT
1 ATATTATGTATGCGATAGGTTTACTATTGATCCGCCGTAATTTAACCTAGTAGATTAAGCT
* *
26345 ATATTATGTATGC-AGTAGGTTTACTATTGATCCGTCGTAATTTGACCTAGTAGATTAA
1 ATATTATGTATGCGA-TAGGTTTACTATTGATCCGCCGTAATTTAACCTAGTAGATTAA
26403 ACTAGTTTTC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
60 1 0.02
61 53 0.98
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.39
Consensus pattern (61 bp):
ATATTATGTATGCGATAGGTTTACTATTGATCCGCCGTAATTTAACCTAGTAGATTAAGCT
Found at i:31901 original size:11 final size:11
Alignment explanation
Indices: 31885--31917 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
31875 CTCTAAAAGA
31885 TAAATATAAAT
1 TAAATATAAAT
*
31896 TAAATACAAAT
1 TAAATATAAAT
31907 TAAATATAAAT
1 TAAATATAAAT
31918 AACATCCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAATATAAAT
Found at i:34143 original size:6 final size:6
Alignment explanation
Indices: 34114--34183 Score: 54
Period size: 6 Copynumber: 11.2 Consensus size: 6
34104 GACAAATAAT
* * *
34114 AAAATA AATAA-A CAAAATAA AAAATTA AAAAT- AAAAGA AAAAGA AAAAGA
1 AAAATA AA-AATA -AAAAT-A AAAA-TA AAAATA AAAATA AAAATA AAAATA
34164 AAGAATA AAAATA AAAATA A
1 AA-AATA AAAATA AAAATA A
34184 TTGGGTTACC
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
5 4 0.07
6 31 0.56
7 18 0.33
8 2 0.04
ACGTcount: A:0.80, C:0.01, G:0.06, T:0.13
Consensus pattern (6 bp):
AAAATA
Found at i:36690 original size:14 final size:15
Alignment explanation
Indices: 36671--36701 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
36661 ATCTGGAGAA
36671 AATTAAAA-AAATAG
1 AATTAAAAGAAATAG
36685 AATTAAAAGAAATAG
1 AATTAAAAGAAATAG
36700 AA
1 AA
36702 GATTGAGGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (15 bp):
AATTAAAAGAAATAG
Found at i:38079 original size:16 final size:16
Alignment explanation
Indices: 38058--38094 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
38048 ACGCAAGAAG
38058 GAAAGGAAAATTTTGA
1 GAAAGGAAAATTTTGA
38074 GAAAGGAAAATTTTGA
1 GAAAGGAAAATTTTGA
38090 GAAAG
1 GAAAG
38095 AAATAAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (16 bp):
GAAAGGAAAATTTTGA
Found at i:47844 original size:15 final size:17
Alignment explanation
Indices: 47824--47856 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
47814 CTTTTTTTTG
47824 TTGTTTT-TA-TTTGCT
1 TTGTTTTCTAGTTTGCT
47839 TTGTTTTCTAGTTTGCT
1 TTGTTTTCTAGTTTGCT
47856 T
1 T
47857 GAGGATAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.06, C:0.09, G:0.15, T:0.70
Consensus pattern (17 bp):
TTGTTTTCTAGTTTGCT
Found at i:56429 original size:27 final size:25
Alignment explanation
Indices: 56372--56429 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
56362 ATTACAATAT
*
56372 TATAATATGAATTTTTTTATATTTG
1 TATAATATGAATTATTTTATATTTG
56397 TA-AATATGAAACTTATTTTATATTT-
1 TATAATATG-AA-TTATTTTATATTTG
56422 TACTAATA
1 TA-TAATA
56430 GATTATGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
24 6 0.21
25 6 0.21
26 12 0.43
27 4 0.14
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.53
Consensus pattern (25 bp):
TATAATATGAATTATTTTATATTTG
Found at i:57550 original size:7 final size:7
Alignment explanation
Indices: 57538--57566 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
57528 TAAATTGCAT
57538 TTTTTTG
1 TTTTTTG
57545 TTTTTTG
1 TTTTTTG
57552 TTTTTTG
1 TTTTTTG
57559 TTTTTTG
1 TTTTTTG
57566 T
1 T
57567 CTTTGTTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (7 bp):
TTTTTTG
Found at i:59246 original size:26 final size:26
Alignment explanation
Indices: 59198--59260 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
59188 TAAAGGACTT
*
59198 AATTAAAATT--AAAAAAAATTAAA-
