Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019373.1 Corchorus olitorius cultivar O-4 contig19406, 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: 50242
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Found at i:642 original size:62 final size:62
Alignment explanation
Indices: 545--668 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
535 TGAGGAAACT
545 CGGTTTGAACATTTTTTGTCCTTTTATGACTTTTCTCATTTGGTTAATTACTAAAAAGGCCC
1 CGGTTTGAACATTTTTTGTCCTTTTATGACTTTTCTCATTTGGTTAATTACTAAAAAGGCCC
*
607 CGGTTTGAACATTTTTTGTCCTTTTATGTCTTTTCTCATTTGGTTAATTACTAAAAAGGCCC
1 CGGTTTGAACATTTTTTGTCCTTTTATGACTTTTCTCATTTGGTTAATTACTAAAAAGGCCC
669 TCATTTAGTT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.22, C:0.18, G:0.15, T:0.46
Consensus pattern (62 bp):
CGGTTTGAACATTTTTTGTCCTTTTATGACTTTTCTCATTTGGTTAATTACTAAAAAGGCCC
Found at i:1167 original size:2 final size:2
Alignment explanation
Indices: 1160--1193 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1150 ATTAATAAGT
1160 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
1194 AAATTGAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1967 original size:30 final size:30
Alignment explanation
Indices: 1928--1988 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1918 TAAGATCATC
1928 AATGAAAATCAGAGCCCTCTTTGATCTTAA
1 AATGAAAATCAGAGCCCTCTTTGATCTTAA
* *
1958 AATGGAAATCAGAGCTCTCTTTGATCTTAA
1 AATGAAAATCAGAGCCCTCTTTGATCTTAA
1988 A
1 A
1989 GGGGTTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (30 bp):
AATGAAAATCAGAGCCCTCTTTGATCTTAA
Found at i:3001 original size:29 final size:30
Alignment explanation
Indices: 2969--3036 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
2959 TTGTATATAA
*
2969 GATCATCAA-TGAAAATCAGAGCCCTCTTT
1 GATCATAAACTGAAAATCAGAGCCCTCTTT
* * *
2998 GATCTTAAACTGGAAATCAGAGTCCTCTTT
1 GATCATAAACTGAAAATCAGAGCCCTCTTT
*
3028 GATCTTAAA
1 GATCATAAA
3037 GGGGTTTGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 7 0.21
30 27 0.79
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.31
Consensus pattern (30 bp):
GATCATAAACTGAAAATCAGAGCCCTCTTT
Found at i:3463 original size:30 final size:31
Alignment explanation
Indices: 3429--3487 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
3419 AGACATATTT
** *
3429 TTTTTAGTATTGTGTATACTTAT-ATCATCC
1 TTTTTAGTATTAAGTATACATATAATCATCC
*
3459 TTTTTATTATTAAGTATACATATAATCAT
1 TTTTTAGTATTAAGTATACATATAATCAT
3488 ATATAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.53
Consensus pattern (31 bp):
TTTTTAGTATTAAGTATACATATAATCATCC
Found at i:4261 original size:54 final size:54
Alignment explanation
Indices: 4203--4312 Score: 202
Period size: 54 Copynumber: 2.0 Consensus size: 54
4193 AACTACATAA
*
4203 GTATTATTCTATTCTACACATTCTTTATCTTAATAATTTCAAGCTCAAAAGAGG
1 GTATTATTCTATTCTACACATTCTTTATCTTAATAATTTCAAGCACAAAAGAGG
*
4257 GTATTATTTTATTCTACACATTCTTTATCTTAATAATTTCAAGCACAAAAGAGG
1 GTATTATTCTATTCTACACATTCTTTATCTTAATAATTTCAAGCACAAAAGAGG
4311 GT
1 GT
4313 TCTGATTCCT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (54 bp):
GTATTATTCTATTCTACACATTCTTTATCTTAATAATTTCAAGCACAAAAGAGG
Found at i:7802 original size:21 final size:21
Alignment explanation
Indices: 7778--7817 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
7768 GGAGGAGGAC
7778 AGTAAAATGCAGGAAGACTTG
