Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003556.1 Kokia drynarioides strain JFW-HI SEQ_116417, 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: 107881
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:602 original size:20 final size:21
Alignment explanation
Indices: 573--616 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
563 ATAATTTGAG
*
573 AATTGAGAATTTAGAATAA-A
1 AATTGAGAATTGAGAATAAGA
*
593 AATTGGGAATTGAGAATAAGA
1 AATTGAGAATTGAGAATAAGA
614 AAT
1 AAT
617 CAACAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.20, T:0.27
Consensus pattern (21 bp):
AATTGAGAATTGAGAATAAGA
Found at i:1016 original size:21 final size:21
Alignment explanation
Indices: 992--1053 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 21
982 TATTTTGGTT
992 CTGTTTTTTATTGTTTTAGTG
1 CTGTTTTTTATTGTTTTAGTG
* *
1013 CTGTTTCTTTTTGTTGTTTTCGTG
1 CTG--T-TTTTTATTGTTTTAGTG
*
1037 CTTTTTTTTATTGTTTT
1 CTGTTTTTTATTGTTTT
1054 GGTGATGCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 15 0.44
22 1 0.03
23 1 0.03
24 17 0.50
ACGTcount: A:0.05, C:0.08, G:0.16, T:0.71
Consensus pattern (21 bp):
CTGTTTTTTATTGTTTTAGTG
Found at i:1062 original size:24 final size:22
Alignment explanation
Indices: 995--1065 Score: 65
Period size: 24 Copynumber: 3.1 Consensus size: 22
985 TTTGGTTCTG
995 TTTTTTATTGTTTTAGTGCTG-TT
1 TTTTTTATTGTTTT-GTG-TGCTT
* *
1018 TCTTTTTGTTGTTTT-CGTGCTT
1 T-TTTTTATTGTTTTGTGTGCTT
1040 TTTTTTATTGTTTTGGTGATGCTT
1 TTTTTTATTGTTTT-GTG-TGCTT
1064 TT
1 TT
1066 GTTGTTAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
21 14 0.36
22 4 0.10
23 2 0.05
24 19 0.49
ACGTcount: A:0.06, C:0.07, G:0.18, T:0.69
Consensus pattern (22 bp):
TTTTTTATTGTTTTGTGTGCTT
Found at i:1065 original size:21 final size:21
Alignment explanation
Indices: 996--1065 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
986 TTGGTTCTGT
*
996 TTTTTATTGTTTTAGTGCTGTTTC
1 TTTTTATTGTTTT-G-G-TGATTC
* * * *
1020 TTTTTGTTGTTTTCGTGCTTT
1 TTTTTATTGTTTTGGTGATTC
*
1041 TTTTTATTGTTTTGGTGATGC
1 TTTTTATTGTTTTGGTGATTC
1062 TTTT
1 TTTT
1066 GTTGTTAATT
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
21 24 0.65
22 1 0.03
24 12 0.32
ACGTcount: A:0.06, C:0.07, G:0.19, T:0.69
Consensus pattern (21 bp):
TTTTTATTGTTTTGGTGATTC
Found at i:1084 original size:15 final size:14
Alignment explanation
Indices: 1064--1113 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
1054 GGTGATGCTT
1064 TTGTTGTTAATTTTG
1 TTGTTGTT-ATTTTG
1079 TTGTTG-T-TTTTG
1 TTGTTGTTATTTTG
*
1091 TTTTTGTTATTTTTG
1 TTGTTGTTA-TTTTG
1106 TTGTTGTT
1 TTGTTGTT
1114 TTTCTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 10 0.33
13 1 0.03
14 1 0.03
15 18 0.60
ACGTcount: A:0.06, C:0.00, G:0.20, T:0.74
Consensus pattern (14 bp):
TTGTTGTTATTTTG
Found at i:1089 original size:12 final size:12
Alignment explanation
Indices: 1062--1156 Score: 79
Period size: 12 Copynumber: 7.8 Consensus size: 12
1052 TTGGTGATGC
**
1062 TTTTGTTGTTAA
1 TTTTGTTGTTGT
1074 TTTTGTTGTTGT
1 TTTTGTTGTTGT
*
1086 TTTTGTTTTTGT
1 TTTTGTTGTTGT
1098 TATTT-TTGTTGT
1 T-TTTGTTGTTGT
* *
1110 TGTTT-TTCTATTT
