Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022801.1 Corchorus olitorius cultivar O-4 contig22834, 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: 17467
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3117 original size:22 final size:21
Alignment explanation
Indices: 3092--4157 Score: 439
Period size: 22 Copynumber: 49.0 Consensus size: 21
3082 ATTTTTTATG
3092 ACCTCCTTATGAAATTTTGATA
1 ACCTCC-TATGAAATTTTGATA
3114 ACCTTCCTATGAAATTTTGATA
1 ACC-TCCTATGAAATTTTGATA
* *
3136 ACATTCCTATGAAATTTTAATA
1 AC-CTCCTATGAAATTTTGATA
* * * * *
3158 ACGATACTATGGAATTTCGAGA
1 AC-CTCCTATGAAATTTTGATA
** * **
3180 ACCTTTTTAT-TAATTTTTTTA
1 ACC-TCCTATGAAATTTTGATA
* *
3201 ACCTTCTTATGAAATTTTGTTA
1 ACC-TCCTATGAAATTTTGATA
* *
3223 ACCTCCCTAAGTAATTTTGA-A
1 ACCT-CCTATGAAATTTTGATA
*
3244 GACCTCACTGTGAAATTTTGATA
1 -ACCTC-CTATGAAATTTTGATA
* * **
3267 ACTTCCCAAAAAATTTTTGATA
1 ACCTCCTATGAAA-TTTTGATA
* * *
3289 ACCAACACTATGAGATGTTGATA
1 ACC-TC-CTATGAAATTTTGATA
* *
3312 ACCTCCATATGATATATTGATA
1 ACCTCC-TATGAAATTTTGATA
* * * * *
3334 ACCACGTTATGAAAATTTAAAA
1 ACCTC-CTATGAAATTTTGATA
3356 ACCTCCATATG-AATTGTT-AGTA
1 ACCTCC-TATGAAATT-TTGA-TA
3378 A--TCAC-ACTGAAATTTTGATA
1 ACCTC-CTA-TGAAATTTTGATA
* * * *
3398 ATCACACTATGAAATTGTAATA
1 ACCTC-CTATGAAATTTTGATA
*
3420 ACCTCGTTATGAAATTTTGATAA
1 ACCTC-CTATGAAATTTTGAT-A
*
3443 ACCTTCCTATAAAATTTTGATAA
1 ACC-TCCTATGAAATTTTGAT-A
3466 ACCTCCCTA--AAATTTTGATA
1 ACCT-CCTATGAAATTTTGATA
*
3486 ACCTCCTTATGAAATCTTGATA
1 ACCTCC-TATGAAATTTTGATA
*
3508 A----CTA-CAAATTTTGATA
1 ACCTCCTATGAAATTTTGATA
* ** *
3524 ATCTCCCTATGATTTTTTGAGA
1 ACCT-CCTATGAAATTTTGATA
* *
3546 ACCTCATTATGAAATTTTGTTA
1 ACCTC-CTATGAAATTTTGATA
* *
3568 ATCTCCCTATGAAATTTTGATTT
1 ACCT-CCTATGAAATTTTGA-TA
* *
3591 ACATACTATGAAATTTTGATA
1 ACCTCCTATGAAATTTTGATA
*
3612 ACCCTCTTATGAAATTTTGA-A
1 A-CCTCCTATGAAATTTTGATA
* *
3633 AACTAAACTATGAAATTTTGATA
1 ACCT--CCTATGAAATTTTGATA
3656 ACCTCCATATGAAATTTTGATA
1 ACCTCC-TATGAAATTTTGATA
* * * *
3678 TCCTCC-CTGAAGTTTTGATT
1 ACCTCCTATGAAATTTTGATA
**
3698 A-CTCCATAAT-AAAAGTT-ATA
1 ACCTCC-T-ATGAAATTTTGATA
*
3718 ACCTTCC--T--AA-TTTGGTA
1 ACC-TCCTATGAAATTTTGATA
* *
3735 ACCATACTATGAAATTTTGGTA
1 ACC-TCCTATGAAATTTTGATA
* * * * *
3757 ATCACATTTTGAAAATTTGATA
1 ACCTC-CTATGAAATTTTGATA
*
3779 ACCTCTTTATGAAATTTTGATA
1 ACCTC-CTATGAAATTTTGATA
* * * *
3801 ACCTCTTTATAAAATTTTGTTG
1 ACCTC-CTATGAAATTTTGATA
*
3823 ACCCCTCTATGAAATTTTGATA
1 ACCTC-CTATGAAATTTTGATA
*** * *
3845 ATAACATTATGTAATTTTGATA
1 ACCTC-CTATGAAATTTTGATA
*
3867 ACCTCGCTTTGAAATTTTGATA
1 ACCTC-CTATGAAATTTTGATA
