Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016608.1 Corchorus olitorius cultivar O-4 contig16641, 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: 85055
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1585 original size:41 final size:41
Alignment explanation
Indices: 1512--1835 Score: 402
Period size: 41 Copynumber: 7.9 Consensus size: 41
1502 GTTTGATTTG
* *
1512 ATTTGATTCAAGGG--TCGAATGACTTGTTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCG-ATGACTTGATCTTGAATTGATA
* * * *
1552 ATTTAATTCAAGGGTGTTGACGACTTGACCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
* *
1593 ATTTAATTCAAGGGTCTTGACGACTTGATCTTGAATTGTTAATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTG---ATA
** *
1637 ATTCGATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
* * **
1678 ATTTAGTTCAAGGGTCTCGAAGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
**
1719 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
*
1760 ATTTAATTCAAGGGTCTCGATGAC-TCATTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTGA-TCTTGAATTGATA
**
1801 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAA
1 ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAA
1836 CAAACGAAAA
Statistics
Matches: 252, Mismatches: 25, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
40 14 0.06
41 199 0.79
42 3 0.01
44 36 0.14
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (41 bp):
ATTTAATTCAAGGGTCTCGATGACTTGATCTTGAATTGATA
Found at i:1755 original size:126 final size:123
Alignment explanation
Indices: 1516--1835 Score: 446
Period size: 126 Copynumber: 2.6 Consensus size: 123
1506 GATTTGATTT
* * * **
1516 GATTCAAGGG--TCGAATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTGTTGACGACTTG
1 GATTCAAGGGTCTCG-ATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCGAAGACTCA
* * **
1579 ACCTTGAATTGATAATTTAATTCAAGGGTCTTGACGACTTGATCTTGAATTGTTAATAATTC
65 ATCTTGAATTGATAATTTAATTCAAGGGTCTCGACGACTCAATCTTGAATTG---ATAATTC
*
1641 GATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATAATTTAGTTCAAGGGTCTCGAAGACTCAA
1 GATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCGAAGACTCAA
* *
1706 TCTTGAATTGATAATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATAATTT
66 TCTTGAATTGATAATTTAATTCAAGGGTCTCGACGACTCAATCTTGAATTGATAATTC
* ** *
1764 AATTCAAGGGTCTCGATGACTCATTCTTGAATTGATAATTTAATTCAAGGGTCTCGATGACTCAA
1 GATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCGAAGACTCAA
1829 TCTTGAA
66 TCTTGAA
1836 CAAACGAAAA
Statistics
Matches: 176, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
123 73 0.41
125 10 0.06
126 90 0.51
127 3 0.02
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (123 bp):
GATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCGAAGACTCAA
TCTTGAATTGATAATTTAATTCAAGGGTCTCGACGACTCAATCTTGAATTGATAATTC
Found at i:3120 original size:2 final size:2
Alignment explanation
Indices: 3113--3139 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3103 ATGAATGATC
3113 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
3140 CTAGTTTTAG
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:3227 original size:22 final size:22
Alignment explanation
Indices: 3199--3396 Score: 97
Period size: 22 Copynumber: 9.1 Consensus size: 22
3189 GAAAATTTAA
3199 ATGAAATTTTGATAACTACCCT
1 ATGAAATTTTGATAACTACCCT
* * ***
3221 ATTAAATTTTGATAACCATGTT
1 ATGAAATTTTGATAACTACCCT
* *
3243 ATGAAAATTTGAT-ACTAACCT
1 ATGAAATTTTGATAACTACCCT
* *
3264 ATGAAATTGTGATAAACT-CCAT
1 ATGAAATTTTGAT-AACTACCCT
* *
3286 ATGAAACTTTGATAACCTA-ACT
1 ATGAAATTTTGATAA-CTACCCT
* * * * *
3308 ATTACATTTTAATAAACCATCCT
1 ATGAAATTTTGAT-AACTACCCT
*
3331 ATGAAATTTTG-TAACCT-TCCT
1 ATGAAATTTTGATAA-CTACCCT
* *
3352 ATG-AGTTTTGATAACCT-CACT
1 ATGAAATTTTGATAA-CTACCCT
* *
3373 ATGAGATTTTGTTAATCT-CCCT
1 ATGAAATTTTGATAA-CTACCCT
3395 AT
1 AT
3397 AATTTTTTGA
Statistics
Matches: 130, Mismatches: 37, Indels: 18
0.70 0.20 0.10
Matches are distributed among these distances:
20 6 0.05
21 37 0.28
22 72 0.55
23 15 0.12
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (22 bp):
ATGAAATTTTGATAACTACCCT
Found at i:5885 original size:2 final size:2
Alignment explanation
Indices: 5870--5905 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
5860 GTCAATAATA
5870 AT AT A- AT A- AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5906 AAAGTCTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:6595 original size:27 final size:26
Alignment explanation
Indices: 6541--6601 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
6531 CTAAATTTCC
6541 ATTATTTTAATAATGGAATAATTAAAAT
1 ATTA-TTTAATAATGGAAT-ATTAAAAT
6569 ATTATTTAATAATGGCAAT-TTAGAAAT
1 ATTATTTAATAATGG-AATATTA-AAAT
6596 A-TATTT
1 ATTATTT
6602 GAAAAAAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.26
27 16 0.52
28 7 0.23
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (26 bp):
ATTATTTAATAATGGAATATTAAAAT
Found at i:6796 original size:22 final size:21
Alignment explanation
