Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1989
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: 22301
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:761 original size:16 final size:15
Alignment explanation
Indices: 740--787 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
730 GATGTGAATA
740 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
756 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
771 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
787 A
1 A
788 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:763 original size:24 final size:24
Alignment explanation
Indices: 736--791 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
726 TAATGATGTG
*
736 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
* *
760 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
784 AATAATAA
1 AATAATAA
792 TAATTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:770 original size:8 final size:8
Alignment explanation
Indices: 736--787 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
726 TAATGATGTG
*
736 AATAATAA
1 AATATTAA
744 AATATATAA
1 AATAT-TAA
753 AATA-TAA
1 AATATTAA
760 AATATTAA
1 AATATTAA
*
768 AATATCAA
1 AATATTAA
*
776 AATATTAG
1 AATATTAA
784 AATA
1 AATA
788 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:1003 original size:22 final size:24
Alignment explanation
Indices: 940--1004 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
930 CGTGATAATA
*
940 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATATATACATAATATAG-G
*
965 TTAAAAATACATACATAATATA-G
1 TTAAAAATATATACATAATATAGG
*
988 TT-AAGATATATACATAA
1 TTAAAAATATATACATAA
1005 GATAACATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 13 0.36
23 3 0.08
25 20 0.56
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (24 bp):
TTAAAAATATATACATAATATAGG
Found at i:1052 original size:29 final size:31
Alignment explanation
Indices: 993--1072 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 31
983 TATAGTTAAG
* * * *
993 ATATATACATAAGATAACATGTAAAATATAT
1 ATATATAAATAATATAATATGTAAAAGATAT
1024 ATATATAAATAATATAATAT-T-AAAGATAT
1 ATATATAAATAATATAATATGTAAAAGATAT
*
1053 ATA-ATAAAATAGTATAATAT
1 ATATAT-AAATAATATAATAT
1073 ATATACGTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
28 2 0.05
29 23 0.53
30 1 0.02
31 17 0.40
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (31 bp):
ATATATAAATAATATAATATGTAAAAGATAT
Found at i:1053 original size:31 final size:31
Alignment explanation
Indices: 993--1072 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
983 TATAGTTAAG
* * *
993 ATATATACATAAGATAACATGTAAAATATAT
1 ATATATAAATAATATAATATGTAAAATATAT
1024 ATATATAAATAATATAATAT-TAAAGATATAT
1 ATATATAAATAATATAATATGTAAA-ATATAT
*
1055 A-ATA-AAATAGTATAATAT
1 ATATATAAATAATATAATAT
1073 ATATACGTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
29 13 0.30
30 7 0.16
31 24 0.55
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (31 bp):
ATATATAAATAATATAATATGTAAAATATAT
Found at i:1054 original size:16 final size:16
Alignment explanation
Indices: 1014--1075 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 16
1004 AGATAACATG
1014 TAAAATATAT-ATATA
1 TAAAATATATAATATA
1029 T-AAATAATATAATAT-
1 TAAAAT-ATATAATATA
*
1044 T-AAAGATAT-ATA-A
1 TAAAATATATAATATA
1057 TAAAATAGTATAATATA
1 TAAAATA-TATAATATA
1074 TA
1 TA
1076 TACGTAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
13 4 0.11
14 12 0.32
15 12 0.32
16 7 0.18
17 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
TAAAATATATAATATA
Found at i:1147 original size:29 final size:29
Alignment explanation
Indices: 1020--1147 Score: 68
Period size: 29 Copynumber: 4.3 Consensus size: 29
1010 CATGTAAAAT
*
1020 ATATATATATAAATAATATAATATTAAAGAT
1 ATATA-ATATAAATAATATAATATT-AAGAA
* *
1051 ATATAATA-AAATAGTATAATATATATACGTA
1 ATATAATATAAATAATATAATAT-TA-A-GAA
* **
1082 ATATAGA-ATTTAA-AATACCTAATA-TATTAA
1 ATATA-ATA-TAAATAATA--TAATATTAAGAA
* *
1112 A-AGAATATATATAATATAATATTAAGAA
1 ATATAATATAAATAATATAATATTAAGAA
1140 ATATAATA
1 ATATAATA
1148 ATAACAAAAA
Statistics
Matches: 71, Mismatches: 14, Indels: 26
0.64 0.13 0.23
Matches are distributed among these distances:
27 5 0.07
28 8 0.11
29 26 0.37
30 7 0.10
31 12 0.17
32 6 0.08
33 2 0.03
34 5 0.07
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (29 bp):
ATATAATATAAATAATATAATATTAAGAA
Found at i:1148 original size:23 final size:25
Alignment explanation
Indices: 1105--1150 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1095 AATACCTAAT
