Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020458.1 Corchorus olitorius cultivar O-4 contig20491, 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: 30705
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:1142 original size:238 final size:231
Alignment explanation
Indices: 700--1169 Score: 694
Period size: 238 Copynumber: 2.0 Consensus size: 231
690 ATTTCTACAA
* *
700 AATCAAGCATGAAATCGTTCCAATAGTTTTCAAAAAAAATTGAAATACTTGCAAGATAGATGAAT
1 AATCAAGCATGAAATCGTTCCAATAGTTTTCAAAAAAAATTGAAATACTTACAAGATAAATGAAT
* *
765 AAACGTAGAATCTCACAAATCAAATGTCCAAGAGATTGAAAGTCTTAAAATATGAATTAACTAGA
66 AAACGCAGAATCTCACAAATCAAATGCCCAAGAGATTGAAAGTCTTAAAATATGAATTAACTAGA
830 AAAGATTGTTTACAAACAAATCAAGAATAGAGAAAACCTCCATTCTTGAGAGAAAGCAACGAAAA
131 AAAGATTGTTTACAAACAAATC---AATAGAGAAAACCTCCATTCTTGAGAGAAAGCAACG---A
*
895 AACCTAAAACTAAAACTTAAGAACTATCTTAATTGGCGGCTAT
190 AA-CTAAAACTAAAACTTAAGAACTATCTTAACTGGCGGCTAT
* ***
938 AATCAAGCATGAAATCGTTCCAATAGTTTTTAGTGAAAATTGAAATACTTACAAGATAAATGAAT
1 AATCAAGCATGAAATCGTTCCAATAGTTTTCAAAAAAAATTGAAATACTTACAAGATAAATGAAT
* *
1003 AAGCGCAGAGTCTCACAAATCAAATGCCCAAGAGATTG-AAGTCTTAAAATATGAATTAACTAGA
66 AAACGCAGAATCTCACAAATCAAATGCCCAAGAGATTGAAAGTCTTAAAATATGAATTAACTAGA
* * *
1067 AAAGATTGTTTACAAA-AGAGTC-ATAGTGAAAACCTCCATTCTTGAGAGAAAGTAACGAAAAAC
131 AAAGATTGTTTACAAACA-AATCAATAGAGAAAACCTCCATTCTTGAGAGAAAGCAACG--AAA-
1130 CTAAAACTAAAACTTAAGAACTATCTTAACTGGCGGCTAT
192 CTAAAACTAAAACTTAAGAACTATCTTAACTGGCGGCTAT
1170 CCCCCTTAAA
Statistics
Matches: 217, Mismatches: 14, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
232 45 0.21
233 33 0.15
236 1 0.00
237 45 0.21
238 93 0.43
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.25
Consensus pattern (231 bp):
AATCAAGCATGAAATCGTTCCAATAGTTTTCAAAAAAAATTGAAATACTTACAAGATAAATGAAT
AAACGCAGAATCTCACAAATCAAATGCCCAAGAGATTGAAAGTCTTAAAATATGAATTAACTAGA
AAAGATTGTTTACAAACAAATCAATAGAGAAAACCTCCATTCTTGAGAGAAAGCAACGAAACTAA
AACTAAAACTTAAGAACTATCTTAACTGGCGGCTAT
Found at i:1236 original size:21 final size:21
Alignment explanation
Indices: 1195--1245 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
1185 GTTTTAACCT
*
1195 AATTAAAATAATTAATTATAA
1 AATTAAAATAATTAATAATAA
*
1216 AATTAAAA-AATTACCTAAT-A
1 AATTAAAATAATTA-ATAATAA
1236 AA-TAAAATAA
1 AATTAAAATAA
1246 CCAACAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 5 0.19
20 10 0.38
21 11 0.42
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (21 bp):
AATTAAAATAATTAATAATAA
Found at i:3295 original size:22 final size:21
Alignment explanation
Indices: 3264--3413 Score: 113
Period size: 22 Copynumber: 6.8 Consensus size: 21
3254 CTCTAACGTA
* *
3264 GAAATATTGATAACCACACCGC
1 GAAAT-TTGATAACCACACTGT
* *
3286 GAAAATTTGATAACCTCATTGT
1 G-AAATTTGATAACCACACTGT
* *
3308 GAAATTTCGATAACCTC-CTTAT
