Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011218.1 Corchorus olitorius cultivar O-4 contig11251, 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: 37925
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:2016 original size:43 final size:43
Alignment explanation
Indices: 1862--2577 Score: 834
Period size: 43 Copynumber: 16.5 Consensus size: 43
1852 ACTGTTTTTC
*
1862 TTTC-TTTCCAAAAATG-CCCTTCCTGGTTGGAAGGTCCCTGT
1 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGT
*
1903 TTT-A-TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGT
1 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGT
*
1944 TTT-TTATTCCAAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGT
1 TTTCAT-TTCC-AAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGT
1988 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGT-CTCTGTT
1 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCT-TG-T
* * * *
2032 TTTCATTCCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTTTT
1 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTC-C--TTGT
* * *
2078 CTTTC-TTTCCAGAAATGCCCCATCATGGTTGGAAGGTCCTTGT
1 -TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGT
* * * *
2121 TTTCATTTCCAGAAATGCCCATTCCTAGTTGGAAGGTCCCTGT
1 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGT
* **
2164 TTT-A-TTCCAAAAATTCCCCTTCCTGGTTGGAAGGTCCCAGT
1 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGT
* *
2205 TTTCTTCTATTCCAAGAATGCCCCTTCCTGGTTGGAAGGTCCTTGT
1 TTTC--AT-TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGT
* *
2251 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTAT
1 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGT
* * *
2294 TTTTA-TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCACAGTTTT
1 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTC-C--TTGT
2339 CTTTC-TTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGT
1 -TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGT
*
2382 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAAGT-CTCTG-
1 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCT-TGT
* ** * **
2424 TTT-ATATTCCAAAAATGCCCATTCCCAGTCGGAAGGTCAC-AAT
1 TTTCAT-TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTC-CTTGT
2467 TTTC-TTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGT
1 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGT
*
2509 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGT
1 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGT
*
2552 TTTCTTTCATCCCAAAAATGCCCCTT
1 TTTCATT--T-CCAAAAATGCCCCTT
2578 TTTGGTCAGA
Statistics
Matches: 583, Mismatches: 56, Indels: 67
0.83 0.08 0.09
Matches are distributed among these distances:
40 11 0.02
41 69 0.12
42 106 0.18
43 193 0.33
44 76 0.13
45 7 0.01
46 115 0.20
47 5 0.01
48 1 0.00
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (43 bp):
TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGT
Found at i:2357 original size:261 final size:258
Alignment explanation
Indices: 1862--2577 Score: 1109
Period size: 261 Copynumber: 2.7 Consensus size: 258
1852 ACTGTTTTTC
1862 TTTC-TTTCCAAAAATGCCCTTCCTGGTTGGAAGGTCCCTGTTTTATTCCAAAAATGCCCCTTCC
1 TTTCATTTCCAAAAATGCCCTTCCTGGTTGGAAGGTCCCTGTTTTATTCCAAAAATGCCCCTTCC