1105 ATATTAAAAGAATATATATAATATA
1 ATATTAAAAGAATATATATAATATA
*
1130 ATATTAAGA-AATATA-ATAATA
1 ATATTAAAAGAATATATATAATA
1151 ACAAAAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATTAAAAGAATATATATAATATA
Found at i:1712 original size:30 final size:30
Alignment explanation
Indices: 1634--1748 Score: 144
Period size: 30 Copynumber: 3.8 Consensus size: 30
1624 TAGGTACAAG
* *
1634 TGGTGGTGGAGCAAGTGTGGTTAGTGGAGT
1 TGGTGGTGGAGAAAGTGTGGCTAGTGGAGT
* ** *
1664 AGGTAATGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGAAAGTGTGGCTAGTGGAGT
1694 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGAAA-GTGTGGCTAGTGGAGT
1724 TGGTGGTGGA-AAAGGTGTGGCTAGT
1 TGGTGGTGGAGAAA-GTGTGGCTAGT
1749 TGAGAAAAGT
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
29 2 0.03
30 74 0.97
ACGTcount: A:0.21, C:0.04, G:0.48, T:0.27
Consensus pattern (30 bp):
TGGTGGTGGAGAAAGTGTGGCTAGTGGAGT
Found at i:2461 original size:15 final size:15
Alignment explanation
Indices: 2437--2469 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2427 GAGTGATTTG
*
2437 AAAAATATAAATTGA
1 AAAAAAATAAATTGA
2452 AAAAAAATAAATTGA
1 AAAAAAATAAATTGA
2467 AAA
1 AAA
2470 GCAGAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (15 bp):
AAAAAAATAAATTGA
Found at i:2552 original size:103 final size:102
Alignment explanation
Indices: 2369--2556 Score: 252
Period size: 103 Copynumber: 1.8 Consensus size: 102
2359 CATTAAAAAT
* * *
2369 AGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACATCTCTCGCAATATGAGTGAT
1 AGAAATTAAAAAGACCTCAGCACGTGAGCCAAGGCTCAACTCACA-CTCTCGCAATATGAGTGAT
* *
2434 TTGAAAAATATAAATTGAAAAAAAATAAATTGAAAAGC
65 TTGAAAAACAGAAATTGAAAAAAAATAAATTGAAAAGC
* ** *
2472 AGAAATTAAAAAGACCTCAGCATGTGAGCTGAGGCTCAACTCAC-CTCTCGCAATATGAGTTATT
1 AGAAATTAAAAAGACCTCAGCACGTGAGCCAAGGCTCAACTCACACTCTCGCAATATGAGTGA--
*
2536 TTTGACAAACAGAAATTGAAA
64 TTTGAAAAACAGAAATTGAAA
2557 TTACCTCAGC
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
101 17 0.23
103 56 0.77
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (102 bp):
AGAAATTAAAAAGACCTCAGCACGTGAGCCAAGGCTCAACTCACACTCTCGCAATATGAGTGATT
TGAAAAACAGAAATTGAAAAAAAATAAATTGAAAAGC
Found at i:2637 original size:73 final size:73
Alignment explanation
Indices: 2463--2684 Score: 320
Period size: 73 Copynumber: 3.0 Consensus size: 73
2453 AAAAAATAAA
* * **
2463 TTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCTGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTAAAAATACCTCAGC--GTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
2528 GAGTT-ATTT
64 GAGTTGATTT
* * * * * *
2537 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCTCCTTTCGCAATATGA
1 TTGAAAAACAGAAATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
2602 GTTGATTT
66 GTTGATTT
*
2610 TTGAAAAACAGAAATTTAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
2675 GTTGATTT
66 GTTGATTT
2683 TT
1 TT
2685 TTTTTTACGA
Statistics
Matches: 131, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
72 33 0.25
73 73 0.56
74 25 0.19
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.29
Consensus pattern (73 bp):
TTGAAAAACAGAAATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTT
Found at i:2963 original size:128 final size:124
Alignment explanation
Indices: 2708--3024 Score: 366
Period size: 127 Copynumber: 2.5 Consensus size: 124
2698 GAAATTGAAG
* *
2708 AACAGAAATT-AAA-ACCTCAGCATGTGAGCC-GA-GCTCAACTCACCTCTCGCAATATGAGTTA
1 AACAAAAATTAAAATACCTCAGC--GTGA-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
* * *
2769 ATTTTTGACAAACAGAAATTAAAAGGCTTAACTCACTTCTCGCAATCATGAGTTGATTTTTGA
63 A-TTTTGACAAACAGAAATTAAAAGGCTTAACCCACCTCTCGCAATCATGAGTTGATTCTTGA
*
2832 AACAACAAAATTAAGAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCTG
1 AAC-A-AAAATTAA-AATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
2897 ATTTTGA-AAA-AGTAGAATTAAAAGG-TTCAACCCACCTCTCGCAAT-ATGAGTTGATTCTTGA
63 ATTTTGACAAACAG-A-AATTAAAAGGCTT-AACCCACCTCTCGCAATCATGAGTTGATTCTTG-
2958 CA
124 -A
* * **
2960 AACAGAAATTGAAATACCTCAGCGTGTTCTGAGGCTCAACTCA--TCTCGCAATATGAGTTGATT
1 AACAAAAATTAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
3023 TT
66 TT
3025 TTGAAAAACA
Statistics
Matches: 170, Mismatches: 11, Indels: 25
0.83 0.05 0.12
Matches are distributed among these distances:
123 21 0.12
124 3 0.02
125 32 0.19
126 33 0.19
127 39 0.23
128 34 0.20
129 8 0.05
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.27
Consensus pattern (124 bp):
AACAAAAATTAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
TTGACAAACAGAAATTAAAAGGCTTAACCCACCTCTCGCAATCATGAGTTGATTCTTGA
Found at i:3015 original size:70 final size:70
Alignment explanation
Indices: 2923--3332 Score: 328
Period size: 72 Copynumber: 5.5 Consensus size: 70
2913 ATTAAAAGGT
* *
2923 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATACCTCAGCGTGTT
1 TCAACTCA-CTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATACCTCAGCGTG-T
2988 CTGAGGC
64 CTGAGGC
* *
2995 TCAACTCA-TCTCGCAATATGAGTTGATTTTTTGAAAAACA-AAATTTAAAATA-CTCAGCGTGT
1 TCAACTCACTCTCGCAATATGAGTTGA-TTTTTGACAAACAGAAA-TTGAAATACCTCAGCGTGT
3057 CTTGAGGC
64 C-TGAGGC
* * *
3065 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTACGAACAGAAATTGAAGA-ACAAAATTGAA
1 TCAACTCA-CTCTCGCAATATGAGTTGA-TTTTTGACAAACAGAAATTGAA-ATAC----CT---
* * *
3129 AAGACCTCAG-CATGTGAGC
56 CAG-CGT--GTC-TGAG-GC
* *
3148 -CGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTC
1 TC-A-ACTCA------CTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAA-TACCTC
*
3212 AGCGTGTCCGAGGC
57 AGCGTGTCTGAGGC
* * *
3226 TCAACTCACCTTTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTG
1 TCAACTCA-CTCTCGCAATATGAGTTGATTTTTGACAAACAGAAA-TT-GAAATACCTCAGCGTG
3291 TCCTGAGGC
63 T-CTGAGGC
3300 TCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 TCAACTCA-CTCTCGCAATATGAGTTGATTTTT
3333 TTTTTACGAA
Statistics
Matches: 276, Mismatches: 29, Indels: 64
0.75 0.08 0.17
Matches are distributed among these distances:
69 2 0.01
70 44 0.16
71 18 0.07
72 75 0.27
73 19 0.07
74 41 0.15
77 5 0.02
78 3 0.01
79 4 0.01
80 3 0.01
81 4 0.01
82 7 0.03
83 4 0.01
84 4 0.01
85 1 0.00
87 1 0.00
88 20 0.07
89 21 0.08
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (70 bp):
TCAACTCACTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATACCTCAGCGTGTCT
GAGGC
Found at i:3043 original size:125 final size:126
Alignment explanation
Indices: 2740--3044 Score: 388
Period size: 125 Copynumber: 2.4 Consensus size: 126
2730 TGTGAGCCGA
* * *
2740 GCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGACAAACAGAAATTAAAAGGCTTAACTCAC
1 GCTCAACTCA-CTCTCGCAATATGAGTTGATTTTTGAAAAACA-AAATTAAAAGGCTTAACCCAC
* *
2805 TTCTCGCAATCATGAGTTGATTTTTGAAACAACAAAATTAAGAATACCTCAGCGTGACCTGAG
64 CTCTCGCAATCATGAGTTGATTCTTGAAACAACAAAATTAAGAATACCTCAGCGTGACCTGAG
* * *
2868 GCTCAACTCACCTCTCGCAATATGAGCTGA-TTTTGAAAAAGTAGAATTAAAAGG-TTCAACCCA
1 GCTCAACTCA-CTCTCGCAATATGAGTTGATTTTTGAAAAA-CAAAATTAAAAGGCTT-AACCCA
* * **
2931 CCTCTCGCAAT-ATGAGTTGATTCTTGACA-AACAGAAATTGA-AATACCTCAGCGTGTTCTGAG
63 CCTCTCGCAATCATGAGTTGATTCTTGAAACAACA-AAATTAAGAATACCTCAGCGTGACCTGAG
2993 GCTCAACTCA-TCTCGCAATATGAGTTGATTTTTTGAAAAACAAAATTTAAAA
1 GCTCAACTCACTCTCGCAATATGAGTTGA-TTTTTGAAAAACAAAA-TTAAAA
3045 TACTCAGCGT
Statistics
Matches: 156, Mismatches: 15, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
123 17 0.11
124 3 0.02
125 49 0.31
126 24 0.15
127 34 0.22
128 29 0.19
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (126 bp):
GCTCAACTCACTCTCGCAATATGAGTTGATTTTTGAAAAACAAAATTAAAAGGCTTAACCCACCT
CTCGCAATCATGAGTTGATTCTTGAAACAACAAAATTAAGAATACCTCAGCGTGACCTGAG
Found at i:3235 original size:72 final size:73
Alignment explanation
Indices: 3147--3574 Score: 343
Period size: 72 Copynumber: 5.6 Consensus size: 73
3137 AGCATGTGAG
* * * *
3147 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTGACAAACAGAAA-TTGAAATTACCT
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCT
3211 CAGCGTGT
66 CAGCGTGT
*
3219 CCGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCT
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCT
3284 CAGCGTGT
66 CAGCGTGT
* ** *
3292 CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTACGAACAGAAATTGAAGAA
1 CC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTGAAAAACAGAAATTTAA-AA
* ** * *
3357 CAGAAATTGAAAAGACCTCAG-
60 -A-TACCT---CAG-CGT--GT
* * *
3378 CATGTGAGC-CGAGGCTCAACTCACCTCTCGCAATATGAGTT-ATTTTTG-AAAACAGAAA-TT-
1 C-CGAG-GCTC-A-ACTC-----ACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTA
* *
3438 GAATTACCTCAGCGTGT
57 AAAATACCTCAGCGTGT
* * * *
3455 CTTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAA-TTGAAATTAC
1 C--CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATAC
3519 CTCAGCGTGT
64 CTCAGCGTGT
*
3529 CCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTGAAAAA
1 CC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
3575 ACAATGAGTT
Statistics
Matches: 288, Mismatches: 37, Indels: 62
0.74 0.10 0.16
Matches are distributed among these distances:
71 19 0.07
72 65 0.23
73 63 0.22
74 49 0.17
76 4 0.01
77 4 0.01
78 24 0.08
79 4 0.01
80 1 0.00
81 2 0.01
82 2 0.01
84 4 0.01
85 2 0.01
86 5 0.02
87 12 0.04
88 8 0.03
92 1 0.00
93 19 0.07
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (73 bp):
CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCT
CAGCGTGT
Found at i:3359 original size:14 final size:14
Alignment explanation
Indices: 3340--3367 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3330 TTTTTTTTAC
3340 GAACAGAAATTGAA
1 GAACAGAAATTGAA
3354 GAACAGAAATTGAA
1 GAACAGAAATTGAA
3368 AAGACCTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
GAACAGAAATTGAA
Found at i:3415 original size:93 final size:91
Alignment explanation
Indices: 3257--3424 Score: 250
Period size: 93 Copynumber: 1.8 Consensus size: 91
3247 GAGTTGATTT
* *
3257 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTCGCAATATG
3322 AGTTGATTTTTTTTTTACGAACAGAAA
66 AGTT-ATTTTTTTTTTACGAACAGAAA
* *
3349 TTGAAGAACAGAAA-TTGAAAAGACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTCGCAAT
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGC--GTG-GCCTGAGGCTCAACTCACCTCTCGCAAT
3412 ATGAGTTATTTTT
63 ATGAGTTATTTTT
3425 GAAAACAGAA
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
91 14 0.20
92 19 0.28
93 34 0.49
94 2 0.03
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (91 bp):
TTGAAAAACAGAAATTTAAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTCGCAATATG
AGTTATTTTTTTTTTACGAACAGAAA
Found at i:3467 original size:164 final size:164
Alignment explanation
Indices: 3191--3496 Score: 485
Period size: 164 Copynumber: 1.9 Consensus size: 164
3181 ATTTTTGACA
** * *
3191 AACAGAAATTGAAATTACCTCAGCGTGTCCGAGGCTCAACTCACCTTTCGCAATATGAGTTGATT
1 AACAGAAATTGAAAAGACCTCAGCGTGGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
3256 TTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
66 TTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
3321 GAGTTGATTTTTTTTTTACGAACAGAAATTGAAG
131 GAGTTGATTTTTTTTTTACGAACAGAAATTGAAG
3355 AACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTT-
1 AACAGAAATTGAAAAGACCTCAGC--GTG-GCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
* * *
3419 ATTTTTG-AAAACAGAAA-TT-GAATTACCTCAGCGTGTCTTTGAGGCTCAACTCACCTCTCGCA
63 ATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTC-CTGAGGCTCAACTCACCTCTCGCA
3481 ATATGAGTTGATTTTT
127 ATATGAGTTGATTTTT
3497 GACAAACAGA
Statistics
Matches: 131, Mismatches: 7, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
163 16 0.12
164 63 0.48
165 10 0.08
166 10 0.08
167 32 0.24
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (164 bp):
AACAGAAATTGAAAAGACCTCAGCGTGGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
TTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
GAGTTGATTTTTTTTTTACGAACAGAAATTGAAG
Found at i:3511 original size:73 final size:72
Alignment explanation
Indices: 3349--3573 Score: 323
Period size: 73 Copynumber: 3.1 Consensus size: 72
3339 CGAACAGAAA
** *
3349 TTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTCGCAATA
1 TTGAA-AACAGAAATTGAAATTACCTCAGC--GTG-TCCTGAGGCTCAACTCACCTCTCGCAATA
3413 TGAGTT-ATTT
62 TGAGTTGATTT
*
3423 TTGAAAACAGAAATTG-AATTACCTCAGCGTGTCTTTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAACAGAAATTGAAATTACCTCAGCGTGTC-CTGAGGCTCAACTCACCTCTCGCAATATGA
3487 GTTGATTT
65 GTTGATTT
*
3495 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGA
1 TTGA-AAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
3560 GTTGA-TT
65 GTTGATTT
3567 TTGAAAA
1 TTGAAAA
3574 AACAATGAGT
Statistics
Matches: 140, Mismatches: 6, Indels: 13
0.88 0.04 0.08
Matches are distributed among these distances:
69 1 0.01
70 3 0.02
71 34 0.24
72 24 0.17
73 56 0.40
74 22 0.16
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (72 bp):
TTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTT
Found at i:3582 original size:22 final size:22
Alignment explanation
Indices: 3556--3600 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
3546 CTCTAGCAAT
3556 ATGAGTTGATTTTGAAAAAACA
1 ATGAGTTGATTTTGAAAAAACA
3578 ATGAGTTGATTTTGAAAAAACA
1 ATGAGTTGATTTTGAAAAAACA
3600 A
1 A
3601 AAATTAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.31
Consensus pattern (22 bp):
ATGAGTTGATTTTGAAAAAACA
Found at i:3633 original size:238 final size:235
Alignment explanation
Indices: 2923--3662 Score: 961
Period size: 238 Copynumber: 3.1 Consensus size: 235
2913 ATTAAAAGGT
* * *