1 GAAATTT-GATAACCACAC-TGT
3330 GAAAATTTGATAACCACACTGT
1 G-AAATTTGATAACCACACTGT
**
3352 GAAATTCTGATAACCACACAAT
1 GAAATT-TGATAACCACACTGT
* * *
3374 GAAGTTTTGATAACCTCAGTGT
1 GAA-ATTTGATAACCACACTGT
*
3396 GAAATTTTGATAATCACA
1 GAAA-TTTGATAACCACA
3414 TTAAAAAATT
Statistics
Matches: 102, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
21 11 0.11
22 78 0.76
23 13 0.13
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (21 bp):
GAAATTTGATAACCACACTGT
Found at i:3334 original size:44 final size:44
Alignment explanation
Indices: 3264--3413 Score: 144
Period size: 44 Copynumber: 3.4 Consensus size: 44
3254 CTCTAACGTA
*** *
3264 GAAATATT-GATAACCACACCGCGAAAATTTGATAACCTCATTGT
1 GAAAT-TTCGATAACCACACAATGAAAATTTGATAACCTCACTGT
* * *
3308 GAAATTTCGATAACCTC-CTTATGAAAATTTGATAACCACACTGT
1 GAAATTTCGATAACCACAC-AATGAAAATTTGATAACCTCACTGT
** *
3352 GAAA-TTCTGATAACCACACAATGAAGTTTTGATAACCTCAGTGT
1 GAAATTTC-GATAACCACACAATGAAAATTTGATAACCTCACTGT
* *
3396 GAAATTTTGATAATCACA
1 GAAATTTCGATAACCACA
3414 TTAAAAAATT
Statistics
Matches: 87, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
43 6 0.07
44 78 0.90
45 3 0.03
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (44 bp):
GAAATTTCGATAACCACACAATGAAAATTTGATAACCTCACTGT
Found at i:3386 original size:66 final size:66
Alignment explanation
Indices: 3265--3413 Score: 156
Period size: 66 Copynumber: 2.2 Consensus size: 66
3255 TCTAACGTAG
* *** **
3265 AAATATTGATAACCACACCGCGAAAATTTGATAACCTCATTGTGAAATTTCGATAACCTCCTTAT
1 AAAT-TTGATAACCACACCGCGAAAATTTGATAACCACACAATGAAATTTCGATAACCTCAGTAT
3330 GA
65 GA
* * * * *
3332 AAATTTGATAACCACACTGTG-AAATTCTGATAACCACACAATGAAGTTTTGATAACCTCAGTGT
1 AAATTTGATAACCACACCGCGAAAATT-TGATAACCACACAATGAAATTTCGATAACCTCAGTAT
3396 GA
65 GA
* *
3398 AATTTTGATAATCACA
1 AAATTTGATAACCACA
3414 TTAAAAAATT
Statistics
Matches: 68, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
65 5 0.07
66 59 0.87
67 4 0.06
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (66 bp):
AAATTTGATAACCACACCGCGAAAATTTGATAACCACACAATGAAATTTCGATAACCTCAGTATG
A
Found at i:3487 original size:22 final size:22
Alignment explanation
Indices: 3264--3489 Score: 93
Period size: 22 Copynumber: 10.3 Consensus size: 22
3254 CTCTAACGTA
* **
3264 GAAATATTGATAACCACACCGC
1 GAAATTTTGATAACCACACCAT
* * ***
3286 GAAAATTTGATAACCTCATTGT
1 GAAATTTTGATAACCACACCAT
* * *
3308 GAAATTTCGATAACCTC-CTTAT
1 GAAATTTTGATAACCACAC-CAT
* **
3330 GAAAATTTGATAACCACACTGT
1 GAAATTTTGATAACCACACCAT
* *
3352 GAAATTCTGATAACCACACAAT
1 GAAATTTTGATAACCACACCAT
* * ***
3374 GAAGTTTTGATAACCTCAGTGT
1 GAAATTTTGATAACCACACCAT
* *
3396 GAAATTTTGATAATCACA--TT
1 GAAATTTTGATAACCACACCAT
* ** * * *
3416 AAAAAATTGGTAATCGCACTC-T
1 GAAATTTTGATAACCACAC-CAT
* *
3438 GAAAATTTTGATAATCTC-CTCAT
1 G-AAATTTTGATAACCACAC-CAT
*