1 T-TTTGTTGT-TGT
*
1123 TTTTGTTGCTG-
1 TTTTGTTGTTGT
1134 TTTTGATTGTTGT
1 TTTTG-TTGTTGT
1147 TTTTGTTGTT
1 TTTTGTTGTT
1157 TGAATGTTAT
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
11 5 0.07
12 49 0.73
13 13 0.19
ACGTcount: A:0.05, C:0.02, G:0.19, T:0.74
Consensus pattern (12 bp):
TTTTGTTGTTGT
Found at i:1089 original size:45 final size:46
Alignment explanation
Indices: 993--1089 Score: 103
Period size: 45 Copynumber: 2.2 Consensus size: 46
983 ATTTTGGTTC
* * * *
993 TGTTTTTTATTGTTTTAGTGCTGTTTCTTTTTGTTGTTTTCGTGCT
1 TGTTTTTTATTGTTTTAGTGATGCTTCTTGTTGTTATTTTCGTGCT
*
1039 T-TTTTTTATTGTTTTGGTGATGCTT-TTGTTGTTAATTTT-GTTG-T
1 TGTTTTTTATTGTTTTAGTGATGCTTCTTGTTGTT-ATTTTCG-TGCT
1083 TGTTTTT
1 TGTTTTT
1090 GTTTTTGTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
44 10 0.23
45 32 0.74
46 1 0.02
ACGTcount: A:0.06, C:0.05, G:0.20, T:0.69
Consensus pattern (46 bp):
TGTTTTTTATTGTTTTAGTGATGCTTCTTGTTGTTATTTTCGTGCT
Found at i:1125 original size:22 final size:21
Alignment explanation
Indices: 1082--1137 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
1072 AATTTTGTTG
* *
1082 TTGTTTTTGTTTTTGTTATTT
1 TTGTTGTTGTTTTTCTTATTT
*
1103 TTGTTGTTGTTTTTCTATTTTT
1 TTGTTGTTGTTTTTCT-TATTT
*
1125 TTGTTGCTGTTTT
1 TTGTTGTTGTTTT
1138 GATTGTTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.04, C:0.04, G:0.16, T:0.77
Consensus pattern (21 bp):
TTGTTGTTGTTTTTCTTATTT
Found at i:1164 original size:20 final size:20
Alignment explanation
Indices: 1135--1175 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1125 TTGTTGCTGT
* *
1135 TTTGATTGTTGTTTTTGTTG
1 TTTGAATGTTATTTTTGTTG
*
1155 TTTGAATGTTATTTTTTTTG
1 TTTGAATGTTATTTTTGTTG
1175 T
1 T
1176 ATTTTTACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.10, C:0.00, G:0.20, T:0.71
Consensus pattern (20 bp):
TTTGAATGTTATTTTTGTTG
Found at i:1643 original size:44 final size:44
Alignment explanation
Indices: 1593--1681 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
1583 CTAGTGAAAA
1593 CGCACCATGTAAGACGTACTTTCTTTTCTTTCCCAGAAGCACAT
1 CGCACCATGTAAGACGTACTTTCTTTTCTTTCCCAGAAGCACAT
*
1637 CGCACCATGTAAGATGTACTTTCTTTTCTTTCCCAGAAGCACAT
1 CGCACCATGTAAGACGTACTTTCTTTTCTTTCCCAGAAGCACAT
1681 C
1 C
1682 CTACGTGACG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.25, C:0.29, G:0.13, T:0.33
Consensus pattern (44 bp):
CGCACCATGTAAGACGTACTTTCTTTTCTTTCCCAGAAGCACAT
Found at i:7977 original size:24 final size:25
Alignment explanation
Indices: 7944--7991 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
7934 TCAATTAAAG
* *
7944 TATATTAAATTTTATTTTATAATTT
1 TATATTAAATTTAATTCTATAATTT
7969 TATA-TAAATTTAATTCTATAATT
1 TATATTAAATTTAATTCTATAATT
7992 AATATTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
TATATTAAATTTAATTCTATAATTT
Found at i:7996 original size:23 final size:24
Alignment explanation
Indices: 7949--7996 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
7939 TAAAGTATAT
* * *
7949 TAAATTTTATTTTATAATTTTATA
1 TAAATTTAATTCTATAATTTAATA
7973 TAAATTTAATTCTATAA-TTAATA
1 TAAATTTAATTCTATAATTTAATA
7996 T
1 T
7997 TATATACAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TAAATTTAATTCTATAATTTAATA