Indices: 6766--7925 Score: 281
Period size: 22 Copynumber: 53.4 Consensus size: 21
6756 ATTACACTAT
*
6766 TTTTTATAACCTCCTTATGAAA
1 TTTTGATAACCTCC-TATGAAA
* *
6788 TTTTAATAACCTTCCTATAAAA
1 TTTTGATAACC-TCCTATGAAA
* * * *
6810 TTTTAATAACGATACTATGGAA
1 TTTTGATAAC-CTCCTATGAAA
* * **
6832 TTTCGAGAACCTTTTTAT-AAA
1 TTTTGATAACC-TCCTATGAAA
** * *
6853 TTTTTTTTAACCTTCTTATAAAA
1 -TTTTGATAACC-TCCTATGAAA
* * *
6876 TTTTGTTAACCTCCTTAAGGAA
1 TTTTGATAACCTCC-TATGAAA
6898 TTTTGA-ATACCTCACTATGAAA
1 TTTTGATA-ACCTC-CTATGAAA
* *
6920 TTTTTTGATAACTTCCCAATGAAA
1 --TTTTGATAACCT-CCTATGAAA
* *
6944 TTTTGATAACCAACACTATGAGA
1 TTTTGATAACC-TC-CTATGAAA
* *
6967 TGTTGATAACCTCCATATGATA
1 TTTTGATAACCTCC-TATGAAA
* * *
6989 TATTGATAACCACGTTATGAAA
1 TTTTGATAACCTC-CTATGAAA
* * * *
7011 ATTTAAAAACGTCCATATG-AA
1 TTTTGATAACCTCC-TATGAAA
* *
7032 TTGTT-AGTAA-TTACACTCTGAAA
1 TT-TTGA-TAACCT-C-CTATGAAA
* *
7055 -TTTGATAATCACACTATGAAA
1 TTTTGATAACCTC-CTATGAAA
* * *
7076 TTGT-ACAACCTCGTTATGAAA
1 TTTTGATAACCTC-CTATGAAA
*
7097 TTTTGATAAACCTTCCTATAAAA
1 TTTTGAT-AACC-TCCTATGAAA
7120 TTTTGATAACCTCCTTATGAAA
1 TTTTGATAACCTCC-TATGAAA
* *
7142 TCTTGATAA----CTA-CAAA
1 TTTTGATAACCTCCTATGAAA
* *
7158 TTTTGATAACCTCCCCATG-AT
1 TTTTGATAACCT-CCTATGAAA
* * *
7179 TTTTTATAACCTCGTTATGCAA
1 TTTTGATAACCTC-CTATGAAA
* *
7201 TTTTGTTAATCTCCCTATGAAA
1 TTTTGATAACCT-CCTATGAAA
* * **
7223 TTTTGATCTACATATTATGAAA
1 TTTTGAT-AACCTCCTATGAAA
* *
7245 TTTTGATAACCCTCTTATGATA
1 TTTTGATAA-CCTCCTATGAAA
* * *
7267 TTTTGAAAACTTAGCTATGAAA
1 TTTTGATAACCT-CCTATGAAA
*
7289 TTTTGATAACCTTCATATGAAA
1 TTTTGATAACC-TCCTATGAAA
*
7311 TTTTGATATCCTCC-ATGAAA
1 TTTTGATAACCTCCTATGAAA
* *
7331 TTTTGATTA-CTCCATAATTAAA
1 TTTTGATAACCTCC-T-ATGAAA
* *
7353 GTTTAATAACCTTCC--T--AA
1 TTTTGATAACC-TCCTATGAAA
* *
7371 -TTTGCTAACCATACTATGAAA
1 TTTTGATAACC-TCCTATGAAA
*
7392 TTTTGATAA--TCATATTGATAA
1 TTTTGATAACCTCCTA-TGA-AA
*** * *
7413 CCTCCCCAGAAATACC-ACTATGAAA
1 --T--TTTGATA-ACCTCCTATGAAA
* * ** *
7438 TTTTGGTAATCATATTTTGAAA
1 TTTTGATAA-CCTCCTATGAAA
* *
7460 ATTTGATAACCTCTTTATGAAA
1 TTTTGATAACCTC-CTATGAAA
* *
7482 GTTTGATAACCT-CTATAAAA
1 TTTTGATAACCTCCTATGAAA
* * *
7502 TTTTGTTGACCCCTCTATGAAA
1 TTTTGATAACCTC-CTATGAAA
* * *
7524 TTTTGATAATCACATTAT-ATAA
1 TTTTGATAACCTC-CTATGA-AA
* *
7546 TTTTGATAACCTTGCTTTGAAA
1 TTTTGATAACC-TCCTATGAAA
** *
7568 TTTTGATAACAACACTATAAAA
1 TTTTGATAACCTC-CTATGAAA
* *
7590 TTTTGATAATCTTCTTAT-AAA
1 TTTTGATAA-CCTCCTATGAAA
*
7611 TTTTGATAAACCGATCTCTAGGAAA
1 TTTTGAT-AACC--TC-CTATGAAA
* *
7636 TTTCGATAATCACT-CTATGAGA
1 TTTTGATAA-C-CTCCTATGAAA
* *
7658 -TTTGATAACCTTCTATCAAA
1 TTTTGATAACCTCCTATGAAA
*
7678 TTTTGGT-A-CTCCTTATGAAA
1 TTTTGATAACCTCC-TATGAAA
* * *
7698 TTTT-AGT-ACTTCTTAAGAAA
1 TTTTGA-TAACCTCCTATGAAA
* * * *
7718 TTTTTGGT-ACTTCTTATGAGA
1 -TTTTGATAACCTCCTATGAAA
* *
7739 -TTTGATAACCTTCTATCAAA
1 TTTTGATAACCTCCTATGAAA
*
7759 TTTTGCT-A-CTCCTTATGAAA
1 TTTTGATAACCTCC-TATGAAA
* * *
7779 TTGAGACTTTTATAATCTTCATATGAAA
1 -T-----TTTGATAA-CCTCCTATGAAA
* *
7807 TTTTGATAACCACACTATCAAA
1 TTTTGATAACCTC-CTATGAAA
*
7829 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCT-CCTATGAAA
*
7851 TATT-AGTAACCTCCTTATGAAA
1 TTTTGA-TAACCTCC-TATGAAA
* *
7873 TTTTGTTAACCACACTATGAAA
1 TTTTGATAACCTC-CTATGAAA
* *
7895 TTCTT-ATAACCTCGTTATGACA
1 TT-TTGATAACCTC-CTATGAAA
*
7917 TTTTAATAA
1 TTTTGATAA
7926 TCTCTTTGAT
Statistics
Matches: 824, Mismatches: 209, Indels: 210
0.66 0.17 0.17
Matches are distributed among these distances:
16 11 0.01
17 12 0.01
18 3 0.00
19 21 0.03
20 74 0.09
21 129 0.16
22 450 0.55
23 59 0.07
24 26 0.03
25 17 0.02
26 9 0.01
27 4 0.00
28 7 0.01
29 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (21 bp):
TTTTGATAACCTCCTATGAAA
Found at i:6964 original size:23 final size:22
Alignment explanation
Indices: 6938--7000 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
6928 TAACTTCCCA
*
6938 ATGAAATTTTGATAACCAACACT
1 ATGAAATATTGATAACCAACA-T
* * **
6961 ATGAGATGTTGATAACCTCCAT
1 ATGAAATATTGATAACCAACAT
*
6983 ATGATATATTGATAACCA
1 ATGAAATATTGATAACCA
7001 CGTTATGAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
22 16 0.48
23 17 0.52
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.32
Consensus pattern (22 bp):
ATGAAATATTGATAACCAACAT
Found at i:7120 original size:23 final size:23
Alignment explanation
Indices: 7082--7150 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
7072 GAAATTGTAC
* *
7082 AACCTCGTTATGAAATTTTGATA
1 AACCTCCTTATAAAATTTTGATA
7105 AACCTTCC-TATAAAATTTTGAT-
1 AACC-TCCTTATAAAATTTTGATA
* *
7127 AACCTCCTTATGAAATCTTGATA
1 AACCTCCTTATAAAATTTTGATA
7150 A
1 A
7151 CTACAAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 3 0.08
22 16 0.41
23 18 0.46
24 2 0.05
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (23 bp):
AACCTCCTTATAAAATTTTGATA
Found at i:7553 original size:86 final size:86
Alignment explanation
Indices: 7430--7594 Score: 210
Period size: 86 Copynumber: 1.9 Consensus size: 86
7420 AGAAATACCA
* * *