1 AGTAAAATGCAGGAAGACTTG
*
7799 AGTAGAATGCAGGAAGACT
1 AGTAAAATGCAGGAAGACT
7818 ATTGGAAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.10, G:0.30, T:0.17
Consensus pattern (21 bp):
AGTAAAATGCAGGAAGACTTG
Found at i:7972 original size:22 final size:21
Alignment explanation
Indices: 7947--7988 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
7937 GATATTTAGC
7947 AACGCCCTAAATTTGTTGCATA
1 AACG-CCTAAATTTGTTGCATA
* *
7969 AACGCTTTAATTTGTTGCAT
1 AACGCCTAAATTTGTTGCAT
7989 TAGGGAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (21 bp):
AACGCCTAAATTTGTTGCATA
Found at i:8486 original size:22 final size:22
Alignment explanation
Indices: 8459--8550 Score: 62
Period size: 22 Copynumber: 4.2 Consensus size: 22
8449 ATAATTTTAA
8459 GCAACACTATTTTCTACTATAT
1 GCAACACTATTTTCTACTATAT
* * *
8481 GCAACAATAGTTT-TACTA-AG
1 GCAACACTATTTTCTACTATAT
* ** ** * *
8501 GCAACCCCCTTTAATAATTGTAT
1 GCAACACTATTTTCT-ACTATAT
*
8524 GCAACACTATTTTCCACTATAT
1 GCAACACTATTTTCTACTATAT
8546 GCAAC
1 GCAAC
8551 GATTTTCTTA
Statistics
Matches: 47, Mismatches: 20, Indels: 6
0.64 0.27 0.08
Matches are distributed among these distances:
20 8 0.17
21 6 0.13
22 23 0.49
23 10 0.21
ACGTcount: A:0.34, C:0.24, G:0.09, T:0.34
Consensus pattern (22 bp):
GCAACACTATTTTCTACTATAT
Found at i:8562 original size:65 final size:64
Alignment explanation
Indices: 8416--8615 Score: 175
Period size: 65 Copynumber: 3.0 Consensus size: 64
8406 ATAAAATGGA
* * * * * *
8416 CAACGATTTTTTTACTTTAGGCAACATCTTTTGATAATTTTAAGCAACACTATTTTCTACTATAT
1 CAACGA-TTTTTTAC-TAAGGCAACACCCTTTAATAATTGTAAGCAACACTATTTTCCACTATAT
8481 G
64 G
* * * *
8482 CAACAATAGTTTTACTAAGGCAACCCCCTTTAATAATTGTATGCAACACTATTTTCCACTATATG
1 CAACGAT-TTTTTACTAAGGCAACACCCTTTAATAATTGTAAGCAACACTATTTTCCACTATATG
** *** * * * * *
8547 CAACGATTTTCTTACTTCTGGCAACAATTTTTGATAATTGCAAGCAACACTATTATCTACAATAT
1 CAACGATTTT-TTAC-TAAGGCAACACCCTTTAATAATTGTAAGCAACACTATTTTCCACTATAT
8612 G
64 G
8613 CAA
1 CAA
8616 TGCTTTTGCA
Statistics
Matches: 107, Mismatches: 24, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
64 2 0.02
65 53 0.50
66 52 0.49
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.38
Consensus pattern (64 bp):
CAACGATTTTTTACTAAGGCAACACCCTTTAATAATTGTAAGCAACACTATTTTCCACTATATG
Found at i:8612 original size:66 final size:63
Alignment explanation
Indices: 8416--8615 Score: 202
Period size: 66 Copynumber: 3.0 Consensus size: 63
8406 ATAAAATGGA
*
8416 CAACGATTTTTTTACTTTAGGCAACATCTTTTGATAATTTTAAGCAACACTATTTTCTACTATAT
1 CAACGA-TTTTTTACTTT-GGCAACAT-TTTTGATAATTGTAAGCAACACTATTTTCTACTATAT
8481 G
63 G
* * ** *** * * *
8482 CAACAATAGTTTTACTAAGGCAACCCCCTTTAATAATTGTATGCAACACTATTTTCCACTATATG
1 CAACGAT-TTTTTACTTTGGCAA-CATTTTTGATAATTGTAAGCAACACTATTTTCTACTATATG
* * *
8547 CAACGATTTTCTTACTTCTGGCAACAATTTTTGATAATTGCAAGCAACACTATTATCTACAATAT
1 CAACGATTTT-TTACTT-TGGCAAC-ATTTTTGATAATTGTAAGCAACACTATTTTCTACTATAT
8612 G
63 G
8613 CAA
1 CAA
8616 TGCTTTTGCA
Statistics
Matches: 105, Mismatches: 24, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
64 2 0.02
65 51 0.49
66 52 0.50
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.38
Consensus pattern (63 bp):
CAACGATTTTTTACTTTGGCAACATTTTTGATAATTGTAAGCAACACTATTTTCTACTATATG
Found at i:14912 original size:15 final size:15
Alignment explanation
Indices: 14892--14952 Score: 79