Found at i:8731 original size:23 final size:23
Alignment explanation
Indices: 8716--8766 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
8706 TTCACTCAAT
8716 TTTCTCTTTAAATTTCACATAAA
1 TTTCTCTTTAAATTTCACATAAA
* *
8739 TTTCTCTTTAAAATTCTCA-AAA
1 TTTCTCTTTAAATTTCACATAAA
8761 -TTCTCT
1 TTTCTCT
8767 AAAATTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 6 0.23
22 3 0.12
23 17 0.65
ACGTcount: A:0.31, C:0.20, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTCTCTTTAAATTTCACATAAA
Found at i:8772 original size:10 final size:9
Alignment explanation
Indices: 8748--8782 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
8738 ATTTCTCTTT
8748 AAAATTCTC
1 AAAATTCTC
8757 AAAATTCTC
1 AAAATTCTC
*
8766 TAAAATTTTC
1 -AAAATTCTC
8776 AAAATTC
1 AAAATTC
8783 ATTTAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (9 bp):
AAAATTCTC
Found at i:8801 original size:14 final size:14
Alignment explanation
Indices: 8784--8828 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
8774 TCAAAATTCA
8784 TTTAATTTAATTAT
1 TTTAATTTAATTAT
* *
8798 TTTATTTTTATT-T
1 TTTAATTTAATTAT
8811 TTATAATTTAATTAT
1 TT-TAATTTAATTAT
8826 TTT
1 TTT
8829 TAACAATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 3 0.12
14 19 0.76
15 3 0.12
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTAATTTAATTAT
Found at i:8822 original size:28 final size:28
Alignment explanation
Indices: 8786--8876 Score: 90
Period size: 28 Copynumber: 3.5 Consensus size: 28
8776 AAAATTCATT
*
8786 TAATTTAATTATTTTATTTTTATTTTTA
1 TAATTTAATTATTTTATTTTTATTTCTA
* *
8814 TAATTT-A--A--TTATTTTTA--ACAA
1 TAATTTAATTATTTTATTTTTATTTCTA
*
8835 T-ATTTAATTATTTTATTTTTATTTGTA
1 TAATTTAATTATTTTATTTTTATTTCTA
8862 TAATTTAATTATTTT
1 TAATTTAATTATTTT
8877 TAATAATATT
Statistics
Matches: 49, Mismatches: 6, Indels: 16
0.69 0.08 0.23
Matches are distributed among these distances:
20 4 0.08
21 3 0.06
23 10 0.20
25 10 0.20
27 3 0.06
28 19 0.39
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (28 bp):
TAATTTAATTATTTTATTTTTATTTCTA
Found at i:8840 original size:48 final size:48
Alignment explanation
Indices: 8788--8892 Score: 192
Period size: 48 Copynumber: 2.2 Consensus size: 48
8778 AATTCATTTA
*
8788 ATTTAATTATTTTATTTTTATTTTTATAATTTAATTATTTTTAACAAT
1 ATTTAATTATTTTATTTTTATTTGTATAATTTAATTATTTTTAACAAT
*
8836 ATTTAATTATTTTATTTTTATTTGTATAATTTAATTATTTTTAATAAT
1 ATTTAATTATTTTATTTTTATTTGTATAATTTAATTATTTTTAACAAT
8884 ATTTAATTA
1 ATTTAATTA
8893 ACTATCTCGA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (48 bp):
ATTTAATTATTTTATTTTTATTTGTATAATTTAATTATTTTTAACAAT
Found at i:8873 original size:23 final size:23
Alignment explanation
Indices: 8799--8878 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 23
8789 TTTAATTATT
*
8799 TTATTTTTATTTTTATAATTTAA
1 TTATTTTTATTTATATAATTTAA
** * *
8822 TTATTTTTAACAATATTTAA-TTATT
1 TTATTTTT-A-TTTATATAATTTA-A
*
8847 TTATTTTTATTTGTATAATTTAA
1 TTATTTTTATTTATATAATTTAA
8870 TTATTTTTA
1 TTATTTTTA
8879 ATAATATTTA
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
23 22 0.51
24 8 0.19
25 13 0.30