2923 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATACCTCAGCGTGT-
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAATTACCTCAGCGTGTC
*
2987 TCTGAGGCTCAACTCA--TCTCGCAATATGAGTTGATTTTTTGAAAAACA-AAATTTAAAATA-C
66 T-TGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTAAAAATACC
* **
3048 TCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTACGAAC-AGA-AA
129 TCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTAAAAACAAGAGAA
3111 TTGAAGAAC-AAAATTGAAAAGACCTCAGCATGTGAGCCGAGGC
193 TTGAAGAACAAAAATTGAAAAGACCTCAGCA-GTGAGCCGAGGC
*
3154 TCAACTCACCTCTCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTG-AATTACCTCAGCGTGT
* *
3219 C-CGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACC
65 CTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA-TTAAAAATACC
**** *
3283 TCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTACGAACAGAA
129 TCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAAC-AAGAG-A
*
3348 ATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGC
192 ATTGAAGAACAAAAATTGAAAAGACCTCAGCA-GTGAGCCGAGGC
3393 TCAACTCACCTCTCGCAATATGAGTT-ATTTTTGA-AAACAGAAATTGAATTACCTCAGCGTGTC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAATTACCTCAGCGTGTC
* * *
3456 TTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCT
66 -TTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAATACCT
* **
3521 CAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAACAATGAGTTG
130 CAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAACAA-GA---G
* * * * *
3586 ATTTTGAAAAAACAAAAATT-AAAAGTATCTCA-C-GTG-TCTTGAGGC
191 A-ATTG-AAGAACAAAAATTGAAAAG-ACCTCAGCAGTGAGC-CGAGGC
*
3631 TCAACTCATCTCTCGCAATATGAGTTGATTTT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTT
3663 CCTTGAAAAG
Statistics
Matches: 452, Mismatches: 34, Indels: 38
0.86 0.06 0.07
Matches are distributed among these distances:
231 58 0.13
232 28 0.06
233 20 0.04
234 16 0.04
235 45 0.10
236 21 0.05
237 73 0.16
238 100 0.22
239 65 0.14
240 10 0.02
241 16 0.04
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.29
Consensus pattern (235 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAATTACCTCAGCGTGTC
TTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAATACCTC
AGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAACAAGAGAATTG
AAGAACAAAAATTGAAAAGACCTCAGCAGTGAGCCGAGGC
Found at i:3649 original size:94 final size:95
Alignment explanation
Indices: 3483--3662 Score: 265
Period size: 94 Copynumber: 1.9 Consensus size: 95
3473 CTCTCGCAAT
* * * *
3483 ATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCT
1 ATGAGTTGATTTTTGAAAAACAAAAATTAAAAGTACCTCAGCGTGTCCTGAGGCTCAACTCACCT
3548 CTAGCAATATGAGTTGATTTTGAAAAAACA
66 CTAGCAATATGAGTTGATTTTGAAAAAACA
* * *
3578 ATGAGTTGA-TTTTGAAAAAACAAAAATTAAAAGTATCTCA-CGTGTCTTGAGGCTCAACTCATC
1 ATGAGTTGATTTTTG-AAAAACAAAAATTAAAAGTACCTCAGCGTGTCCTGAGGCTCAACTCACC
*
3641 TCTCGCAATATGAGTTGATTTT
65 TCTAGCAATATGAGTTGATTTT
3663 CCTTGAAAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
94 47 0.62
95 29 0.38
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (95 bp):
ATGAGTTGATTTTTGAAAAACAAAAATTAAAAGTACCTCAGCGTGTCCTGAGGCTCAACTCACCT
CTAGCAATATGAGTTGATTTTGAAAAAACA
Found at i:5046 original size:690 final size:690
Alignment explanation
Indices: 3724--5096 Score: 2600
Period size: 690 Copynumber: 2.0 Consensus size: 690
3714 TAGAACTCGG
3724 GTGTCTTTTCCTTTGATTCAGTGCGACTCTCATTCAAGATTTCTTGCTCTGCTGGAGTACCTGTA
1 GTGTCTTTTCCTTTGATTCAGTGCGACTCTCATTCAAGATTTCTTGCTCTGCTGGAGTACCTGTA
3789 TATGCTATGTATGATGTTATCATGATATGCACATGTTTGTCTTAATGCTTTTATGCCTACATGAT
66 TATGCTATGTATGATGTTATCATGATATGCACATGTTTGTCTTAATGCTTTTATGCCTACATGAT
3854 TATGCAGTGCTCCTTAAGCATGTTGTCGTATGTCCATTTAGCCACGATTGTTGAGGATCTGTGTT
131 TATGCAGTGCTCCTTAAGCATGTTGTCGTATGTCCATTTAGCCACGATTGTTGAGGATCTGTGTT
3919 TCATTGCTTTGATTCTCGACTTTCTCTTAGGCCTGTATACCTGCCTTCAAGCTTCACGAGTAATC
196 TCATTGCTTTGATTCTCGACTTTCTCTTAGGCCTGTATACCTGCCTTCAAGCTTCACGAGTAATC
3984 GACGTTCCTCAGATATCACTCTTCTGCCCCCGATTGAACTTTGTTCTTACTTTGAGACTCTTGTG
261 GACGTTCCTCAGATATCACTCTTCTGCCCCCGATTGAACTTTGTTCTTACTTTGAGACTCTTGTG
4049 CTTATCAAATTTTCATCCAGGTAATGCTTAACATTTCTTTTGTTTAGAGTTGTCATTTCTCCATT
326 CTTATCAAATTTTCATCCAGGTAATGCTTAACATTTCTTTTGTTTAGAGTTGTCATTTCTCCATT
4114 TATCATGTAAATAAACACATAATGAGATGCATGAAAAAGGTCAGGTAGGGAAAAAATGATATTTC
391 TATCATGTAAATAAACACATAATGAGATGCATGAAAAAGGTCAGGTAGGGAAAAAATGATATTTC
4179 ATATTCATCTATTTCAAATGTGGCAAAAGCAAGTTAACCAATGAGAGTAAAAAATGTCAAAAAGA
456 ATATTCATCTATTTCAAATGTGGCAAAAGCAAGTTAACCAATGAGAGTAAAAAATGTCAAAAAGA