1 AATTAAAATTAAAAAAAAAAATAAAG
*
59221 AGTTAAAATTAAAAAAACAAAATAAAG
1 AATTAAAATTAAAAAAA-AAAATAAAG
59248 AATT-AAATTAAAA
1 AATTAAAATTAAAA
59261 TAATATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 9 0.27
25 5 0.15
26 16 0.48
27 3 0.09
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (26 bp):
AATTAAAATTAAAAAAAAAAATAAAG
Found at i:59261 original size:6 final size:6
Alignment explanation
Indices: 59198--59234 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
59188 TAAAGGACTT
59198 AATTAA AATTAA AA--AA AATTAA AAGTTAA AATTAA AA
1 AATTAA AATTAA AATTAA AATTAA AA-TTAA AATTAA AA
59235 AAACAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
4 4 0.14
6 18 0.64
7 6 0.21
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (6 bp):
AATTAA
Found at i:60368 original size:6 final size:6
Alignment explanation
Indices: 60357--60387 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
60347 TTATTACAAT
60357 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG T
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG T
60388 CTTTCTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:61318 original size:50 final size:51
Alignment explanation
Indices: 60991--61329 Score: 173
Period size: 50 Copynumber: 6.7 Consensus size: 51
60981 TCACAATTTC
* * * * * * *
60991 ATCTTGCTCCACTGCATCTTCAGGGAGATAAGATTTGCTTCTGTAGCTTGA
1 ATCTTGATCCACTACAACTTCAAGGAGATAAGATTTGGTCCTGTAGCTTTA
* * ** *
61042 ATC-TGATCTACTACAACTTC-A-GAGATATAGGATCTGGTGTTGTATCTTT-
1 ATCTTGATCCACTACAACTTCAAGGAGATA-A-GATTTGGTCCTGTAGCTTTA
* * * ** *
61091 ATCTTGATCCACTGCATCTTCAAGGAGATAAAATTTGGTGTTGTAGC-TTC
1 ATCTTGATCCACTACAACTTCAAGGAGATAAGATTTGGTCCTGTAGCTTTA
* ** * *
61141 ATCTTGCTTTACTACAACTT-TAGAGAGATAAAGATTT-GTCACTGTTAGTTTTA
1 ATCTTGATCCACTACAACTTCAAG-GAGAT-AAGATTTGGTC-CTG-TAGCTTTA
* * * * * *
61194 ATC-TAATCCACTGCAACTTCAGGGATATAAGATTTAACGT-C-ATAGCTTT-
1 ATCTTGATCCACTACAACTTCAAGGAGATAAGATTT--GGTCCTGTAGCTTTA
* * * * * *
61243 ATCTTGCTTCATTACGACTTTAAGGAGATAAGATTCT-CTCCTGTAGCTTTA
1 ATCTTGATCCACTACAACTTCAAGGAGATAAGATT-TGGTCCTGTAGCTTTA
* *
61294 ATC-TGATCCACTACAACTTCAAGGACATAGGATTTG
1 ATCTTGATCCACTACAACTTCAAGGAGATAAGATTTG
61330 CTGTTTTACT
Statistics
Matches: 211, Mismatches: 56, Indels: 43
0.68 0.18 0.14
Matches are distributed among these distances:
48 7 0.03
49 13 0.06
50 134 0.64
51 24 0.11
52 25 0.12
53 6 0.03
54 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (51 bp):
ATCTTGATCCACTACAACTTCAAGGAGATAAGATTTGGTCCTGTAGCTTTA
Found at i:61328 original size:100 final size:102
Alignment explanation
Indices: 61134--61328 Score: 245
Period size: 100 Copynumber: 1.9 Consensus size: 102
61124 TTTGGTGTTG
* * *
61134 TAGCTTCATCTTGCTTTACTACAACTTTAGAGAGATAAAGATTTGTCACTGTTAGTTTTAATCTA
1 TAGCTTCATCTTGCTTCACTACAACTTTAGAGAGATAAAGATTTCTCACTGTTAGCTTTAATCTA
* * *
61199 ATCCACTGCAACTTCAGGGATATAAGATTTAACGTCA
66 ATCCACTACAACTTCAAGGACATAAGATTTAACGTCA
* * *
61236 TAGCTTTATCTTGCTTCATTACGACTTTA-AGGAGAT-AAGATTCTCTC-CTG-TAGCTTTAATC
1 TAGCTTCATCTTGCTTCACTACAACTTTAGA-GAGATAAAGATT-TCTCACTGTTAGCTTTAATC
* *
61297 TGATCCACTACAACTTCAAGGACATAGGATTT
64 TAATCCACTACAACTTCAAGGACATAAGATTT
61329 GCTGTTTTAC
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
100 37 0.46
101 10 0.12
102 33 0.41
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (102 bp):
TAGCTTCATCTTGCTTCACTACAACTTTAGAGAGATAAAGATTTCTCACTGTTAGCTTTAATCTA
ATCCACTACAACTTCAAGGACATAAGATTTAACGTCA
Found at i:67827 original size:13 final size:13
Alignment explanation
Indices: 67809--67853 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
67799 TATACATATA
67809 TTTTTTTTTCTTT
