Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold198
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: 1648337
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 499 characters in sequence are not A, C, G, or T
File 11 of 11
Found at i:1584062 original size:40 final size:40
Alignment explanation
Indices: 1584007--1584096 Score: 162
Period size: 40 Copynumber: 2.2 Consensus size: 40
1583997 GATACATTGT
*
1584007 ATCGATACAACACTTATGTATCGATATATTTACTGTTTGC
1 ATCGATACAACACTTATGTATCGATACATTTACTGTTTGC
*
1584047 ATCGATACAACACTTATGTATCGATACATTTACTGTTTGT
1 ATCGATACAACACTTATGTATCGATACATTTACTGTTTGC
1584087 ATCGATACAA
1 ATCGATACAA
1584097 ATTGTTGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (40 bp):
ATCGATACAACACTTATGTATCGATACATTTACTGTTTGC
Found at i:1584854 original size:52 final size:49
Alignment explanation
Indices: 1584715--1585112 Score: 219
Period size: 49 Copynumber: 8.4 Consensus size: 49
1584705 ATATGCGGCT
* * * * *
1584715 AGCGATATTGGGCTCAAAGATGCGAAGAATGACAATGTGCTGA-TCATGGCC
1 AGCGACATTGGACTTAAAGAT--GAA-AATGCCAATGTGCTGATTCAAGGCC
* * * **
1584766 AGCGACATTAGATTTAAAGA--AGAATGCCAATGTGCTGAGACAAGGCC
1 AGCGACATTGGACTTAAAGATGAAAATGCCAATGTGCTGATTCAAGGCC
* ** *
1584813 AGCGACATTGGGCTTAGGGATGTTAAAGATGCCAATATGCTGATTCAAGGCC
1 AGCGACATTGGACTTAAAGATG--AAA-ATGCCAATGTGCTGATTCAAGGCC
* * * *
1584865 AACGATATCGGACTTAAAGATGAAAATGCTAATGTGCTGATTCAAGGCC
1 AGCGACATTGGACTTAAAGATGAAAATGCCAATGTGCTGATTCAAGGCC
* * ** * * *
1584914 AGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCCGATTCAAAGCC
1 AGCGACATTGGACTTAAAGATGAAAATGCCAATGTGCTGATTCAAGGCC
* *
1584962 AGCGATATTAGG-C-T-----T----ATGCCAATGTGCTAATTCAAGGCC
1 AGCGACATT-GGACTTAAAGATGAAAATGCCAATGTGCTGATTCAAGGCC
* * **** *
1585001 AGCAACATTGGTCTTAAAGATGCCGGTGCCAATATGCTGATTCAAGGCC
1 AGCGACATTGGACTTAAAGATGAAAATGCCAATGTGCTGATTCAAGGCC
** * *
1585050 AATGACATT-GACTTAAAG--G----TGCCAATATGTTGATTCAAGGCC
1 AGCGACATTGGACTTAAAGATGAAAATGCCAATGTGCTGATTCAAGGCC
*
1585092 AGCGATATTGGACTTAGAAGA
1 AGCGACATTGGACTTA-AAGA
1585113 AGATGCCACT
Statistics
Matches: 269, Mismatches: 56, Indels: 50
0.72 0.15 0.13
Matches are distributed among these distances:
38 2 0.01
39 27 0.10
40 1 0.00
42 28 0.10
43 6 0.02
44 3 0.01
45 1 0.00
46 16 0.06
47 23 0.09
48 38 0.14
49 67 0.25
50 3 0.01
51 17 0.06
52 37 0.14
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (49 bp):
AGCGACATTGGACTTAAAGATGAAAATGCCAATGTGCTGATTCAAGGCC
Found at i:1585168 original size:29 final size:29
Alignment explanation
Indices: 1585116--1585570 Score: 165
Period size: 28 Copynumber: 15.9 Consensus size: 29
1585106 TAGAAGAAGA
*
1585116 TGCCACTAACTTGTGTGGGCTTTTGAAAGGGT
1 TGCCACCAACTTGTGT--GCTTTTGAAA-GGT
1585148 TG-CACCAACTTGTGTGCTTTTG-AAGGT
1 TGCCACCAACTTGTGTGCTTTTGAAAGGT
* * * *
1585175 TGCCACTAACTTGTGGGCTTTTGAAAAGA
1 TGCCACCAACTTGTGTGCTTTTGAAAGGT
* * ** * *
1585204 TACTACTGACTTGTGGGC--TTGAAAGGGG
1 TGCCACCAACTTGTGTGCTTTTGAAA-GGT
*** * * *
1585232 TGCCATTGACTTGTGGGC-TTTGGAAGAT
1 TGCCACCAACTTGTGTGCTTTTGAAAGGT
* ** * * * *