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (23 bp):
TTATTTTTATTTATATAATTTAA
Found at i:8880 original size:10 final size:10
Alignment explanation
Indices: 8788--8892 Score: 60
Period size: 10 Copynumber: 10.9 Consensus size: 10
8778 AATTCATTTA
8788 ATTTAATTAT
1 ATTTAATTAT
* *
8798 -TTTATTTTT
1 ATTTAATTAT
8807 ATTT--TTAT
1 ATTTAATTAT
8815 AATTTAATTAT
1 -ATTTAATTAT
* **
8826 TTTTAACAAT
1 ATTTAATTAT
8836 ATTTAATTAT
1 ATTTAATTAT
* *
8846 -TTTATTTTT
1 ATTTAATTAT
*
8855 ATTT--GTAT
1 ATTTAATTAT
8863 AATTTAATTAT
1 -ATTTAATTAT
* *
8874 TTTTAATAAT
1 ATTTAATTAT
8884 ATTTAATTA
1 ATTTAATTA
8893 ACTATCTCGA
Statistics
Matches: 69, Mismatches: 18, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
8 5 0.07
9 22 0.32
10 35 0.51
11 7 0.10
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (10 bp):
ATTTAATTAT
Found at i:12686 original size:21 final size:20
Alignment explanation
Indices: 12642--12697 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
12632 TTAAAATACC
*
12642 AAACCCTAATTTTAATAACAT
1 AAACCCTAA-TTTAAAAACAT
*
12663 AAACCCTAATTTAAAAACCCT
1 AAACCCTAATTTAAAAA-CAT
12684 AAA-CCTAA-TTAAAA
1 AAACCCTAATTTAAAA
12698 CAAAAACACC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.19
20 12 0.38
21 14 0.44
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (20 bp):
AAACCCTAATTTAAAAACAT
Found at i:15339 original size:29 final size:28
Alignment explanation
Indices: 15264--15444 Score: 150
Period size: 29 Copynumber: 6.2 Consensus size: 28
15254 GCCACTATTT
* * * *
15264 TTTTCTAGATTTTACAGTTTTACCACTA
1 TTTTCCAGATTTTAAAGTTTTGCCACTG
* * *
15292 TTTTCTAGATTTCACAGTTTTGCCACTAG
1 TTTTCCAGATTTTAAAGTTTTGCCACT-G
*
15321 TTTTCCAGATTTTAAAGTTCTGCCACTGG
1 TTTTCCAGATTTTAAAGTTTTGCCACT-G
*
15350 TTTTCCCAGATTTTACAA-TTTTGGCACTG
1 TTTT-CCAGATTTTA-AAGTTTTGCCACTG
* * * *
15379 ATTTTCTAGATTTTATAGTTCTACCACTG
1 -TTTTCCAGATTTTAAAGTTTTGCCACTG
*
15408 TTATTCCAGATTTTACAA-TTTTGCTACTG
1 TT-TTCCAGATTTTA-AAGTTTTGCCACTG
15437 ATTTTCCA
1 -TTTTCCA
15445 AATCTCTGTG
Statistics
Matches: 125, Mismatches: 20, Indels: 15
0.78 0.12 0.09
Matches are distributed among these distances:
28 28 0.22
29 70 0.56
30 25 0.20
31 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.46
Consensus pattern (28 bp):
TTTTCCAGATTTTAAAGTTTTGCCACTG
Found at i:15361 original size:59 final size:57
Alignment explanation
Indices: 15264--15444 Score: 211
Period size: 59 Copynumber: 3.1 Consensus size: 57
15254 GCCACTATTT
* * * * * * *
15264 TTTTCTAGATTTTACAGTTTTACCACTATTTTCTAGATTTCACAGTTTTGCCACT-A
1 TTTTCCAGATTTTAAAGTTCTACCACTGTTTTCCAGATTTTACAATTTTGCCACTGA
* *
15320 GTTTTCCAGATTTTAAAGTTCTGCCACTGGTTTTCCCAGATTTTACAATTTTGGCACTGA
1 -TTTTCCAGATTTTAAAGTTCTACCACT-GTTTT-CCAGATTTTACAATTTTGCCACTGA
* * *
15380 TTTTCTAGATTTTATAGTTCTACCACTGTTATTCCAGATTTTACAATTTTGCTACTGA
1 TTTTCCAGATTTTAAAGTTCTACCACTGTT-TTCCAGATTTTACAATTTTGCCACTGA
15438 TTTTCCA
1 TTTTCCA
15445 AATCTCTGTG
Statistics
Matches: 105, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
57 23 0.22
58 36 0.34
59 45 0.43
60 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.46
Consensus pattern (57 bp):
