Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019057.1 Corchorus olitorius cultivar O-4 contig19090, 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: 97587
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Found at i:568 original size:13 final size:12
Alignment explanation
Indices: 547--581 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
537 AATAAAGTAA
547 TAATACTATTAT
1 TAATACTATTAT
559 TAATTACTATTAT
1 TAA-TACTATTAT
572 TAATACTATT
1 TAATACTATT
582 TCAATGTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (12 bp):
TAATACTATTAT
Found at i:3120 original size:20 final size:20
Alignment explanation
Indices: 3091--3136 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
3081 GGGAAGGGCC
* *
3091 AAACAGGAATAAAAGGTTGA
1 AAACAAGAATAAAAGATTGA
*
3111 AAACAAGAATAAAATATTGA
1 AAACAAGAATAAAAGATTGA
3131 AAACAA
1 AAACAA
3137 CACCTTCCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.63, C:0.07, G:0.15, T:0.15
Consensus pattern (20 bp):
AAACAAGAATAAAAGATTGA
Found at i:3154 original size:68 final size:68
Alignment explanation
Indices: 3064--3713 Score: 767
Period size: 68 Copynumber: 9.8 Consensus size: 68
3054 AGAGAATAGG
** * ** *
3064 AACAAC-CTCTTCCGATGGGGAAGGGCCAAACAGGAATAAAAGGTTGAAAACAAGAATAAAATAT
1 AACAACAC-CTTCCGACCGGGAAGGGCAAAACAGGAATAAAATATTGAAAACAGGAATAAAATAT
3128 TGAA
65 TGAA
* * * * *
3132 AACAACACCTTCCGACCGGGAAGGGCAAAACGGGAATAAGACATCGAAAACAAGAATAAAATATT
1 AACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAATATTGAAAACAGGAATAAAATATT
3197 GAA
66 GAA
* * ** *
3200 AACAACACCTTCCGACCGAGAAGGGCAAAACAAGAATAAAAGGTTGAAAACAGGAATAAAACATT
1 AACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAATATTGAAAACAGGAATAAAATATT
3265 GAA
66 GAA
* * * * * *
3268 AAGAACACCTTCCGACCAGAAAGGGCAAAAC-GG-----GA-ATTGAAAATAGGAATAAAATAAT
1 AACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAATATTGAAAACAGGAATAAAATATT
3326 GAA
66 GAA
* * *
3329 AACAACACCTTCCGACCGTGAAGGGCAAAACATGAATAAAATATTGAAAACAGGAATAAAACATT
1 AACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAATATTGAAAACAGGAATAAAATATT
3394 GAA
66 GAA
* * *
3397 AACAACACCTTCCAACCAGGAATGGCAAAACAGG------A-ATTGAAAACAGGAATAAAATATT
1 AACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAATATTGAAAACAGGAATAAAATATT
*
3455 GGA
66 GAA
* * * *
3458 AACAACACCTTCCGACCAGGAAGGGCAAAACATGAATAAAATATTGAAAACAGGAAAAAAACATT
1 AACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAATATTGAAAACAGGAATAAAATATT
3523 GAA
66 GAA
* * * * *
3526 AACAACACCTTTCGACCGGGAAGGGTAAAA-TGGGA-AAAATATTGAAAACAGGAATAAAACATT
1 AACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAATATTGAAAACAGGAATAAAATATT
3589 GAA
66 GAA
* *
3592 AACAACACCTTCCGACCGGGAAGGGCAAAACATGAATAATATATTGAAAACAGGAATAAAATATT
1 AACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAATATTGAAAACAGGAATAAAATATT
3657 GAA
66 GAA
* * * *
3660 GACAACACCTTCCGATCGGGAAGGGCAAAACTGGGAATAAAACATTGAAAACAG
1 AACAACACCTTCCGACCGGGAAGGGCAAAAC-AGGAATAAAATATTGAAAACAG
3714 CACCTTCCGG
Statistics