7430 CTATGAAATTTTGGTAATCATATTTTGAAAATTTGATAACC-TCTTTATGAAAGTTTGATAAC-C
1 CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTTC-TT-TGAAAGTTTGATAACAC
*
7493 TCTATAAAATTTTGTTGACCCCT
64 ACTATAAAATTTTGTTGACCCCT
* *
7516 CTATGAAATTTTGATAATCACATTAT-ATAATTTTGATAACCTTGCTTTGAAATTTTGATAACAA
1 CTATGAAATTTTGATAATCACATTATGA-AAATTTGATAACCTT-CTTTGAAAGTTTGATAAC-A
7580 CACTATAAAATTTTG
63 CACTATAAAATTTTG
7595 ATAATCTTCT
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
85 1 0.01
86 49 0.72
87 3 0.04
88 15 0.22
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (86 bp):
CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTTCTTTGAAAGTTTGATAACACAC
TATAAAATTTTGTTGACCCCT
Found at i:7698 original size:20 final size:20
Alignment explanation
Indices: 7675--7780 Score: 90
Period size: 20 Copynumber: 5.2 Consensus size: 20
7665 ACCTTCTATC
7675 AAATTTTGGTACTCCTTATG
1 AAATTTTGGTACTCCTTATG
* * *
7695 AAATTTTAGTACTTCTTAAG
1 AAATTTTGGTACTCCTTATG
*
7715 AAATTTTTGGTACTTCTTATG
1 AAA-TTTTGGTACTCCTTATG
* * * *
7736 AGA-TTTGATAAC-CTTCTATC
1 AAATTTTGGT-ACTCCT-TATG
*
7756 AAATTTTGCTACTCCTTATG
1 AAATTTTGGTACTCCTTATG
7776 AAATT
1 AAATT
7781 GAGACTTTTA
Statistics
Matches: 67, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
19 6 0.09
20 37 0.55
21 24 0.36
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.45
Consensus pattern (20 bp):
AAATTTTGGTACTCCTTATG
Found at i:7741 original size:21 final size:20
Alignment explanation
Indices: 7678--7741 Score: 74
Period size: 21 Copynumber: 3.1 Consensus size: 20
7668 TTCTATCAAA
* *
7678 TTTTGGTACTCCTTATGAAA
1 TTTTGGTACTTCTTATGAAT
* *
7698 TTTTAGTACTTCTTAAGAAAT
1 TTTTGGTACTTCTTATG-AAT
7719 TTTTGGTACTTCTTATGAGAT
1 TTTTGGTACTTCTTATGA-AT
7740 TT
1 TT
7742 GATAACCTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 15 0.42
21 21 0.58
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.50
Consensus pattern (20 bp):
TTTTGGTACTTCTTATGAAT
Found at i:8002 original size:22 final size:22
Alignment explanation
Indices: 7930--8161 Score: 138
Period size: 22 Copynumber: 10.5 Consensus size: 22
7920 TAATAATCTC
* * *
7930 TTTGATAACATTTCTATAAAAT
1 TTTGATAACCTTCCTATGAAAT
* * *
7952 TGTGATAAAC-ACACTATG-AAT
1 TTTGATAACCTTC-CTATGAAAT
* *
7973 TTTCAATAACCTTCCTAAGAAAT
1 TTT-GATAACCTTCCTATGAAAT
* *
7996 TTTAATAACCTGATACTATGAAAT
1 TTTGATAACCT--TCCTATGAAAT
* *
8020 TTTGGTAACC-ACACTATGAAAT
1 TTTGATAACCTTC-CTATGAAAT
8042 TTTGATAACCTTCCTATGAAA-
1 TTTGATAACCTTCCTATGAAAT
8063 TTTGATAA-CTTCCATATGAAAT
1 TTTGATAACCTTCC-TATGAAAT
* * * *
8085 TTTGGTAACC-ACATTATGGAAT
1 TTTGATAACCTTC-CTATGAAAT
* *
8107 TTCGATAACC-TCATCATGAAAT
1 TTTGATAACCTTCCT-ATGAAAT
* * *
8129 TAT-ATTAACCATCTTATGAAAT
1 TTTGA-TAACCTTCCTATGAAAT
8151 TTTGATAACCT
1 TTTGATAACCT
8162 CATAGAGATA
Statistics
Matches: 161, Mismatches: 33, Indels: 32
0.71 0.15 0.14
Matches are distributed among these distances:
20 5 0.03
21 22 0.14
22 104 0.65
23 13 0.08
24 17 0.11
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (22 bp):
TTTGATAACCTTCCTATGAAAT
Found at i:8057 original size:68 final size:63
Alignment explanation
Indices: 7934--8117 Score: 188
Period size: 68 Copynumber: 2.8 Consensus size: 63
7924 AATCTCTTTG
* * * * * *
7934 ATAACATTTCTATAAAATTGTGATAAACACACTATGAATTTTCAATAACCTTCCTAAGAAATTTT
1 ATAAC-TTACTATGAAATTTTGGTAACCACACTATGAATTTT-GATAACCTTCCTAAGAAA-TTT
7999 A
63 A
*
8000 ATAACCTGATACTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCTATGAAATT
1 ATAA-CT--TACTATGAAATTTTGGTAACCACACTATG-AATTTTGATAACCTTCCTAAGAAATT
*
8065 TG
62 TA
* * *
8067 ATAACTTCCATATGAAATTTTGGTAACCACATTATGGAATTTCGATAACCT
1 ATAACTTAC-TATGAAATTTTGGTAACCACACTAT-GAATTTTGATAACCT
8118 CATCATGAAA
Statistics
Matches: 101, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
64 2 0.02
65 37 0.37
66 8 0.08
67 8 0.08
68 40 0.40
69 6 0.06
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (63 bp):
ATAACTTACTATGAAATTTTGGTAACCACACTATGAATTTTGATAACCTTCCTAAGAAATTTA
Found at i:8365 original size:20 final size:20
Alignment explanation
Indices: 8327--8366 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
8317 TATTGACATT
8327 TAAAAAATTGAAATTAAAAA
1 TAAAAAATTGAAATTAAAAA
*
8347 TAAAATATT-AAATTCAAAAA
1 TAAAAAATTGAAATT-AAAAA
8367 ATAATAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAA
Found at i:8692 original size:166 final size:172
Alignment explanation
Indices: 8379--8719 Score: 455
Period size: 166 Copynumber: 2.0 Consensus size: 172
8369 AATAGTAAAG
*** * *
8379 GAAATTTGCATGTTCATCAACGAAAATCAATTTGACAAACTTATAATTCGGTTTAAATTGAAAGT
1 GAAATTTGCATGAAAATCAACGAAAATCAATTTGACAAACTTATAATCCGGTCTAAATTGAAAGT
8444 TTTAATTAATTTTTAATAATAAAATTATACTAAATTTTAATAATGGCAATTTAGAATATATTTGA
66 TTTAATTAA-TTTT-AT-ATAAAATTATACTAAATTTTAATAATGGCAATTTAGAATATATTTGA
8509 AAAAAAGGGTACAATCGGAAAACATAAAGTTCCCCATTATTCGTA
128 AAAAAAGGGTACAATCGGAAAACATAAAGTTCCCCATTATTCGTA
* * * *
8554 GAAATTTGCATGAAAATCAATGAAAATCAATTTTACAAAGTTATAATCCGGTCTAAATTGAAATT
1 GAAATTTGCATGAAAATCAACGAAAATCAATTTGACAAACTTATAATCCGGTCTAAATTGAAAGT