TTTTCCAGATTTTAAAGTTCTACCACTGTTTTCCAGATTTTACAATTTTGCCACTGA
Found at i:15383 original size:88 final size:87
Alignment explanation
Indices: 15226--15422 Score: 225
Period size: 88 Copynumber: 2.2 Consensus size: 87
15216 ATGACCATGC
* * ** ** * * *
15226 ACCATTGTTTTACAGATTTTGTAGTTCTGCCACTATTTTTTTCTAGATTTTACAGTTTTACCACT
1 ACCACTGTTTTCCAGATTTTAAAGTTCTGCCACTAGGTTTTCCCAGATTTTACAATTTTACCACT
*
15291 ATTTTCTAGATTTCACAGTTTT
66 ATTTTCTAGATTTCACAGTTCT
* **
15313 GCCACTAGTTTTCCAGATTTTAAAGTTCTGCCACT-GGTTTTCCCAGATTTTACAATTTTGGCAC
1 ACCACT-GTTTTCCAGATTTTAAAGTTCTGCCACTAGGTTTTCCCAGATTTTACAATTTTACCAC
* *
15377 TGATTTTCTAGATTTTATAGTTCT
65 T-ATTTTCTAGATTTCACAGTTCT
15401 ACCACTGTTATTCCAGATTTTA
1 ACCACTGTT-TTCCAGATTTTA
15423 CAATTTTGCT
Statistics
Matches: 91, Mismatches: 16, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
87 30 0.33
88 61 0.67
ACGTcount: A:0.22, C:0.19, G:0.12, T:0.47
Consensus pattern (87 bp):
ACCACTGTTTTCCAGATTTTAAAGTTCTGCCACTAGGTTTTCCCAGATTTTACAATTTTACCACT
ATTTTCTAGATTTCACAGTTCT
Found at i:28133 original size:33 final size:33
Alignment explanation
Indices: 28064--28138 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
28054 TGAAGGTAGT
* *
28064 TTCATCAATGATTGGAACATCCATCGAGGTAAC
1 TTCATCATTGATTGGAACATCCATCGAGGCAAC
* * *
28097 TTCATCATTGTTTGGAACATCTC-TCGGGGCAGC
1 TTCATCATTGATTGGAACATC-CATCGAGGCAAC
28130 TTCATCATT
1 TTCATCATT
28139 CTGTTCGACT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
33 35 0.97
34 1 0.03
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (33 bp):
TTCATCATTGATTGGAACATCCATCGAGGCAAC
Found at i:68972 original size:21 final size:21
Alignment explanation
Indices: 68939--68979 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
68929 TTTCAGTACA
*
68939 TAGTTTAGTTGCA-TGTCATG
1 TAGTTTAATTGCATTGTCATG
68959 TAGTTATAATTGCATTGTCAT
1 TAGTT-TAATTGCATTGTCAT
68980 CACATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.46
Consensus pattern (21 bp):
TAGTTTAATTGCATTGTCATG
Found at i:76392 original size:130 final size:130
Alignment explanation
Indices: 76155--76401 Score: 476
Period size: 130 Copynumber: 1.9 Consensus size: 130
76145 ATCAAGAAAG
76155 CAATAAAATGCATTACCTGCTAATCTATCCAACATTTGATCTATAAACGACAAAGGAAAATGATC
1 CAATAAAATGCATTACCTGCTAATCTATCCAACATTTGATCTATAAACGACAAAGGAAAATGATC
*
76220 CTTCCTCATAGCTTTGTTGAGTTTCTTATAATCCATATAAAATCTCCAACCTTTAATAATCCATA
66 CTTCCTCATAGCTTTGTTGAGTTTCTTATAATCCATACAAAATCTCCAACCTTTAATAATCCATA
*
76285 CAATAAAATGCATTACCTGCTAATCTATCCAACATTTGATCTATAAACGACAAATGAAAATGATC
1 CAATAAAATGCATTACCTGCTAATCTATCCAACATTTGATCTATAAACGACAAAGGAAAATGATC
76350 CTTCCTCATAGCTTTGTTGAGTTTCTTATAATCCATACAAAATCTCCAACCT
66 CTTCCTCATAGCTTTGTTGAGTTTCTTATAATCCATACAAAATCTCCAACCT
76402 GTAACAGTCC
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 115 1.00
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.33
Consensus pattern (130 bp):
CAATAAAATGCATTACCTGCTAATCTATCCAACATTTGATCTATAAACGACAAAGGAAAATGATC
CTTCCTCATAGCTTTGTTGAGTTTCTTATAATCCATACAAAATCTCCAACCTTTAATAATCCATA
Found at i:80830 original size:36 final size:36
Alignment explanation
Indices: 80779--81017 Score: 183