3461 AAAATTTTGATAACCACACCAT
1 GAAATTTTGATAACCACACCAT
3483 GAAATTT
1 GAAATTT
3490 CGCTAACTTC
Statistics
Matches: 154, Mismatches: 42, Indels: 16
0.73 0.20 0.08
Matches are distributed among these distances:
20 14 0.09
22 125 0.81
23 15 0.10
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.31
Consensus pattern (22 bp):
GAAATTTTGATAACCACACCAT
Found at i:3561 original size:22 final size:22
Alignment explanation
Indices: 3530--3617 Score: 81
Period size: 22 Copynumber: 4.0 Consensus size: 22
3520 ATGTCCTCTA
*
3530 TATGTAATTTTGATAACCTCTCC
1 TATGAAATTTTGATAACCTC-CC
*
3553 -AT-AACATTTTCATAACCTCCC
1 TATGAA-ATTTTGATAACCTCCC
* *
3574 TATGAAATTTTGTTAACCTTCC
1 TATGAAATTTTGATAACCTCCC
* **
3596 TAGGATTTTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCCC
3618 ACCCTGTGAA
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
21 3 0.06
22 47 0.90
23 2 0.04
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCC
Found at i:3702 original size:22 final size:22
Alignment explanation
Indices: 3677--3830 Score: 84
Period size: 22 Copynumber: 7.0 Consensus size: 22
3667 TAAAATTTCA
3677 ATAACCTTCGTATGAAATTTTG
1 ATAACCTTCGTATGAAATTTTG
* *
3699 ATAACATAT-TTATGAAATTTTG
1 ATAACCT-TCGTATGAAATTTTG
* *
3721 GTTACC-TCTGTATGAAATTTTG
1 ATAACCTTC-GTATGAAATTTTG
* * *
3743 ATAA-CTACATTATGAAGTTTTG
1 ATAACCTTC-GTATGAAATTTTG
* * * *
3765 ATAACGTCCATATGAAGTTTTG
1 ATAACCTTCGTATGAAATTTTG
* *
3787 GTAA--TTACAGTATGAAATTTTA
1 ATAACCTT-C-GTATGAAATTTTG
* * *
3809 ATAACTTTCCTATGTAATTTTG
1 ATAACCTTCGTATGAAATTTTG
3831 GTTTTATTGT
Statistics
Matches: 99, Mismatches: 24, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
20 2 0.02
21 2 0.02
22 89 0.90
23 4 0.04
24 2 0.02
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
ATAACCTTCGTATGAAATTTTG
Found at i:3756 original size:44 final size:44
Alignment explanation
Indices: 3648--3830 Score: 154
Period size: 44 Copynumber: 4.2 Consensus size: 44
3638 TGTTCTAATT
* * * ** *
3648 AATTTTGATAATTACACTATAAAATTTCAATAACCTTCGTATGA
1 AATTTTGATAACTACATTATGAAATTTTGATAACCTCCGTATGA
* * * *
3692 AATTTTGATAACATA-TTTATGAAATTTTGGTTACCTCTGTATGA
1 AATTTTGATAAC-TACATTATGAAATTTTGATAACCTCCGTATGA
* * *
3736 AATTTTGATAACTACATTATGAAGTTTTGATAACGTCCATATGA
1 AATTTTGATAACTACATTATGAAATTTTGATAACCTCCGTATGA
* * * * * * *
3780 AGTTTTGGTAATTACAGTATGAAATTTTAATAACTTTCC-TATGT
1 AATTTTGATAACTACATTATGAAATTTTGATAAC-CTCCGTATGA
3824 AATTTTG
1 AATTTTG
3831 GTTTTATTGT
Statistics
Matches: 110, Mismatches: 26, Indels: 6
0.77 0.18 0.04
Matches are distributed among these distances:
43 2 0.02
44 103 0.94
45 5 0.05
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (44 bp):
AATTTTGATAACTACATTATGAAATTTTGATAACCTCCGTATGA
Found at i:3830 original size:66 final size:64
Alignment explanation
Indices: 3648--3830 Score: 152
