Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009789.1 Kokia drynarioides strain JFW-HI SEQ_124510, 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: 83022
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1240 original size:16 final size:15
Alignment explanation
Indices: 1219--1258 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1209 AAAAATACAA
1219 AAAAAGAAGAAAAAAG
1 AAAAAGAA-AAAAAAG
*
1235 AAAAAGAAAAAAATG
1 AAAAAGAAAAAAAAG
1250 AAAAA-AAAA
1 AAAAAGAAAA
1259 TAGAAAGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.17
15 11 0.48
16 8 0.35
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:1244 original size:21 final size:20
Alignment explanation
Indices: 1204--1264 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 20
1194 TGTTTAAATC
*
1204 AAGAAAAAAATACAAA-AAAAG
1 AAGAAAAAAA-A-AAAGAAAAA
1225 AAGAAAAAAGAAAAAGAAAAA
1 AAGAAAAAA-AAAAAGAAAAA
*
1246 AATGAAAAAAAAATAGAAA
1 AA-GAAAAAAAAAAAGAAA
1265 GAGAGAGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 3 0.09
21 24 0.69
22 8 0.23
ACGTcount: A:0.82, C:0.02, G:0.11, T:0.05
Consensus pattern (20 bp):
AAGAAAAAAAAAAAGAAAAA
Found at i:1716 original size:42 final size:42
Alignment explanation
Indices: 1656--2395 Score: 766
Period size: 42 Copynumber: 17.4 Consensus size: 42
1646 AAAGAAATCA
*
1656 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCTATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
1698 TTCATTTCATTTAAAGGCCCAGGTGTGGAGGTCCGTTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
1740 TTCATAGCATTTAGAGGCCCAGGTGTGGAAGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * ** *
1782 TTCGTTGCATTTAAACACCCAGATGTGGAGG-CTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTC-CATTTACTT
** * * ** * *
1824 TTCACCGCATTCAAAGGCTTA-GTAGTGGAGGCCCACTTACTT
1 TTCATTGCATTTAGAGGCCCAGGT-GTGGAGGTCCATTTACTT
* *
1866 TTCATTGCATTTAGAGGCCCAGGCGTGGAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
** * *
1908 TTTGTTGCATTTAAAGGCCCAGGTGTGGAAGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
1950 TTGATTGTATTTAGAGGCCCAGGTGTGGAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCC--------AGGTGTGGAGGTCCATTTACTT
*
2000 TTCATTGCATTTAGAGGCTCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
2042 TTAATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
2084 TTCATCGCATTTAGAGGCCTAGGTGTGGAGGTCAATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * * * *
2126 TTCATCGCATTCAGAGGCCTAAGTGTAGAGGCCCATTCACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
2168 TTCATCGCATTCACAGGCCCAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
2210 TTCATTGCATTCAGAGGCCTAGGTGTAGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
2252 TTCATTGCATTCAGAGGCCCAGCTGTGAAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
** * * * * *
2294 TTTGTTGCATTTAGAGGACTAAGTGT-GAGGGTTCATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGA-GGTCCATTTACTT
** * * *
2336 TTCATTGCATTCGGAGGCCTAGGTGTGGAGGTTCATTTACCT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