Period size: 15 Copynumber: 4.0 Consensus size: 15
14882 TTTGATAAAA
14892 TATACTTTACATTAT
1 TATACTTTACATTAT
14907 TATACTTTACATTA-
1 TATACTTTACATTAT
* *
14921 TATACTTTATATTGTT
1 TATACTTTACATT-AT
14937 ATATACTTTACATTAT
1 -TATACTTTACATTAT
14953 CATCAGCCTG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
14 12 0.31
15 14 0.36
16 1 0.03
17 12 0.31
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.54
Consensus pattern (15 bp):
TATACTTTACATTAT
Found at i:14923 original size:29 final size:31
Alignment explanation
Indices: 14891--14952 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
14881 TTTTGATAAA
14891 ATATACTTTACATT-AT-TATACTTTACATT
1 ATATACTTTACATTGATATATACTTTACATT
* *
14920 ATATACTTTATATTGTTATATACTTTACATT
1 ATATACTTTACATTGATATATACTTTACATT
14951 AT
1 AT
14953 CATCAGCCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 13 0.45
30 1 0.03
31 15 0.52
ACGTcount: A:0.34, C:0.11, G:0.02, T:0.53
Consensus pattern (31 bp):
ATATACTTTACATTGATATATACTTTACATT
Found at i:15390 original size:2 final size:2
Alignment explanation
Indices: 15383--15407 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15373 GTTAGTACTA
15383 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 A
15408 ATCATTAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24484 original size:22 final size:22
Alignment explanation
Indices: 24456--24500 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
24446 CCATCGTGAC
*
24456 TTCCCCTTTTTTACTTCCCATT
1 TTCCCCTTTTTTACTTCACATT
24478 TTCCCCTTTTTTACTTCACATT
1 TTCCCCTTTTTTACTTCACATT
24500 T
1 T
24501 CTTTCCACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.11, C:0.33, G:0.00, T:0.56
Consensus pattern (22 bp):
TTCCCCTTTTTTACTTCACATT
Found at i:26150 original size:21 final size:20
Alignment explanation
Indices: 26120--26160 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
26110 GTGTTTTAGA
26120 TATTTTGTTGGATAATTGTT
1 TATTTTGTTGGATAATTGTT
26140 TATTTCTGTTGGATAATTGTT
1 TATTT-TGTTGGATAATTGTT
26161 CAATTATCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.20, C:0.02, G:0.20, T:0.59
Consensus pattern (20 bp):
TATTTTGTTGGATAATTGTT
Found at i:26467 original size:27 final size:27
Alignment explanation
Indices: 26437--26491 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
26427 GCACTTCTGT
26437 AGCTTTGGTTTAAGAACACTCTGCTTG
1 AGCTTTGGTTTAAGAACACTCTGCTTG
26464 AGCTTTGGTTTAAGAACACTCTGCTTG
1 AGCTTTGGTTTAAGAACACTCTGCTTG
26491 A
1 A
26492 TAAGCAAGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (27 bp):
AGCTTTGGTTTAAGAACACTCTGCTTG
Found at i:26766 original size:39 final size:40
Alignment explanation
Indices: 26696--26775 Score: 144
Period size: 39 Copynumber: 2.0 Consensus size: 40
26686 TTCAACTACA
26696 AATACACAAAAACAGTTTTAAGTTGCCTACTTTAATAAGT
1 AATACACAAAAACAGTTTTAAGTTGCCTACTTTAATAAGT
*
26736 AATACACAAAAAGAG-TTTAAGTTGCCTACTTTAATAAGT
1 AATACACAAAAACAGTTTTAAGTTGCCTACTTTAATAAGT
26775 A
1 A
26776 GGCAAACATA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 25 0.64
40 14 0.36
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (40 bp):
AATACACAAAAACAGTTTTAAGTTGCCTACTTTAATAAGT
Found at i:32668 original size:19 final size:20
Alignment explanation
Indices: 32626--32679 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
32616 TTATATTGTG
