Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_188 ID=scaffold_188-JGI_221_v2.0
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: 9799
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.33
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:129 original size:16 final size:16
Alignment explanation
Indices: 104--141 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
94 TCCCCTTTTC
*
104 TTTCTCCCTTT-TTCAT
1 TTTCTTCCTTTCTTC-T
120 TTTCTTCCTTTCTTCT
1 TTTCTTCCTTTCTTCT
136 TTTCTT
1 TTTCTT
142 TCTTCCCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTCTTCCTTTCTTCT
Found at i:157 original size:16 final size:16
Alignment explanation
Indices: 138--177 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
128 TTTCTTCTTT
*
138 TCTTTCTTCCCTCTCC
1 TCTTTCTTCCATCTCC
*
154 TCTTTCTTCTATCTCC
1 TCTTTCTTCCATCTCC
170 TCTTTCTT
1 TCTTTCTT
178 TTGTAATTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.03, C:0.40, G:0.00, T:0.57
Consensus pattern (16 bp):
TCTTTCTTCCATCTCC
Found at i:775 original size:29 final size:28
Alignment explanation
Indices: 729--798 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 28
719 TATAGGGCTA
729 AAGTGTAATTTCTAAAAAGT-TTAGGGGCCC
1 AAGTGTAATTTC-AAAAA-TATTAGGGG-CC
*
759 AAGTGTAATTT-ACAAAATATTAGGGGTC
1 AAGTGTAATTTCA-AAAATATTAGGGGCC
787 AAGATGTAATTT
1 AAG-TGTAATTT
799 TTATTTTTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
28 6 0.17
29 19 0.53
30 11 0.31
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (28 bp):
AAGTGTAATTTCAAAAATATTAGGGGCC
Found at i:827 original size:11 final size:10
Alignment explanation
Indices: 802--826 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
792 GTAATTTTTA
802 TTTTTGAATT
1 TTTTTGAATT
812 TTTTTGAATT
1 TTTTTGAATT
822 TTTTT
1 TTTTT
827 TTTTAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (10 bp):
TTTTTGAATT
Found at i:1387 original size:73 final size:74
Alignment explanation
Indices: 965--1746 Score: 984
Period size: 76 Copynumber: 10.3 Consensus size: 74
955 TTTTTATTTG
* * * * *
965 AAAA-ACAGAAATTGAAAATACCTCGGCGTGTGGCCCGAGGCTCAACTCACCTCTAGCAATATGA
1 AAAAGACAGAAATTAAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCT-GTATTATGA
**
1029 GTTGATTTT-TG
63 GTTGATTTTAAA
* * ** *
1040 AAAA-ACAGAAATTTAAAAGAAATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTCGTAATAT
1 AAAAGACAGAAA-TT--AA-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTAT
1104 GAGTTGATTTTTTTGAAA
61 GAGTTGA---TTTT-AAA
*
1122 AAAAG-CAGAAATTTAAAAGAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTTTGTATTATG
1 AAAAGACAGAAA-TT--AA-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATG
1186 AGTTGATTTTTAAAAAA
62 AGTTGA-TTTT---AAA
*
1203 AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACATCTGTATTATGAGTT
1 AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
*
1268 GATTTTTTTAA