Matches: 495, Mismatches: 69, Indels: 35
0.83 0.12 0.06
Matches are distributed among these distances:
61 104 0.21
62 3 0.01
66 58 0.12
67 7 0.01
68 304 0.61
69 19 0.04
ACGTcount: A:0.49, C:0.17, G:0.20, T:0.14
Consensus pattern (68 bp):
AACAACACCTTCCGACCGGGAAGGGCAAAACAGGAATAAAATATTGAAAACAGGAATAAAATATT
GAA
Found at i:3188 original size:20 final size:20
Alignment explanation
Indices: 3165--3204 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3155 GGCAAAACGG
*
3165 GAATAAGACATCGAAAACAA
1 GAATAAAACATCGAAAACAA
* *
3185 GAATAAAATATTGAAAACAA
1 GAATAAAACATCGAAAACAA
3205 CACCTTCCGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.10, G:0.12, T:0.15
Consensus pattern (20 bp):
GAATAAAACATCGAAAACAA
Found at i:3266 original size:20 final size:20
Alignment explanation
Indices: 3226--3269 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3216 CGAGAAGGGC
**
3226 AAAACAAGAATAAAAGGTTG
1 AAAACAAGAATAAAACATTG
*
3246 AAAACAGGAATAAAACATTG
1 AAAACAAGAATAAAACATTG
3266 AAAA
1 AAAA
3270 GAACACCTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.64, C:0.07, G:0.16, T:0.14
Consensus pattern (20 bp):
AAAACAAGAATAAAACATTG
Found at i:3379 original size:129 final size:128
Alignment explanation
Indices: 3082--3697 Score: 818
Period size: 129 Copynumber: 4.7 Consensus size: 128
3072 CTTCCGATGG
* * ** * *
3082 GGAAGGGCCAAACAGGAATAAAAGGTTGAAAACAAGAATAAAATATTGAAAACAACACCTTCCGA
1 GGAAGGGCAAAACATGAATAAAATATTGAAAACAGGAATAAAACATTGAAAACAACACCTTCCGA
*
3147 CCGGGAAGGGCAAAACGGGAATAAGACATCGAAAACAAGAATAAAATATTGAAAACAACACCTTC
66 CCGGGAAGGGCAAAACGGGAAT------T-GAAAACAGGAATAAAATATTGAAAACAACACCTTC
3212 CGACC
124 CGACC
* ** *
3217 GAGAAGGGCAAAACAAGAATAAAAGGTTGAAAACAGGAATAAAACATTGAAAAGAACACCTTCCG
1 G-GAAGGGCAAAACATGAATAAAATATTGAAAACAGGAATAAAACATTGAAAACAACACCTTCCG
* * * *
3282 ACCAGAAAGGGCAAAACGGGAATTGAAAATAGGAATAAAATAATGAAAACAACACCTTCCGACC
65 ACCGGGAAGGGCAAAACGGGAATTGAAAACAGGAATAAAATATTGAAAACAACACCTTCCGACC
*
3346 GTGAAGGGCAAAACATGAATAAAATATTGAAAACAGGAATAAAACATTGAAAACAACACCTTCCA
1 G-GAAGGGCAAAACATGAATAAAATATTGAAAACAGGAATAAAACATTGAAAACAACACCTTCCG
* * * *
3411 ACCAGGAATGGCAAAACAGGAATTGAAAACAGGAATAAAATATTGGAAACAACACCTTCCGACC
65 ACCGGGAAGGGCAAAACGGGAATTGAAAACAGGAATAAAATATTGAAAACAACACCTTCCGACC
* *
3475 AGGAAGGGCAAAACATGAATAAAATATTGAAAACAGGAAAAAAACATTGAAAACAACACCTTTCG
1 -GGAAGGGCAAAACATGAATAAAATATTGAAAACAGGAATAAAACATTGAAAACAACACCTTCCG
* * *
3540 ACCGGGAAGGGTAAAATGGGAAAAATATTGAAAACAGGAATAAAACATTGAAAACAACACCTTCC
65 ACCGGGAAGGGCAAAACGGG----A-ATTGAAAACAGGAATAAAATATTGAAAACAACACCTTCC
3605 GACC
125 GACC
* * *
3609 GGGAAGGGCAAAACATGAATAATATATTGAAAACAGGAATAAAATATTGAAGACAACACCTTCCG
1 -GGAAGGGCAAAACATGAATAAAATATTGAAAACAGGAATAAAACATTGAAAACAACACCTTCCG
*
3674 ATCGGGAAGGGCAAAACTGGGAAT
65 ACCGGGAAGGGCAAAAC-GGGAAT
3698 AAAACATTGA
Statistics
Matches: 432, Mismatches: 41, Indels: 21
0.87 0.08 0.04
Matches are distributed among these distances:
129 229 0.53
130 4 0.01
131 1 0.00
133 1 0.00
134 114 0.26
135 4 0.01
136 79 0.18
ACGTcount: A:0.49, C:0.17, G:0.20, T:0.14