2378 TTGATTGCATTTAGAGGC
1 TTCATTGCATTTAGAGGC
2396 TTAAGCATAG
Statistics
Matches: 584, Mismatches: 100, Indels: 28
0.82 0.14 0.04
Matches are distributed among these distances:
41 3 0.01
42 539 0.92
43 4 0.01
50 38 0.07
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:3544 original size:146 final size:146
Alignment explanation
Indices: 3343--3871 Score: 601
Period size: 146 Copynumber: 3.6 Consensus size: 146
3333 ATTTTTTTAG
*
3343 AAAAGTTTAAATTTTTAAAACAAAGTTTTGA-TTTTTTTAACTATTTC-AATATAAAAGTTTAGA
1 AAAAATTTAAATTTTT-AAACAAAGTTTTGATTTTTTTTAACTATTTCGAA-ATAAAAGTTTAGA
*
3406 TTTTTAAG-AAAGTAGTGATTTTCATTAAAAAATGAGAAAGTTTATATTTTTAAAAAATAAAATC
64 TTTTTAAGTAAAGTAGTGATTTTCATTAAAAAA-GAGAAAGTTTAGATTTTT-AAAAATAAAATC
*
3470 TGTTTTAATTATTTTAAAG-
127 TTTTTTAATTATTTTAAAGA
* * *
3489 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTGGATT
1 AAAAATTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATT
* * * * *
3554 TTTAAGTAAAATAGTGATTTACTTTAAAAAAGAGAATGCTTT-GCATTTTTATAAATAAAAATCC
66 TTTAAGTAAAGTAGTGATTTTCATTAAAAAAGAGAAAG-TTTAG-ATTTTTAAAAAT-AAAAT-C
* *
3618 GTTTTTTTTAGTTATTTTAAGGA
127 ---TTTTTTAATTATTTTAAAGA
* * * * *
3641 AAAAATTTAAATTTTTAAATAAAGTTTTTATTTTTTTAAACTATTT-GAAATAAAAATTTAGAAT
1 AAAAATTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATT
*
3705 TTTAAGTAAAGTAGTGATTTTCATTAAAAAAGAAAGAAAGTTTAGA--TTTAAAAA-AAATATAT
66 TTTAAGTAAAGTAGTGATTTTCATTAAAAAAG--AGAAAGTTTAGATTTTTAAAAATAAA-ATCT
* *
3767 TTTTTAGTGATTTTAAAGA
128 TTTTTAATTATTTTAAAGA
* * * * * *
3786 AAAAATTAAAATTTTTAAACAAAGTTTTTA-TTTTTTTATACTATTTTGAATTAAAAATTTTGAT
1 AAAAATTTAAATTTTTAAACAAAGTTTTGATTTTTTTTA-ACTATTTCGAAATAAAAGTTTAGAT
*
3850 TTTGAAGTAAAGTAGTGATTTT
65 TTTTAAGTAAAGTAGTGATTTT
3872 GTTTTAATCA
Statistics
Matches: 334, Mismatches: 32, Indels: 34
0.83 0.08 0.09
Matches are distributed among these distances:
144 7 0.02
145 66 0.20
146 98 0.29
147 37 0.11
148 4 0.01
149 2 0.01
150 7 0.02
151 60 0.18
152 47 0.14
153 6 0.02
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (146 bp):
AAAAATTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATT
TTTAAGTAAAGTAGTGATTTTCATTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAATCTTTT
TTAATTATTTTAAAGA
Found at i:3572 original size:52 final size:51
Alignment explanation
Indices: 3341--3573 Score: 126
Period size: 52 Copynumber: 4.7 Consensus size: 51
3331 CTATTTTTTT
** *
3341 AGAAAAGTTTAAATTTTTAAA-ACAAAGTTTTGA-TTTTTTTAACTATTTCAA
1 AGAAAAGTTTAAATTTTTAAATA-AAA-TAGTGATTTTTTTTAACTATTTGAA
* * * * ** * **
3392 TATAAAAGTTTAGATTTTT-AAGAAAGTAGTGATTTTCATTAA-AAAATG--
1 -AGAAAAGTTTAAATTTTTAAATAAAATAGTGATTTTTTTTAACTATTTGAA
* ** * * * *
3440 AG-AAAGTTTATATTTTT-AA-AAAATA-AAATCTGTTTTAATTATTTTAA
1 AGAAAAGTTTAAATTTTTAAATAAAATAGTGATTTTTTTTAACTATTTGAA
* **
3487 AGAAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTCGAA
1 AGAAAAGTTTAAATTTTTAAATAAAATAGTGATTTTTTTTAACTATTT-GAA
* ** *
3539 ATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTT
1 AGAAAAGTTTAAATTTTTAAATAAAATAGTGATTT
3574 ACTTTAAAAA
Statistics
Matches: 131, Mismatches: 40, Indels: 20