*
8619 TTATAATTAA-TTT-T-T-AAA-TA-A-TAAATTTTAATAATGTCAATTTAGAAATATATTTG-A
66 TT-TAATTAATTTTATATAAAATTATACTAAATTTTAATAATGGCAATTTAG-AATATATTTGAA
* ***
8676 AAAAAGGGTGCAATCGGAAAACATAAAGTTTGGCATTATTCGTA
129 AAAAAGGGTACAATCGGAAAACATAAAGTTCCCCATTATTCGTA
8720 CTTTTGTATA
Statistics
Matches: 150, Mismatches: 14, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
166 64 0.43
167 11 0.07
168 2 0.01
169 3 0.02
170 1 0.01
172 1 0.01
174 3 0.02
175 58 0.39
176 7 0.05
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.35
Consensus pattern (172 bp):
GAAATTTGCATGAAAATCAACGAAAATCAATTTGACAAACTTATAATCCGGTCTAAATTGAAAGT
TTTAATTAATTTTATATAAAATTATACTAAATTTTAATAATGGCAATTTAGAATATATTTGAAAA
AAAGGGTACAATCGGAAAACATAAAGTTCCCCATTATTCGTA
Found at i:9456 original size:2 final size:2
Alignment explanation
Indices: 9421--9445 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9411 AGTAGACAAT
9421 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
9446 TTGATTATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10022 original size:108 final size:109
Alignment explanation
Indices: 9896--10110 Score: 353
Period size: 108 Copynumber: 2.0 Consensus size: 109
9886 ATCATTTTGA
9896 TGCTTGTAATTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTACTTAT
1 TGCTTGTAATTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTACTTAT
* *
9961 TTAATAGGTTCAATTGAATAAA-CAACA-CATTAATAATAATAGG
66 TTAATAAGTTCAATTGAATAAATC-ACATAATTAATAATAATAGG
* * **
10004 TGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCATTTTGTATTGTTTGGTATGTGTGTTTAT
1 TGCTTGTAATTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTACTTAT
10069 TTAATAAGTTCAATTGAATAAATCACATAATTAATAATAATA
66 TTAATAAGTTCAATTGAATAAATCACATAATTAATAATAATA
10111 TATATAATAG
Statistics
Matches: 99, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
108 85 0.86
109 14 0.14
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (109 bp):
TGCTTGTAATTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTACTTAT
TTAATAAGTTCAATTGAATAAATCACATAATTAATAATAATAGG
Found at i:10774 original size:22 final size:21
Alignment explanation
Indices: 10749--11902 Score: 286
Period size: 22 Copynumber: 53.8 Consensus size: 21
10739 ATGACTTTCT
10749 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACC-TCC
* * *
10771 TATGAAATTTTAATAACGATAC
1 TATGAAATTTTGATAAC-CTCC
* * * *
10793 TATGGAATTTCGAGAACCTTTC
1 TATGAAATTTTGATAACC-TCC
* * *
10815 TAT-ATATATTTT-TTAACTTTCT
1 TATGA-A-ATTTTGATAAC-CTCC
*
10837 TATGAAATTTTGTTAACCTCTC
1 TATGAAATTTTGATAACCTC-C
*
10859 TAATG-AATTTTGA-AGACATCAC
1 T-ATGAAATTTTGATA-ACCTC-C
* *
10881 TATAAAATTTTGATAACTTCCC
1 TATGAAATTTTGATAACCT-CC
* *
10903 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TC-C
* *
10926 TATGAGATGTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
* * * *
10947 ATATGATATATTGATAACCACGT
1 -TATGAAATTTTGATAACCTC-C
* * *
10970 TATGAAAATTTAAAAACCTCC
1 TATGAAATTTTGATAACCTCC
* *
10991 ATATG-AATTGTTAGA-AATCACAC
1 -TATGAAATT-TT-GATAACCTC-C
* ***
11014 TCTGAAATTTTGATAATGACAC
1 TATGAAATTTTGATAACCTC-C
*
11036 TATG-AATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTC-C
11057 TATGAAATTTTGATAAACCTTCC
1 TATGAAATTTTGAT-AACC-TCC
*
11080 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCT-CC
*
11103 TATAAAATTTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
*
11124 TTATGAAATCTTGATAA----C
1 -TATGAAATTTTGATAACCTCC
*
11142 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCT-CC
** *
11163 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTC-C
11185 TATGAAATTTT--T-A----C
1 TATGAAATTTTGATAACCTCC
*
11199 TATGAAATTTTGATAATCCTCT
1 TATGAAATTTTGATAA-CCTCC
* *
11221 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT--CC
*
11243 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACC-TCC
* *
11265 TATGAAATTTTGCTATCCTCC
1 TATGAAATTTTGATAACCTCC
* *
11286 -CTGAAATTTTGATTA-CTCC
1 TATGAAATTTTGATAACCTCC
* * * *
11305 ATAATAAAAGTTTAATAATCTTCC
1 -T-ATGAAATTTTGATAA-CCTCC
* *
11329 --T--AA-TTTGGTAACCATAC
1 TATGAAATTTTGATAACC-TCC
11346 TATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCT-CC
** *
11368 TA-GAAA---T-ACCA-CT-A
1 TATGAAATTTTGATAACCTCC
* * * *
11382 TGA--AATTTTGGTAATCACAT--
1 T-ATGAAATTT--TGATAACCTCC
** *
11402 TTGGCAAA-TTTGATAACCTCTT
1 TATG-AAATTTTGATAACCTC-C
*
11424 TATGAAATTTTGATAACATCTC
1 TATGAAATTTTGATAACCTC-C
* * * *
11446 TATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACCTC-C
*
11468 TATGAAATTTTGATAGCCTCGC
1 TATGAAATTTTGATAACCTC-C
* ** *
11490 TTTGAAATTTTGATAACAACAT
1 TATGAAATTTTGATAACCTC-C
* *
11512 TATGAAATTTTGACAATCTTCC
1 TATGAAATTTTGATAA-CCTCC
** * *
11534 -AAAAAATTTTGATAATTCAATCTT
1 TATGAAATTTTGATAA--C-CTC-C
*
11558 TATGAAATTTCGATAATCACT-C
1 TATGAAATTTTGATAA-C-CTCC
* *
11580 TATGAGA-TTTGATAACCTTC
1 TATGAAATTTTGATAACCTCC
* * *
11600 TATCAATTTTTGGT-A-CTCC
1 TATGAAATTTTGATAACCTCC
* *
11619 TTATGAAATTGAAACTTTTATAACCTTCA
1 -TATGAAA-T-----TTTGATAACC-TCC
*