Consensus pattern (128 bp):
GGAAGGGCAAAACATGAATAAAATATTGAAAACAGGAATAAAACATTGAAAACAACACCTTCCGA
CCGGGAAGGGCAAAACGGGAATTGAAAACAGGAATAAAATATTGAAAACAACACCTTCCGACC
Found at i:3380 original size:20 final size:20
Alignment explanation
Indices: 3355--3400 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
3345 CGTGAAGGGC
* *
3355 AAAACATGAATAAAATATTG
1 AAAACAGGAATAAAACATTG
3375 AAAACAGGAATAAAACATTG
1 AAAACAGGAATAAAACATTG
3395 AAAACA
1 AAAACA
3401 ACACCTTCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.63, C:0.09, G:0.11, T:0.17
Consensus pattern (20 bp):
AAAACAGGAATAAAACATTG
Found at i:3441 original size:13 final size:14
Alignment explanation
Indices: 3413--3446 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3403 ACCTTCCAAC
3413 CAGGAATGGCAAAA
1 CAGGAATGGCAAAA
*
3427 CAGGAATTG-AAAA
1 CAGGAATGGCAAAA
3440 CAGGAAT
1 CAGGAAT
3447 AAAATATTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.50, C:0.12, G:0.26, T:0.12
Consensus pattern (14 bp):
CAGGAATGGCAAAA
Found at i:3506 original size:197 final size:195
Alignment explanation
Indices: 3082--3713 Score: 708
Period size: 197 Copynumber: 3.2 Consensus size: 195
3072 CTTCCGATGG
* * * *
3082 GGAAGGGCCAAACAGGAATAAAAGGTTGAAAACAAGAATAAAATATTGAAAACAACACCTTCCGA
1 GGAAGGGCAAAAC-TGAATAAAA-ATTGAAAACAGGAATAAAATATTGAAAACAACACCTTCCGA
** * * * * *
3147 CCGGGAAGGGCAAAACGGGAATAAGACATCGAAAACAAGAATAAAATATTGAAAACAACACCTTC
64 CCGGGAAGGGCAAAACATGAATAAAATATTGAAAACAGGAATAAAACATTGAAAACAACACCTTC
* * *
3212 CGACCGAGAAGGGCAAAACAAGAATAAAAGGTTGAAAACAGGAATAAAACATTGAAAAGAACACC
129 CGACCG-GAAGGGCAAAAC-AG---AAAA--TTGAAAACAGGAATAAAATATTGGAAACAACACC
3277 TTCCGACCA
187 TTCCGACCA
* ** * *
3286 GAAAGGGCAAAAC-G----GGAATTGAAAATAGGAATAAAATAATGAAAACAACACCTTCCGACC
1 GGAAGGGCAAAACTGAATAAAAATTGAAAACAGGAATAAAATATTGAAAACAACACCTTCCGACC
* *
3346 GTGAAGGGCAAAACATGAATAAAATATTGAAAACAGGAATAAAACATTGAAAACAACACCTTCCA
66 GGGAAGGGCAAAACATGAATAAAATATTGAAAACAGGAATAAAACATTGAAAACAACACCTTCCG
* *
3411 ACCAGGAATGGCAAAACAG-GAATTGAAAACAGGAATAAAATATTGGAAACAACACCTTCCGACC
131 ACC-GGAAGGGCAAAACAGAAAATTGAAAACAGGAATAAAATATTGGAAACAACACCTTCCGACC
3475 A
195 A
* * *
3476 GGAAGGGCAAAACATGAATAAAATATTGAAAACAGGAAAAAAACATTGAAAACAACACCTTTCGA
1 GGAAGGGCAAAAC-TGAATAAAA-ATTGAAAACAGGAATAAAATATTGAAAACAACACCTTCCGA
* *
3541 CCGGGAAGGG-TAAA-ATGGGA-AAAATATTGAAAACAGGAATAAAACATTGAAAACAACACCTT
64 CCGGGAAGGGCAAAACAT-GAATAAAATATTGAAAACAGGAATAAAACATTGAAAACAACACCTT
3603 CCGACCGGGAAGGGCAAAACATGAATAATATATTGAAAACAGGAATAAAATATT-GAAGACAACA
128 CCGACC-GGAAGGGCAAAACA-G---AA-A-ATTGAAAACAGGAATAAAATATTGGAA-ACAACA
* *
3667 CCTTCCGATCG
185 CCTTCCGACCA
3678 GGAAGGGCAAAACTGGGAATAAAACATTGAAAACAG
1 GGAAGGGCAAAACT--GAATAAAA-ATTGAAAACAG
3714 CACCTTCCGG
Statistics
Matches: 369, Mismatches: 40, Indels: 39
0.82 0.09 0.09
Matches are distributed among these distances:
190 52 0.14
192 3 0.01
195 62 0.17
196 9 0.02
197 154 0.42
198 2 0.01
201 5 0.01
202 52 0.14
203 19 0.05
204 11 0.03
ACGTcount: A:0.50, C:0.16, G:0.20, T:0.14
Consensus pattern (195 bp):