32626 TGTTAGGGTTTGGCTTCATCTCA
1 TGTTAGGGTTT-G--TCATCTCA
*
32649 T-TTAGGGTTTGTCATGTCA
1 TGTTAGGGTTTGTCATCTCA
32668 TGGTTAGGGTTT
1 T-GTTAGGGTTT
32680 AGATTTCATG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 8 0.29
21 10 0.36
22 9 0.32
23 1 0.04
ACGTcount: A:0.13, C:0.11, G:0.30, T:0.46
Consensus pattern (20 bp):
TGTTAGGGTTTGTCATCTCA
Found at i:32689 original size:25 final size:25
Alignment explanation
Indices: 32660--32746 Score: 70
Period size: 25 Copynumber: 3.4 Consensus size: 25
32650 TTAGGGTTTG
32660 TCATGTCATGGTTAGGGTTTAGATT
1 TCATGTCATGGTTAGGGTTTAGATT
* *** *
32685 TCATGTCAT-GTCATTTTTTTTG-TCT
1 TCATGTCATGGTTA-GGGTTTAGAT-T
*
32710 CCCTATGTCATGGTTAGGGTTTAGATT
1 -TC-ATGTCATGGTTAGGGTTTAGATT
32737 TCATGTCATG
1 TCATGTCATG
32747 TCATTTTTTT
Statistics
Matches: 44, Mismatches: 12, Indels: 12
0.65 0.18 0.18
Matches are distributed among these distances:
24 4 0.09
25 22 0.50
26 2 0.05
27 12 0.27
28 4 0.09
ACGTcount: A:0.17, C:0.14, G:0.22, T:0.47
Consensus pattern (25 bp):
TCATGTCATGGTTAGGGTTTAGATT
Found at i:32692 original size:30 final size:30
Alignment explanation
Indices: 32658--32750 Score: 85
Period size: 30 Copynumber: 3.4 Consensus size: 30
32648 ATTTAGGGTT
32658 TGTCATGTCATGGTTAGGGTTTAGATTTCA
1 TGTCATGTCATGGTTAGGGTTTAGATTTCA
* * *
32688 TGTCATGTCAT--TT---TTTTTG-TCTC-
1 TGTCATGTCATGGTTAGGGTTTAGATTTCA
**
32711 CCT-ATGTCATGGTTAGGGTTTAGATTTCA
1 TGTCATGTCATGGTTAGGGTTTAGATTTCA
32740 TGTCATGTCAT
1 TGTCATGTCAT
32751 TTTTTTTTGT
Statistics
Matches: 45, Mismatches: 10, Indels: 16
0.63 0.14 0.23
Matches are distributed among these distances:
22 7 0.16
23 1 0.02
24 5 0.11
25 4 0.09
27 4 0.09
28 5 0.11
29 1 0.02
30 18 0.40
ACGTcount: A:0.17, C:0.14, G:0.22, T:0.47
Consensus pattern (30 bp):
TGTCATGTCATGGTTAGGGTTTAGATTTCA
Found at i:32721 original size:52 final size:53
Alignment explanation
Indices: 32662--32766 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 53
32652 AGGGTTTGTC
32662 ATGTCATGGTTAGGGTTTAGATTTCATGTCATGTCA-TTTTTTTTGTCTCCCT
1 ATGTCATGGTTAGGGTTTAGATTTCATGTCATGTCATTTTTTTTTGTCTCCCT
32714 ATGTCATGGTTAGGGTTTAGATTTCATGTCATGTCATTTTTTTTTGTCTCCCT
1 ATGTCATGGTTAGGGTTTAGATTTCATGTCATGTCATTTTTTTTTGTCTCCCT
32767 TACTATTTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 36 0.69
53 16 0.31
ACGTcount: A:0.15, C:0.15, G:0.19, T:0.50
Consensus pattern (53 bp):
ATGTCATGGTTAGGGTTTAGATTTCATGTCATGTCATTTTTTTTTGTCTCCCT
Found at i:33832 original size:18 final size:20
Alignment explanation
Indices: 33796--33837 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
33786 TTCTGTCTTG
33796 TTTCTTCTTTGATTTTCCT-
1 TTTCTTCTTTGATTTTCCTA
33815 TTTCTCTCTTT-A-TTTCCTA
1 TTTCT-TCTTTGATTTTCCTA
33834 TTTC
1 TTTC
33838 CTATTCATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.29
19 10 0.48
20 5 0.24
ACGTcount: A:0.07, C:0.24, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTCTTCTTTGATTTTCCTA
Found at i:35116 original size:11 final size:11
Alignment explanation
Indices: 35100--35140 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
35090 TCAATTATTT
35100 TTGTTGTTTCA
1 TTGTTGTTTCA
* *
35111 TTGTTGTCATGA
1 TTGTTGT-TTCA
35123 TTGTTGTTTCA
1 TTGTTGTTTCA
35134 TTGTTGT
1 TTGTTGT
35141 CAATTATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.10, C:0.07, G:0.22, T:0.61