*
4244 AAGAAAGGATCGTATTCAACGGATACAAATACTTTAGATATTCGACACATGAACTCTTCCACGTT
521 AAGAAAGGATCGTATTCAACGGATACAAATACTTTAGATATTCAACACATGAACTCTTCCACGTT
4309 CCTCAATCAAGAATCTTTTCGAGTCTGGCTCTTTGCGTAGAAGATTTCGAGCTTTCAGAAATGCT
586 CCTCAATCAAGAATCTTTTCGAGTCTGGCTCTTTGCGTAGAAGATTTCGAGCTTTCAGAAATGCT
4374 TCAAATACTGTAGTCTCACTGTTGACCCGCTGTTAAAACGC
651 TCAAATACTGTAGTCTCACTGTTGA-CCGCTGTTAAAACGC
4415 GTGTC-TTTCCTTTGATTCAGTGCGACTCTCATTCAAGATTTCTTGCTCTGCTGGAGTACCTGTA
1 GTGTCTTTTCCTTTGATTCAGTGCGACTCTCATTCAAGATTTCTTGCTCTGCTGGAGTACCTGTA
4479 TATGCTATGTATGATGTTATCATGATATGCACATGTTTGTCTTAAATGCTTTTATGCCTACATGA
66 TATGCTATGTATGATGTTATCATGATATGCACATGTTTGTCTT-AATGCTTTTATGCCTACATGA
4544 TTATGCAGTGCTCCTTAAGCATGTTTGTCGTATGTCCATTTAGCCACGATTGTTGAGGATCTGTG
130 TTATGCAGTGCTCCTTAAGCATG-TTGTCGTATGTCCATTTAGCCACGATTGTTGAGGATCTGTG
4609 -TTCATTGCTTTGATTCTCGACTTTCTCTTCAGGCCT-TATACCTG-CTTCAAGCTTCACGAGTA
194 TTTCATTGCTTTGATTCTCGACTTTCTCTT-AGGCCTGTATACCTGCCTTCAAGCTTCACGAGTA
4671 ATCGACGTTCCTCAGATATCACTCTTCTGCCCCCGATTGAACTTTGTTCTTACTTTGAGACTCTT
258 ATCGACGTTCCTCAGATATCACTCTTCTGCCCCCGATTGAACTTTGTTCTTACTTTGAGACTCTT
4736 GTGCTTATCAAATTTTCATCCAGGTAATGCTTAACATTTCTTTTGTTTAGAGTATGTCA-TT-TC
323 GTGCTTATCAAATTTTCATCCAGGTAATGCTTAACATTTCTTTTGTTTAGAGT-TGTCATTTCTC
4799 CATTTATCATGTAAATAAACACATAATGAGATGCATGAAAAAGGTCAGGTAGGGAAAAAATGATA
387 CATTTATCATGTAAATAAACACATAATGAGATGCATGAAAAAGGTCAGGTAGGGAAAAAATGATA
4864 TTTCATATTCATCTATTTCAAATGTGGCAAACAAAGCAAGTTAACCAATGAGAGTAAAAAATGTC
452 TTTCATATTCATCTATTTCAAATGTGGC--A-AAAGCAAGTTAACCAATGAGAGTAAAAAATGTC
*
4929 AAAAAGAAAGAAAGGATCGTATTCAATGGATACAAATACTTTAGATATTCAACACATGAACTCTT
514 AAAAAGAAAGAAAGGATCGTATTCAACGGATACAAATACTTTAGATATTCAACACATGAACTCTT
4994 CCACGTTCCTCAATCAA-AATCTTTTCGAGTCTGGCTC-TTGCGTAGAAGATTTCGAGCTTTCAG
579 CCACGTTCCTCAATCAAGAATCTTTTCGAGTCTGGCTCTTTGCGTAGAAGATTTCGAGCTTTCAG
5057 AAATGCTTCAAATACTGTAGTCTCACTGTTGACCGCTGTT
644 AAATGCTTCAAATACTGTAGTCTCACTGTTGACCGCTGTT
5097 CGCCACTCTT
Statistics
Matches: 673, Mismatches: 2, Indels: 16
0.97 0.00 0.02
Matches are distributed among these distances:
689 103 0.15
690 298 0.44
691 112 0.17
692 160 0.24
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (690 bp):
GTGTCTTTTCCTTTGATTCAGTGCGACTCTCATTCAAGATTTCTTGCTCTGCTGGAGTACCTGTA
TATGCTATGTATGATGTTATCATGATATGCACATGTTTGTCTTAATGCTTTTATGCCTACATGAT
TATGCAGTGCTCCTTAAGCATGTTGTCGTATGTCCATTTAGCCACGATTGTTGAGGATCTGTGTT
TCATTGCTTTGATTCTCGACTTTCTCTTAGGCCTGTATACCTGCCTTCAAGCTTCACGAGTAATC
GACGTTCCTCAGATATCACTCTTCTGCCCCCGATTGAACTTTGTTCTTACTTTGAGACTCTTGTG
CTTATCAAATTTTCATCCAGGTAATGCTTAACATTTCTTTTGTTTAGAGTTGTCATTTCTCCATT
TATCATGTAAATAAACACATAATGAGATGCATGAAAAAGGTCAGGTAGGGAAAAAATGATATTTC
ATATTCATCTATTTCAAATGTGGCAAAAGCAAGTTAACCAATGAGAGTAAAAAATGTCAAAAAGA
AAGAAAGGATCGTATTCAACGGATACAAATACTTTAGATATTCAACACATGAACTCTTCCACGTT
CCTCAATCAAGAATCTTTTCGAGTCTGGCTCTTTGCGTAGAAGATTTCGAGCTTTCAGAAATGCT
TCAAATACTGTAGTCTCACTGTTGACCGCTGTTAAAACGC
Found at i:12615 original size:12 final size:12
Alignment explanation
Indices: 12595--12630 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
12585 ATGGATATGC
*
12595 AATGTATGAATG
1 AATGCATGAATG
12607 AATGCATGAATG
1 AATGCATGAATG
12619 AATGCATGAATG
1 AATGCATGAATG
12631 TCAAATGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:14215 original size:16 final size:15
Alignment explanation
Indices: 14194--14241 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
14184 GATGTGAATA
14194 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
14210 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
14225 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
14241 A
1 A
14242 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:14217 original size:24 final size:24
Alignment explanation
Indices: 14190--14245 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
14180 TAATGATGTG
*
14190 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
* *
14214 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
14238 AATAATAA
1 AATAATAA
14246 TAATTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:14224 original size:8 final size:8
Alignment explanation
Indices: 14190--14241 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
14180 TAATGATGTG
*
14190 AATAATAA
1 AATATTAA
14198 AATATATAA
1 AATAT-TAA
14207 AATA-TAA
1 AATATTAA
14214 AATATTAA
1 AATATTAA
*
14222 AATATCAA
1 AATATTAA
*
14230 AATATTAG
1 AATATTAA
14238 AATA
1 AATA
14242 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:14431 original size:24 final size:22