**
3889 ACAACACTATGAAATTTTGATA
1 ACCTC-CTATGAAATTTTGATA
* *
3911 ATCTTCCAAT-AAATTTTGATA
1 A-CCTCCTATGAAATTTTGATA
*
3932 ATCCGATCTCTATGAAATTTCGATA
1 A-CC--TC-CTATGAAATTTTGATA
* *
3957 ATCACT-TTATGAGA-TTTGATA
1 A-C-CTCCTATGAAATTTTGATA
* * *
3978 ACCTTCTATCAAATTTTGGT-
1 ACCTCCTATGAAATTTTGATA
*
3998 A-CTCCTCATGAAATTGAGACTTTTATA
1 ACCTCCT-ATGAAA-T-----TTTGATA
*
4025 ACCTTCATATGAAATTTTGATA
1 ACC-TCCTATGAAATTTTGATA
*
4047 ACCACACTATGAAATTTTGATA
1 ACCTC-CTATGAAATTTTGATA
* * *
4069 ACCTCCCCATGATATATT-AGTA
1 ACCT-CCTATGAAATTTTGA-TA
*
4091 ACCTCCTTATGAAATTTTGTTA
1 ACCTCC-TATGAAATTTTGATA
*
4113 ACCACACTATGAAATTCTT-ATA
1 ACCTC-CTATGAAATT-TTGATA
*
4135 ACCTCGCTATGACATTTTGATA
1 ACCTC-CTATGAAATTTTGATA
4157 A
1 A
4158 TCCCTTTGAT
Statistics
Matches: 785, Mismatches: 178, Indels: 162
0.70 0.16 0.14
Matches are distributed among these distances:
16 13 0.02
17 11 0.01
18 2 0.00
19 14 0.02
20 44 0.06
21 92 0.12
22 511 0.65
23 58 0.07
24 10 0.01
25 13 0.02
26 5 0.01
27 2 0.00
28 7 0.01
29 3 0.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.39
Consensus pattern (21 bp):
ACCTCCTATGAAATTTTGATA
Found at i:3148 original size:44 final size:43
Alignment explanation
Indices: 3099--4394 Score: 374
Period size: 44 Copynumber: 29.9 Consensus size: 43
3089 ATGACCTCCT
3099 TATGAAATTTTGATAACCTTCCTATGAAATTTTGATAACATTCC
1 TATGAAATTTTGATAACCTTCCTATGAAATTTTGATAAC-TTCC
* ** * * * * **
3143 TATGAAATTTTAATAACGATACTATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCCTATGAAATTTTGATAA-CTTCC
* ** * * *
3187 TAT-TAATTTTTTTAACCTTCTTATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCCTATGAAATTTTGATAA-CTTCC
* * *
3230 TAAGTAATTTTGA-AGACC-TCACTGTGAAATTTTGATAACTTCC
1 TATGAAATTTTGATA-ACCTTC-CTATGAAATTTTGATAACTTCC
* ** ** * * *
3273 CAAAAAATTTTTGATAACCAACACTATGAGATGTTGATAACCTCC
1 TATGAAA-TTTTGATAACCTTC-CTATGAAATTTTGATAACTTCC
* * * * * * * *
3318 ATATGATATATTGATAACC-ACGTTATGAAAATTTAAAAACCTCC
1 -TATGAAATTTTGATAACCTTC-CTATGAAATTTTGATAACTTCC
*
3362 ATATG-AATTGTT-AGTAA---TCAC-ACTGAAATTTTGATAA-TCACAC
1 -TATGAAATT-TTGA-TAACCTTC-CTA-TGAAATTTTGATAACT-TC-C
* * *
3405 TATGAAATTGTAATAACC-TCGTTATGAAATTTTGATAAACCTTCC
1 TATGAAATTTTGATAACCTTC-CTATGAAATTTTGAT-AA-CTTCC
* * *
3450 TATAAAATTTTGATAAACCTCCCTA--AAATTTTGATAACCTCC
1 TATGAAATTTTGAT-AACCTTCCTATGAAATTTTGATAACTTCC
* * *
3492 TTATGAAATCTTGATAA-----CTA-CAAATTTTGATAATCTCCC
1 -TATGAAATTTTGATAACCTTCCTATGAAATTTTGATAA-CTTCC
** * * * *
3531 TATGATTTTTTGAGAACC-TCATTATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTC-CTATGAAATTTTGATAA-CTTCC
* * * * *