Period size: 36 Copynumber: 6.6 Consensus size: 36
80769 TTCAAATGAA
* * * * *
80779 GCATACGTCTCGGTTAGAGCGTCTTGCTATGACGTT
1 GCATATGTCTCGGTTAGAGCATATTGCTACGAAGTT
* * *
80815 GCATATGTCTTGGTTAGAGCATATCGCTACAAAGTT
1 GCATATGTCTCGGTTAGAGCATATTGCTACGAAGTT
*
80851 GCATATGTCTCGATTAGAGCATATTGCTACGAAGTT
1 GCATATGTCTCGGTTAGAGCATATTGCTACGAAGTT
* * * * * *
80887 ACATATGTCCCGGTTAGAGCATATTACTATGATGCT
1 GCATATGTCTCGGTTAGAGCATATTGCTACGAAGTT
* * * * *
80923 GCATATATCTCGATTAGAGTATATTTCTATGATA-TT
1 GCATATGTCTCGGTTAGAGCATATTGCTACGA-AGTT
* ** * * * *
80959 ACATACATCTTGGTTAGAGCATATTGTTATGATGTT
1 GCATATGTCTCGGTTAGAGCATATTGCTACGAAGTT
** * *
80995 GCATACATCTCAGTTAAAGCATA
1 GCATATGTCTCGGTTAGAGCATA
81018 ATGTTAAGTG
Statistics
Matches: 162, Mismatches: 39, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
36 162 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36
Consensus pattern (36 bp):
GCATATGTCTCGGTTAGAGCATATTGCTACGAAGTT
Found at i:80902 original size:72 final size:72
Alignment explanation
Indices: 80779--80982 Score: 212
Period size: 72 Copynumber: 2.8 Consensus size: 72
80769 TTCAAATGAA
* * * * * * *
80779 GCATACGTCTCGGTTAGAGCGTCTTGCTATGACGTTGCATATGTCTTGGTTAGAGCATATCGCTA
1 GCATATGTCTCGATTAGAGCATATTGCTATGAAGTTACATATGTCTTGGTTAGAGCATATCACTA
*
80844 CAAAGTT
66 CAAAGCT
* ** *
80851 GCATATGTCTCGATTAGAGCATATTGCTACGAAGTTACATATGTCCCGGTTAGAGCATATTACTA
1 GCATATGTCTCGATTAGAGCATATTGCTATGAAGTTACATATGTCTTGGTTAGAGCATATCACTA
** *
80916 TGATGCT
66 CAAAGCT
* * * **
80923 GCATATATCTCGATTAGAGTATATTTCTATGATA-TTACATACATCTTGGTTAGAGCATAT
1 GCATATGTCTCGATTAGAGCATATTGCTATGA-AGTTACATATGTCTTGGTTAGAGCATAT
80983 TGTTATGATG
Statistics
Matches: 108, Mismatches: 23, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
72 107 0.99
73 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (72 bp):
GCATATGTCTCGATTAGAGCATATTGCTATGAAGTTACATATGTCTTGGTTAGAGCATATCACTA
CAAAGCT
Found at i:80983 original size:72 final size:72
Alignment explanation
Indices: 80786--81005 Score: 208
Period size: 72 Copynumber: 3.1 Consensus size: 72
80776 GAAGCATACG
* * * * * * ** * ** *
80786 TCTCGGTTAGAGCGTCTTGCTATGACGTTGCATATGTCTTGGTTAGAGCATATCGCTACAAAGTT
1 TCTCGATTAGAGCATATTGCTACGAAGTTACATACATCTTGGTTAGAGCATATTGCTATGATGTT
*
80851 GCATATG
66 GCATATA
** ** * *
80858 TCTCGATTAGAGCATATTGCTACGAAGTTACATATGTCCCGGTTAGAGCATATTACTATGATGCT
1 TCTCGATTAGAGCATATTGCTACGAAGTTACATACATCTTGGTTAGAGCATATTGCTATGATGTT
80923 GCATATA
66 GCATATA
* * * *
80930 TCTCGATTAGAGTATATTTCTATGATA-TTACATACATCTTGGTTAGAGCATATTGTTATGATGT
1 TCTCGATTAGAGCATATTGCTACGA-AGTTACATACATCTTGGTTAGAGCATATTGCTATGATGT
*
80994 TGCATACA
65 TGCATATA
81002 TCTC
1 TCTC
81006 AGTTAAAGCA
Statistics
Matches: 121, Mismatches: 26, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
72 120 0.99
73 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (72 bp):
TCTCGATTAGAGCATATTGCTACGAAGTTACATACATCTTGGTTAGAGCATATTGCTATGATGTT
GCATATA
Found at i:84984 original size:40 final size:40
Alignment explanation
Indices: 84939--85029 Score: 157
Period size: 40 Copynumber: 2.3 Consensus size: 40
84929 TGAGAATATA