Period size: 66 Copynumber: 2.8 Consensus size: 64
3638 TGTTCTAATT
* * * * * **
3648 AATTTTGATAATTACACTATAAAATTTCAATAACCTTCGTATGAAATTTTGATAACATATTTATG
1 AATTTTGGTAATTACAGTATGAAATTTTAATAA-CTTCCTATG-AATTTTGATAACATACATATG
3713 A
64 A
** * * * * * *
3714 AATTTTGGTTACCT-CTGTATGAAATTTTGATAACTACATTATGAAGTTTTGATAACGTCCATAT
1 AATTTTGG-TAATTACAGTATGAAATTTTAATAACTTC-CTATGAA-TTTTGATAACATACATAT
3778 GA
63 GA
*
3780 AGTTTTGGTAATTACAGTATGAAATTTTAATAACTTTCCTATGTAATTTTG
1 AATTTTGGTAATTACAGTATGAAATTTTAATAAC-TTCCTATG-AATTTTG
3831 GTTTTATTGT
Statistics
Matches: 90, Mismatches: 21, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
65 8 0.09
66 75 0.83
67 7 0.08
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (64 bp):
AATTTTGGTAATTACAGTATGAAATTTTAATAACTTCCTATGAATTTTGATAACATACATATGA
Found at i:5824 original size:65 final size:65
Alignment explanation
Indices: 5749--5981 Score: 274
Period size: 65 Copynumber: 3.6 Consensus size: 65
5739 TTTCTTAATT
** *
5749 ACTATGAAATTTTGGTAACCTCCATATGAAATTTTGGTAACCTGACTATGAAA-TTTGGTGACCT
1 ACTATGAAATTTTGGTAACCTCCATATGAAATTTTGGTAACCTCCCCATGAAATTTTGGT-ACCT
5813 C
65 C
* * * *
5814 ACTATGAAATTTCGGTAACTTGCC-TATGAAATTTTGGTAACCTTCCCATGAAATTTTGGTAACT
1 ACTATGAAATTTTGGTAACCT-CCATATGAAATTTTGGTAACCTCCCCATGAAATTTTGGTACCT
5878 CC
65 -C
* * *
5880 ACTATGAAACTTTTGGCAACCTCCCTATGAAATTTTGGTAACC-CCCGATGAAATTTTGGTAACC
1 ACTATGAAA-TTTTGGTAACCTCCATATGAAATTTTGGTAACCTCCCCATGAAATTTTGGT-ACC
5944 TC
64 TC
* * * *
5946 CCTATGAAGTTTTGGTAACCTCAATGTGAAATTTTG
1 ACTATGAAATTTTGGTAACCTCCATATGAAATTTTG
5982 ATAATCACAA
Statistics
Matches: 144, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
65 71 0.49
66 43 0.30
67 30 0.21
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (65 bp):
ACTATGAAATTTTGGTAACCTCCATATGAAATTTTGGTAACCTCCCCATGAAATTTTGGTACCTC
Found at i:6064 original size:22 final size:22
Alignment explanation
Indices: 5749--6066 Score: 285
Period size: 22 Copynumber: 14.5 Consensus size: 22
5739 TTTCTTAATT
5749 ACTATGAAATTTTGGTAACCTC
1 ACTATGAAATTTTGGTAACCTC
*
5771 -CATATGAAATTTTGGTAACCTG
1 AC-TATGAAATTTTGGTAACCTC
*
5793 ACTATGAAA-TTTGGTGACCTC
1 ACTATGAAATTTTGGTAACCTC
* *
5814 ACTATGAAATTTCGGTAACTTGC
1 ACTATGAAATTTTGGTAACCT-C
5837 -CTATGAAATTTTGGTAACCTTC
1 ACTATGAAATTTTGGTAACC-TC
*
5859 -CCATGAAATTTTGGTAA-CTCC
1 ACTATGAAATTTTGGTAACCT-C
*
5880 ACTATGAAACTTTTGGCAACCTC
1 ACTATGAAA-TTTTGGTAACCTC
*
5903 CCTATGAAATTTTGGTAACC-C
1 ACTATGAAATTTTGGTAACCTC
* *
5924 CCGATGAAATTTTGGTAACCTC
1 ACTATGAAATTTTGGTAACCTC
* *
5946 CCTATGAAGTTTTGGTAACCTC
1 ACTATGAAATTTTGGTAACCTC
* * *
5968 AATGTGAAATTTTGATAA--TC
1 ACTATGAAATTTTGGTAACCTC
* * ** * *
5988 ACAATAAAAAATTGGTAATCGC
1 ACTATGAAATTTTGGTAACCTC
* *
6010 ACTATGAAAAGTTTGATAACCTC
1 ACTATG-AAATTTTGGTAACCTC
* * *
6033 -CTCATAAAATTTTGATAACCAC