11648 TATGAAATTTTGATAACC-AC
1 TATGAAATTTTGATAACCTCC
*
11668 -ACT---ACTTTGATAACCTTTCC
1 TA-TGAAATTTTGATAACC--TCC
* *
11688 -A-GAAAATTGTGATAACCACAC
1 TATG-AAATTTTGATAACCTC-C
**
11709 TATGAAATTTCAATAACCTTCC
1 TATGAAATTTTGATAACC-TCC
* **
11731 TAAGAAATTTCAATAACCTGATCC
1 TATGAAATTTTGATAACC---TCC
* *
11755 TATGAAATTTTGGTAACCACAC
1 TATGAAATTTTGATAACCTC-C
11777 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACC-TCC
* *
11799 CATGAAATTTTGATAACTTCC
1 TATGAAATTTTGATAACCTCC
* * * *
11820 ATATGAAATTTTGGTAAGCACAG
1 -TATGAAATTTTGATAACCTC-C
*
11843 TATGGAATTTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
* * **
11864 TCATGAAATTATAATAACCATTT
1 T-ATGAAATTTTGATAACC-TCC
11887 TATGAAATTTTGATAA
1 TATGAAATTTTGATAA
11903 TCACACAGAG
Statistics
Matches: 828, Mismatches: 193, Indels: 222
0.67 0.16 0.18
Matches are distributed among these distances:
14 14 0.02
15 1 0.00
16 15 0.02
17 24 0.03
18 4 0.00
19 19 0.02
20 35 0.04
21 86 0.10
22 492 0.59
23 83 0.10
24 27 0.03
25 12 0.01
26 4 0.00
27 2 0.00
28 8 0.01
29 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (21 bp):
TATGAAATTTTGATAACCTCC
Found at i:10855 original size:44 final size:44
Alignment explanation
Indices: 10731--10866 Score: 116
Period size: 44 Copynumber: 3.0 Consensus size: 44
10721 ATAATTACAC
*
10731 TATTTTTTATGACTTTCTTATGAAATTTTGATAACCTTCCTATGAA
1 TATTTTTTA--ACTTTCTTATGAAATTTTGATAACCTTTCTATGAA
* * * * * *
10777 -ATTTTAATAACGATAC-TATGGAATTTCGAGAACCTTTCTAT-ATA
1 TATTTT-TTAAC-TTTCTTATGAAATTTTGATAACCTTTCTATGA-A
* *
10821 TATTTTTTAACTTTCTTATGAAATTTTGTTAACCTCTCTAATGAA
1 TATTTTTTAACTTTCTTATGAAATTTTGATAACCTTTCT-ATGAA
10866 T
1 T
10867 TTTGAAGACA
Statistics
Matches: 68, Mismatches: 15, Indels: 15
0.69 0.15 0.15
Matches are distributed among these distances:
43 3 0.04
44 46 0.68
45 16 0.24
46 3 0.04
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (44 bp):
TATTTTTTAACTTTCTTATGAAATTTTGATAACCTTTCTATGAA
Found at i:11231 original size:60 final size:62
Alignment explanation
Indices: 11079--11231 Score: 169
Period size: 60 Copynumber: 2.5 Consensus size: 62
11069 ATAAACCTTC
* *
11079 CTATAAAATTTTGATAAACCTCCCTAT-AAA-ATTTTGATAACCTCCTTATGAAATCTTGATAA
1 CTATAAAATTTTGAT-AACCTCCCTATGAAATTTTTTGATAACCTCATTATGAAATCTT-ATAA
* *
11141 CTA-CAAATTTTGATAACCTCCCTATG--ATTTTTTGATAACCTCATTATGAAAT-TT-TTA
1 CTATAAAATTTTGATAACCTCCCTATGAAATTTTTTGATAACCTCATTATGAAATCTTATAA
* *
11198 CTATGAAATTTTGATAATCCT-CTTATGAAATTTT
1 CTATAAAATTTTGATAA-CCTCCCTATGAAATTTT
11232 GAAAACTAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
57 5 0.06
58 17 0.22
59 6 0.08
60 38 0.48
61 10 0.13
62 3 0.04
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (62 bp):
CTATAAAATTTTGATAACCTCCCTATGAAATTTTTTGATAACCTCATTATGAAATCTTATAA
Found at i:12109 original size:20 final size:20
Alignment explanation
Indices: 12071--12109 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12061 TATTGACATT
12071 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
12091 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
12110 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:20203 original size:15 final size:15
Alignment explanation
Indices: 20183--20211 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20173 AAAGTACCTT
20183 TATAATTAATTAAAG
1 TATAATTAATTAAAG
20198 TATAATTAATTAAA
1 TATAATTAATTAAA
20212 TACATGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
TATAATTAATTAAAG
Found at i:20424 original size:31 final size:33
Alignment explanation
Indices: 20386--20450 Score: 98
Period size: 31 Copynumber: 2.0 Consensus size: 33
20376 TTAGCTTTTA
20386 ATTTGTTTAATTTAAGGC-T-TTCATTTTAATT
1 ATTTGTTTAATTTAAGGCTTATTCATTTTAATT
*
20417 ATTTGTTTAATTTAATGCTTAATTCATTTTAATT
1 ATTTGTTTAATTTAAGGCTT-ATTCATTTTAATT
20451 TGCAATAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 17 0.57
32 1 0.03
34 12 0.40
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (33 bp):
ATTTGTTTAATTTAAGGCTTATTCATTTTAATT
Found at i:20977 original size:16 final size:15
Alignment explanation
Indices: 20920--20979 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 15
20910 CGTACCCGAG
20920 ACCGAACCCGAAAAT
1 ACCGAACCCGAAAAT
* *
20935 ACCCGAATCCG-ACAT
1 A-CCGAACCCGAAAAT
*
20950 AACCCAAGCCCGAAAAT
1 -ACCGAA-CCCGAAAAT
20967 ACCTGAACCCGAA
1 ACC-GAACCCGAA
20980 CCCACCCAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 9
0.69 0.12 0.18
Matches are distributed among these distances:
15 8 0.24
16 21 0.62
17 5 0.15
ACGTcount: A:0.42, C:0.37, G:0.13, T:0.08
Consensus pattern (15 bp):
ACCGAACCCGAAAAT
Found at i:22703 original size:92 final size:93
Alignment explanation
Indices: 22596--22774 Score: 211
Period size: 93 Copynumber: 1.9 Consensus size: 93
22586 AAAGTTTTAA
* * * ** * *
22596 TTTTCGAATTAAGATT-AGCTCAAAAA-GATTTGA-TAATCTATTTCTGAATTAATTTTAAACTA
1 TTTTCAAATTAAGATTAATC-CAAAAAGGATTT-ACTAATCGATTTCCAAACTAATTTTAAACCA
* *
22658 AAAGTCAAATCTTTAAATCAAAGACTTGAT
64 AAAATCAAACCTTTAAATCAAAGACTTGAT
* *