1 TTTTTTTTTCTTT
*
67822 TTTTTTCTTCTTT
1 TTTTTTTTTCTTT
* *
67835 TCTTTTTCTCTTT
1 TTTTTTTTTCTTT
67848 TTTTTT
1 TTTTTT
67854 ATGTGATTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTTTTTCTTT
Found at i:68546 original size:141 final size:140
Alignment explanation
Indices: 68293--68574 Score: 492
Period size: 141 Copynumber: 2.0 Consensus size: 140
68283 CTTTCATTAA
*
68293 ACTCAAAAGGACAAATTTTCAAAATGTCATGGATTTGAATTTTCAGCCCATATACATTCCCCCCA
1 ACTCAAAAGGACAAATTTTCAAAATGTCATGGATTTGAATTTCCAGCCCATATACATTCCCCCCA
*
68358 AACTTAAAGTCTGCATTGTCCCCAATACACTGACATTAATTTACAAAGACATATGGAAATGCAAT
66 AAATTAAAGTCTGCATTGTCCCCAATACACTGACATTAATTTACAAAGACATATGGAAATGCAAT
68423 GACAATGTAG
131 GACAATGTAG
** * *
68433 ACTCAAAAGGACAAATTTTCAAAATGTGGGTGGATTTGCATTTCCAGCCCATATACATTCCCCTC
1 ACTCAAAAGGACAAATTTTCAAAATGT-CATGGATTTGAATTTCCAGCCCATATACATTCCCCCC
*
68498 AAAATTAAAGTCTGCATTGTCCCCAATGCACTGACATTAATTTACAAAGACATATGGAAATGCAA
65 AAAATTAAAGTCTGCATTGTCCCCAATACACTGACATTAATTTACAAAGACATATGGAAATGCAA
68563 TGACAATGTAG
130 TGACAATGTAG
68574 A
1 A
68575 TGCAGTGACA
Statistics
Matches: 134, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
140 27 0.20
141 107 0.80
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (140 bp):
ACTCAAAAGGACAAATTTTCAAAATGTCATGGATTTGAATTTCCAGCCCATATACATTCCCCCCA
AAATTAAAGTCTGCATTGTCCCCAATACACTGACATTAATTTACAAAGACATATGGAAATGCAAT
GACAATGTAG
Found at i:68617 original size:17 final size:17
Alignment explanation
Indices: 68578--68620 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
68568 ATGTAGATGC
68578 AGTGACAATAAAAATGT
1 AGTGACAATAAAAATGT
*
68595 AATGACAA-AAGAAATGT
1 AGTGACAATAA-AAATGT
*
68612 GGTGACAAT
1 AGTGACAAT
68621 TACACTACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.51, C:0.07, G:0.21, T:0.21
Consensus pattern (17 bp):
AGTGACAATAAAAATGT
Found at i:69080 original size:24 final size:24
Alignment explanation
Indices: 69039--69084 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
69029 TCGACATCAG
*
69039 TTCCTTCTCTTCTTTCTTCCTCCT
1 TTCCTTCTCTTCTGTCTTCCTCCT
69063 TTCCTTCTTCTT-TGTCTTCCTC
1 TTCCTTC-TCTTCTGTCTTCCTC
69085 TATCTCCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.00, C:0.39, G:0.02, T:0.59
Consensus pattern (24 bp):
TTCCTTCTCTTCTGTCTTCCTCCT
Found at i:70826 original size:22 final size:22
Alignment explanation
Indices: 70801--70842 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
70791 GTCTATAAGG
70801 AGCTTTGTATGCATCGACAAGA
1 AGCTTTGTATGCATCGACAAGA
*
70823 AGCTTTGTATGCGTCGACAA
1 AGCTTTGTATGCATCGACAA
70843 AAGAAAGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (22 bp):
AGCTTTGTATGCATCGACAAGA
Found at i:74752 original size:10 final size:10
Alignment explanation
Indices: 74737--74774 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
74727 CAACAAAATC
74737 AAATAATTCA
1 AAATAATTCA
*
74747 AAATAATTTTA
1 AAATAA-TTCA
74758 AAA-AATTCA
1 AAATAATTCA
74767 AAATAATT
1 AAATAATT
74775 TTAAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 6 0.25
10 12 0.50
11 6 0.25
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (10 bp):
AAATAATTCA
Found at i:74788 original size:19 final size:19
Alignment explanation
Indices: 74741--74808 Score: 84
Period size: 19 Copynumber: 3.5 Consensus size: 19
74731 AAAATCAAAT
74741 AATTCAAAATAATTTTAAAA
1 AATTCAAAATAATTTT-AAA
74761 AATTCAAAATAATTTTAAA
1 AATTCAAAATAATTTTAAA
* *
74780 ATTTTAAAAT-ATTTATAAA
1 AATTCAAAATAATTT-TAAA
*
74799 AATTCCAAAT
1 AATTCAAAAT
74809 TTTATTTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
18 4 0.10
19 22 0.52
20 16 0.38
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTCAAAATAATTTTAAA
Found at i:74802 original size:20 final size:20
Alignment explanation
Indices: 74743--74807 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
74733 AATCAAATAA
*
74743 TTCAAAATAATTTTAAAAAA
1 TTCAAAATAATTTTAAAAAT
74763 TTCAAAATAATTTT-AAAAT
1 TTCAAAATAATTTTAAAAAT
*
74782 TTTAAAAT-ATTTATAAAAAT
1 TTCAAAATAATTT-TAAAAAT
*
74802 TCCAAA
1 TTCAAA
74808 TTTTATTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
18 4 0.10
19 12 0.31
20 23 0.59
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.38
Consensus pattern (20 bp):
TTCAAAATAATTTTAAAAAT
Found at i:75058 original size:5 final size:5
Alignment explanation
Indices: 75042--75090 Score: 53
Period size: 5 Copynumber: 9.8 Consensus size: 5
75032 ACAATTTCAC
* * * * *
75042 TCGAT TCAAT TCGAT TCGAT TCGAT TCGAC TCGAC TCGAA TCGAA TCGA
1 TCGAT TCGAT TCGAT TCGAT TCGAT TCGAT TCGAT TCGAT TCGAT TCGA
75091 AAATTTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (5 bp):
TCGAT
Found at i:80466 original size:3 final size:3
Alignment explanation
Indices: 80460--80508 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
80450 AGCAAATAAT
* *
80460 AGA AGA AGA AGT AGA AGA AGA AGA AGA AGA AGA AGA AGA GGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
80508 A
1 A
80509 ATCCTTAGCG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.63, C:0.00, G:0.35, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:88553 original size:11 final size:12
Alignment explanation
Indices: 88535--88563 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
88525 TTTAAATATT
88535 ATATAATAAATA
1 ATATAATAAATA
88547 A-ATAATAAATA
1 ATATAATAAATA
88558 ATATAA
1 ATATAA
88564 AAAGTGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
ATATAATAAATA
Found at i:89282 original size:31 final size:30
Alignment explanation
Indices: 89247--89306 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
89237 TTACAAAACG
89247 ATTACTAAACTATTCAAAAGTTTTCATTTAA
1 ATTACTAAACTATTCAAAAGTTTT-ATTTAA
* *
89278 ATTACTTAACTATTCTAAAGTTTTATTTA
1 ATTACTAAACTATTCAAAAGTTTTATTTA
89307 GGTCATTAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 5 0.19
31 22 0.81
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (30 bp):
ATTACTAAACTATTCAAAAGTTTTATTTAA
Found at i:92208 original size:2 final size:2
Alignment explanation
Indices: 92201--92242 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
92191 AAACAATTAA
92201 AT AT 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 AT AT
92243 TAAAAAAATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:97744 original size:2 final size:2
Alignment explanation
Indices: 97737--97767 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
97727 TTTGATTATA
97737 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
97768 ATTTATGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:101625 original size:2 final size:2
Alignment explanation
Indices: 101618--101654 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
101608 GGTATAAATT
101618 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
101655 ATACTCAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:105696 original size:24 final size:24
Alignment explanation
Indices: 105668--105728 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
105658 TTTAACTTAT
105668 ATACTTTAATTTTGACATAATTTG
1 ATACTTTAATTTTGACATAATTTG
105692 ATACTTTAATTTTGACATAATTTG
1 ATACTTTAATTTTGACATAATTTG
105716 ATACTTTAATTTT
1 ATACTTTAATTTT
105729 TATAATGCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.33, C:0.08, G:0.07, T:0.52
Consensus pattern (24 bp):
ATACTTTAATTTTGACATAATTTG