1 ACT-ATGAAATTTTGGTAACCTC
6055 ACTATGAAATTT
1 ACTATGAAATTT
6067 CGCTAACTTC
Statistics
Matches: 241, Mismatches: 40, Indels: 30
0.77 0.13 0.10
Matches are distributed among these distances:
20 14 0.06
21 42 0.17
22 148 0.61
23 35 0.15
24 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (22 bp):
ACTATGAAATTTTGGTAACCTC
Found at i:6253 original size:22 final size:22
Alignment explanation
Indices: 5750--6297 Score: 186
Period size: 22 Copynumber: 24.8 Consensus size: 22
5740 TTCTTAATTA
*
5750 CTATGAAATTTTGGTAACC-TC
1 CTATGAAATTTTGATAACCTTC
* **
5771 CATATGAAATTTTGGTAACCTGA
1 C-TATGAAATTTTGATAACCTTC
* *
5794 CTATGAAA-TTTGGTGACC-TC
1 CTATGAAATTTTGATAACCTTC
* *
5814 ACTATGAAATTTCGGTAA-CTTGC
1 -CTATGAAATTTTGATAACCTT-C
*
5837 CTATGAAATTTTGGTAACCTTC
1 CTATGAAATTTTGATAACCTTC
* * *
5859 CCATGAAATTTTGGTAA-CTCC
1 CTATGAAATTTTGATAACCTTC
** *
5880 ACTATGAAACTTTTGGCAACCTCC
1 -CTATGAAA-TTTTGATAACCTTC
* *
5904 CTATGAAATTTTGGTAACC-CC
1 CTATGAAATTTTGATAACCTTC
* * *
5925 CGATGAAATTTTGGTAACCTCC
1 CTATGAAATTTTGATAACCTTC
* *
5947 CTATGAAGTTTTGGTAACC-TC
1 CTATGAAATTTTGATAACCTTC
* *
5968 AATGTGAAATTTTGATAA---TC
1 -CTATGAAATTTTGATAACCTTC
* * ** * * *
5988 ACAATAAAAAATTGGTAATC-GC
1 -CTATGAAATTTTGATAACCTTC
*
6010 ACTATGAAAAGTTTGATAACC-TC
1 -CTATG-AAATTTTGATAACCTTC
* *
6033 CTCATAAAATTTTGATAACC-AC
1 CT-ATGAAATTTTGATAACCTTC
* *
6055 ACTATGAAATTTCGCTAA-CTTCC
1 -CTATGAAATTTTGATAACCTT-C
* * *
6078 CTATGGGAATGAAACTGTGATATCC-TC
1 C--T----ATGAAATTTTGATAACCTTC
* *
6105 TATATGTAATTTTGATAACCTCTC
1 -CTATGAAATTTTGATAACCT-TC
* * *
6129 CGTA--ACATTTTCATAACCTCC
1 C-TATGAAATTTTGATAACCTTC
*
6150 CTATGAAATTTTGTTAACCTTC
1 CTATGAAATTTTGATAACCTTC
* * *
6172 CTAGGAAATTTTGTTAACGTT-
1 CTATGAAATTTTGATAACCTTC
* *
6193 CTAAT-TAATTTTGATAA--TGAC
1 CT-ATGAAATTTTGATAACCT-TC
* **
6214 ACTATAAAATTTCAATAACCTTC
1 -CTATGAAATTTTGATAACCTTC
* * *
6237 GTATGAAATTTTGATAACATTT
1 CTATGAAATTTTGATAACCTTC
* *
6259 TTATGAAATTTTGGTAACC-TC
1 CTATGAAATTTTGATAACCTTC
*
6280 TATATGAAATTTTGATAA
1 -CTATGAAATTTTGATAA
6298 TTACATTATG
Statistics
Matches: 403, Mismatches: 84, Indels: 79
0.71 0.15 0.14
Matches are distributed among these distances:
19 1 0.00
20 15 0.04
21 61 0.15
22 264 0.66
23 38 0.09
24 10 0.02
26 1 0.00
27 1 0.00
28 11 0.03
29 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCTTC
Found at i:6307 original size:22 final size:21
Alignment explanation
Indices: 6281--6363 Score: 58
Period size: 22 Copynumber: 3.8 Consensus size: 21
6271 GGTAACCTCT
*
6281 ATATGAAATTTTGATAATTAC
1 ATATGAAATTTTAATAATTAC
* * *
6302 ATTATGAAGTTTTAATAACCTCC
1 A-TATGAAATTTTAATAA-TTAC
* **
6325 ATATGAAGTTTTGGTAATTAC
1 ATATGAAATTTTAATAATTAC
* *
6346 GGTATGAAAATTTAATAA
1 -ATATGAAATTTTAATAA
6364 CCATCCTATG
Statistics
Matches: 46, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