22688 TTTTCAAATTAAGATTAATCCAAAAAGGATTTACTGATCGATTTCCAAACTAATTTTAATCCAAA
1 TTTTCAAATTAAGATTAATCCAAAAAGGATTTACTAATCGATTTCCAAACTAATTTTAAACCAAA
*
22753 AATCAAACCTTTAATTCAAAGA
66 AATCAAACCTTTAAATCAAAGA
22775 ATTTACTTTT
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
92 22 0.31
93 50 0.69
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.36
Consensus pattern (93 bp):
TTTTCAAATTAAGATTAATCCAAAAAGGATTTACTAATCGATTTCCAAACTAATTTTAAACCAAA
AATCAAACCTTTAAATCAAAGACTTGAT
Found at i:26890 original size:16 final size:16
Alignment explanation
Indices: 26865--26904 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
26855 TACCCTTATC
*
26865 TTTTTATTTTTCGTTA
1 TTTTTCTTTTTCGTTA
*
26881 TTTTTCTTTTTCTTTA
1 TTTTTCTTTTTCGTTA
26897 TTTTTCTT
1 TTTTTCTT
26905 AGTTACTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.07, C:0.10, G:0.03, T:0.80
Consensus pattern (16 bp):
TTTTTCTTTTTCGTTA
Found at i:30616 original size:21 final size:21
Alignment explanation
Indices: 30591--30635 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
30581 CTTCTATTAC
*
30591 CTTTATTCAT-AAATTCACTCA
1 CTTTAATCATCAAATTCACT-A
*
30612 CTTTAATCATCAATTTCACTA
1 CTTTAATCATCAAATTCACTA
30633 CTT
1 CTT
30636 CATCACTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.31, C:0.24, G:0.00, T:0.44
Consensus pattern (21 bp):
CTTTAATCATCAAATTCACTA
Found at i:31938 original size:12 final size:13
Alignment explanation
Indices: 31916--31945 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
31906 ACTAACAACT
31916 AAAATCAATCAAG
1 AAAATCAATCAAG
31929 AAAA-CAATCAAG
1 AAAATCAATCAAG
31941 AAAAT
1 AAAAT
31946 TAAAGAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAATCAATCAAG
Found at i:35881 original size:76 final size:76
Alignment explanation
Indices: 35787--35938 Score: 180
Period size: 76 Copynumber: 2.0 Consensus size: 76
35777 TGATGAGCTA
* * * *
35787 TGACACAGCCCATCTGGGTGATCAGGCGAAACACATGGCTCTTCAG-ACAAACCATGTGGGCACC
1 TGACACAGCCCACCTGGGTCATCAAGCGAAACACATGGATCTTCAGAAC-AACCATGTGGGCACC
*
35851 CAGCTGGAGTCG
65 CAGCTAGAGTCG
* * * * * *
35863 TGACACTGCCCACCTGGGTCCTCAAGCTAACCACATGGATGTTCAGAACAACCATGTGGGCGCCC
1 TGACACAGCCCACCTGGGTCATCAAGCGAAACACATGGATCTTCAGAACAACCATGTGGGCACCC
*
35928 AGGTAGAGTCG
66 AGCTAGAGTCG
35939 GGGACAGCCA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
76 61 0.97
77 2 0.03
ACGTcount: A:0.26, C:0.30, G:0.27, T:0.18
Consensus pattern (76 bp):
TGACACAGCCCACCTGGGTCATCAAGCGAAACACATGGATCTTCAGAACAACCATGTGGGCACCC
AGCTAGAGTCG
Found at i:38219 original size:18 final size:19
Alignment explanation
Indices: 38184--38222 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
38174 CTCCCTATTT
38184 TTTTTTCTTTCTCTCTTCC
1 TTTTTTCTTTCTCTCTTCC
38203 TTTTTTCTGTT-TC-CTTCC
1 TTTTTTCT-TTCTCTCTTCC
38221 TT
1 TT
38223 GATCATGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
19 10 0.53
20 2 0.11
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.69
Consensus pattern (19 bp):
TTTTTTCTTTCTCTCTTCC
Found at i:39283 original size:39 final size:39
Alignment explanation
Indices: 39240--39613 Score: 217
Period size: 39 Copynumber: 10.2 Consensus size: 39
39230 ATTAACCGAT
* *
39240 AAGCAATGATCCTAAATCAGGATCGAAATAAAACTGACA
1 AAGCAATGATCCTAAATCAGGATTGAAATAAAACTGATA
* * ** *
39279 AAGCAATAATCCTAAATCATGATTGAAATTGAA-TCATA
1 AAGCAATGATCCTAAATCAGGATTGAAATAAAACTGATA
* * * *
39317 AAGCAACGAT-CAAAAT-AAGATTGAAA-ATAAACAGATA
1 AAGCAATGATCCTAAATCAGGATTGAAATA-AAACTGATA
*
39354 AAGCAATGATCCTAAACCAGGATTGAAA-ATAAACTGATA
1 AAGCAATGATCCTAAATCAGGATTGAAATA-AAACTGATA
* * * *
39393 AAGCAATAATCCTGAA-CTAGGATCGAGAAT-AAACTCATA
1 AAGCAATGATCCTAAATC-AGGATTGA-AATAAAACTGATA
*
39432 AAGCAATGATCCTAAACCAGGATTG-----AAA---ATA
1 AAGCAATGATCCTAAATCAGGATTGAAATAAAACTGATA
*
39463 AAGCAATGATCCTAAATCAAGATTG-----AAA-TG---
1 AAGCAATGATCCTAAATCAGGATTGAAATAAAACTGATA
* * * *
39493 AAGCAAAGATCATAAACCAGGATTGAAA-ATAAACTGAAA
1 AAGCAATGATCCTAAATCAGGATTGAAATA-AAACTGATA
* * * * * * *
39532 AAACTATGACCCTAAACCAGGATAGAAAT-AAATTAATA
1 AAGCAATGATCCTAAATCAGGATTGAAATAAAACTGATA
* * * *
39570 AAGCAATGATCCTAAACCAGGATCGAAA-ATAATTGATA
1 AAGCAATGATCCTAAATCAGGATTGAAATAAAACTGATA
39608 AAGCAA
1 AAGCAA
39614 AAGTTCTTGA
Statistics
Matches: 266, Mismatches: 48, Indels: 43
0.75 0.13 0.12
Matches are distributed among these distances:
30 21 0.08
31 29 0.11
34 3 0.01
35 3 0.01
36 13 0.05
37 17 0.06
38 59 0.22
39 118 0.44
40 3 0.01
ACGTcount: A:0.51, C:0.15, G:0.14, T:0.20
Consensus pattern (39 bp):
AAGCAATGATCCTAAATCAGGATTGAAATAAAACTGATA
Found at i:39467 original size:31 final size:31
Alignment explanation
Indices: 39429--39525 Score: 142
Period size: 31 Copynumber: 3.2 Consensus size: 31
39419 GAATAAACTC
39429 ATAAAGCAATGATCCTAAACCAGGATTGAAA
1 ATAAAGCAATGATCCTAAACCAGGATTGAAA
* *
39460 ATAAAGCAATGATCCTAAATCAAGATTG-AA
1 ATAAAGCAATGATCCTAAACCAGGATTGAAA
* * *
39490 ATGAAGCAAAGATCATAAACCAGGATTGAAA
1 ATAAAGCAATGATCCTAAACCAGGATTGAAA
39521 ATAAA
1 ATAAA
39526 CTGAAAAAAC