66 GA--TTTTAAA
* * *
1279 AAAAGACAAAAATTAAAAATACCTCAGCATGACCCGAGGCTCAACTCACCTTTGTATTATGAGTT
1 AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
1344 GATTTT-AA
66 GATTTTAAA
*
1352 AAAAGACCGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
1 AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
1417 GATTTTAAA
66 GATTTTAAA
*
1426 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
1 AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
*
1491 GATTTAAAAAA
66 GATTT--TAAA
* * *
1502 AAAAGACATAAATTAAAAAAACCTCAGCGTAACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
1 AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
1567 GATTTTTAAA
66 GA-TTTTAAA
* *
1577 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAAGCTCAACTCACCTCTGTATTATGAGTT
1 AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
1642 GA-TTTAAA
66 GATTTTAAA
* * *
1650 AAAAGACCGAAATTAAAAATACTTCAGCGTGACCCGAGGTTCAACTCACCTCTCGTATTATGAGT
1 AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGT
*
1715 TGATATTTGAA
65 TGAT-TTTAAA
*
1726 AAAA-ACAGAAAGTGAAAAATA
1 AAAAGACAGAAA-TTAAAAATA
1747 TTTCTTGAAA
Statistics
Matches: 643, Mismatches: 42, Indels: 43
0.88 0.06 0.06
Matches are distributed among these distances:
73 123 0.19
74 88 0.14
75 84 0.13
76 152 0.24
77 39 0.06
78 50 0.08
79 24 0.04
80 4 0.01
81 23 0.04
82 56 0.09
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (74 bp):
AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
GATTTTAAA
Found at i:1470 original size:223 final size:226
Alignment explanation
Indices: 965--1730 Score: 1003
Period size: 223 Copynumber: 3.4 Consensus size: 226
955 TTTTTATTTG
* * * * *
965 AAAA-ACAGAAATTGAAAATACCTCGGCGTGTGGCCCGAGGCTCAACTCACCTCTAGCAATATGA
1 AAAAGACAGAAATTAAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTAGTATTATGA
* * * * **
1029 GTTGATTTTTGAAAAACAGA-AATTTAAA--AGAAATACCTCGGCATGGTCCGAGGCTCAACTCA
64 GTTGATTTTTTAAAAAAAGACAA---AAATTAAAAATACCTCAGCATGACCCGAGGCTCAACTCA
* *
1091 CCTCTCGTAATATGAGTTGATTTTTTTGAAAAAAAG-CAGAAATTTAAAAGAAATACCTCAGCGT
126 CCT-TTGTATTATGAGTTGA--TTTTT-AAAAAAAGACAGAAA-TT--AA-AAATACCTCAGCGT
*
1155 GACCCGAGGCTCAACTCACCTTTGTATTATGAGTTGATTTTTAAAAAA
183 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTT---AAA
*
1203 AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACATCT-GTATTATGAGT
1 AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGTATTATGAGT
*
1267 TGATTTTTTTAAAAAAGACAAAAATTAAAAATACCTCAGCATGACCCGAGGCTCAACTCACCTTT
66 TGATTTTTTAAAAAAAGACAAAAATTAAAAATACCTCAGCATGACCCGAGGCTCAACTCACCTTT
*
1332 GTATTATGAGTTGA-TTTT-AAAAAAGACCGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCA
131 GTATTATGAGTTGATTTTTAAAAAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCA
1395 ACTCACCTCTGTATTATGAGTTGATTTTAAA
196 ACTCACCTCTGTATTATGAGTTGATTTTAAA
*
1426 AAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGT
1 AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGTATTATGAGT
*** * * * * *
1490 TGATTTAAAAAAAAAAGACATAAATTAAAAAAACCTCAGCGTAACCCGAGGCTCAACTCACCTCT
66 TGATTTTTTAAAAAAAGACAAAAATTAAAAATACCTCAGCATGACCCGAGGCTCAACTCACCTTT
* *
1555 GTATTATGAGTTGATTTTTAAAAAAAGACATAAATTAAAAATACCTCAGCGTGACCCGAAGCTCA
131 GTATTATGAGTTGATTTTTAAAAAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCA
1620 ACTCACCTCTGTATTATGAGTTGA-TTTAAA
196 ACTCACCTCTGTATTATGAGTTGATTTTAAA
* * * *
1650 AAAAGACCGAAATTAAAAATACTTCAGCGTGACCCGAGGTTCAACTCACCTCTCGTATTATGAGT
1 AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGTATTATGAGT
* *
1715 TGATATTTGAAAAAAA
66 TGATTTTTTAAAAAAA
1731 CAGAAAGTGA
Statistics
Matches: 481, Mismatches: 39, Indels: 29
0.88 0.07 0.05
Matches are distributed among these distances:
223 135 0.28
224 59 0.12
225 89 0.19
226 4 0.01
227 50 0.10
228 2 0.00
230 9 0.02
231 5 0.01
232 4 0.01
234 3 0.01
235 14 0.03
236 57 0.12
237 25 0.05
238 4 0.01
239 21 0.04
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (226 bp):
AAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGTATTATGAGT
TGATTTTTTAAAAAAAGACAAAAATTAAAAATACCTCAGCATGACCCGAGGCTCAACTCACCTTT
GTATTATGAGTTGATTTTTAAAAAAAGACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCA
ACTCACCTCTGTATTATGAGTTGATTTTAAA
Found at i:2586 original size:43 final size:45
Alignment explanation
Indices: 2521--2609 Score: 119
Period size: 44 Copynumber: 2.0 Consensus size: 45
2511 TAAGTCCGAA
* *
2521 TCTGTTTCATTAGGATGCCC-TTTCAGGTTTTCATCCTAATCTTT
1 TCTGTTTCATTAAGACGCCCTTTTCAGGTTTTCATCCTAATCTTT
* * *
2565 TCTGTTT-ATTAAGACGCCCTTTTCGGGTTTTCATCTTAATGTTT
1 TCTGTTTCATTAAGACGCCCTTTTCAGGTTTTCATCCTAATCTTT
2609 T
1 T
2610 TCTTCTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 10 0.26
44 29 0.74
ACGTcount: A:0.16, C:0.20, G:0.15, T:0.49
Consensus pattern (45 bp):
TCTGTTTCATTAAGACGCCCTTTTCAGGTTTTCATCCTAATCTTT
Found at i:2627 original size:18 final size:17
Alignment explanation
Indices: 2604--2681 Score: 84
Period size: 18 Copynumber: 4.2 Consensus size: 17
2594 TTCATCTTAA
2604 TGTTTTTCTTCTTTTTTT
1 TGTTTTT-TTCTTTTTTT
2622 TGTTTTTTTCTTGTTTTT
1 TGTTTTTTTCTT-TTTTT
*
2640 TGTTTGTTTGTTTTTTTTT
1 TGTTT-TTT-TCTTTTTTT
*
2659 TGTTTTTTGTTTTGTTTTT
1 TGTTTTTT-TCTT-TTTTT
2678 TGTT
1 TGTT
2682 AGGCATAATA
Statistics
Matches: 55, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
17 5 0.09
18 25 0.45
19 22 0.40
20 3 0.05
ACGTcount: A:0.00, C:0.04, G:0.13, T:0.83
Consensus pattern (17 bp):
TGTTTTTTTCTTTTTTT
Found at i:2629 original size:11 final size:11
Alignment explanation
Indices: 2615--2681 Score: 82
Period size: 11 Copynumber: 6.0 Consensus size: 11
2605 GTTTTTCTTC
2615 TTTTTTTTGTT
1 TTTTTTTTGTT
*
2626 TTTTTCTTGTT
1 TTTTTTTTGTT
*
2637 TTTTGTTTGTT
1 TTTTTTTTGTT
2648 TGTTTTTTT-TT
1 T-TTTTTTTGTT
*
2659 TGTTTTTTGTT
1 TTTTTTTTGTT
2670 TTGTTTTTTGTT