Alignment explanation
Indices: 14404--14456 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 22
14394 TAAAAATATG
14404 TACATAATATAGTGTTAAAATACA
1 TACATAATATA--GTTAAAATACA
* *
14428 TACATAATATAGTTAAGATATA
1 TACATAATATAGTTAAAATACA
14450 TACATAA
1 TACATAA
14457 GATAACATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 16 0.59
24 11 0.41
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.34
Consensus pattern (22 bp):
TACATAATATAGTTAAAATACA
Found at i:14452 original size:22 final size:23
Alignment explanation
Indices: 14396--14456 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 23
14386 GATAATATTA
*
14396 AAAATATGTACATAATATAGTGTT
1 AAAATATATACATAATATAG-GTT
*
14420 AAAATACATACATAATATA-GTT
1 AAAATATATACATAATATAGGTT
*
14442 AAGATATATACATAA
1 AAAATATATACATAA
14457 GATAACATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 16 0.48
24 17 0.52
ACGTcount: A:0.52, C:0.07, G:0.08, T:0.33
Consensus pattern (23 bp):
AAAATATATACATAATATAGGTT
Found at i:14499 original size:23 final size:21
Alignment explanation
Indices: 14473--14526 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 21
14463 ATGTAAAAAA
14473 AATATATATATAAATATAATATT
1 AATATATATATAAA-ATAATA-T
* *
14496 AATATATACATAAAATAGTAT
1 AATATATATATAAAATAATAT
14517 AATATATATA
1 AATATATATA
14527 CGTAATATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 10 0.36
22 5 0.18
23 13 0.46
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
AATATATATATAAAATAATAT
Found at i:14502 original size:19 final size:21
Alignment explanation
Indices: 14478--14524 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
14468 AAAAAAATAT
*
14478 ATATATAAATATAATA-T-TA
1 ATATATAAATAAAATAGTATA
*
14497 ATATATACATAAAATAGTATA
1 ATATATAAATAAAATAGTATA
14518 ATATATA
1 ATATATA
14525 TACGTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 14 0.58
20 1 0.04
21 9 0.38
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
ATATATAAATAAAATAGTATA
Found at i:14520 original size:8 final size:7
Alignment explanation
Indices: 14474--14584 Score: 51
Period size: 7 Copynumber: 16.3 Consensus size: 7
14464 TGTAAAAAAA
14474 ATAT-AT
1 ATATAAT
14480 ATATAA-
1 ATATAAT
14486 ATATAAT
1 ATATAAT
14493 AT-TAAT
1 ATATAAT
14499 ATATACAT
1 ATATA-AT
14507 A-A-AAT
1 ATATAAT
14512 AGTATAAT
1 A-TATAAT
14520 ATAT-AT
1 ATATAAT
**
14526 ACGTAAT
1 ATATAAT
*
14533 ATAGAAT
1 ATATAAT
* *
14540 TTAAAAT
1 ATATAAT
14547 ATACCTAAT
1 ATA--TAAT
14556 ATATTAA-
1 ATA-TAAT
*
14563 A-AGAAT
1 ATATAAT
14569 ATAT-AT
1 ATATAAT
14575 AATATAAT
1 -ATATAAT
14583 AT
1 AT
14585 TAAGAAATAT
Statistics
Matches: 79, Mismatches: 12, Indels: 27
0.67 0.10 0.23
Matches are distributed among these distances:
5 5 0.06
6 25 0.32
7 31 0.39
8 12 0.15
9 6 0.08
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (7 bp):
ATATAAT
Found at i:14527 original size:23 final size:22
Alignment explanation
Indices: 14472--14536 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
14462 CATGTAAAAA
* *
14472 AAATATATATATAAATATAATAT
1 AAATATATACATAAA-ATAGTAT
*
14495 TAATATATACATAAAATAGTAT
1 AAATATATACATAAAATAGTAT
* *
14517 AATATATATACGTAATATAG
1 AA-ATATATACATAAAATAG
14537 AATTTAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 7 0.20
23 28 0.80
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (22 bp):
AAATATATACATAAAATAGTAT
Found at i:14595 original size:46 final size:43
Alignment explanation
Indices: 14470--14587 Score: 112
Period size: 46 Copynumber: 2.6 Consensus size: 43
14460 AACATGTAAA
*
14470 AAAAATATATATATAAATATAATATTAATATATACATAAAATAGT
1 AAAAA-ATATATAT-AATATAATATTAAAATATACATAAAATAGT
* * * * *
14515 ATAATATATATACGTAATATAGA-ATTTAAAATATACCTAATATATT
1 AAAAAATATATA--TAATATA-ATA-TTAAAATATACATAAAATAGT
14561 AAAAGAATATATATAATATAATATTAA
1 AAAA-AATATATATAATATAATATTAA
14588 GAAATATAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
44 12 0.20
45 18 0.31
46 22 0.37
47 7 0.12
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.36
Consensus pattern (43 bp):
AAAAAATATATATAATATAATATTAAAATATACATAAAATAGT
Found at i:14599 original size:23 final size:25
Alignment explanation
Indices: 14556--14601 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
14546 TATACCTAAT
14556 ATATTAAAAGAATATATATAATATA
1 ATATTAAAAGAATATATATAATATA
*
14581 ATATTAAGA-AATATA-ATAATA
1 ATATTAAAAGAATATATATAATA
14602 ACAAAAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATTAAAAGAATATATATAATATA
Found at i:15171 original size:59 final size:60