21 3 0.07
22 40 0.87
23 3 0.07
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (21 bp):
ATATGAAATTTTAATAATTAC
Found at i:6307 original size:44 final size:44
Alignment explanation
Indices: 6199--6381 Score: 165
Period size: 44 Copynumber: 4.2 Consensus size: 44
6189 CGTTCTAATT
* * * * * *
6199 AATTTTGATAATGACACTATAAAATTTCAATAACCTTCGTATGA
1 AATTTTGATAATTACATTATGAAATTTTAATAACCTCCATATGA
* ** *
6243 AATTTTGATAACATT--TTTATGAAATTTTGGTAACCTCTATATGA
1 AATTTTGAT-A-ATTACATTATGAAATTTTAATAACCTCCATATGA
*
6287 AATTTTGATAATTACATTATGAAGTTTTAATAACCTCCATATGA
1 AATTTTGATAATTACATTATGAAATTTTAATAACCTCCATATGA
* * ** * *
6331 AGTTTTGGTAATTACGGTATGAAAATTTAATAACCATCC-TATGT
1 AATTTTGATAATTACATTATGAAATTTTAATAACC-TCCATATGA
6375 AATTTTG
1 AATTTTG
6382 GTTTGATTGT
Statistics
Matches: 111, Mismatches: 23, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
42 3 0.03
43 1 0.01
44 101 0.91
45 4 0.04
46 2 0.02
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (44 bp):
AATTTTGATAATTACATTATGAAATTTTAATAACCTCCATATGA
Found at i:9478 original size:322 final size:322
Alignment explanation
Indices: 8886--9529 Score: 1209
Period size: 322 Copynumber: 2.0 Consensus size: 322
8876 AGTCCAACCA
* *
8886 AAACTGGTATACTATTCCCACTATTAAGTTTTAACTTTAGTGATCAAAAATAAAAGTTTTAACTT
1 AAACTGATATACTATTCCCACTATTAAGTTTTAACTTCAGTGATCAAAAATAAAAGTTTTAACTT
8951 CAAATCTCATCCAGTTTTTTATTTGATGGAATATTTTTTTTGTTTAATTCAAATTTTTACGTAAA
66 CAAATCTCATCCAGTTTTTTATTTGATGGAATATTTTTTTTGTTTAATTCAAATTTTTACGTAAA
* *
9016 ACAAATTAGTTATAAATAAAAAAATATAAATAATAAATAATTATGAGAAGTAAATTAATAATTAA
131 ACAAATTAGTAATAAATAAAAAAATATAAATAACAAATAATTATGAGAAGTAAATTAATAATTAA
9081 ATTTGTAGTGAATTTACAATATTTTTTCATAGTTAATAATAAAAGTTAAATGACTAAAAAGAACA
196 ATTTGTAGTGAATTTACAATATTTTTTCATAGTTAATAATAAAAGTTAAATGACTAAAAAGAACA
9146 CCAATTAAAAAATTATTATACTATAATAAAAAGGGTATTTAGGAAATTTCCCAATTAAAATT
261 CCAATTAAAAAATTATTATACTATAATAAAAAGGGTATTTAGGAAATTTCCCAATTAAAATT
*
9208 AAACTGATATACTATTCCCACTTTTAAGTTTTAACTTCAGTGATCAAAAATAAAAGTTTTAACTT
1 AAACTGATATACTATTCCCACTATTAAGTTTTAACTTCAGTGATCAAAAATAAAAGTTTTAACTT
9273 CAAATCTCATCCAGTTTTTTATTTGATGGAATA-TTTTTTTGTTTAATTCAAATTTTTACGTAAA
66 CAAATCTCATCCAGTTTTTTATTTGATGGAATATTTTTTTTGTTTAATTCAAATTTTTACGTAAA
9337 ACAAATTAGTAAATAAATAAAAAAATATAAATAACAAATAATTATGAGAAGTAAATTAATAATTA
131 ACAAATTAGT-AATAAATAAAAAAATATAAATAACAAATAATTATGAGAAGTAAATTAATAATTA
9402 AATTTGTAGTGAATTTACAATATTTTTTCATAGTTAATAATAAAAGTTAAATGACTAAAAAGAAC
195 AATTTGTAGTGAATTTACAATATTTTTTCATAGTTAATAATAAAAGTTAAATGACTAAAAAGAAC
* *
9467 ACCAATTAAAAAATTATTATACTATAATAAAAAGGGTATTTATGAAATTTCCTAATTAAAATT
260 ACCAATTAAAAAATTATTATACTATAATAAAAAGGGTATTTAGGAAATTTCCCAATTAAAATT
9530 TTGGAGTTCG
Statistics
Matches: 314, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
321 41 0.13