0.69 0.21 0.10
Matches are distributed among these distances:
44 7 0.05
45 7 0.05
46 16 0.12
47 3 0.02
48 14 0.11
49 2 0.02
50 10 0.08
51 25 0.19
52 47 0.36
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.45
Consensus pattern (51 bp):
AGAAAAGTTTAAATTTTTAAATAAAATAGTGATTTTTTTTAACTATTTGAA
Found at i:4502 original size:20 final size:21
Alignment explanation
Indices: 4464--4503 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4454 ATAATTTTTA
* *
4464 TTTATTTTTATTTCATATTTG
1 TTTATTTTCATGTCATATTTG
4485 TTTATTTTCATGTC-TATTT
1 TTTATTTTCATGTCATATTT
4504 ATATTTAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTATTTTCATGTCATATTTG
Found at i:8240 original size:4 final size:4
Alignment explanation
Indices: 8231--8301 Score: 79
Period size: 4 Copynumber: 17.8 Consensus size: 4
8221 GTGCCCCAAT
* * *
8231 TTCA TTCA TTCA CTCA TTCA TTCA TTCA TTCA CTCA CTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
* * * *
8279 TTCA CTCA CTCA CTCA CTCA TTC
1 TTCA TTCA TTCA TTCA TTCA TTC
8302 GCTCATTTGT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 61 1.00
ACGTcount: A:0.24, C:0.35, G:0.00, T:0.41
Consensus pattern (4 bp):
TTCA
Found at i:8256 original size:20 final size:20
Alignment explanation
Indices: 8231--8306 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
8221 GTGCCCCAAT
*
8231 TTCATTCATTCACTCATTCA
1 TTCATTCATTCACTCACTCA
8251 TTCATTCATTCACTCACTCA
1 TTCATTCATTCACTCACTCA
8271 TTCATTCATTCACTCACTCA
1 TTCATTCATTCACTCACTCA
* * *
8291 CTCACTCATTCGCTCA
1 TTCATTCATTCACTCA
8307 TTTGTTTATT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.24, C:0.36, G:0.01, T:0.39
Consensus pattern (20 bp):
TTCATTCATTCACTCACTCA
Found at i:16594 original size:19 final size:20
Alignment explanation
Indices: 16550--16587 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16540 TGTTTAAATT
*
16550 AAGAAAAAATACAAAAAAAG
1 AAGAAAAAAGACAAAAAAAG
16570 AAGAAAAAAGA-AAAAAAA
1 AAGAAAAAAGACAAAAAAA
16588 ATAGAAAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.84, C:0.03, G:0.11, T:0.03
Consensus pattern (20 bp):
AAGAAAAAAGACAAAAAAAG
Found at i:17056 original size:42 final size:42
Alignment explanation
Indices: 16997--17690 Score: 767
Period size: 42 Copynumber: 16.5 Consensus size: 42
16987 AAAGAAAGCA
* * *
16997 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTAACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * *
17039 TTCATCGCATTTAGAGGCCTAGGTGTGAAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * * *
17081 TTCATTGTATTCAGACGCCCAGGTGTGGAAGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * ***
17123 TTCGTTACATTTAGAGGCCCATAAGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
*** **
17165 TTCATCATATTTAGAGGCCCAATTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * *
17207 TTCATTGCATTTAGAGGCCTAGGTTTGGAGGCCTATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * **
17249 TTCGTTGCATTTAAAGGCCCAATTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
*
17291 TTCGTTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