1 TT-TTTTTTGTT
2682 AGGCATAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
10 6 0.13
11 26 0.55
12 15 0.32
ACGTcount: A:0.00, C:0.01, G:0.13, T:0.85
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:2652 original size:26 final size:27
Alignment explanation
Indices: 2615--2675 Score: 97
Period size: 26 Copynumber: 2.3 Consensus size: 27
2605 GTTTTTCTTC
*
2615 TTTTTTTTGTTTTTTTCTTGTTTTTTG
1 TTTTGTTTGTTTTTTTCTTGTTTTTTG
*
2642 -TTTGTTTGTTTTTTTTTTGTTTTTTG
1 TTTTGTTTGTTTTTTTCTTGTTTTTTG
2668 TTTTGTTT
1 TTTTGTTT
2676 TTTGTTAGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 24 0.77
27 7 0.23
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85
Consensus pattern (27 bp):
TTTTGTTTGTTTTTTTCTTGTTTTTTG
Found at i:8216 original size:18 final size:20
Alignment explanation
Indices: 8186--8227 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
8176 CACAATATTT
*
8186 TTTTTTTGAAAAC-ATAGAA
1 TTTTTTTGAAAACAAGAGAA
8205 TTTTTTTG-AAACAAGAGAA
1 TTTTTTTGAAAACAAGAGAA
8224 TTTT
1 TTTT
8228 AGAAACACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
TTTTTTTGAAAACAAGAGAA
Found at i:8362 original size:34 final size:35
Alignment explanation
Indices: 8237--8384 Score: 110
Period size: 35 Copynumber: 4.2 Consensus size: 35
8227 TAGAAACACA
* * * *
8237 AAAATTTTTGAAAAC-CTGAAAATTTTTACAACACG
1 AAAATTTTGGAGAACAC-GAAAATTTTTAAAATACG
* *
8272 AAAA-TTTGCGA-AACAC-AACAATTTTTTGAAACACG
1 AAAATTTTG-GAGAACACGAA-AA-TTTTTAAAATACG
* *
8307 AGAAATTTTTGAGAACGCGAAAA-TTTTAAAATACG
1 A-AAATTTTGGAGAACACGAAAATTTTTAAAATACG
*
8342 CAAAATTTTGGA-AACACGAAAATTTTTGAAATACG
1 -AAAATTTTGGAGAACACGAAAATTTTTAAAATACG
*
8377 AAATTTTT
1 AAAATTTT
8385 TCTTTTAAAA
Statistics
Matches: 92, Mismatches: 11, Indels: 21
0.74 0.09 0.17
Matches are distributed among these distances:
33 2 0.02
34 24 0.26
35 49 0.53
36 6 0.07
37 9 0.10
38 2 0.02
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (35 bp):
AAAATTTTGGAGAACACGAAAATTTTTAAAATACG
Found at i:8385 original size:17 final size:17
Alignment explanation
Indices: 8207--8384 Score: 150
Period size: 17 Copynumber: 10.3 Consensus size: 17
8197 ACATAGAATT
* *
8207 TTTTTGAAACAAGAGAA
1 TTTTTGAAACACGAAAA
* *
8224 TTTTAGAAACACAAAAA
1 TTTTTGAAACACGAAAA
8241 TTTTTGAAA-ACCTGAAAA
1 TTTTTGAAACA-C-GAAAA
8259 TTTTT-ACAACACGAAAA
1 TTTTTGA-AACACGAAAA
**
8276 TTTGCGAAACAC-AACAA
1 TTTTTGAAACACGAA-AA
8293 TTTTTTGAAACACGAGAAA
1 -TTTTTGAAACACGA-AAA
*
8312 TTTTTGAGAACGCGAAAA
1 TTTTTGA-AACACGAAAA
* *
8330 -TTTTAAAATACGCAAAA
1 TTTTTGAAACACG-AAAA
*
8347 TTTTGGAAACACGAAAA
1 TTTTTGAAACACGAAAA
*
8364 TTTTTGAAATACG-AAA
1 TTTTTGAAACACGAAAA
8380 TTTTT
1 TTTTT
8385 TCTTTTAAAA
Statistics
Matches: 130, Mismatches: 19, Indels: 25
0.75 0.11 0.14
Matches are distributed among these distances:
16 15 0.12
17 62 0.48
18 42 0.32
19 10 0.08
20 1 0.01