GGAAGGGCAAAACTGAATAAAAATTGAAAACAGGAATAAAATATTGAAAACAACACCTTCCGACC
GGGAAGGGCAAAACATGAATAAAATATTGAAAACAGGAATAAAACATTGAAAACAACACCTTCCG
ACCGGAAGGGCAAAACAGAAAATTGAAAACAGGAATAAAATATTGGAAACAACACCTTCCGACCA
Found at i:3509 original size:20 final size:20
Alignment explanation
Indices: 3484--3529 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
3474 CAGGAAGGGC
* * *
3484 AAAACATGAATAAAATATTG
1 AAAACAGGAAAAAAACATTG
3504 AAAACAGGAAAAAAACATTG
1 AAAACAGGAAAAAAACATTG
3524 AAAACA
1 AAAACA
3530 ACACCTTTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.65, C:0.09, G:0.11, T:0.15
Consensus pattern (20 bp):
AAAACAGGAAAAAAACATTG
Found at i:3643 original size:20 final size:20
Alignment explanation
Indices: 3618--3659 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3608 CGGGAAGGGC
* *
3618 AAAACATGAATAATATATTG
1 AAAACAGGAATAAAATATTG
3638 AAAACAGGAATAAAATATTG
1 AAAACAGGAATAAAATATTG
3658 AA
1 AA
3660 GACAACACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.05, G:0.12, T:0.24
Consensus pattern (20 bp):
AAAACAGGAATAAAATATTG
Found at i:3718 original size:49 final size:48
Alignment explanation
Indices: 3638--3808 Score: 243
Period size: 48 Copynumber: 3.5 Consensus size: 48
3628 TAATATATTG
* *
3638 AAAACAGGAATAAAATATTGAAGACAACACCTTCCGATCGGGAAGGGC
1 AAAACTGGAATAAAATATTGAAAACAACACCTTCCGATCGGGAAGGGC
* * **
3686 AAAACTGGGAATAAAACATTGAAAACAGCACCTTCCGGCCGGGAAGGGC
1 AAAACT-GGAATAAAATATTGAAAACAACACCTTCCGATCGGGAAGGGC
* *
3735 AAAACTGGAATAGAATATTGAAAACAACACCTTCCGATTGGGAAGGGC
1 AAAACTGGAATAAAATATTGAAAACAACACCTTCCGATCGGGAAGGGC
**
3783 AAAACAAGAATAAAATATTGAAAACA
1 AAAACTGGAATAAAATATTGAAAACA
3809 GGAATATAGT
Statistics
Matches: 107, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
48 64 0.60
49 43 0.40
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (48 bp):
AAAACTGGAATAAAATATTGAAAACAACACCTTCCGATCGGGAAGGGC
Found at i:3808 original size:20 final size:20
Alignment explanation
Indices: 3783--3829 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
3773 TGGGAAGGGC
3783 AAAACAAGAATAAAATATTG
1 AAAACAAGAATAAAATATTG
* * *
3803 AAAACAGGAATATAGTATTG
1 AAAACAAGAATAAAATATTG
3823 AAAACAA
1 AAAACAA
3830 CACTGATTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.62, C:0.06, G:0.13, T:0.19
Consensus pattern (20 bp):
AAAACAAGAATAAAATATTG
Found at i:14901 original size:50 final size:50
Alignment explanation
Indices: 14813--15419 Score: 973
Period size: 50 Copynumber: 12.1 Consensus size: 50
14803 ATATTTCCTT
* * ** * *
14813 TTTATTTACAAATTGCTTAGAAGGTTGAATCTTTTAATCAAAAATCCAATC
1 TTTATTTACAAATTTCTTA-AAAGTTTCATCTTTTAATTAAAAACCCAATC
* * * *
14864 TTTATTCATAAATTTCTTGAAAGTTTCATCTTTTAATCAAAAACCCAATC
1 TTTATTTACAAATTTCTTAAAAGTTTCATCTTTTAATTAAAAACCCAATC
*
14914 TTTATTTACAAATTTCTTAAAAG-TTCAGTCTTTTGATTAAAAACCCAATC
1 TTTATTTACAAATTTCTTAAAAGTTTCA-TCTTTTAATTAAAAACCCAATC
*
14964 TTTATTTACAAATTTCTTAAAAGTTTCATCTTTTAATCAAAAACCCAATC
1 TTTATTTACAAATTTCTTAAAAGTTTCATCTTTTAATTAAAAACCCAATC
* *