Found at i:109638 original size:23 final size:23
Alignment explanation
Indices: 109612--109656 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
109602 CCAACTTAAC
109612 CCAAAACC-TTTAAACCCAATAAG
1 CCAAAACCATTT-AACCCAATAAG
* *
109635 CCAAACCCATTTGACCCAATAA
1 CCAAAACCATTTAACCCAATAA
109657 CTCAAATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.44, C:0.33, G:0.04, T:0.18
Consensus pattern (23 bp):
CCAAAACCATTTAACCCAATAAG
Found at i:109707 original size:6 final size:6
Alignment explanation
Indices: 109696--109757 Score: 61
Period size: 6 Copynumber: 9.7 Consensus size: 6
109686 CCATTGACCG
* * *
109696 TTGACT TTGACT TTGACCG TTGACT ATTGACC TTGACT GTTGATCG TTGACT
1 TTGACT TTGACT TTGA-CT TTGACT -TTGACT TTGACT -TTGA-CT TTGACT
109748 TTGACT TTGA
1 TTGACT TTGA
109758 ATCGTTGACT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
6 27 0.59
7 18 0.39
8 1 0.02
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.44
Consensus pattern (6 bp):
TTGACT
Found at i:109718 original size:13 final size:14
Alignment explanation
Indices: 109702--109752 Score: 63
Period size: 13 Copynumber: 3.9 Consensus size: 14
109692 ACCGTTGACT
109702 TTGACT-TTGACCG
1 TTGACTATTGACCG
109715 TTGACTATTGACC-
1 TTGACTATTGACCG
* *
109728 TTGACTGTTGATCG
1 TTGACTATTGACCG
109742 TTGACT-TTGAC
1 TTGACTATTGAC
109753 TTTGAATCGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 21 0.64
14 12 0.36
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.41
Consensus pattern (14 bp):
TTGACTATTGACCG
Found at i:109718 original size:26 final size:27
Alignment explanation
Indices: 109684--109766 Score: 80
Period size: 26 Copynumber: 3.1 Consensus size: 27
109674 CAAGTTGACC
* *
109684 GACCATTGACCGTTGACTTTGACT-TT
1 GACCGTTGACCATTGACTTTGACTGTT
* *
109710 GACCGTTGACTATTGACCTTGACTGTT
1 GACCGTTGACCATTGACTTTGACTGTT
* * *
109737 GATCGTTGA-CTTTGACTTTGAATCGTT
1 GACCGTTGACCATTGACTTTGACT-GTT
109764 GAC
1 GAC
109767 TTTTTTCGAG
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
26 30 0.67
27 15 0.33
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (27 bp):
GACCGTTGACCATTGACTTTGACTGTT
Found at i:109767 original size:20 final size:20
Alignment explanation
Indices: 109689--109769 Score: 78
Period size: 20 Copynumber: 4.1 Consensus size: 20
109679 TGACCGACCA
* *
109689 TTGACCGTTGA-CTTTGACT
1 TTGACTGTTGATCGTTGACT
* * *
109708 TTGACCGTTGA-CTATTGACC
1 TTGACTGTTGATC-GTTGACT
109728 TTGACTGTTGATCGTTGACT
1 TTGACTGTTGATCGTTGACT
109748 TTGACT-TTGAATCGTTGACT
1 TTGACTGTTG-ATCGTTGACT
109768 TT
1 TT
109770 TTTCGAGGAA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.28
20 38 0.70
21 1 0.02
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (20 bp):
TTGACTGTTGATCGTTGACT
Found at i:113878 original size:27 final size:28
Alignment explanation
Indices: 113819--113905 Score: 106
Period size: 28 Copynumber: 3.1 Consensus size: 28
113809 TATGCTCAAT
* *
113819 ACTCGTCCAGCA-CATAAGTGCGGTAAAA
1 ACTCGTCCAGCACCA-AAGTGAGGTAATA
*
113847 ACTCGTCCAGCACCAAAGTG-GGTATTA
1 ACTCGTCCAGCACCAAAGTGAGGTAATA
* *
113874 ACTCGTACAGCACAAAAGTGAGGTAATA
1 ACTCGTCCAGCACCAAAGTGAGGTAATA
113902 ACTC
1 ACTC
113906 ATATCACAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
27 23 0.44
28 27 0.52
29 2 0.04
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.20
Consensus pattern (28 bp):
ACTCGTCCAGCACCAAAGTGAGGTAATA
Found at i:120668 original size:8 final size:8
Alignment explanation
Indices: 120649--120727 Score: 52
Period size: 9 Copynumber: 9.1 Consensus size: 8
120639 TTATTTTAGA
120649 AAATTTTT
1 AAATTTTT
120657 -AATTTTT
1 AAATTTTT