** ** *
17333 TTTGTTGCATTTAGAGGCCCAGGTGTGGAGATCCATTTCCTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* ** * *
17375 TTCATTGTATTTAGAGGCCCAAATGTGGAGGTCCATTTGCTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * **
17417 TTCAGTGCATTTAGAGGCCTAGGTGTGGAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * * * *
17459 TTCATCGCATTCAAAGGCCCAGGTGTGGAGGTCCATTTACAT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
** *
17501 TTCATCACATTCAGAGGCCCAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * * * *
17543 TTCATTGCATTCATAGGCCTAGGTGTGAAGGCTCATTTACTCTTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTA--C-TT
** ** * *
17588 TTTTTTGCATTTAGAGGCCCAAATGTGGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
** * *
17630 TTCATTGCATTCGGAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
*
17672 TTCATTGCAATTAGAGGCC
1 TTCATTGCATTTAGAGGCC
17691 TAAGCATAGA
Statistics
Matches: 550, Mismatches: 99, Indels: 6
0.84 0.15 0.01
Matches are distributed among these distances:
42 518 0.94
44 1 0.00
45 31 0.06
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
Found at i:18678 original size:133 final size:137
Alignment explanation
Indices: 18516--18915 Score: 355
Period size: 149 Copynumber: 2.8 Consensus size: 137
18506 TTGGGAAAAA
* *
18516 TTTTGATTTTTTTAAAATAATTTCGAAATAAAAACTTT-TATTTTTAAGTAAAATAGTGATTTTC
1 TTTTGATTTTTTTAAAATAATTTCAAAAT-AAAACTTTAGATTTTTAAG-AAAATAGTGATTTTC
* **
18580 TTTTTAAAA-A-AAAGCTTAGATTTTT-AAAAATAAAAATCTGTTTTTTTAGAAAAGTTAAAAAT
64 ATTAAAAAAGAGAAAGCTTAGATTTTTAAAAAATAAAAATCTGTTTTTTTAGAAAAGTTAAAAAT
18642 TAAACAAAG
129 TAAACAAAG
* * *
18651 TTTTGA-TTTTTTAAACT-ATTTCAAAATAAAAGTTTAGATTTTTAAGAAAGTAGTGATTTTCAT
1 TTTTGATTTTTTTAAAATAATTTCAAAATAAAACTTTAGATTTTTAAGAAAATAGTGATTTTCAT
* * *
18714 TAAAAAATGAGAAAGTTTATATTTTTAAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAGAA
66 TAAAAAA-GAGAAAGCTTAGATTTTTAAAAAATAAAAATCTG-----T--TT-TTTT--AGAAAA
**
18779 GTTTAAATTTTTAAACAAAG
120 G-TTAAA-AATTAAACAAAG
* * * * * * *
18799 TTTTGATTTTTTTTAACT-ATTTCGAAATAAAAATTTAGAATTTTAAGTAAAGTATTGATTTTCA
1 TTTTGATTTTTTTAAAATAATTTCAAAATAAAACTTTAGATTTTTAAG-AAAATAGTGATTTTCA
** *
18863 TTTAAAAAAGAAAGAAAATTTAGATTTTAGAAAAAAATAAAAATCTGTTTTTT
65 -TTAAAAAAG--AGAAAGCTTAGATTTT--TAAAAAATAAAAATCTGTTTTTT
18916 AGTGATTTCA
Statistics
Matches: 220, Mismatches: 21, Indels: 37
0.79 0.08 0.13
Matches are distributed among these distances:
132 27 0.12
133 18 0.08
134 11 0.05
135 19 0.09
136 15 0.07
141 1 0.00
143 2 0.01
144 4 0.02
146 9 0.04
147 7 0.03
148 16 0.07
149 37 0.17
150 16 0.07
151 8 0.04
152 14 0.06
154 16 0.07
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (137 bp):
TTTTGATTTTTTTAAAATAATTTCAAAATAAAACTTTAGATTTTTAAGAAAATAGTGATTTTCAT
TAAAAAAGAGAAAGCTTAGATTTTTAAAAAATAAAAATCTGTTTTTTTAGAAAAGTTAAAAATTA
AACAAAG
Found at i:18953 original size:155 final size:151
Alignment explanation
Indices: 18641--19037 Score: 497
Period size: 155 Copynumber: 2.6 Consensus size: 151
18631 AAGTTAAAAA
* * * *