15014 TTTATTTACAAATTTCTTAAAAGTTTCATCTTTTAATCAAAAATCCAATC
1 TTTATTTACAAATTTCTTAAAAGTTTCATCTTTTAATTAAAAACCCAATC
*
15064 TTTATTTACAAATTTCTTAAAAATTTCATCTTTTAATTAAAAACCCAATC
1 TTTATTTACAAATTTCTTAAAAGTTTCATCTTTTAATTAAAAACCCAATC
* * *
15114 TTTATTTACAAATTTCTTAAAAGTTTAATCTTTTAATCAAAAATCCAATC
1 TTTATTTACAAATTTCTTAAAAGTTTCATCTTTTAATTAAAAACCCAATC
* * *
15164 TTTATTTACAAATTTCATAGAAGTTTCATCTTTTAATTAAAAATCCAATC
1 TTTATTTACAAATTTCTTAAAAGTTTCATCTTTTAATTAAAAACCCAATC
* *
15214 TTTATTTACAAATTTCTTAGAAGTTTCATCTTTTAATTAAAACCCCAATC
1 TTTATTTACAAATTTCTTAAAAGTTTCATCTTTTAATTAAAAACCCAATC
15264 TTTATTTACAAATTTCTTAAAAGTTTCATCTTTTAATTAAAAACCCAATC
1 TTTATTTACAAATTTCTTAAAAGTTTCATCTTTTAATTAAAAACCCAATC
15314 TTTATTTACAAATTTCTTAAAAGTTTCATCTTTTAATTAAAAACCCAATC
1 TTTATTTACAAATTTCTTAAAAGTTTCATCTTTTAATTAAAAACCCAATC
*
15364 TTTATTTACAAATTTCTTAAAAGTTTCATCTTTTAATTAAAAAACCAATC
1 TTTATTTACAAATTTCTTAAAAGTTTCATCTTTTAATTAAAAACCCAATC
15414 TTTATT
1 TTTATT
15420 CACTAAGGTG
Statistics
Matches: 521, Mismatches: 33, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
49 4 0.01
50 498 0.96
51 19 0.04
ACGTcount: A:0.38, C:0.16, G:0.03, T:0.43
Consensus pattern (50 bp):
TTTATTTACAAATTTCTTAAAAGTTTCATCTTTTAATTAAAAACCCAATC
Found at i:25390 original size:15 final size:15
Alignment explanation
Indices: 25360--25401 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
25350 TTACTTTGTT
25360 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
25376 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
25391 TTGTTTTCTGT
1 TTGTTTTCTGT
25402 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:33834 original size:19 final size:18
Alignment explanation
Indices: 33805--33840 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
33795 TTGAAATAAT
33805 TCTTCAATAGTCTTCAAG
1 TCTTCAATAGTCTTCAAG
33823 TCTTCAAATAGTCTTCAA
1 TCTTC-AATAGTCTTCAA
33841 ACACAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (18 bp):
TCTTCAATAGTCTTCAAG
Found at i:39516 original size:14 final size:14
Alignment explanation
Indices: 39488--39532 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 14
39478 TAAAAGACTC
39488 AAAACC-TTT-TTG
1 AAAACCTTTTCTTG
39500 AAAACCTTTTCTTG
1 AAAACCTTTTCTTG
*
39514 AAAACAATTTTCTTG
1 AAAAC-CTTTTCTTG
39529 AAAA
1 AAAA
39533 ACATGTCTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 6 0.21
13 3 0.10
14 8 0.28
15 12 0.41
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.38
Consensus pattern (14 bp):
AAAACCTTTTCTTG
Found at i:40801 original size:22 final size:22
Alignment explanation
Indices: 40768--40835 Score: 65
Period size: 21 Copynumber: 3.2 Consensus size: 22
40758 AATGCATGAA
40768 GGATGTAT-GACATATATCAAT
1 GGATGTATGGACATATATCAAT
*
40789 GGA-GATATGGACA-ATCCATGAA-
1 GGATG-TATGGACATAT--ATCAAT
40811 GGATGTATGG-CATATATCAAT
1 GGATGTATGGACATATATCAAT
40832 GGAT
1 GGAT
40836 ATGATGATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
20 5 0.13
21 14 0.37
22 14 0.37
23 5 0.13
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.28
Consensus pattern (22 bp):