3575 TATGAAATTTTGATTTA-CATACTATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGA-TAACCTTCCTATGAAATTTTGATAA-CTTCC
* ** *
3619 TATGAAATTTTGA-AAACTAAACTATGAAATTTTGATAACCTCC
1 TATGAAATTTTGATAACCT-TCCTATGAAATTTTGATAACTTCC
* * * *
3662 ATATGAAATTTTGATATCC-TCC-CTGAAGTTTTGATTAC-TCC
1 -TATGAAATTTTGATAACCTTCCTATGAAATTTTGATAACTTCC
** * * *
3703 ATAAT-AAAAGTT-ATAACCTTCC--T--AA-TTTGGTAACCATAC
1 -T-ATGAAATTTTGATAACCTTCCTATGAAATTTTGATAA-CTTCC
* * * *
3742 TATGAAATTTTGGTAATCACATT--T-TGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAA-C-C-TTCCTATGAAATTTTGATAACTTC-C
* * * * **
3786 TATGAAATTTTGATAACC-TCTTTATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACCTTC-CTATGAAATTTTGATAACTTC-C
* * * *
3830 TATGAAATTTTGATAA--TAACATTATGTAATTTTGATAACCTCGC
1 TATGAAATTTTGATAACCT-TC-CTATGAAATTTTGATAACTTC-C
* **
3874 TTTGAAATTTTGATAA-CAACACTATGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAACCTTC-CTATGAAATTTTGATAA-CTTCC
* * *
3918 AAT-AAATTTTGATAATCCGATCTCTATGAAATTTCGATAA--TCAC
1 TATGAAATTTTGATAA-CC-TTC-CTATGAAATTTTGATAACTTC-C
* * *
3962 TTTATGAGA-TTTGATAACCTT-CTATCAAATTTTGGT-AC-TCC
1 --TATGAAATTTTGATAACCTTCCTATGAAATTTTGATAACTTCC
* * **
4003 TCATGAAATTGAGACTTTTATAACCTTCATATGAAATTTTGATAACCACAC
1 T-ATGAAA-T-----TTTGATAACCTTCCTATGAAATTTTGATAACTTC-C
* * * * *
4054 TATGAAATTTTGATAACCTCCCCATGATATATT-AGTAACCTCC
1 TATGAAATTTTGATAACCTTCCTATGAAATTTTGA-TAACTTCC
* * *
4097 TTATGAAATTTTGTTAACC-ACACTATGAAATTCTT-ATAACCTCGC
1 -TATGAAATTTTGATAACCTTC-CTATGAAATT-TTGATAACTTC-C
* * *
4142 TATGACATTTTGATAA---TCC-------CTTTGATAACTTTTC
1 TATGAAATTTTGATAACCTTCCTATGAAATTTTGATAAC-TTCC
* * * **
4176 TATAAAATTGTGATAACC-ACACTATGAAATTTCAATAACCTTCC
1 TATGAAATTTTGATAACCTTC-CTATGAAATTTTGATAA-CTTCC
* * * * **
4220 TAAGAAATTTTAATAACCTAATCTTATGAAATTTTGGTAACCACAC
1 TATGAAATTTTGATAACCT--TCCTATGAAATTTTGATAACTTC-C
*
4266 TATGAAATTTTGATAACCTTCCCATGAAATTTTGATAACTTCC
1 TATGAAATTTTGATAACCTTCCTATGAAATTTTGATAACTTCC
* ** * *
4309 ATATGAAATTTTGGTAACCACACACTATGGAATTTTGATAACCTCC
1 -TATGAAATTTTGATAACC-TTC-CTATGAAATTTTGATAACTTCC
* * * * *
4355 TCATGAAATTATAATAACCATCTTATGAAATCTTGATAAC
1 T-ATGAAATTTTGATAACCTTCCTATGAAATTTTGATAAC
4395 CACACAAAGA
Statistics
Matches: 934, Mismatches: 212, Indels: 212
0.69 0.16 0.16
Matches are distributed among these distances:
33 2 0.00
34 20 0.02
35 1 0.00
36 1 0.00
37 12 0.01
38 32 0.03
39 9 0.01
40 13 0.01
41 19 0.02
42 61 0.07
43 94 0.10
44 461 0.49
45 67 0.07
46 102 0.11
47 16 0.02
48 12 0.01
49 3 0.00
50 7 0.01
51 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (43 bp):