120664 AAATTTTTTT
1 AAA--TTTTT
120674 ATATATTTTT
1 A-A-ATTTTT
120684 AGAATTTTT
1 A-AATTTTT
120693 ATAATTTTT
1 A-AATTTTT
** *
120702 AAAAAATAT
1 -AAATTTTT
*
120711 AAATTTTG
1 AAATTTTT
120719 AAATTTTT
1 AAATTTTT
120727 A
1 A
120728 TAAATATTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
7 7 0.13
8 14 0.25
9 18 0.33
10 14 0.25
11 1 0.02
12 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (8 bp):
AAATTTTT
Found at i:120731 original size:18 final size:18
Alignment explanation
Indices: 120657--120745 Score: 74
Period size: 19 Copynumber: 4.8 Consensus size: 18
120647 GAAAATTTTT
120657 AATTTTTAAATTTTTTTATA
1 AATTTTTAAA--TTTTTATA
*
120677 TATTTTTAGAATTTTTAT-
1 AATTTTTA-AATTTTTATA
***
120695 AATTTTTAAA-AAATATA
1 AATTTTTAAATTTTTATA
*
120712 AATTTTGAAATTTTTATA
1 AATTTTTAAATTTTTATA
*
120730 AATATTTTTAATTTTT
1 AAT-TTTTAAATTTTT
120746 GAAAATTATT
Statistics
Matches: 54, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
16 3 0.06
17 11 0.20
18 14 0.26
19 17 0.31
20 7 0.13
21 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
AATTTTTAAATTTTTATA
Found at i:121153 original size:18 final size:18
Alignment explanation
Indices: 121130--121165 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
121120 TTAATAAAAT
*
121130 AAAATAAAATTTATTTAA
1 AAAATAAAATTGATTTAA
121148 AAAATAAAATTGATTTAA
1 AAAATAAAATTGATTTAA
121166 TATTTTTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
AAAATAAAATTGATTTAA
Found at i:129156 original size:17 final size:16
Alignment explanation
Indices: 129122--129156 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
129112 GAGCCACTTG
*
129122 TAAAGTATTTTTTTAT
1 TAAAGTATTTTTTGAT
129138 TAAAGTATTTTTATGAT
1 TAAAGTATTTTT-TGAT
129155 TA
1 TA
129157 TTTTTCTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (16 bp):
TAAAGTATTTTTTGAT
Found at i:129611 original size:29 final size:28
Alignment explanation
Indices: 129574--129634 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 28
129564 TATATATTAT
129574 TAATTAATAAAATT-T-TAAATCTATAAAA
1 TAATTAATAAAATTATATAAAT-TA-AAAA
*
129602 TAATTGAATATAATTATATAAATTAAAAA
1 TAATT-AATAAAATTATATAAATTAAAAA
129631 TAAT
1 TAAT
129635 AATTTTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 5 0.17
29 16 0.55
30 3 0.10
31 5 0.17
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (28 bp):
TAATTAATAAAATTATATAAATTAAAAA
Found at i:129666 original size:22 final size:23
Alignment explanation
Indices: 129622--129665 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
129612 TAATTATATA
129622 AATTAAA-AATAATAATTTTTTT
1 AATTAAATAATAATAATTTTTTT
129644 AATTAAATAA-AATTAATTTTTT
1 AATTAAATAATAA-TAATTTTTT
129666 ATATAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AATTAAATAATAATAATTTTTTT
Found at i:129683 original size:16 final size:17
Alignment explanation
Indices: 129662--129694 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
129652 AAAATTAATT
129662 TTTTA-TATAAATATGA
1 TTTTATTATAAATATGA
*
129678 TTTTATTTTAAATATGA
1 TTTTATTATAAATATGA
129695 AAAAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (17 bp):
TTTTATTATAAATATGA
Found at i:136693 original size:52 final size:52
Alignment explanation
Indices: 136636--136746 Score: 159
Period size: 52 Copynumber: 2.1 Consensus size: 52
136626 ATTACACTTA
*
136636 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTTAC
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAC
* * * ** *
136688 ATACTCACGATGGCACATAGTCATTGGACCTCATACTCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAC
136740 ATACTCA
1 ATACTCA
136747 AAGCCCGTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAC
Found at i:141357 original size:11 final size:11
Alignment explanation
Indices: 141333--141371 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
141323 GTCTCTAATA
141333 ATTTTTCTAT-
1 ATTTTTCTATG
141343 ATTTTTCTATG
1 ATTTTTCTATG
141354 ATTTTTCTATG
1 ATTTTTCTATG
141365 ATTTTTC
1 ATTTTTC
141372 AAATTTAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 10 0.36
11 18 0.64
ACGTcount: A:0.18, C:0.10, G:0.05, T:0.67
Consensus pattern (11 bp):
ATTTTTCTATG
Found at i:147656 original size:11 final size:11
Alignment explanation
Indices: 147632--147670 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
147622 GTCTCTAATA
147632 ATTTTTCTAT-
1 ATTTTTCTATG
147642 ATTTTTCTATG
1 ATTTTTCTATG
147653 ATTTTTCTATG
1 ATTTTTCTATG
147664 ATTTTTC
1 ATTTTTC
147671 AAATTTAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 10 0.36
11 18 0.64
ACGTcount: A:0.18, C:0.10, G:0.05, T:0.67
Consensus pattern (11 bp):
ATTTTTCTATG
Found at i:153889 original size:52 final size:52
Alignment explanation
Indices: 153797--153983 Score: 239
Period size: 52 Copynumber: 3.6 Consensus size: 52
153787 ATTACACTTA
* * * * ** *
153797 ATACTCATGATGACACATAGTTATCGGACATCTTGTTCCGTAAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * *
153849 ACACTCACGATGACACATAGTCATTGGACCTCATAATCCGTAAAGGATTTAC
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
153901 ATACTCACAATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
153953 ATACTCACGGTGACACATAGTCATCGAACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
153984 TTCTCATTTA
Statistics
Matches: 114, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 114 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:155955 original size:52 final size:52
Alignment explanation
Indices: 155872--156164 Score: 360
Period size: 52 Copynumber: 5.6 Consensus size: 52
155862 TTCTCATTTA
* *
155872 ATACTCAAGATGACACATAGTCATCGGACCTCATAATCTGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCTGTAAAAGATTCAT
* * * *
155924 ATACTCATGATGACACATAGTCATTGAACCTCGTAATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCTGTAAAAGATTCAT
* * *
155976 ATAGTCACGAATGACACATAGTCATCGAACCTCATAAT-TCATAAAGGATTCAT
1 ATACTCACG-ATGACACATAGTCATCGAACCTCATAATCT-GTAAAAGATTCAT
* * *
156029 ATACTCATGATGACACATAGTCATCGGACCTCATAAT-TCGAAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCT-GTAAAAGATTCAT
* * *
156081 ATACTCACGATGACGCATAGTCATC-AGACCCCGA-AATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGA-ACCTC-ATAATCTGTAAAAGATTCAT
*
156133 ATAACTCACGATGACACATAGTCATCGGACCT
1 AT-ACTCACGATGACACATAGTCATCGAACCT
156165 TTTGCATTTA
Statistics
Matches: 207, Mismatches: 27, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
52 137 0.66
53 70 0.34
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGAACCTCATAATCTGTAAAAGATTCAT
Found at i:156074 original size:105 final size:104
Alignment explanation
Indices: 155872--156164 Score: 394
Period size: 105 Copynumber: 2.8 Consensus size: 104
155862 TTCTCATTTA
* *
155872 ATACTCAAGATGACACATAGTCATCGGACCTCATAA-TCTGTAAAAGATTCATATACTCATGATG
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATTC-GTAAAAGATTCATATACTCATGATG
* * * *
155936 ACACATAGTCATTGAACCTCGTAATCCGTAAAAGATTCAT
65 ACACATAGTCATCGGACCTCATAATCCGAAAAAGATTCAT
* * *
155976 ATAGTCACGAATGACACATAGTCATCGAACCTCATAATTCATAAAGGATTCATATACTCATGATG
1 ATACTCACG-ATGACACATAGTCATCGAACCTCATAATTCGTAAAAGATTCATATACTCATGATG
*
156041 ACACATAGTCATCGGACCTCATAATTCGAAAAAGATTCAT
65 ACACATAGTCATCGGACCTCATAATCCGAAAAAGATTCAT
* * * *
156081 ATACTCACGATGACGCATAGTCATC-AGACCCCGA-AATCCGTAAAAGATTCATATAACTCACGA