322 273 0.87
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (322 bp):
AAACTGATATACTATTCCCACTATTAAGTTTTAACTTCAGTGATCAAAAATAAAAGTTTTAACTT
CAAATCTCATCCAGTTTTTTATTTGATGGAATATTTTTTTTGTTTAATTCAAATTTTTACGTAAA
ACAAATTAGTAATAAATAAAAAAATATAAATAACAAATAATTATGAGAAGTAAATTAATAATTAA
ATTTGTAGTGAATTTACAATATTTTTTCATAGTTAATAATAAAAGTTAAATGACTAAAAAGAACA
CCAATTAAAAAATTATTATACTATAATAAAAAGGGTATTTAGGAAATTTCCCAATTAAAATT
Found at i:12160 original size:42 final size:43
Alignment explanation
Indices: 12109--12202 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
12099 AGTGCATTAC
* *
12109 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTAATCAAAATAAAG
12150 CTAATATTCTACTCCTCCATCTCTAGATAATTAATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTAATCAAAATAAAG
*
12195 TTAATATT
1 CTAATATT
12203 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 36 0.78
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTAATCAAAATAAAG
Found at i:13346 original size:41 final size:43
Alignment explanation
Indices: 13301--13396 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 43
13291 AAAGTACATT
13301 ACCTAA-ATTCTA-CTCCATCTATAAATAATTCATCAAAACAA
1 ACCTAATATTCTATCTCCATCTATAAATAATTCATCAAAACAA
* * * *
13342 ACCTAATATTCTATTCCTCCATTTCTAGATAATTCATCAAAATAA
1 ACCTAATATTCTA-T-CTCCATCTATAAATAATTCATCAAAACAA
*
13387 AGCTAATATT
1 ACCTAATATT
13397 AATTGTTGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
41 6 0.13
42 6 0.13
45 34 0.74
ACGTcount: A:0.42, C:0.22, G:0.02, T:0.34
Consensus pattern (43 bp):
ACCTAATATTCTATCTCCATCTATAAATAATTCATCAAAACAA
Found at i:15461 original size:42 final size:42
Alignment explanation
Indices: 15402--15487 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 42
15392 ACTTTGGGAC
*
15402 GAGGAAGAAATACTTGGAG-AAAGAGACTGATTAGAAGAAGAT
1 GAGGAAGAAATACTTGGAGAAAAG-GACTGATTAGAAGAAAAT
* *
15444 GAGGAAGAAATATTTGGAGAAAAGGACTGATTGGAAGAAAAT
1 GAGGAAGAAATACTTGGAGAAAAGGACTGATTAGAAGAAAAT
15486 GA
1 GA
15488 ACTCGAGGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 36 0.90
43 4 0.10
ACGTcount: A:0.48, C:0.03, G:0.31, T:0.17
Consensus pattern (42 bp):
GAGGAAGAAATACTTGGAGAAAAGGACTGATTAGAAGAAAAT
Found at i:20991 original size:21 final size:21
Alignment explanation
Indices: 20967--21033 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
20957 GGCTTGGAAT
20967 GGTGATGGCACGGGCATGGCC
1 GGTGATGGCACGGGCATGGCC
* * **
20988 GGTGATGGCTCGGGCTTAACC
1 GGTGATGGCACGGGCATGGCC
* *
21009 GGTGGTGGCACGGTGAATGGCC
1 GGTGATGGCACGG-GCATGGCC
21031 GGT
1 GGT
21034 TGTGGCGCGG
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
21 28 0.80
22 7 0.20
ACGTcount: A:0.13, C:0.21, G:0.46, T:0.19
Consensus pattern (21 bp):
GGTGATGGCACGGGCATGGCC
Found at i:21269 original size:21 final size:21
Alignment explanation