18641 TTAAACAAAGTTTTGA-TTTTTTAAACTATTTCAAAATAAAAGTTTAGATTTTTAAG-AAAGTAG
1 TTAAACAAAGTTTTGATTTTTTTTAACTATTTC-AAATAAAAATTTAGAATTTTAAGTAAAGTAT
* * * *
18704 TGATTTTCA-TTAAAAAATG--AGAAAGTTTATATTTTTAAAAAATAAAAATCTGTTTTTTAGTT
65 TGATTTTCATTTAAAAAA-GAAAGAAAATTTAGATTTTAAAAAAATAAAAATCTGTTTTTTAGTG
* *
18766 ATTTTAAAGAGAAGTTTAAATTT
129 ATTTCAAAGAAAAGTTTAAATTT
18789 TTAAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAATTTAGAATTTTAAGTAAAGTAT
1 TTAAACAAAGTTTTGATTTTTTTTAACTATTTC-AAATAAAAATTTAGAATTTTAAGTAAAGTAT
18854 TGATTTTCATTTAAAAAAGAAAGAAAATTTAGATTTTAGAAAAAAATAAAAATCTGTTTTTTAGT
65 TGATTTTCATTTAAAAAAGAAAGAAAATTTAGATTTT--AAAAAAATAAAAATCTGTTTTTTAGT
18919 GATTTCAAAGAAAAAGTTTAAATTT
128 GATTTCAAAG-AAAAGTTTAAATTT
* * *
18944 TTAAGCAAAGTTTTAATTTTTTTTGAACTATTTCAAATTAAAAATTTTG-ATTTTGAAGTAAAGT
1 TTAAACAAAGTTTTGATTTTTTTT-AACTATTTCAAA-TAAAAATTTAGAATTTT-AAGTAAAGT
* **
19008 -TGTGATTTT-ATTTTAATCA-AAAGAAAATTT
63 AT-TGATTTTCATTTAAAAAAGAAAGAAAATTT
19038 TTGGTTTTTT
Statistics
Matches: 220, Mismatches: 17, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
148 16 0.07
149 36 0.16
150 16 0.07
151 8 0.04
152 14 0.06
154 44 0.20
155 51 0.23
156 35 0.16
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (151 bp):
TTAAACAAAGTTTTGATTTTTTTTAACTATTTCAAATAAAAATTTAGAATTTTAAGTAAAGTATT
GATTTTCATTTAAAAAAGAAAGAAAATTTAGATTTTAAAAAAATAAAAATCTGTTTTTTAGTGAT
TTCAAAGAAAAGTTTAAATTT
Found at i:19631 original size:25 final size:23
Alignment explanation
Indices: 19575--19658 Score: 64
Period size: 25 Copynumber: 3.4 Consensus size: 23
19565 TAGTTTAATG
* *
19575 TTTTATATTTATTCACATTTGCATA
1 TTTTTTATTTATTC-TATTT-CATA
*
19600 ATTTTTATTTATTCTTATTTCATA
1 TTTTTTATTTATTC-TATTTCATA
19624 TTTATTTACTTTCATGTCTATTT-ATA
1 TTT-TTTA-TTT-AT-TCTATTTCATA
19650 -TTTTTATTT
1 TTTTTTATTT
19659 TTATTTTTAC
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
23 3 0.06
24 10 0.20
25 22 0.44
26 6 0.12
27 7 0.14
28 2 0.04
ACGTcount: A:0.24, C:0.10, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTTTTATTTATTCTATTTCATA
Found at i:28874 original size:17 final size:17
Alignment explanation
Indices: 28854--28919 Score: 69
Period size: 17 Copynumber: 3.8 Consensus size: 17
28844 ATTGTCACCA
28854 CATTTCCTTTGTCATTG
1 CATTTCCTTTGTCATTG
***
28871 CATTTTAATTGTCATTG
1 CATTTCCTTTGTCATTG
* * *
28888 CATTTGCGTTATCATTG
1 CATTTCCTTTGTCATTG
28905 CATTTCCATTTGTCA
1 CATTTCC-TTTGTCA
28920 ATACATTGAG
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
17 33 0.87
18 5 0.13
ACGTcount: A:0.18, C:0.20, G:0.12, T:0.50
Consensus pattern (17 bp):
CATTTCCTTTGTCATTG
Found at i:28892 original size:34 final size:34
Alignment explanation
Indices: 28840--28909 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 34
28830 GTAGCTGTAA
* *
28840 TTTAATTGTCACCACATTTCCTTTGTCATTGCAT
1 TTTAATTGTCACCACATTTCCGTTATCATTGCAT
*** *
28874 TTTAATTGTCATTGCATTTGCGTTATCATTGCAT
1 TTTAATTGTCACCACATTTCCGTTATCATTGCAT
28908 TT
1 TT
28910 CCATTTGTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.20, C:0.19, G:0.11, T:0.50
Consensus pattern (34 bp):