*
1926 TGGTTGGAAGGTCCCTGTTTTT-TATTCCAAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTT
66 TGGTTGGAAGGTCCCAGTTTTTCTATTCC-AAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTT
*
1990 TCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTTTTCATTCCCAAAAATGCCCCTT
130 TCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCT-TTTTTTTCATT-CCAAAAATGCCCCTT
*
2055 CCCGGTCGGAAGGTCACAGTTTTCTTTCTTTCCAGAAATGCCCCATCATGGTTGGAAGGTCCTTG
193 CCCGGTCGGAAGGTCACAGTTTTCTTTCTTTCCAAAAATGCCCCATCATGGTTGGAAGGTCCTTG
2120 T
258 T
* * *
2121 TTTCATTTCCAGAAATGCCCATTCCTAGTTGGAAGGTCCCTGTTTTATTCCAAAAATTCCCCTTC
1 TTTCATTTCCAAAAATGCCC-TTCCTGGTTGGAAGGTCCCTGTTTTATTCCAAAAATGCCCCTTC
*
2186 CTGGTTGGAAGGTCCCAGTTTTCTTCTATTCCAAGAATGCCCCTTCCTGGTTGGAAGGTCCTTGT
65 CTGGTTGGAAGGTCCCAG-TTT-TTCTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGT
2251 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTATTTTT-ATTCCAAAAATGCCCCT
128 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTTT-TTTTTCATTCCAAAAATGCCCCT
* * *
2315 TCCTGGTCGGAAGGTCACAGTTTTCTTTCTTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTT
192 TCCCGGTCGGAAGGTCACAGTTTTCTTTCTTTCCAAAAATGCCCCATCATGGTTGGAAGGTCCTT
2380 GT
257 GT
* * *
2382 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAAGTCTCTGTTTATATTCCAAAAATGCCCATT
1 TTTCATTTCCAAAAATG-CCCTTCCTGGTTGGAAGGTCCCTGTTT-TATTCCAAAAATGCCCCTT
** * * *
2447 CCCAGTCGGAAGGTCACA-ATTTTCT-TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTT
64 CCTGGTTGGAAGGTCCCAGTTTTTCTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTT
*
2510 TTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCTTTCATCCCAAAAATGCCC
129 TTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGT--CT-TTTT-TTTCATTCCAAAAATGCCC
2575 CTT
190 CTT
2578 TTTGGTCAGA
Statistics
Matches: 421, Mismatches: 23, Indels: 23
0.90 0.05 0.05
Matches are distributed among these distances:
258 73 0.17
259 8 0.02
260 20 0.05
261 178 0.42
262 58 0.14
263 78 0.19
264 6 0.01
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (258 bp):
TTTCATTTCCAAAAATGCCCTTCCTGGTTGGAAGGTCCCTGTTTTATTCCAAAAATGCCCCTTCC
TGGTTGGAAGGTCCCAGTTTTTCTATTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTT
CATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTTTTTTCATTCCAAAAATGCCCCTTCCC
GGTCGGAAGGTCACAGTTTTCTTTCTTTCCAAAAATGCCCCATCATGGTTGGAAGGTCCTTGT
Found at i:2358 original size:131 final size:130
Alignment explanation
Indices: 1862--2546 Score: 1003
Period size: 131 Copynumber: 5.3 Consensus size: 130
1852 ACTGTTTTTC
* *
1862 TTTC-TTTCCAAAAATG-CCCTTCCTGGTTGGAAGGTCCCTGTTTTATTCCAAAAATGCCCCTTC
1 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTCTTTTTTATTCCAAAAATGCCCCTTC
* * * *
1925 CTGGTTGGAAGGTCCCTG-TTT-TTT-ATTCCAAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTG
66 CTGGTCGGAAGGTCACAGTTTTCTTTCTTTCC-AAAAATGCCCCTTCCTGGTTGGAAGGTCCTTG
1987 T
130 T
1988 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTCTGTTTTTCATTCCCAAAAATGCCCC
1 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTCT-TTTTT-ATT-CCAAAAATGCCCC
* * * *
2053 TTCCCGGTCGGAAGGTCACAGTTTTCTTTCTTTCCAGAAATGCCCCATCATGGTTGGAAGGTCCT
63 TTCCTGGTCGGAAGGTCACAGTTTTCTTTCTTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCT
2118 TGT
128 TGT
* * * * * *
2121 TTTCATTTCCAGAAATGCCCATTCCTAGTTGGAAGGTCCCTGTTTTATTCCAAAAATTCCCCTTC
1 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTCTTTTTTATTCCAAAAATGCCCCTTC
* * *
2186 CTGGTTGGAAGGTCCCAGTTTTC-TTCTATTCCAAGAATGCCCCTTCCTGGTTGGAAGGTCCTTG
66 CTGGTCGGAAGGTCACAGTTTTCTTTCT-TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTG
2250 T
130 T
*
2251 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTATTTTTATTCCAAAAATGCCCCTT
1 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTCT-TTTTTATTCCAAAAATGCCCCTT
2316 CCTGGTCGGAAGGTCACAGTTTTCTTTCTTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTG
65 CCTGGTCGGAAGGTCACAGTTTTCTTTCTTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTG
2381 T
130 T
* * *
2382 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAAGTCTCTGTTTATATTCCAAAAATGCCCATT
1 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTCT-TTTTTATTCCAAAAATGCCCCTT
** *
2447 CCCAGTCGGAAGGTCACA---AT-TTTCTTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTG
65 CCTGGTCGGAAGGTCACAGTTTTCTTTCTTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTG
2508 T
130 T
2509 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTC
1 TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTC
2547 CCTGTTTTCT
Statistics
Matches: 506, Mismatches: 42, Indels: 21
0.89 0.07 0.04
Matches are distributed among these distances:
126 4 0.01
127 91 0.18
128 23 0.05
129 8 0.02
130 107 0.21
131 188 0.37
132 11 0.02
133 70 0.14
134 4 0.01
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (130 bp):
TTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCTCTTTTTTATTCCAAAAATGCCCCTTC
CTGGTCGGAAGGTCACAGTTTTCTTTCTTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGT
Found at i:2675 original size:48 final size:49
Alignment explanation
Indices: 2609--2855 Score: 324
Period size: 48 Copynumber: 5.1 Consensus size: 49
2599 AAGTCTACTT
* * *
2609 TTCCCGTTTTGCCATTCCCGGTCGGAAGGTGTTGTTTTCAATG-TTGAA
1 TTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGATTTAA
* *
2657 TTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
1 TTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGATTTAA
* * * *
2706 TTTC-GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTAT
1 TTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGATTTAA
* * *
2754 TTCTTGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTCTTCAATGATTT-A
1 TTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGATTTAA
* * *
2802 TTCCCGTTTTGCCCTT-CCGGTCGGAAGGTGTTATTTTCAAT-ATTTCA
1 TTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGATTTAA
2849 TTCCTGT
1 TTCCTGT
2856 CTTCAATGTT
Statistics
Matches: 179, Mismatches: 17, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
46 4 0.02
47 29 0.16
48 100 0.56
49 46 0.26
ACGTcount: A:0.13, C:0.21, G:0.22, T:0.44
Consensus pattern (49 bp):
TTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGATTTAA
Found at i:12752 original size:418 final size:419
Alignment explanation
Indices: 11975--12801 Score: 1485
Period size: 418 Copynumber: 2.0 Consensus size: 419
11965 TCTTCCTTCC
11975 ATGCTTCATGTATCTTCAAAATATTAATTCCATTTCCACTCATGAAGCTTCCAACTTAAATCCAT