GGATGTATGGACATATATCAAT
Found at i:40809 original size:43 final size:43
Alignment explanation
Indices: 40710--40834 Score: 182
Period size: 43 Copynumber: 2.9 Consensus size: 43
40700 ATACAAAGGA
* *
40710 ATGGATAATGCATGATGGATGTATGAACATATAT--ATGGAGAC
1 ATGGACAATGCATGAAGGATGTATG-ACATATATCAATGGAGAC
*
40752 ATGGACAATGCATGAAGGATGTATGACATATATCAATGGAGAT
1 ATGGACAATGCATGAAGGATGTATGACATATATCAATGGAGAC
* *
40795 ATGGACAATCCATGAAGGATGTATGGCATATATCAATGGA
1 ATGGACAATGCATGAAGGATGTATGACATATATCAATGGA
40835 TATGATGATA
Statistics
Matches: 76, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
41 8 0.11
42 23 0.30
43 45 0.59
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (43 bp):
ATGGACAATGCATGAAGGATGTATGACATATATCAATGGAGAC
Found at i:48551 original size:30 final size:29
Alignment explanation
Indices: 48504--48560 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 29
48494 TTGATGTCCT
48504 TGATAACCCTTGGCGCATCATTCCCTCCA
1 TGATAACCCTTGGCGCATCATTCCCTCCA
*
48533 TGATAAGCCTTGGGCGCATCATTCCCTC
1 TGATAACCCTT-GGCGCATCATTCCCTC
48561 TCCCTTGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.19, C:0.35, G:0.18, T:0.28
Consensus pattern (29 bp):
TGATAACCCTTGGCGCATCATTCCCTCCA
Found at i:48585 original size:15 final size:15
Alignment explanation
Indices: 48565--48597 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
48555 TCCCTCTCCC
*
48565 TTGATACGAGTCTAG
1 TTGATACGAATCTAG
48580 TTGATACGAATCTAG
1 TTGATACGAATCTAG
48595 TTG
1 TTG
48598 TTTAAGATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.36
Consensus pattern (15 bp):
TTGATACGAATCTAG
Found at i:51173 original size:15 final size:15
Alignment explanation
Indices: 51134--51174 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
51124 CAAGAGCAAT
*
51134 AAAACACCA-AAACA
1 AAAACAACACAAACA
*
51148 AAAA-AAAACAAACA
1 AAAACAACACAAACA
51162 AAAACAACACAAA
1 AAAACAACACAAA
51175 GCAACCATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
13 2 0.09
14 13 0.59
15 7 0.32
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAACAACACAAACA
Found at i:55782 original size:27 final size:28
Alignment explanation
Indices: 55714--55787 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 28
55704 GAGTGGACTT
** *
55714 AAAATGACCAACGTGCTCCTGAATATGC
1 AAAATGACCAAAATGCCCCTGAATATGC
*
55742 AAAAATGACCAAAATGCCCCTGAATGTGC
1 -AAAATGACCAAAATGCCCCTGAATATGC
55771 -AAATGACCAAAATGCCC
1 AAAATGACCAAAATGCCC
55788 ATGGATGACC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 17 0.41
29 24 0.59
ACGTcount: A:0.41, C:0.26, G:0.16, T:0.18
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGAATATGC
Found at i:55932 original size:30 final size:32
Alignment explanation
Indices: 55888--55950 Score: 94
Period size: 30 Copynumber: 2.0 Consensus size: 32
55878 TTCGAAACGT
55888 AAGGAATTAATTTGTTCCAAAA-AAAAACATA
1 AAGGAATTAATTTGTTCCAAAAGAAAAACATA
* *
55919 AAGG-ATTATTTTGTTTCAAAAGAAAAACATA
1 AAGGAATTAATTTGTTCCAAAAGAAAAACATA
55950 A
1 A
55951 GAGATTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 15 0.52