1585260 TGCTACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACCAACTTGTGTGCTTTTGAAAGGT
** *
1585289 TGCCACTGACTTGTGGGCTTTTG-AAGGT
1 TGCCACCAACTTGTGTGCTTTTGAAAGGT
* * * * * ***
1585317 TACCACTAACTTTTGGGCTTTGGAAAAAA
1 TGCCACCAACTTGTGTGCTTTTGAAAGGT
** *
1585346 TGCCACTGACTTGTGGGCTTTT-AAAGGT
1 TGCCACCAACTTGTGTGCTTTTGAAAGGT
** * * * *
1585374 TGCCACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACCAACTTGTGTGCTTTTGAAAGGT
** *
1585403 TGCCACTGACTTGTGGGCTTTTG-AAGGT
1 TGCCACCAACTTGTGTGCTTTTGAAAGGT
** * * * *
1585431 TGCCACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACCAACTTGTGTGCTTTTGAAAGGT
** *
1585460 TGCCACTGACTTGTGGGCTTTTG-AAGGT
1 TGCCACCAACTTGTGTGCTTTTGAAAGGT
* ** * * * *
1585488 TGTCACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACCAACTTGTGTGCTTTTGAAAGGT
** *
1585517 TGCCACTGACTTGTGGGCTTTTG-AAGGT
1 TGCCACCAACTTGTGTGCTTTTGAAAGGT
* ** * *
1585545 TGCTACTGACTTGTGGGCTTTGGAAA
1 TGCCACCAACTTGTGTGCTTTTGAAA
1585571 AGATGCCCCT
Statistics
Matches: 350, Mismatches: 63, Indels: 23
0.80 0.14 0.05
Matches are distributed among these distances:
27 11 0.03
28 172 0.49
29 153 0.44
31 12 0.03
32 2 0.01
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.33
Consensus pattern (29 bp):
TGCCACCAACTTGTGTGCTTTTGAAAGGT
Found at i:1585601 original size:57 final size:57
Alignment explanation
Indices: 1585112--1585593 Score: 634
Period size: 57 Copynumber: 8.4 Consensus size: 57
1585102 GACTTAGAAG
* ** * *
1585112 AAGATGCCACTAACTTGTGTGGGCTTTTGAAAGGGTTGC-ACCAACTTGTGTGCTTTTG-A
1 AAGATGCCACTGAC-T-TGTGGGCTTTTG-AA-GGTTGCTACTGACTTGTGGGCTTTGGAA
* * * * * *
1585171 AGGTTGCCACTAACTTGTGGGCTTTTGAAAAGATACTACTGACTTGTGGGC-TT-GAA
1 AAGATGCCACTGACTTGTGGGCTTTTG-AAGGTTGCTACTGACTTGTGGGCTTTGGAA
* * * * *
1585227 AGGGGTGCCATTGACTTGTGGGCTTTGGAAGATTGCTACTGACTTGTGGGCTTTGGAA
1 A-AGATGCCACTGACTTGTGGGCTTTTGAAGGTTGCTACTGACTTGTGGGCTTTGGAA
* * * *
1585285 AAGATGCCACTGACTTGTGGGCTTTTGAAGGTTACCACTAACTTTTGGGCTTTGGAA
1 AAGATGCCACTGACTTGTGGGCTTTTGAAGGTTGCTACTGACTTGTGGGCTTTGGAA
* * *
1585342 AAAATGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTTGGAA
1 AAGATGCCACTGACTTGTGGGCTTTTGAAGGTTGCTACTGACTTGTGGGCTTTGGAA
*
1585399 AAGATGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAA
1 AAGATGCCACTGACTTGTGGGCTTTTGAAGGTTGCTACTGACTTGTGGGCTTTGGAA
1585456 AAGATGCCACTGACTTGTGGGCTTTTGAAGGTTG-TCACTGACTTGTGGGCTTTGGAA
1 AAGATGCCACTGACTTGTGGGCTTTTGAAGGTTGCT-ACTGACTTGTGGGCTTTGGAA
1585513 AAGATGCCACTGACTTGTGGGCTTTTGAAGGTTGCTACTGACTTGTGGGCTTTGGAA
1 AAGATGCCACTGACTTGTGGGCTTTTGAAGGTTGCTACTGACTTGTGGGCTTTGGAA
*
1585570 AAGATGCCCCTGACTTGT-GGCTTT
1 AAGATGCCACTGACTTGTGGGCTTT
1585594 GAAAAGGTGA
Statistics
Matches: 382, Mismatches: 34, Indels: 17
0.88 0.08 0.04
Matches are distributed among these distances:
55 1 0.00
56 32 0.08
57 331 0.87
58 6 0.02
59 12 0.03
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.33
Consensus pattern (57 bp):
AAGATGCCACTGACTTGTGGGCTTTTGAAGGTTGCTACTGACTTGTGGGCTTTGGAA
Found at i:1587036 original size:14 final size:14
Alignment explanation