TATGAAATTTTGATAACCTTCCTATGAAATTTTGATAACTTCC
Found at i:3489 original size:66 final size:63
Alignment explanation
Indices: 3385--4395 Score: 256
Period size: 66 Copynumber: 15.6 Consensus size: 63
3375 GTAATCACAC
* * * * *
3385 TGAAATTTTGATAATCACACTATGAAATTGTAATAACCTCGTTATGAAATTTTGATAAACCTTCC
1 TGAAATTTTGATAACCTCCCTA-GAAATTTTGATAACCTC-TTATGAAATTTTGATAAA-C-TCC
3450 TA
62 TA
* *
3452 TAAAATTTTGATAAACCTCCCTA-AAATTTTGATAACCTCCTTATGAAATCTTGAT-AA---CTA
1 TGAAATTTTGAT-AACCTCCCTAGAAATTTTGATAACCT-CTTATGAAATTTTGATAAACTCCTA
* * ** * * *
3512 -CAAATTTTGATAATCTCCCTATGATTTTTTGAGAACCTCATTATGAAATTTTGTTAATCTCCCT
1 TGAAATTTTGATAACCTCCCTA-GAAATTTTGATAACCTC-TTATGAAATTTTGATAAACT-CCT
3576 A
63 A
* * * *
3577 TGAAATTTTGATTTACAT-ACTATGAAATTTTGATAACCCTCTTATGAAATTTTGA-AAACTAAA
1 TGAAATTTTGA-TAACCTCCCTA-GAAATTTTGATAA-CCTCTTATGAAATTTTGATAAACT--C
3640 CTA
61 CTA
* * ** * *
3643 TGAAATTTTGATAACCTCCATATGAAATTTTGATATCCTC-CCTGAAGTTTTGAT-TACTCCATA
1 TGAAATTTTGATAACCTCCCTA-GAAATTTTGATAACCTCTTATGAAATTTTGATAAACTCC-T-
3706 A
63 A
** * * * * * *
3707 T-AAAAGTT-ATAACCTTCCT---AA-TTTGGTAACCATAC-TATGAAATTTTGGTAATCACATT
1 TGAAATTTTGATAACCTCCCTAGAAATTTTGATAACC-T-CTTATGAAATTTTGATAAACTC-CT
*
3765 T
63 A
* ** * * * * *
3766 TGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCTCT
1 TGAAATTTTGATAACCTCCCTA-GAAATTTTGATAACCTC-TTATGAAATTTTGATAAACTC-CT
3831 A
63 A
*** ** * *
3832 TGAAATTTTGATAATAACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAAC-A
1 TGAAATTTTGATAACCTCCCTA-GAAATTTTGATAACCT--CTTATGAAATTTTGAT-A-AACTC
3895 CTA
61 CTA
* * * * *
3898 TGAAATTTTGATAATCTTCCAATAAATTTTGATAATCCGATCTCTATGAAATTTCGATAATCACT
1 TGAAATTTTGATAACCTCCCTAGAAATTTTGATAA-CC--TCT-TATGAAATTTTGATAA--ACT
*
3963 -TTA
60 CCTA
* * * * * * * *
3966 TGAGA-TTTGATAACCT-TCTATCAAATTTTGGTACTCCTCATGAAATTGAGACTTTT-ATAACC
1 TGAAATTTTGATAACCTCCCTA-GAAATTTTGATA-ACCTC-T--TA-TGA-AATTTTGATAAAC
*
4028 TTCATA
59 -TCCTA
* * ** * * *
4034 TGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGATATATT-AGTAACCTCCT
1 TGAAATTTTGATAACCTCCCTA-GAAATTTTGATAACCT-CTTATGAAATTTTGA-TAAACTCC-
4098 TA
62 TA
* * * * * *
4100 TGAAATTTTGTTAACCACACTATGAAATTCTT-ATAACCTCGCTATGACATTTTGATAATC-CCT
1 TGAAATTTTGATAACCTCCCTA-GAAATT-TTGATAACCTC-TTATGAAATTTTGATAAACTCCT
*
4163 T
63 A
* * * * * ** *
4164 TGATAACTTT--T---CT--ATA-AAATTGTGATAACCACACTATGAAATTTCAATAACCTTCCT
1 TGA-AATTTTGATAACCTCCCTAGAAATTTTGATAACCTC-TTATGAAATTTTGATAAAC-TCCT
4221 A
63 A
* * * * * * * *
4222 AGAAATTTTAATAACCTAATCTTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTC
1 TGAAATTTTGATAACCT--CCCTA-GAAATTTTGATAACCTC-TTATGAAATTTTGATAAAC-TC