1 ATACTCACGATGACACATAGTCATCGA-ACCTC-ATAATTCGTAAAAGATTCATAT-ACTCATGA
156144 TGACACATAGTCATCGGACCT
63 TGACACATAGTCATCGGACCT
156165 TTTGCATTTA
Statistics
Matches: 167, Mismatches: 17, Indels: 9
0.87 0.09 0.05
Matches are distributed among these distances:
103 1 0.01
104 43 0.26
105 121 0.72
106 2 0.01
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.26
Consensus pattern (104 bp):
ATACTCACGATGACACATAGTCATCGAACCTCATAATTCGTAAAAGATTCATATACTCATGATGA
CACATAGTCATCGGACCTCATAATCCGAAAAAGATTCAT
Found at i:156158 original size:157 final size:157
Alignment explanation
Indices: 155872--156164 Score: 457
Period size: 157 Copynumber: 1.9 Consensus size: 157
155862 TTCTCATTTA
* *
155872 ATACTCAAGATGACACATAGTCATCGGACCTCATAATCTGTAAAAGATTCATATACTCATGATGA
1 ATACTCAAGATGACACATAGTCATCGGACCTCATAATCTGAAAAAGATTCATATACTCACGATGA
* * * *
155937 CACATAGTCATTGAACCTCGTAATCCGTAAAAGATTCATATAGTCACGAATGACACATAGTCATC
66 CACATAGTCATAGAACCCCGAAATCCGTAAAAGATTCATATACTCACGAATGACACATAGTCATC
156002 GAACCTCATAATTCATAAAGGATTCAT
131 GAACCTCATAATTCATAAAGGATTCAT
*
156029 ATACTCATGATGACACATAGTCATCGGACCTCATAAT-TCGAAAAAGATTCATATACTCACGATG
1 ATACTCAAGATGACACATAGTCATCGGACCTCATAATCT-GAAAAAGATTCATATACTCACGATG
*
156093 ACGCATAGTCATCAG-ACCCCGAAATCCGTAAAAGATTCATATAACTCACG-ATGACACATAGTC
65 ACACATAGTCAT-AGAACCCCGAAATCCGTAAAAGATTCATAT-ACTCACGAATGACACATAGTC
*
156156 ATCGGACCT
128 ATCGAACCT
156165 TTTGCATTTA
Statistics
Matches: 124, Mismatches: 9, Indels: 6
0.89 0.06 0.04
Matches are distributed among these distances:
156 1 0.01
157 116 0.94
158 7 0.06
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.26
Consensus pattern (157 bp):
ATACTCAAGATGACACATAGTCATCGGACCTCATAATCTGAAAAAGATTCATATACTCACGATGA
CACATAGTCATAGAACCCCGAAATCCGTAAAAGATTCATATACTCACGAATGACACATAGTCATC
GAACCTCATAATTCATAAAGGATTCAT
Found at i:156652 original size:16 final size:16
Alignment explanation
Indices: 156628--156659 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
156618 TCCTTACAAA
*
156628 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
156644 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
156660 AAAAGTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:159192 original size:89 final size:89
Alignment explanation
Indices: 159041--159221 Score: 362
Period size: 89 Copynumber: 2.0 Consensus size: 89
159031 GCATGTATTG
159041 GTAGAGGTACAGGGTAGGAGAGAAGTTGTTCATTGACTTGGGTTGTATCAGTAGTTGAATGGCAA
1 GTAGAGGTACAGGGTAGGAGAGAAGTTGTTCATTGACTTGGGTTGTATCAGTAGTTGAATGGCAA
159106 ATATCGGTAGTTATATGTTTAGAA
66 ATATCGGTAGTTATATGTTTAGAA
159130 GTAGAGGTACAGGGTAGGAGAGAAGTTGTTCATTGACTTGGGTTGTATCAGTAGTTGAATGGCAA
1 GTAGAGGTACAGGGTAGGAGAGAAGTTGTTCATTGACTTGGGTTGTATCAGTAGTTGAATGGCAA
159195 ATATCGGTAGTTATATGTTTAGAA
66 ATATCGGTAGTTATATGTTTAGAA
159219 GTA
1 GTA
159222 TCGGTAGTTT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 92 1.00
ACGTcount: A:0.29, C:0.07, G:0.31, T:0.33
Consensus pattern (89 bp):
GTAGAGGTACAGGGTAGGAGAGAAGTTGTTCATTGACTTGGGTTGTATCAGTAGTTGAATGGCAA
ATATCGGTAGTTATATGTTTAGAA
Found at i:163743 original size:17 final size:17
Alignment explanation
Indices: 163675--163743 Score: 59
Period size: 17 Copynumber: 4.1 Consensus size: 17
163665 CCAATTTTAA
* *
163675 ATTTTAAATTTTAATTT
1 ATTTTGAATTTAAATTT
*
163692 ATTTT-AAGTTTAAACTT
1 ATTTTGAA-TTTAAATTT
* * *
163709 ATTCTGAGTTTAATTTT
1 ATTTTGAATTTAAATTT
*
163726 ATTTTGAATTCAAATTT
1 ATTTTGAATTTAAATTT
163743 A
1 A
163744 AAGTTTAAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
16 2 0.05
17 37 0.93
18 1 0.03
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (17 bp):
ATTTTGAATTTAAATTT
Done.