Indices: 21245--21299 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
21235 GAGGAAGGCA
*
21245 CGGATGACCGGGCAGGCGGCG
1 CGGATGACCGGGCAGGCGACG
* * *
21266 CGGATGGCCGGGCAGGTGACT
1 CGGATGACCGGGCAGGCGACG
*
21287 CGGGTGACCGGGC
1 CGGATGACCGGGC
21300 TTTGGCCGGG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.13, C:0.27, G:0.51, T:0.09
Consensus pattern (21 bp):
CGGATGACCGGGCAGGCGACG
Found at i:24278 original size:35 final size:34
Alignment explanation
Indices: 24205--24284 Score: 105
Period size: 33 Copynumber: 2.4 Consensus size: 34
24195 CCACACAAAA
24205 ATTAAAAACGCA-AAAATCAAAATTTTTTTATAG
1 ATTAAAAACGCAGAAAATCAAAATTTTTTTATAG
*
24238 A--AAAAACGCAGAAAA-CAAAAATTTTTTTTTTAG
1 ATTAAAAACGCAGAAAATC-AAAA-TTTTTTTATAG
24271 ATTAAAAACGCAGA
1 ATTAAAAACGCAGA
24285 GACTAAGAGA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
31 10 0.24
32 8 0.20
33 12 0.29
35 11 0.27
ACGTcount: A:0.53, C:0.10, G:0.09, T:0.29
Consensus pattern (34 bp):
ATTAAAAACGCAGAAAATCAAAATTTTTTTATAG
Found at i:25622 original size:22 final size:22
Alignment explanation
Indices: 25579--25622 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
25569 TAATTTTTCT
*
25579 TTCTTCTTCCCTGTTCATCTTC
1 TTCTTCTTCCCTGTTCAGCTTC
*
25601 TTCTTCTTTCCT-TTCACGCTTC
1 TTCTTCTTCCCTGTTCA-GCTTC
25623 GCTTGCTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.05, C:0.36, G:0.05, T:0.55
Consensus pattern (22 bp):
TTCTTCTTCCCTGTTCAGCTTC
Found at i:28049 original size:10 final size:9
Alignment explanation
Indices: 28025--28082 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
28015 ATTTCTTACC
*
28025 CTTATCTTT
1 CTTATTTTT
28034 -TTATTTTT
1 CTTATTTTT
28042 CGTTATTTTT
1 C-TTATTTTT
28052 CTT-TTTCTT
1 CTTATTT-TT
28061 -TTATTTTT
1 CTTATTTTT
*
28069 GTTTATTTTT
1 -CTTATTTTT
28079 CTTA
1 CTTA
28083 GTTACTTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
8 14 0.34
9 10 0.24
10 17 0.41
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.76
Consensus pattern (9 bp):
CTTATTTTT
Found at i:28056 original size:16 final size:17
Alignment explanation
Indices: 28031--28068 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
28021 TACCCTTATC
28031 TTTTTATTTTTC-GTTA
1 TTTTTATTTTTCTGTTA
* *
28047 TTTTTCTTTTTCTTTTA
1 TTTTTATTTTTCTGTTA
28064 TTTTT
1 TTTTT
28069 GTTTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTTATTTTTCTGTTA
Found at i:29247 original size:21 final size:22
Alignment explanation
Indices: 29208--29248 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
29198 TCAATGCTTT
**
29208 AGGAATGCAAGAGGGATTTCAA
1 AGGAATGCAAGAGCCATTTCAA
29230 AGGAA-GCAAGAGCCATTTC
1 AGGAATGCAAGAGCCATTTC
29249 CAAGAAGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.39, C:0.15, G:0.29, T:0.17
Consensus pattern (22 bp):
AGGAATGCAAGAGCCATTTCAA
Done.