*
4287 CCA
61 CTA
* * * * * * *
4290 TGAAATTTTGATAACTTCCATATGAAATTTTGGTAACCACACACTATGGAATTTTGATAACCTCC
1 TGAAATTTTGATAACCTCCCTA-GAAATTTTGATAA-C-CTC-TTATGAAATTTTGATAAACTCC
4355 TCA
62 T-A
* * * *
4358 TGAAATTATAATAACCAT-CTTATGAAATCTTGATAACC
1 TGAAATTTTGATAACC-TCCCTA-GAAATTTTGATAACC
4396 ACACAAAGAC
Statistics
Matches: 717, Mismatches: 149, Indels: 157
0.70 0.15 0.15
Matches are distributed among these distances:
55 1 0.00
56 27 0.04
57 13 0.02
58 19 0.03
59 24 0.03
60 38 0.05
61 9 0.01
62 12 0.02
63 7 0.01
64 20 0.03
65 47 0.07
66 266 0.37
67 56 0.08
68 145 0.20
69 18 0.03
70 15 0.02
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.38
Consensus pattern (63 bp):
TGAAATTTTGATAACCTCCCTAGAAATTTTGATAACCTCTTATGAAATTTTGATAAACTCCTA
Found at i:3549 original size:126 final size:125
Alignment explanation
Indices: 3387--3637 Score: 290
Period size: 126 Copynumber: 2.0 Consensus size: 125
3377 AATCACACTG
* * *
3387 AAATTTTGATAATCACACTATGAAATTGTAATAACCTCGTTATGAAATTTTGATAAACCTTCCTA
1 AAATTTTGATAATCACACTATGAAATTGTAAGAACCTCATTATGAAATTTTG-TAAACCTCCCTA
* * *
3452 TAAAATTTTGATAAACCTCCCTA-AAATTTTGATAA-CCTCCTTATGAAATCTTGATAACTAC
65 TAAAATTTTGATAAACAT-ACTAGAAATTTTGATAACCCT-CTTATGAAATCTTGAAAACTAC
* * ** * * * *
3513 AAATTTTGATAATCTCCCTATGATTTTTTGAGAACCTCATTATGAAATTTTGTTAATCTCCCTAT
1 AAATTTTGATAATCACACTATGAAATTGTAAGAACCTCATTATGAAATTTTGTAAACCTCCCTAT
* ** *
3578 GAAATTTTGATTTACATACTATGAAATTTTGATAACCCTCTTATGAAATTTTGAAAACTA
66 AAAATTTTGATAAACATACTA-GAAATTTTGATAACCCTCTTATGAAATCTTGAAAACTA
3638 AACTATGAAA
Statistics
Matches: 104, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
124 3 0.03
125 23 0.22
126 75 0.72
127 3 0.03
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (125 bp):
AAATTTTGATAATCACACTATGAAATTGTAAGAACCTCATTATGAAATTTTGTAAACCTCCCTAT
AAAATTTTGATAAACATACTAGAAATTTTGATAACCCTCTTATGAAATCTTGAAAACTAC
Found at i:4299 original size:146 final size:144
Alignment explanation
Indices: 4036--4303 Score: 369
Period size: 146 Copynumber: 1.8 Consensus size: 144
4026 CCTTCATATG
* ** * * *
4036 AAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGATATATTAGTAACCTCCTTAT
1 AAATTGTGATAACCACACTATGAAATTTCAATAACCTCCCCAAGAAATATTAATAACCTCCTTAT
* * *
4101 GAAATTTTGTTAACCACACTATGAAATTCTTATAACCTCGCTATGACATTTTGATAATCCCTTTG
66 GAAATTTTGGTAACCACACTATGAAATTCTTATAACCTCGCCATGAAATTTTGATAATCCCTTTG
4166 ATAACTTTTCTATA
131 ATAACTTTTCTATA
* * * *
4180 AAATTGTGATAACCACACTATGAAATTTCAATAACCTTCCTAAGAAATTTTAATAACCTAATCTT
1 AAATTGTGATAACCACACTATGAAATTTCAATAACCTCCCCAAGAAATATTAATAACCT--CCTT