31 14 0.48
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.29
Consensus pattern (32 bp):
AAGGAATTAATTTGTTCCAAAAGAAAAACATA
Found at i:59523 original size:19 final size:18
Alignment explanation
Indices: 59499--59534 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
59489 TGAAGACTTA
59499 TTGAAGATAATCTGAAGAC
1 TTGAAGATAAT-TGAAGAC
*
59518 TTGAAGATTATTGAAGA
1 TTGAAGATAATTGAAGA
59535 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAC
Found at i:63172 original size:21 final size:21
Alignment explanation
Indices: 63148--63197 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
63138 CCCGACCATG
*
63148 GCCCGGCCATCCGAGCCACCT
1 GCCCGGCCAGCCGAGCCACCT
* **
63169 GCCCTGCCAGCCGAGCCATTT
1 GCCCGGCCAGCCGAGCCACCT
63190 GCCCGGCC
1 GCCCGGCC
63198 CTACCCGGCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.12, C:0.50, G:0.26, T:0.12
Consensus pattern (21 bp):
GCCCGGCCAGCCGAGCCACCT
Found at i:67925 original size:14 final size:15
Alignment explanation
Indices: 67906--67934 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
67896 ACTTAAATGA
67906 TAAAAG-TGTATTTT
1 TAAAAGATGTATTTT
67920 TAAAAGATGTATTTT
1 TAAAAGATGTATTTT
67935 CAATTCTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (15 bp):
TAAAAGATGTATTTT
Found at i:68952 original size:32 final size:32
Alignment explanation
Indices: 68915--69104 Score: 236
Period size: 32 Copynumber: 5.9 Consensus size: 32
68905 TATTAAAGAA
* *
68915 AACGCCACAGATTTGTGGCGTTTTCTTCAAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
* *
68947 TACGCCACAAACTAGTGGCGTTTTCTTCAAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
*
68979 AACGCCACAAATTAGTGGCGTTTTCTTTAAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
* * *
69011 AACGCCAAAAATTAGTGGCGTTTCCTTTAAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
* * * *
69043 GATGCCACAAATTAGTGGCGTTTACTTCAGAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
** * *
69075 AACGCCACTGATTTGTGGCGTTTTATTCAA
1 AACGCCACAAATTAGTGGCGTTTTCTTCAA
69105 TAAACACCAT
Statistics
Matches: 135, Mismatches: 23, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 135 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (32 bp):
AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
Found at i:77036 original size:18 final size:19
Alignment explanation
Indices: 77013--77051 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
77003 TTCTTGAAAT
77013 AATTCTTC-AATGATCTTC
1 AATTCTTCAAATGATCTTC
*
77031 AATTCTTCAAATTATCTTC
1 AATTCTTCAAATGATCTTC
77050 AA
1 AA
77052 CAAATCTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.44
Consensus pattern (19 bp):
AATTCTTCAAATGATCTTC
Found at i:80671 original size:15 final size:15
Alignment explanation
Indices: 80651--80685 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
80641 ATAAATGCTA
*
80651 TCATTTTGAAATGAT
1 TCATTTTAAAATGAT
*
80666 TCATTTTAAAATGTT
1 TCATTTTAAAATGAT
80681 TCATT
1 TCATT
80686 CCTAAAGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (15 bp):