TTTAATTGTCACCACATTTCCGTTATCATTGCAT
Found at i:30237 original size:26 final size:26
Alignment explanation
Indices: 30200--30253 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
30190 CACCCAAAAA
* *
30200 TGTCGCTGCATGAACATGTCTAGAAT
1 TGTCGCTACATGAACATGTCCAGAAT
30226 TGTCGCTACATGAACATGTCCAGAAT
1 TGTCGCTACATGAACATGTCCAGAAT
30252 TG
1 TG
30254 CACCTTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (26 bp):
TGTCGCTACATGAACATGTCCAGAAT
Found at i:41612 original size:193 final size:195
Alignment explanation
Indices: 41352--41716 Score: 585
Period size: 193 Copynumber: 1.9 Consensus size: 195
41342 TTGAAAACAA
* *
41352 TTTCCCTAACGATGTTGCTCACACGAGCTATCGAGAATATGCATTTAAGCATAGATCCCAGCCAT
1 TTTCCCTAACGATGTTGCTCACACGAGCTATCGAGAATATGCATTTAAGCATAAATCCCAACCAT
*
41417 CGTAGGGCCTATAATCCATT-TAAG-ATTTCATATCTC-TTT-CCGACTCACGATGCTGCTCACA
66 CGTAGGGCCTATAATCCATTAT-AGTA-TTCATATCTCATTTCCCAACTCACGATGCTGCTCACA
* ** *
41478 CGAGCTGTTGAGGACTCGCAACATATGTGGTACCTCAACCATCGATACGATAAATGTGTATATAT
129 CGAGCTGTCGAGGACTCGCAACATATCCGGTACATCAACCATCGATACGATAAATGTGTATATAT
41543 TG
194 TG
*
41545 TTTCCCTAACGATGTTGCTCAGACGAGCTATCGAGAATATGCATTTAAGCATAAATCCCAACCAT
1 TTTCCCTAACGATGTTGCTCACACGAGCTATCGAGAATATGCATTTAAGCATAAATCCCAACCAT
* * *
41610 CGTAGGGCCTATAATCCATTATTGTATTCATTTCTCATTTCCCAACTCACGATGTTGCTCACACG
66 CGTAGGGCCTATAATCCATTATAGTATTCATATCTCATTTCCCAACTCACGATGCTGCTCACACG
41675 AGCTGTCGAGGACTCGCAACATATCCGGTACATCAACCATCG
131 AGCTGTCGAGGACTCGCAACATATCCGGTACATCAACCATCG
41717 CGTCGATTCA
Statistics
Matches: 157, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
193 92 0.59
194 5 0.03
195 60 0.38
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (195 bp):
TTTCCCTAACGATGTTGCTCACACGAGCTATCGAGAATATGCATTTAAGCATAAATCCCAACCAT
CGTAGGGCCTATAATCCATTATAGTATTCATATCTCATTTCCCAACTCACGATGCTGCTCACACG
AGCTGTCGAGGACTCGCAACATATCCGGTACATCAACCATCGATACGATAAATGTGTATATATTG
Found at i:46763 original size:194 final size:193
Alignment explanation
Indices: 46405--46850 Score: 474
Period size: 194 Copynumber: 2.3 Consensus size: 193
46395 TACCAGTACC
* * * * * *
46405 CGATGTGCTCACACGAGCTGTCGAGGACTCGCAACATATGTGGTACCCCAGCCATCAATACGGTG
1 CGATGTGCTCACACAAGCTGTCGAGGACTCACAACATATGTCGTACCTCAGCCATCGATACGGTA
* * * * * * *
46470 TCTGTCTGTAAATTGTTTCCCTAATGATGCTGCTCACACGAGCTGTTGAGAATATGCATCTAAGC
66 TATGTCTATAAACTATTTCCCTAACGAAGCTGCTCACACGAGCTGTCGAGAATAT-CATCTAAGC
* * ** * * * *
46535 TTAGATCCCAACCATTGTAGGGCTTATAATCCATT-TAAGATTTCAAATCTC-TTT-TCGACTTA
130 ATAAATCCCAACCATCATAAGGCCTATAATCCATTCTAAGA-TTCAAATCTCATTTCCCGACTCA
*
46597 CGATGTTGCTCACACAAGCTGTCGAGGACTC-CTAACATATGTCGTACCTTAGCCATCGATACGG
1 CGATG-TGCTCACACAAGCTGTCGAGGACTCAC-AACATATGTCGTACCTCAGCCATCGATACGG
*
46661 TATATGTGC-ATATAACTATTTCCCTAACGAAGCTGCTCACACGAGTTGTCGAGAATAT-ATACT
64 TATATGT-CTATA-AACTATTTCCCTAACGAAGCTGCTCACACGAGCTGTCGAGAATATCAT-C-
* * * ** **
46724 TATGCATAAATCTCAACCATCATAAGGCCTGTAATCCATTCTTGGATTCATTTCTCATTTCCCGA
125 TAAGCATAAATCCCAACCATCATAAGGCCTATAATCCATTCTAAGATTCAAATCTCATTTCCCGA
46789 CTCA
190 CTCA
*