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
30 25 0.44
31 32 0.56
ACGTcount: A:0.52, C:0.13, G:0.15, T:0.20
Consensus pattern (31 bp):
ATAAAGCAATGATCCTAAACCAGGATTGAAA
Found at i:39609 original size:38 final size:39
Alignment explanation
Indices: 39493--39613 Score: 138
Period size: 38 Copynumber: 3.2 Consensus size: 39
39483 GATTGAAATG
* * * * *
39493 AAGCAAAGATCATAAACCAGGATTGAAAATAAACTGAAA
1 AAGCAATGATCCTAAACCAGGATAGAAAATAAATTGATA
* * * *
39532 AAACTATGACCCTAAACCAGGATAG-AAATAAATTAATA
1 AAGCAATGATCCTAAACCAGGATAGAAAATAAATTGATA
*
39570 AAGCAATGATCCTAAACCAGGATCGAAAAT-AATTGATA
1 AAGCAATGATCCTAAACCAGGATAGAAAATAAATTGATA
39608 AAGCAA
1 AAGCAA
39614 AAGTTCTTGA
Statistics
Matches: 67, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
38 44 0.66
39 23 0.34
ACGTcount: A:0.53, C:0.15, G:0.14, T:0.18
Consensus pattern (39 bp):
AAGCAATGATCCTAAACCAGGATAGAAAATAAATTGATA
Found at i:40332 original size:169 final size:170
Alignment explanation
Indices: 39783--40397 Score: 876
Period size: 170 Copynumber: 3.6 Consensus size: 170
39773 TGAAATGGTA
* * *
39783 CCCGGAGGACTTATCAGAATTAATACCCGAAGGTTTCTAAATTTGTGCCCGGAGGACATACCAAT
1 CCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAAT
* * * * * *
39848 GTGAACTTTGAATTGAGACCTTGAACAAGGATTTTAAGCTTAAACATGAACCTTTTTATGAAAAA
66 GTAAACTCTGAATAGAGACCTTGAACAAGGATTTTAAACTTAAACATGAATCTTTTGATGAAAAA
* *
39913 CATGATGAAATGAAATGGTACCCGGAGGTTTTACCGATTT
131 CTTGATGAAATGAAATGGTACCCGGAGGTTTTACCGATTG
* * *
39953 CCCGGAGGACTTATCAAAATTAATACTCAGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAAT
1 CCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAAT
* * * * * *
40018 GCAACCTTTGGATTGAAACCTTGAACAAGGATTTTAAACTTAAACATGAATCTTTTGATGAAAAA
66 GTAAACTCTGAATAGAGACCTTGAACAAGGATTTTAAACTTAAACATGAATCTTTTGATGAAAAA
*
40083 CTTGATTAAATGAAATGGTACCCGGAGGTTTTACCGATTG
131 CTTGATGAAATGAAATGGTACCCGGAGGTTTTACCGATTG
* * *
40123 CCTGGAGGACTTATCAGAATTAATACTCGGTGGTTTCTGAATTTGTGCCCGGAGGACTTACCAAT
1 CCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAAT
* *
40188 GTAAACTCTGAACAGAGACCTTGACCAAGGATTTTAAACTTAAACATGAATC-TTTGATGAAAAA
66 GTAAACTCTGAATAGAGACCTTGAACAAGGATTTTAAACTTAAACATGAATCTTTTGATGAAAAA
* * * *
40252 CTTGATGAAATGAAACGATACCCGGAGGTTTTATCAATTG
131 CTTGATGAAATGAAATGGTACCCGGAGGTTTTACCGATTG
* * *
40292 CCCGAAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGTCTTATCAAT
1 CCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAAT
* * * *
40357 G-CAATTCTGAAAAGAGACCTTAAACAAGGATTTT-AACTTAA
66 GTAAACTCTGAATAGAGACCTTGAACAAGGATTTTAAACTTAA
40398 CTTAATATGG
Statistics
Matches: 400, Mismatches: 45, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
167 7 0.02
168 28 0.07
169 107 0.27
170 258 0.64
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.29
Consensus pattern (170 bp):
CCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAAT
GTAAACTCTGAATAGAGACCTTGAACAAGGATTTTAAACTTAAACATGAATCTTTTGATGAAAAA
CTTGATGAAATGAAATGGTACCCGGAGGTTTTACCGATTG
Found at i:40640 original size:69 final size:69
Alignment explanation
Indices: 40490--40643 Score: 166
Period size: 69 Copynumber: 2.2 Consensus size: 69
40480 CTCATTTAAC
* * * * *
40490 TTGACTTATGGAAAAACCCTTGATGGTTGGATGGAATCAAAACTTCAACTATCTCGTATGGAAAC
1 TTGACTTATGGAAAAGCCCATGATGCTGGGATGGAACCAAAACTTCAACTATCTCGTATGGAAAC
40555 GAAT
66 GAAT
* * * * ** *
40559 TTGGCCTGTGGAAAAGCCCATGTTGCTGGGATGGAACCAAGGCTTGAACTGA-CTCGTATGGAAA
1 TTGACTTATGGAAAAGCCCATGATGCTGGGATGGAACCAAAACTTCAACT-ATCTCGTATGGAAA
* *
40623 TGACT
65 CGAAT
40628 TTGACTTATGGAAAAG
1 TTGACTTATGGAAAAG
40644 TCAAGCATTC
Statistics
Matches: 67, Mismatches: 17, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
69 66 0.99
70 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.27
Consensus pattern (69 bp):
TTGACTTATGGAAAAGCCCATGATGCTGGGATGGAACCAAAACTTCAACTATCTCGTATGGAAAC
GAAT
Found at i:40930 original size:35 final size:35
Alignment explanation
Indices: 40796--40983 Score: 182
Period size: 35 Copynumber: 5.3 Consensus size: 35
40786 ACCAATTTGC
* *
40796 GGTCAACTGAAATAAACTTAA-AAACGACCACCCTC
1 GGTCAACTGAAATAAACTGAAGAAA-GACCACCCTG
* * * * *
40831 GATCATTCTGACATAAACTGGAGAAAGACCACCCTA
1 GGTCA-ACTGAAATAAACTGAAGAAAGACCACCCTG
* * *
40867 AGTCAACTAAAAT-AACTGAAGAACGACCACCCTG
1 GGTCAACTGAAATAAACTGAAGAAAGACCACCCTG
* * * *
40901 GGCCAACTGAAATAAAATGAAGAGAGACCACCCGG
1 GGTCAACTGAAATAAACTGAAGAAAGACCACCCTG
** *
40936 GGTCAACTGAAATAGGCTGAAGAAAGACCGCCCTG
1 GGTCAACTGAAATAAACTGAAGAAAGACCACCCTG
40971 GGTCAACCTGAAA
1 GGTCAA-CTGAAA
40984 GTCAAAATTG
Statistics
Matches: 121, Mismatches: 28, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
34 28 0.23
35 60 0.50
36 30 0.25
37 3 0.02
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.15
Consensus pattern (35 bp):
GGTCAACTGAAATAAACTGAAGAAAGACCACCCTG
Found at i:42262 original size:9 final size:8
Alignment explanation
Indices: 42241--42285 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
42231 ATTTTTTTGA
42241 TTGATTTT