TCATTTTAAAATGAT
Found at i:81943 original size:2 final size:2
Alignment explanation
Indices: 81936--81962 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
81926 ACTAAAGAAA
81936 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
81963 ATTAACAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:82102 original size:21 final size:22
Alignment explanation
Indices: 82073--82137 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
82063 TTTACCTTCA
82073 TATATTTCTTTACCTTTTTTTT
1 TATATTTCTTTACCTTTTTTTT
*** * *
82095 TA-ATTTCTTT-TGGTTTGTGT
1 TATATTTCTTTACCTTTTTTTT
82115 TATATTTCTTTACCTTTTTTTT
1 TATATTTCTTTACCTTTTTTTT
82137 T
1 T
82138 TTTTAAATTT
Statistics
Matches: 31, Mismatches: 10, Indels: 4
0.69 0.22 0.09
Matches are distributed among these distances:
20 7 0.23
21 16 0.52
22 8 0.26
ACGTcount: A:0.12, C:0.11, G:0.06, T:0.71
Consensus pattern (22 bp):
TATATTTCTTTACCTTTTTTTT
Found at i:82120 original size:42 final size:44
Alignment explanation
Indices: 82073--82163 Score: 141
Period size: 47 Copynumber: 2.0 Consensus size: 44
82063 TTTACCTTCA
82073 TATATTTCTTTACC-TTTTTTTTT-AATTTCTTTTGGTTTGTGT
1 TATATTTCTTTACCTTTTTTTTTTAAATTTCTTTTGGTTTGTGT
82115 TATATTTCTTTACCTTTTTTTTTTTTTAAATTTCTTTTGGTTTGTGT
1 TATATTTCTTTACC---TTTTTTTTTTAAATTTCTTTTGGTTTGTGT
82162 TA
1 TA
82164 GTGTTATTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
42 14 0.32
46 9 0.20
47 21 0.48
ACGTcount: A:0.13, C:0.09, G:0.09, T:0.69
Consensus pattern (44 bp):
TATATTTCTTTACCTTTTTTTTTTAAATTTCTTTTGGTTTGTGT
Found at i:93399 original size:37 final size:37
Alignment explanation
Indices: 93355--93425 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
93345 CTTGATCAAC
*
93355 ATACATGTCTTTT-CATATAGACATAACTTTATGATCA
1 ATACATGT-TTTTCCAAATAGACATAACTTTATGATCA
93392 ATACATGTTTTTCCAAATAGACATAACTTTATGA
1 ATACATGTTTTTCCAAATAGACATAACTTTATGA
93426 ATAATTATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 4 0.12
37 28 0.88
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.39
Consensus pattern (37 bp):
ATACATGTTTTTCCAAATAGACATAACTTTATGATCA
Found at i:95217 original size:26 final size:25
Alignment explanation
Indices: 95179--95230 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
95169 ATTTCTTACA
95179 AAATAATAGAAATAAACATTAGATAT
1 AAATAATAGAAATAAAC-TTAGATAT
* * * *
95205 AAATCATATAAATGAACTTATATAT
1 AAATAATAGAAATAAACTTAGATAT
95230 A
1 A
95231 TCTCATTGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (25 bp):
AAATAATAGAAATAAACTTAGATAT
Found at i:95901 original size:37 final size:37
Alignment explanation
Indices: 95857--95927 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
95847 CTTGATCAAC
* *
95857 ATACATGTCTTTTCATATAGACATAACTTTATGATCA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
95894 ATACATGTCTTTCCAAATAGACATAACTTTATGA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGA
95928 ATAATCATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (37 bp):
ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
Done.