4245 ATGAAATTTTGGTAACCACACTATGAAATT-TTGATAACCTTC-CCATGAAATTTTGATAA
64 ATGAAATTTTGGTAACCACACTATGAAATTCTT-ATAACC-TCGCCATGAAATTTTGATAA
4304 CTTCCATATG
Statistics
Matches: 107, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
144 50 0.47
145 2 0.02
146 53 0.50
147 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.37
Consensus pattern (144 bp):
AAATTGTGATAACCACACTATGAAATTTCAATAACCTCCCCAAGAAATATTAATAACCTCCTTAT
GAAATTTTGGTAACCACACTATGAAATTCTTATAACCTCGCCATGAAATTTTGATAATCCCTTTG
ATAACTTTTCTATA
Found at i:4393 original size:22 final size:22
Alignment explanation
Indices: 4175--4396 Score: 173
Period size: 22 Copynumber: 9.9 Consensus size: 22
4165 GATAACTTTT
* *
4175 CTATAAAATTGTGATAACCA-C
1 CTATGAAATTTTGATAACCATC
** *
4196 ACTATGAAATTTCAATAACCTTC
1 -CTATGAAATTTTGATAACCATC
* *
4219 CTAAGAAATTTTAATAACCTAATC
1 CTATGAAATTTTGATAACC--ATC
* *
4243 TTATGAAATTTTGGTAACCA-C
1 CTATGAAATTTTGATAACCATC
*
4264 ACTATGAAATTTTGATAACCTTC
1 -CTATGAAATTTTGATAACCATC
* *
4287 CCATGAAATTTTGATAA-CTTC
1 CTATGAAATTTTGATAACCATC
* *
4308 CATATGAAATTTTGGTAACCACAC
1 C-TATGAAATTTTGATAACCA-TC
*
4332 ACTATGGAATTTTGATAACC-TC
1 -CTATGAAATTTTGATAACCATC
* *
4354 CTCATGAAATTATAATAACCATC
1 CT-ATGAAATTTTGATAACCATC
* *
4377 TTATGAAATCTTGATAACCA
1 CTATGAAATTTTGATAACCA
4397 CACAAAGACA
Statistics
Matches: 159, Mismatches: 30, Indels: 22
0.75 0.14 0.10
Matches are distributed among these distances:
21 8 0.05
22 110 0.69
23 6 0.04
24 34 0.21
25 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.34
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCATC
Found at i:4400 original size:68 final size:67
Alignment explanation
Indices: 4180--4399 Score: 259
Period size: 68 Copynumber: 3.3 Consensus size: 67
4170 CTTTTCTATA
* ** *
4180 AAATTGTGATAACCACACTATGAAATTTCAATAACCTTCCT-AAGAAATTTTAATAACCTAATCT
1 AAATTTTGATAACCACACTATGAAATTTTGATAACCTTCCTCATGAAATTTTAATAACC--ATCT
4244 TATG
64 TATG
* * * *
4248 AAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCC-CATGAAATTTTGATAA-CTTCCAT
1 AAATTTTGATAACCACACTATGAAATTTTGATAACCTTCCTCATGAAATTTTAATAACCAT-CTT
4311 ATG
65 ATG
* * *
4314 AAATTTTGGTAACCACACACTATGGAATTTTGATAACC-TCCTCATGAAATTATAATAACCATCT
1 AAATTTTGATAA-C-CACACTATGAAATTTTGATAACCTTCCTCATGAAATTTTAATAACCATCT
4378 TATG
64 TATG
*
4382 AAATCTTGATAACCACAC
1 AAATTTTGATAACCACAC
4400 AAAGACAAGG
Statistics
Matches: 131, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
65 1 0.01
66 22 0.17
67 6 0.05
68 100 0.76
69 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (67 bp):