1 TTGATTTT
42249 TTGATTTT
1 TTGATTTT
42257 TGTGATTTTT
1 T-TGA-TTTT
*
42267 TTGATTTGA
1 TTGATTT-T
42276 TTGATTTT
1 TTGATTTT
42284 TT
1 TT
42286 TTTTGATGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
8 14 0.44
9 13 0.41
10 5 0.16
ACGTcount: A:0.13, C:0.00, G:0.16, T:0.71
Consensus pattern (8 bp):
TTGATTTT
Found at i:42266 original size:18 final size:18
Alignment explanation
Indices: 42236--42286 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
42226 TTGAAATTTT
42236 TTTGATTGA-TTTTTTGA
1 TTTGATTGATTTTTTTGA
*
42253 TTT-TTGTGATTTTTTTGA
1 TTTGAT-TGATTTTTTTGA
42271 TTTGATTGATTTTTTT
1 TTTGATTGATTTTTTT
42287 TTTGATGGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 1 0.03
17 6 0.21
18 21 0.72
19 1 0.03
ACGTcount: A:0.14, C:0.00, G:0.16, T:0.71
Consensus pattern (18 bp):
TTTGATTGATTTTTTTGA
Found at i:42287 original size:30 final size:29
Alignment explanation
Indices: 42231--42292 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
42221 TTACTTTGAA
*
42231 ATTTTTTTGATTGATTTTTTGATTTTTGTG
1 ATTTTTTTGATTGATTATTT-ATTTTTGTG
*
42261 ATTTTTTTGATTTGATTGATTT-TTTTTTTG
1 ATTTTTTTGA-TTGATT-ATTTATTTTTGTG
42291 AT
1 AT
42293 GGAGTGAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 19 0.68
31 6 0.21
32 3 0.11
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.71
Consensus pattern (29 bp):
ATTTTTTTGATTGATTATTTATTTTTGTG
Found at i:42595 original size:15 final size:14
Alignment explanation
Indices: 42577--42626 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 14
42567 CCGAGTTTCC
42577 GAAAACCATTTTTTT
1 GAAAACCA-TTTTTT
42592 GAAAA--ATATTTTT
1 GAAAACCAT-TTTTT
*
42605 GAAAAACA-TTTTT
1 GAAAACCATTTTTT
42618 GAAAACCAT
1 GAAAACCAT
42627 GACTCTTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
12 1 0.03
13 23 0.77
15 6 0.20
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (14 bp):
GAAAACCATTTTTT
Found at i:42623 original size:12 final size:13
Alignment explanation
Indices: 42587--42622 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
42577 GAAAACCATT
*
42587 TTTTTGAAAAATA
1 TTTTTGAAAAACA
42600 TTTTTGAAAAACA
1 TTTTTGAAAAACA
42613 TTTTTGAAAA
1 TTTTTGAAAA
42623 CCATGACTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (13 bp):
TTTTTGAAAAACA
Found at i:42725 original size:9 final size:9
Alignment explanation
Indices: 42679--42717 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
42669 AGTGCCTTTA
42679 TTTTCATTT
1 TTTTCATTT
42688 TTTTCA-TT
1 TTTTCATTT
**
42696 CATTCATTT
1 TTTTCATTT
42705 TTTTCATTT
1 TTTTCATTT
42714 TTTT
1 TTTT
42718 TTATTTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
8 6 0.24
9 19 0.76
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTCATTT
Found at i:44417 original size:19 final size:18
Alignment explanation
Indices: 44393--44428 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
44383 TGAAGTCTTA
44393 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
44412 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
44429 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:48688 original size:16 final size:16
Alignment explanation
Indices: 48669--48699 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48659 CATCTTTTTA
*
48669 ATTTTTTGATTTTTCC
1 ATTTTTTCATTTTTCC
48685 ATTTTTTCATTTTTC
1 ATTTTTTCATTTTTC
48700 ATCAATTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.71
Consensus pattern (16 bp):
ATTTTTTCATTTTTCC
Found at i:51095 original size:18 final size:19
Alignment explanation
Indices: 51060--51098 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
51050 ATTTCTATTT
51060 TTTTTTCTTTCTCTCTTCC
1 TTTTTTCTTTCTCTCTTCC
51079 TTTTTTCTGTT-TC-CTTCC
1 TTTTTTCT-TTCTCTCTTCC
51097 TT
1 TT
51099 GATCATGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
19 10 0.53
20 2 0.11
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.69
Consensus pattern (19 bp):
TTTTTTCTTTCTCTCTTCC
Found at i:81813 original size:29 final size:30
Alignment explanation
Indices: 81781--81850 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 30
81771 TGTTTGGATG
*
81781 TTTTGCTCCCTAAACT-TCAATTTTGGGCA
1 TTTTGCCCCCTAAACTCTCAATTTTGGGCA
*
81810 TTTTGCCCCCTAAACTCTCAATTTTGGGCG
1 TTTTGCCCCCTAAACTCTCAATTTTGGGCA
*
81840 TTTTTCCCCCT
1 TTTTGCCCCCT
81851 CTTAGGCTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 15 0.41
30 22 0.59
ACGTcount: A:0.16, C:0.30, G:0.13, T:0.41
Consensus pattern (30 bp):
TTTTGCCCCCTAAACTCTCAATTTTGGGCA
Found at i:81918 original size:32 final size:32
Alignment explanation
Indices: 81875--81968 Score: 152
Period size: 32 Copynumber: 2.9 Consensus size: 32
81865 ACCGTCATGC
*
81875 CGATGACGTGGCATTGCCACGTCAGATCAAAT
1 CGATGACGTGGCATTGCCACGTCGGATCAAAT
* *
81907 CGATGATGTGGCATTGTCACGTCGGATCAAAT
1 CGATGACGTGGCATTGCCACGTCGGATCAAAT
*
81939 CGATGAGGTGGCATTGCCACGTCGGATCAA
1 CGATGACGTGGCATTGCCACGTCGGATCAA
81969 GAGTAATTGC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (32 bp):
CGATGACGTGGCATTGCCACGTCGGATCAAAT
Done.