46793 CGATGCTGCTCACACAAGCTGTCGAGGACTCACAACATATG-CGGTACCTCAACCATCG
1 CGATG-TGCTCACACAAGCTGTCGAGGACTCACAACATATGTC-GTACCTCAGCCATCG
46851 TGTCAGTTCA
Statistics
Matches: 211, Mismatches: 32, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
192 8 0.04
193 59 0.28
194 79 0.37
195 7 0.03
196 57 0.27
197 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (193 bp):
CGATGTGCTCACACAAGCTGTCGAGGACTCACAACATATGTCGTACCTCAGCCATCGATACGGTA
TATGTCTATAAACTATTTCCCTAACGAAGCTGCTCACACGAGCTGTCGAGAATATCATCTAAGCA
TAAATCCCAACCATCATAAGGCCTATAATCCATTCTAAGATTCAAATCTCATTTCCCGACTCA
Found at i:50579 original size:27 final size:28
Alignment explanation
Indices: 50557--50619 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
50547 GTCAAATTAA
50557 AATTTGTTT-CTTTTTACTACAAATTGT
1 AATTTGTTTACTTTTTACTACAAATTGT
* *
50584 AATTTATTTATTTTTTACTACAAATTGT
1 AATTTGTTTACTTTTTACTACAAATTGT
50612 AATTTGTT
1 AATTTGTT
50620 CATTTTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 8 0.25
28 24 0.75
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.57
Consensus pattern (28 bp):
AATTTGTTTACTTTTTACTACAAATTGT
Found at i:50607 original size:28 final size:28
Alignment explanation
Indices: 50567--50625 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
50557 AATTTGTTTC
*
50567 TTTTTACTACAAATTGTAATTTATTTAT
1 TTTTTACTACAAATTGTAATTTATTCAT
*
50595 TTTTTACTACAAATTGTAATTTGTTCAT
1 TTTTTACTACAAATTGTAATTTATTCAT
50623 TTT
1 TTT
50626 ATTAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.29, C:0.08, G:0.05, T:0.58
Consensus pattern (28 bp):
TTTTTACTACAAATTGTAATTTATTCAT
Found at i:53555 original size:13 final size:13
Alignment explanation
Indices: 53537--53561 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53527 TAAGTTAAAA
53537 ATGCTAAAAATGC
1 ATGCTAAAAATGC
53550 ATGCTAAAAATG
1 ATGCTAAAAATG
53562 ATAAAATGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (13 bp):
ATGCTAAAAATGC
Found at i:53909 original size:10 final size:10
Alignment explanation
Indices: 53891--53924 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
53881 AATATAAATA
*
53891 TTTTCCTTTT
1 TTTTTCTTTT
53901 TTTTTCTTTT
1 TTTTTCTTTT
*
53911 CTTTTCTTTT
1 TTTTTCTTTT
53921 TTTT
1 TTTT
53925 ATAAAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:65419 original size:24 final size:24
Alignment explanation
Indices: 65374--65591 Score: 211
Period size: 24 Copynumber: 9.1 Consensus size: 24
65364 GCAAGTTCAT
* ** *
65374 TACGTTTACACTCTTCAACATGAA
1 TACGTTTACGCTCACCAGCATGAA
* *
65398 TTCGTTTACGCTCGCCAGCATGAA
1 TACGTTTACGCTCACCAGCATGAA
* * * *
65422 TACATTCACGCTCTCCAACATGAA
1 TACGTTTACGCTCACCAGCATGAA
*
65446 TATGTTTACGCTCACCAGCATGAA
1 TACGTTTACGCTCACCAGCATGAA
* *** *
65470 TACGTTTATGCTCGTTAACATGAA
1 TACGTTTACGCTCACCAGCATGAA
* ** *
65494 TACGTTTACACTTGCTAGCATGAA
1 TACGTTTACGCTCACCAGCATGAA
**
65518 TACGTTTACGCTCATTAGCATGAA
1 TACGTTTACGCTCACCAGCATGAA
* *
65542 TACGTTTAAGCTCATCAGCATGAA
1 TACGTTTACGCTCACCAGCATGAA
*
65566 TACGTTTACGCTCATCAGCATGAA
1 TACGTTTACGCTCACCAGCATGAA
65590 TA
1 TA
65592 TTCGAAACAT
Statistics