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:9296 original size:13 final size:13
Alignment explanation
Indices: 9278--9336 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
9268 GTTGATTTTT
9278 CTTTTTTCTTTCC
1 CTTTTTTCTTTCC
9291 C-TTTTTCTTT--
1 CTTTTTTCTTTCC
9301 C-TTTTTCTTCTCC
1 CTTTTTTCTT-TCC
* *
9314 TTTTTTTCTTTCT
1 CTTTTTTCTTTCC
*
9327 TTTTTTTCTT
1 CTTTTTTCTT
9337 CTTCTTCGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
10 9 0.22
11 1 0.03
12 9 0.22
13 13 0.32
14 8 0.20
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
CTTTTTTCTTTCC
Found at i:9297 original size:12 final size:12
Alignment explanation
Indices: 9280--9325 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 12
9270 TGATTTTTCT
9280 TTTTTCTTTCCC
1 TTTTTCTTTCCC
9292 TTTTTCTTT--C
1 TTTTTCTTTCCC
*
9302 TTTTTCTTCTCCTT
1 TTTTTCTT-TCC-C
9316 TTTTTCTTTC
1 TTTTTCTTTC
9326 TTTTTTTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
10 9 0.31
11 1 0.03
12 9 0.31
13 2 0.07
14 8 0.28
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:9301 original size:23 final size:25
Alignment explanation
Indices: 9275--9335 Score: 85
Period size: 24 Copynumber: 2.6 Consensus size: 25
9265 ACTGTTGATT
9275 TTTCTTTTTTCTT-TCC-CTTTTTC
1 TTTCTTTTTTCTTCTCCTCTTTTTC
*
9298 TTTC-TTTTTCTTCTCCTTTTTTTC
1 TTTCTTTTTTCTTCTCCTCTTTTTC
9322 TTTCTTTTTT-TTCT
1 TTTCTTTTTTCTTCT
9336 TCTTCTTCGG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
22 8 0.24
23 7 0.21
24 14 0.41
25 5 0.15
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTCTTTTTTCTTCTCCTCTTTTTC
Found at i:9328 original size:12 final size:12
Alignment explanation
Indices: 9275--9332 Score: 66
Period size: 12 Copynumber: 4.9 Consensus size: 12
9265 ACTGTTGATT
9275 TTTC-TTTTTTC
1 TTTCTTTTTTTC
**
9286 TTTCCCTTTTTC
1 TTTCTTTTTTTC
9298 TTTCTTTTTCTTC
1 TTTCTTTTT-TTC
*
9311 -TCCTTTTTTTC
1 TTTCTTTTTTTC
9322 TTTCTTTTTTT
1 TTTCTTTTTTT
9333 TCTTCTTCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 7 0.18
12 29 0.74
13 3 0.08
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTCTTTTTTTC
Found at i:9488 original size:16 final size:16
Alignment explanation
Indices: 9469--9508 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
9459 TTTCTTCTTT
* *
9469 TCTTTTTTCCCTCTCC
1 TCTTTCTTCCATCTCC
*
9485 TCTTTCTTCTATCTCC
1 TCTTTCTTCCATCTCC
9501 TCTTTCTT
1 TCTTTCTT
9509 TTGTAATTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.03, C:0.38, G:0.00, T:0.60
Consensus pattern (16 bp):
TCTTTCTTCCATCTCC
Found at i:9488 original size:21 final size:22
Alignment explanation
Indices: 9444--9489 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
9434 CTTTCTCCCT
* * *
9444 TTTTCATTTTTTTCCTTTCTTC
1 TTTTCATTTTTTCCCTCTCCTC
9466 TTTTC-TTTTTTCCCTCTCCTC
1 TTTTCATTTTTTCCCTCTCCTC
9487 TTT
1 TTT
9490 CTTCTATCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTCATTTTTTCCCTCTCCTC
Done.