84939 GTTAAAAAGGAAGACTTATGACTCAATAGAGCATAAGATT
1 GTTAAAAAGGAAGACTTATGACTCAATAGAGCATAAGATT
**
84979 GTTAAAAAGGAAGACTTATGACTCGGTAGAGCATAAGATT
1 GTTAAAAAGGAAGACTTATGACTCAATAGAGCATAAGATT
85019 GTT-AAAAGGAA
1 GTTAAAAAGGAA
85030 AACACATGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
39 8 0.16
40 41 0.84
ACGTcount: A:0.44, C:0.09, G:0.23, T:0.24
Consensus pattern (40 bp):
GTTAAAAAGGAAGACTTATGACTCAATAGAGCATAAGATT
Found at i:90050 original size:21 final size:21
Alignment explanation
Indices: 90009--90050 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
89999 GATATACAAA
*
90009 ACTAACAGTGAGTACCGAAGT
1 ACTAACAGTGAGTACAGAAGT
* *
90030 ACTATCAGTGAGTACATAAGT
1 ACTAACAGTGAGTACAGAAGT
90051 GCTGATGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (21 bp):
ACTAACAGTGAGTACAGAAGT
Found at i:90193 original size:23 final size:24
Alignment explanation
Indices: 90058--90204 Score: 132
Period size: 23 Copynumber: 6.5 Consensus size: 24
90048 AGTGCTGATG
90058 AAAT-AGTAAGCACACACAGTGC-
1 AAATCAGTAAGCACACACAGTGCT
* * *
90080 AAATCAGTAGGCACACACAGTCCA
1 AAATCAGTAAGCACACACAGTGCT
*
90104 AAAT-AGTAAGCACACACAATGC-
1 AAATCAGTAAGCACACACAGTGCT
* *
90126 AAATCAGTAAGCACATATAGTG-T
1 AAATCAGTAAGCACACACAGTGCT
* *
90149 GAATCAATAAG--CACACAGTGCT
1 AAATCAGTAAGCACACACAGTGCT
* *
90171 GAA-CAGTAAGCACACACAATGCT
1 AAATCAGTAAGCACACACAGTGCT
*
90194 GAA-CAGTAAGC
1 AAATCAGTAAGC
90205 GAGCTAATGT
Statistics
Matches: 104, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
21 13 0.12
22 12 0.12
23 75 0.72
24 4 0.04
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.16
Consensus pattern (24 bp):
AAATCAGTAAGCACACACAGTGCT
Found at i:91211 original size:27 final size:24
Alignment explanation
Indices: 91181--91232 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 24
91171 TCTTTTTGCC
91181 CTTTTCTTCCTTTTGGTCCCTCTCCTT
1 CTTTT-TTCC-TTT-GTCCCTCTCCTT
91208 C---TTTCCTTTGTCCCTCTCCTT
1 CTTTTTTCCTTTGTCCCTCTCCTT
91229 CTTT
1 CTTT
91233 CCTTTCTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 9
0.71 0.00 0.29
Matches are distributed among these distances:
21 13 0.59
22 3 0.14
23 4 0.18
24 1 0.05
27 1 0.05
ACGTcount: A:0.00, C:0.38, G:0.06, T:0.56
Consensus pattern (24 bp):
CTTTTTTCCTTTGTCCCTCTCCTT
Found at i:91222 original size:21 final size:22
Alignment explanation
Indices: 91187--91237 Score: 86
Period size: 21 Copynumber: 2.3 Consensus size: 22
91177 TGCCCTTTTC
91187 TTCCTTTTGGTCCCTCTCCTTCT
1 TTCC-TTTGGTCCCTCTCCTTCT
91210 TTCCTTT-GTCCCTCTCCTTCT
1 TTCCTTTGGTCCCTCTCCTTCT
91231 TTCCTTT
1 TTCCTTT
91238 CTAATCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.75
22 3 0.11
23 4 0.14
ACGTcount: A:0.00, C:0.39, G:0.06, T:0.55
Consensus pattern (22 bp):
TTCCTTTGGTCCCTCTCCTTCT
Found at i:94190 original size:6 final size:6
Alignment explanation
Indices: 94179--94205 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
94169 ATGTCTCAGG
94179 ATGAGA ATGAGA ATGAGA ATGAGA ATG
1 ATGAGA ATGAGA ATGAGA ATGAGA ATG
94206 TGATAAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.33, T:0.19
Consensus pattern (6 bp):
ATGAGA