Matches: 161, Mismatches: 33, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 161 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (24 bp):
TACGTTTACGCTCACCAGCATGAA
Found at i:65445 original size:48 final size:48
Alignment explanation
Indices: 65374--65591 Score: 249
Period size: 48 Copynumber: 4.5 Consensus size: 48
65364 GCAAGTTCAT
* * * *
65374 TACGTTTACACTCTTCAACATGAATTCGTTTACGCTCGCCAGCATGAA
1 TACGTTTACGCTCATCAACATGAATACGTTTACGCTCACCAGCATGAA
* * *
65422 TACATTCACGCTC-TCCAACATGAATATGTTTACGCTCACCAGCATGAA
1 TACGTTTACGCTCAT-CAACATGAATACGTTTACGCTCACCAGCATGAA
* * * * ** *
65470 TACGTTTATGCTCGTTAACATGAATACGTTTACACTTGCTAGCATGAA
1 TACGTTTACGCTCATCAACATGAATACGTTTACGCTCACCAGCATGAA
* * * *
65518 TACGTTTACGCTCATTAGCATGAATACGTTTAAGCTCATCAGCATGAA
1 TACGTTTACGCTCATCAACATGAATACGTTTACGCTCACCAGCATGAA
*
65566 TACGTTTACGCTCATCAGCATGAATA
1 TACGTTTACGCTCATCAACATGAATA
65592 TTCGAAACAT
Statistics
Matches: 143, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
47 1 0.01
48 141 0.99
49 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (48 bp):
TACGTTTACGCTCATCAACATGAATACGTTTACGCTCACCAGCATGAA
Found at i:65494 original size:72 final size:72
Alignment explanation
Indices: 65392--65592 Score: 235
Period size: 72 Copynumber: 2.8 Consensus size: 72
65382 CACTCTTCAA
* * * * * *
65392 CATGAATTCGTTTACGCTCGCCAGCATGAATACATTCACGCTCTCCAACATGAATATGTTTACGC
1 CATGAATACGTTTAAGCTCGTCAGCATGAATACGTTTACGCTCTCCAGCATGAATATGTTTACGC
65457 TCACCAG
66 TCACCAG
* * * * * *
65464 CATGAATACGTTTATGCTCGTTAACATGAATACGTTTACACT-TGCTAGCATGAATACGTTTACG
1 CATGAATACGTTTAAGCTCGTCAGCATGAATACGTTTACGCTCT-CCAGCATGAATATGTTTACG
**
65528 CTCATTAG
65 CTCACCAG
*
65536 CATGAATACGTTTAAGCTCATCAGCATGAATACGTTTACGCTCAT-CAGCATGAATAT
1 CATGAATACGTTTAAGCTCGTCAGCATGAATACGTTTACGCTC-TCCAGCATGAATAT
65593 TCGAAACATT
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
71 1 0.01
72 104 0.98
74 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (72 bp):
CATGAATACGTTTAAGCTCGTCAGCATGAATACGTTTACGCTCTCCAGCATGAATATGTTTACGC
TCACCAG
Found at i:74298 original size:6 final size:6
Alignment explanation
Indices: 74281--74338 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
74271 GGACATTTAA
* * *
74281 TTAAATT TTAAAT TTAAAT TTAAA- ATAAAT TTAAAC TTAAA- AT-AAT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
74327 TTAAAAT TTAAA
1 TT-AAAT TTAAA
74339 ATTAGATTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
4 2 0.05
5 6 0.14
6 24 0.57
7 10 0.24
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (6 bp):
TTAAAT
Found at i:74309 original size:17 final size:17
Alignment explanation
Indices: 74289--74340 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
74279 AATTAAATTT
74289 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
74306 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
74323 T-AATTTAAAATTTAAAA
1 TAAATTT-AAATTTAAAA
74340 T
1 T
74341 TAGATTCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.16
17 27 0.84
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Done.