Consensus pattern (11 bp):
TTGTTGTTTCA
Found at i:35126 original size:23 final size:24
Alignment explanation
Indices: 35099--35170 Score: 101
Period size: 23 Copynumber: 2.9 Consensus size: 24
35089 TTCAATTATT
35099 TTTGTTGTTTCATTGTTGTCATGA
1 TTTGTTGTTTCATTGTTGTCATGA
*
35123 -TTGTTGTTTCATTGTTGTCAATTA
1 TTTGTTGTTTCATTGTTGTC-ATGA
35147 TTTTTGTTGTTTCATTGTTGTCAT
1 --TTTGTTGTTTCATTGTTGTCAT
35171 AAATTATTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
23 19 0.44
24 3 0.07
26 2 0.05
27 19 0.44
ACGTcount: A:0.12, C:0.08, G:0.18, T:0.61
Consensus pattern (24 bp):
TTTGTTGTTTCATTGTTGTCATGA
Found at i:35179 original size:30 final size:27
Alignment explanation
Indices: 35090--35169 Score: 123
Period size: 27 Copynumber: 3.1 Consensus size: 27
35080 TTTCTTTATT
35090 TCAATTATTTTTGTTGTTTCATTGTTG
1 TCAATTATTTTTGTTGTTTCATTGTTG
*
35117 TC-ATGA---TTGTTGTTTCATTGTTG
1 TCAATTATTTTTGTTGTTTCATTGTTG
35140 TCAATTATTTTTGTTGTTTCATTGTTG
1 TCAATTATTTTTGTTGTTTCATTGTTG
35167 TCA
1 TCA
35170 TAAATTATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
23 19 0.40
24 3 0.06
26 3 0.06
27 22 0.47
ACGTcount: A:0.15, C:0.09, G:0.16, T:0.60
Consensus pattern (27 bp):
TCAATTATTTTTGTTGTTTCATTGTTG
Found at i:36205 original size:36 final size:37
Alignment explanation
Indices: 36158--36230 Score: 139
Period size: 36 Copynumber: 2.0 Consensus size: 37
36148 AGCACTGGAG
36158 AAAGTTAAAGCAGGTGAGAG-TTTTTTCAAGATTTGA
1 AAAGTTAAAGCAGGTGAGAGTTTTTTTCAAGATTTGA
36194 AAAGTTAAAGCAGGTGAGAGTTTTTTTCAAGATTTGA
1 AAAGTTAAAGCAGGTGAGAGTTTTTTTCAAGATTTGA
36231 GCAATGTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 20 0.56
37 16 0.44
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (37 bp):
AAAGTTAAAGCAGGTGAGAGTTTTTTTCAAGATTTGA
Found at i:39012 original size:2 final size:2
Alignment explanation
Indices: 39007--39036 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
38997 TGTGAGTGTG
*
39007 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39037 AGATCAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:41267 original size:21 final size:22
Alignment explanation
Indices: 41242--41283 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41232 CATTTTTCAG
41242 ATTTTAC-AAATTACAAATTTT
1 ATTTTACAAAATTACAAATTTT
* *
41263 ATTTTCCAAAATTACTAATTT
1 ATTTTACAAAATTACAAATTT
41284 CTTAAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTTACAAAATTACAAATTTT
Found at i:46624 original size:17 final size:17
Alignment explanation
Indices: 46602--46635 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
46592 GGATCATCAT
46602 GGAAAATCT-TGAGAAAA
1 GGAAAAT-TATGAGAAAA
46619 GGAAAATTATGAGAAAA
1 GGAAAATTATGAGAAAA
46636 ATTTTATGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 15 0.94
ACGTcount: A:0.56, C:0.03, G:0.24, T:0.18
Consensus pattern (17 bp):
GGAAAATTATGAGAAAA
Found at i:47591 original size:28 final size:28
Alignment explanation
Indices: 47532--47592 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
47522 AAAGAAATTT
* * * *
47532 AAAAAAAACGCATAAAAGTTATATATAT
1 AAAAAAAACGCAGAAAAGTTATAAAAAA
47560 AAAAAAAACGCAGAAAAGTTATAAAAAA
1 AAAAAAAACGCAGAAAAGTTATAAAAAA
47588 AAAAA
1 AAAAA
47593 GTCAGGTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.69, C:0.07, G:0.08, T:0.16
Consensus pattern (28 bp):
AAAAAAAACGCAGAAAAGTTATAAAAAA
Done.