1 ATGCTTCATGTATCTTCAAAATATTAATTCCATTTCCACTCATGAAGCTTCCAACTTAAATCCAT
* *
12040 TAAGCCTTTGATGAGAAAGCTAGTAATCTGTAAGGTATCCAATCTAATTACATCTTGCTTTGCTT
66 TAAGCCTTTGATGAGAAAGCTAGTAATCTGTAAGGTATCCAATCCAATCACATCTTGCTTTGCTT
*
12105 GACTTCATTTCTATTCCACTTCAATTTTCTCATTGACCTTCTTCATGCTTCATATTCCCTTAATA
131 GACTTCATTTCTATTCCACTCCAATTTTCTCATTGACCTTCTTCATGCTTCATATTCCCTTAATA
*
12170 AATTGATCATGGAGTCCTCTCTTATTAAGCTTCGAGTCTATATCTTTAAGTCCTTCAATGAGCTT
196 AATTGATCATGGAGTCCTCTCTTATGAAGCTTCGAGTCTATATCTTTAAGTCCTTCAATGAGCTT
* *
12235 CTTAATATCACCAAGCAAGGCATCAAGAAAGGCTGTTAGTGCAGTCAATAATATGTTAATATTGT
261 CTTAATATCACCAAGCAAGACATCAAGAAAGGCTGTTAGTGCAGTCAATAATATGCTAATATTGT
* * *
12300 ACCTGCACACTTAGGAGCTTTGTTAGACTTAAATGAAGAGAATCTTTTGTTATCATCAAAAACAC
326 ACCAGCACACTTAGGAGCTTTGTTAGACTTAAATGAAGAGAATCGTTTGTAATCATCAAAAACAC
12365 ATGGAGTCAACA-ATCTCCCCCTTTTTTG
391 ATGGAGTCAACACATCTCCCCCTTTTTTG
*
12393 ATGCTTCATGTATCTTCAAAATATTAATTCCATTTCCACTCATGAAGCTTCCAATTTAAATCCAT
1 ATGCTTCATGTATCTTCAAAATATTAATTCCATTTCCACTCATGAAGCTTCCAACTTAAATCCAT
*
12458 TAAGCCTTTGATGAGAAAGCTAGTAATCTGTAAGGTATCCAATCCAGTCACATCTTGCTTTGCTT
66 TAAGCCTTTGATGAGAAAGCTAGTAATCTGTAAGGTATCCAATCCAATCACATCTTGCTTTGCTT
* * *
12523 GACTTCCTTTCTATTCCACTCCAATTTTCTCATTGTCCTTTTTCATGCTTCATATTCCCTTAATA
131 GACTTCATTTCTATTCCACTCCAATTTTCTCATTGACCTTCTTCATGCTTCATATTCCCTTAATA
12588 AATTGATCATGGAGTCCTCTCTTATGAAGCTTCGAGTCTATATCTTTAAGTCCTTCAATGAGCTT
196 AATTGATCATGGAGTCCTCTCTTATGAAGCTTCGAGTCTATATCTTTAAGTCCTTCAATGAGCTT
* *
12653 CTTAATATCACCAAGCAAGACATCTAGAAAGGTTGTTAGTGCAGTCAATAATATGCTAATATTGT
261 CTTAATATCACCAAGCAAGACATCAAGAAAGGCTGTTAGTGCAGTCAATAATATGCTAATATTGT
* *
12718 ACCAGCACACTTAGGAGCTTTGTTAGACTTAAATGAAGAGAATGGTTTGTAATCATCAGAAACAC
326 ACCAGCACACTTAGGAGCTTTGTTAGACTTAAATGAAGAGAATCGTTTGTAATCATCAAAAACAC
12783 ATGGAGTCAACACATCTCC
391 ATGGAGTCAACACATCTCC
12802 TGTTCGAAAA
Statistics
Matches: 390, Mismatches: 18, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
418 384 0.98
419 6 0.02
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (419 bp):
ATGCTTCATGTATCTTCAAAATATTAATTCCATTTCCACTCATGAAGCTTCCAACTTAAATCCAT
TAAGCCTTTGATGAGAAAGCTAGTAATCTGTAAGGTATCCAATCCAATCACATCTTGCTTTGCTT
GACTTCATTTCTATTCCACTCCAATTTTCTCATTGACCTTCTTCATGCTTCATATTCCCTTAATA
AATTGATCATGGAGTCCTCTCTTATGAAGCTTCGAGTCTATATCTTTAAGTCCTTCAATGAGCTT
CTTAATATCACCAAGCAAGACATCAAGAAAGGCTGTTAGTGCAGTCAATAATATGCTAATATTGT
ACCAGCACACTTAGGAGCTTTGTTAGACTTAAATGAAGAGAATCGTTTGTAATCATCAAAAACAC
ATGGAGTCAACACATCTCCCCCTTTTTTG
Found at i:25114 original size:29 final size:30
Alignment explanation
Indices: 25077--25136 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
25067 AATTCTTTCC
* *
25077 TCTTGAAATAATTCTTCAAT-GTCTTCAAA
1 TCTTCAAATAAGTCTTCAATAGTCTTCAAA
25106 TCTTCAAATAAGTCTTCAATGAGTCTTCAAA
1 TCTTCAAATAAGTCTTCAAT-AGTCTTCAAA
25137 CACGAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 18 0.67
31 9 0.33
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.38
Consensus pattern (30 bp):
TCTTCAAATAAGTCTTCAATAGTCTTCAAA
Found at i:27000 original size:21 final size:21
Alignment explanation
Indices: 26976--27030 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
26966 GGCTTGGAAT
* *
26976 GGTGATGGCACGGGCATAGCC
1 GGTGGTGGCACGGGCATAACC
* *
26997 GGTGGTAGCACGGGCTTAACC