Alignment explanation
Indices: 15100--15229 Score: 174
Period size: 59 Copynumber: 2.2 Consensus size: 60
15090 GGTGGAGCAA
* ** *
15100 GTGTGGTTAGTGGAGTAGGTAATGGAGCAAGTGTGGCTAGTGGA-TTTG-GTGTGGAAAAG
1 GTGTGGCTAGTGGAGTAGGTAATGGAAAAAGAGTGGCTAGTGGAGTTTGTG-GTGGAAAAG
* **
15159 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGTTTGTGGTGGAAAAG
1 GTGTGGCTAGTGGAGTAGGTAATGGAAAAAGAGTGGCTAGTGGAGTTTGTGGTGGAAAAG
15219 GTGTGGCTAGT
1 GTGTGGCTAGT
15230 TGAGAAAAGT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
59 37 0.60
60 24 0.39
61 1 0.02
ACGTcount: A:0.22, C:0.04, G:0.45, T:0.28
Consensus pattern (60 bp):
GTGTGGCTAGTGGAGTAGGTAATGGAAAAAGAGTGGCTAGTGGAGTTTGTGGTGGAAAAG
Found at i:15186 original size:30 final size:29
Alignment explanation
Indices: 15086--15229 Score: 155
Period size: 30 Copynumber: 4.8 Consensus size: 29
15076 TAGGTACAAG
* *
15086 TGGTGGTGGAGCAAGTGTGGTTAGTGGAGT
1 TGGTGGTGGA-AAAGTGTGGCTAGTGGAGT
* ** * *
15116 AGGTAATGGAGCAAGTGTGGCTAGTGGATT
1 TGGTGGTGGA-AAAGTGTGGCTAGTGGAGT
15146 TGGT-GTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAA-GTGTGGCTAGTGGAGT
*
15175 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGG-AAAAGTGTGGCTAGTGGAGT
*
15205 TTGTGGTGGAAAAGGTGTGGCTAGT
1 TGGTGGTGGAAAA-GTGTGGCTAGT
15230 TGAGAAAAGT
Statistics
Matches: 98, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.02
29 27 0.28
30 65 0.66
31 4 0.04
ACGTcount: A:0.22, C:0.04, G:0.46, T:0.28
Consensus pattern (29 bp):
TGGTGGTGGAAAAGTGTGGCTAGTGGAGT
Found at i:19066 original size:32 final size:32
Alignment explanation
Indices: 19026--19177 Score: 216
Period size: 32 Copynumber: 4.8 Consensus size: 32
19016 AAAAAATATG
* *
19026 ATACATTAGGTTTACGTATAAAAAAGTAGATC
1 ATACATTAGTTTTACATATAAAAAAGTAGATC
* *
19058 ATACATTAGTTTTGCATATAAAAAAGTAGATA
1 ATACATTAGTTTTACATATAAAAAAGTAGATC
* *
19090 ATACATTAGGTTCACATAT-AAAAAGTAGATC
1 ATACATTAGTTTTACATATAAAAAAGTAGATC
* * *
19121 ATACATTAGTTTTGCAAATGAAAAAGTAGATC
1 ATACATTAGTTTTACATATAAAAAAGTAGATC
19153 ATACATTAGTTTTACATATAAAAAA
1 ATACATTAGTTTTACATATAAAAAA
19178 CTAGTATAGT
Statistics
Matches: 104, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
31 26 0.25
32 78 0.75
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.32
Consensus pattern (32 bp):
ATACATTAGTTTTACATATAAAAAAGTAGATC
Found at i:19128 original size:63 final size:63
Alignment explanation
Indices: 19026--19176 Score: 239
Period size: 63 Copynumber: 2.4 Consensus size: 63
19016 AAAAAATATG
* *
19026 ATACATTAGGTTTACGTATAAAAAAGTAGATCATACATTAGTTTTGCATATAAAAAAGTAGATA
1 ATACATTAGGTTTACATAT-AAAAAGTAGATCATACATTAGTTTTGCAAATAAAAAAGTAGATA
* * *
19090 ATACATTAGGTTCACATATAAAAAGTAGATCATACATTAGTTTTGCAAATGAAAAAGTAGATC
1 ATACATTAGGTTTACATATAAAAAGTAGATCATACATTAGTTTTGCAAATAAAAAAGTAGATA
*
19153 ATACATTAGTTTTACATATAAAAA
1 ATACATTAGGTTTACATATAAAAA
19177 ACTAGTATAG
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
63 63 0.79
64 17 0.21
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.32
Consensus pattern (63 bp):
ATACATTAGGTTTACATATAAAAAGTAGATCATACATTAGTTTTGCAAATAAAAAAGTAGATA
Found at i:20166 original size:11 final size:11
Alignment explanation
Indices: 20152--20176 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20142 TTTTCCATAA
20152 TTTTTTTGTGT
1 TTTTTTTGTGT
20163 TTTTTTTGTGT
1 TTTTTTTGTGT
20174 TTT
1 TTT
20177 AGTTGTCGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (11 bp):
TTTTTTTGTGT
Found at i:21463 original size:18 final size:19
Alignment explanation
Indices: 21428--21463 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
21418 ATGATATTAA
21428 TGATATACCTACAAGGTAG
1 TGATATACCTACAAGGTAG
21447 TGATATACCTA-AAGGTA
1 TGATATACCTACAAGGTA
21464 TGAAAACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (19 bp):
TGATATACCTACAAGGTAG
Found at i:21786 original size:61 final size:61
Alignment explanation
Indices: 21687--21821 Score: 216
Period size: 61 Copynumber: 2.2 Consensus size: 61
21677 TCTATCACAG
21687 AACTCAGATCAAAAGAAATTATTAAGCTGAAACCTATAAAAAAACACTAAAGAGTTTTCCA
1 AACTCAGATCAAAAGAAATTATTAAGCTGAAACCTATAAAAAAACACTAAAGAGTTTTCCA
* * * * * *
21748 AACTCAGATCAAAAGACATTATTGAGCTGAAACTTATAAAAAAGCAGTAAAGAGTTTTCCG
1 AACTCAGATCAAAAGAAATTATTAAGCTGAAACCTATAAAAAAACACTAAAGAGTTTTCCA
21809 AACTCAGATCAAA
1 AACTCAGATCAAA
21822 CTCAGATCAA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 68 1.00
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (61 bp):
AACTCAGATCAAAAGAAATTATTAAGCTGAAACCTATAAAAAAACACTAAAGAGTTTTCCA
Done.