AAATTTTGATAACCACACTATGAAATTTTGATAACCTTCCTCATGAAATTTTAATAACCATCTTA
TG
Found at i:5232 original size:21 final size:22
Alignment explanation
Indices: 5192--5232 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5182 CACAAACTCG
*
5192 TAACCCGAATAACCCGAGAAGA
1 TAACCCGAATAACCCAAGAAGA
*
5214 TAACCCG-ATGACCCAAGAA
1 TAACCCGAATAACCCAAGAA
5233 TATTATAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.44, C:0.29, G:0.17, T:0.10
Consensus pattern (22 bp):
TAACCCGAATAACCCAAGAAGA
Found at i:5986 original size:16 final size:15
Alignment explanation
Indices: 5967--6009 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
5957 GATTATTGTT
5967 TTTGTTGTTTCTTCCC
1 TTTGTT-TTTCTTCCC
* *
5983 TTTGTTTGTTCTTGCT
1 TTTGTTT-TTCTTCCC
5999 TTTGTTTTTCT
1 TTTGTTTTTCT
6010 ATTTCTCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.00, C:0.16, G:0.14, T:0.70
Consensus pattern (15 bp):
TTTGTTTTTCTTCCC
Found at i:7241 original size:161 final size:160
Alignment explanation
Indices: 7074--7384 Score: 385
Period size: 161 Copynumber: 1.9 Consensus size: 160
7064 TATTTCTTAA
* * * * *
7074 AAAAAATTGTAAAATTTAATCAATGT-CA-TTTAAGAAATATATTTTAAAAATACTAATATATCT
1 AAAAAATAG-AAAATTTAATCAA-GTAAACTATAA-AAATATATTTAAAAAATACTAATATATAT
* *
7137 AAGT-TTTTTAATTAAATTAGTAAATTGATAAAAATAAAATAGGTATAAGGATATTAGATTTAAT
63 AA-TATTTTTAATTAAAATAGTAAAATGATAAAAATAAAATAGGTATAAGGATATTAGATTTAAT
*
7201 TAAATAAAAATAGATTTTTTAGTGGCTTTTGGCC
127 TAAATAAAAATAGAGTTTTTAGTGGCTTTTGGCC
*** * ** *
7235 AAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAATATATTTAAAAAATTCTAATATATATAA
1 AAAAAATAGAAAATTTAATCAAGT-AAACTATAAAAATATATTTAAAAAATACTAATATATATAA
* * * *
7300 TATTTTTAATTAAAATAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATTATATTTAATTAA
65 TATTTTTAATTAAAATAGTAAAATGATAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAA
7365 ATAAAAATAGAGTTTTTAGT
130 ATAAAAATAGAGTTTTTAGT
7385 TGAGTAAAAC
Statistics
Matches: 127, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
159 2 0.02
160 8 0.06
161 113 0.89
162 4 0.03
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (160 bp):
AAAAAATAGAAAATTTAATCAAGTAAACTATAAAAATATATTTAAAAAATACTAATATATATAAT
ATTTTTAATTAAAATAGTAAAATGATAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAA
TAAAAATAGAGTTTTTAGTGGCTTTTGGCC
Found at i:17426 original size:2 final size:2
Alignment explanation
Indices: 17419--17464 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
17409 GGCATCTTTC
17419 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17461 TA TA
1 TA TA
17465 GTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.