1 GGTGGTGGCACGGGCATAACC
27018 GGTGGTGGCACGG
1 GGTGGTGGCACGG
27031 TAGTGGCGCG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.16, C:0.22, G:0.45, T:0.16
Consensus pattern (21 bp):
GGTGGTGGCACGGGCATAACC
Found at i:30122 original size:24 final size:23
Alignment explanation
Indices: 30095--30177 Score: 96
Period size: 24 Copynumber: 3.5 Consensus size: 23
30085 AGGAAAATAT
30095 ATTTTTTTTTATGACGCAGAAACA
1 ATTTTTTTTTATGACGCA-AAACA
*
30119 ATTTATTTTTATGACGCAAAA-A
1 ATTTTTTTTTATGACGCAAAACA
* *
30141 CTCTTTTTTTTATGACGCAAAAACT
1 AT-TTTTTTTTATGACGC-AAAACA
*
30166 CTTTTTTTTTAT
1 ATTTTTTTTTAT
30178 ATATCCAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
22 2 0.04
23 17 0.33
24 31 0.60
25 2 0.04
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.48
Consensus pattern (23 bp):
ATTTTTTTTTATGACGCAAAACA
Found at i:30127 original size:23 final size:24
Alignment explanation
Indices: 30095--30164 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
30085 AGGAAAATAT
* *
30095 ATTTTTTTTTATGACGCAGAAACA
1 ATTTATTTTTATGACGCAAAAACA
*
30119 ATTTATTTTTATGACGCAAAAACT
1 ATTTATTTTTATGACGCAAAAACA
*
30143 CTTT-TTTTTATGACGCAAAAAC
1 ATTTATTTTTATGACGCAAAAAC
30165 TCTTTTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 18 0.43
24 24 0.57
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (24 bp):
ATTTATTTTTATGACGCAAAAACA
Found at i:30165 original size:23 final size:23
Alignment explanation
Indices: 30097--30174 Score: 120
Period size: 23 Copynumber: 3.3 Consensus size: 23
30087 GAAAATATAT
* **
30097 TTTTTTTTATGACGCAGAAACAA
1 TTTTTTTTATGACGCAAAAACTC
30120 TTTATTTTTATGACGCAAAAACTC
1 TTT-TTTTTATGACGCAAAAACTC
30144 TTTTTTTTATGACGCAAAAACTC
1 TTTTTTTTATGACGCAAAAACTC
30167 TTTTTTTT
1 TTTTTTTT
30175 TATATATCCA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
23 31 0.61
24 20 0.39
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.47
Consensus pattern (23 bp):
TTTTTTTTATGACGCAAAAACTC
Found at i:30544 original size:15 final size:16
Alignment explanation
Indices: 30520--30559 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
30510 AGAGGTTGAA
*
30520 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
30535 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
30551 AGAAAACAA
1 AGAAAACAA
30560 AACAAAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:31975 original size:29 final size:30
Alignment explanation
Indices: 31938--31997 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
31928 AATTCTTTCC
* *
31938 TCTTGAAATAATTCTTCAAT-GTCTTCAAA
1 TCTTCAAATAAGTCTTCAATAGTCTTCAAA
31967 TCTTCAAATAAGTCTTCAATGAGTCTTCAAA
1 TCTTCAAATAAGTCTTCAAT-AGTCTTCAAA
31998 CACGAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 18 0.67
31 9 0.33
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.38
Consensus pattern (30 bp):
TCTTCAAATAAGTCTTCAATAGTCTTCAAA
Found at i:33987 original size:18 final size:18
Alignment explanation
Indices: 33964--33999 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
33954 TAACCTTACG
33964 AAGGATATAACGTT-ATAT
1 AAGGATAT-ACGTTCATAT
33982 AAGGATATACGTTCATAT
1 AAGGATATACGTTCATAT
34000 TGCTTTAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (18 bp):
AAGGATATACGTTCATAT
Done.