Found at i:94309 original size:41 final size:40
Alignment explanation
Indices: 94210--94383 Score: 215
Period size: 40 Copynumber: 4.2 Consensus size: 40
94200 AGAATGTGAT
* * *
94210 AAAGGAAGACTCATGACTCGAAAGGAGCATGAGAATATTGTTAA
1 AAAGGAAGACTTATGACTCGATA-GAGCAT---AAGATTGTTAA
* * *
94254 AAAGGAAGACTTATGACTCGGTAGAGCATATGATTGTTTA
1 AAAGGAAGACTTATGACTCGATAGAGCATAAGATTGTTAA
94294 AAAGGAAGACTTTATGACTCGATAGAGCATAAGATTGTTAA
1 AAAGGAAGAC-TTATGACTCGATAGAGCATAAGATTGTTAA
* * *
94335 AAATGAAGACTTATGACTAGATAGAGCATAAGATTATT-A
1 AAAGGAAGACTTATGACTCGATAGAGCATAAGATTGTTAA
94374 AAAGGAAGAC
1 AAAGGAAGAC
94384 ACATGAACCT
Statistics
Matches: 116, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
39 10 0.09
40 44 0.38
41 36 0.31
43 6 0.05
44 20 0.17
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.25
Consensus pattern (40 bp):
AAAGGAAGACTTATGACTCGATAGAGCATAAGATTGTTAA
Found at i:94348 original size:81 final size:81
Alignment explanation
Indices: 94210--94389 Score: 229
Period size: 81 Copynumber: 2.2 Consensus size: 81
94200 AGAATGTGAT
* * *
94210 AAAGGAAGACTCATGACTCGAAAGGAGCATGAGAATATTGTTAAAAAGGAAGACTTATGACTCGG
1 AAAGGAAGACTCATGACTCGAAAGGAGCAT--GAAGATTGTTAAAAAGGAAGACTTATGACTAGA
* *
94275 TAGAGCATATGATTGTTTA
64 TAGAGCATAAGATT-ATTA
* * *
94294 AAAGGAAGACTTTATGACTCGATA-GAGCAT-AAGATTGTTAAAAATGAAGACTTATGACTAGAT
1 AAAGGAAGAC-TCATGACTCGAAAGGAGCATGAAGATTGTTAAAAAGGAAGACTTATGACTAGAT
94357 AGAGCATAAGATTATTA
65 AGAGCATAAGATTATTA
*
94374 AAAGGAAGACACATGA
1 AAAGGAAGACTCATGA
94390 ACCTGTGTAG
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
79 4 0.05
80 13 0.15
81 41 0.48
84 16 0.19
85 11 0.13
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.24
Consensus pattern (81 bp):
AAAGGAAGACTCATGACTCGAAAGGAGCATGAAGATTGTTAAAAAGGAAGACTTATGACTAGATA
GAGCATAAGATTATTA
Found at i:94539 original size:9 final size:9
Alignment explanation
Indices: 94527--94551 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
94517 TATTGTTGTT
94527 ATTTTGTAG
1 ATTTTGTAG
94536 ATTTTGTAG
1 ATTTTGTAG
94545 ATTTTGT
1 ATTTTGT
94552 TTTGGCTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (9 bp):
ATTTTGTAG
Found at i:94984 original size:24 final size:22
Alignment explanation
Indices: 94957--95009 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
94947 TATATAGGTG
*
94957 TCGGTAGATTTGTGTATGCTTGTA
1 TCGGTAGA-TTATG-ATGCTTGTA
94981 TCGGTAG-TTATGATGCTTGTA
1 TCGGTAGATTATGATGCTTGTA
95002 TCGGTAGA
1 TCGGTAGA
95010 AGTTACAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 16 0.59
22 4 0.15
24 7 0.26
ACGTcount: A:0.19, C:0.09, G:0.30, T:0.42
Consensus pattern (22 bp):
TCGGTAGATTATGATGCTTGTA
Found at i:97143 original size:38 final size:38
Alignment explanation
Indices: 97092--97168 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
97082 AGGGACAAAG
*
97092 TATGTGTTCTTAATAATCTAGATTTGAGACGAGATATC
1 TATGTGTTCTTAATAATCTAGATTTGAGACGAGACATC
97130 TATGTGTTCTTAATAATCTAGATTTGAGACGAGACATC
1 TATGTGTTCTTAATAATCTAGATTTGAGACGAGACATC
97168 T
1 T
97169 CGGTAGAGGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (38 bp):
TATGTGTTCTTAATAATCTAGATTTGAGACGAGACATC
Done.