Indices: 1587017--1587089 Score: 53
Period size: 14 Copynumber: 5.2 Consensus size: 14
1587007 CATCCGGACC
1587017 CTTTTTGTTGTTTT
1 CTTTTTGTTGTTTT
*
1587031 CTTTTT-TGGTTTT
1 CTTTTTGTTGTTTT
*
1587044 -TTTTTGTTATTTT
1 CTTTTTGTTGTTTT
1587057 -TTGTTTGTTAGTTGTT
1 CTT-TTTGTT-GTT-TT
* * *
1587073 TTTTTTCTTTTTTT
1 CTTTTTGTTGTTTT
1587087 CTT
1 CTT
1587090 CTTTCTTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
12 5 0.11
13 13 0.28
14 16 0.34
15 4 0.09
16 7 0.15
17 2 0.04
ACGTcount: A:0.03, C:0.05, G:0.12, T:0.79
Consensus pattern (14 bp):
CTTTTTGTTGTTTT
Found at i:1587096 original size:15 final size:14
Alignment explanation
Indices: 1587071--1587106 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
1587061 TTGTTAGTTG
1587071 TTTTT-TTTCTTTT
1 TTTTTCTTTCTTTT
1587084 TTTCTTCTTTCTTTT
1 TTT-TTCTTTCTTTT
1587099 TTTTTCTT
1 TTTTTCTT
1587107 GCGGAGGACG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.14
14 7 0.33
15 11 0.52
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTCTTTCTTTT
Found at i:1595487 original size:13 final size:13
Alignment explanation
Indices: 1595469--1595493 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1595459 CAAAGATCAG
1595469 TGTATCGATACAA
1 TGTATCGATACAA
1595482 TGTATCGATACA
1 TGTATCGATACA
1595494 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1595574 original size:33 final size:33
Alignment explanation
Indices: 1595532--1595601 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1595522 TGCAGTAGCT
1595532 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
1595565 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
1595598 TACA
1 TACA
1595602 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:1595575 original size:13 final size:13
Alignment explanation
Indices: 1595557--1595581 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1595547 CAAAAAAATA
1595557 TGTATCGATACAT
1 TGTATCGATACAT
1595570 TGTATCGATACA
1 TGTATCGATACA
1595582 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1605740 original size:33 final size:33
Alignment explanation
Indices: 1605681--1605747 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
1605671 GCCGTTGGGC
* *
1605681 ATAATGTATCGATACAATTCTTCATGTATTGAT
1 ATAATGTATCGATACAATTCTCCATGTATCGAT
*
1605714 ATAATGTATCGATAC-ATTGTCCCATGTATCGAT
1 ATAATGTATCGATACAATTCT-CCATGTATCGAT
1605747 A
1 A
1605748 CATTTCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 4 0.13
33 26 0.87
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (33 bp):
ATAATGTATCGATACAATTCTCCATGTATCGAT
Found at i:1606412 original size:89 final size:89
Alignment explanation
Indices: 1606245--1606706 Score: 550
Period size: 89 Copynumber: 5.2 Consensus size: 89
1606235 GGTGTCTACA
* * * * *
1606245 GTATCGATGCATCATAAAGCCTAATTTCCTTGGGGGCAAGGAGCAACCCATACATTCCCAATCAT
1 GTATTGATGCATCAGAAAGCCTAATTTCCTT-GGGGCAAGGTGCAGCCCACACATTCCCAATCAT
1606310 ATCCCCTTCACTTAACCACTAGATG
65 ATCCCCTTCACTTAACCACTAGATG
* * * * *
1606335 GTATTGATGCATCAGAAAGCCTAATTTCCTTAGGGCAAGGTGTAGCCTACATATTCCCAATAATA
1 GTATTGATGCATCAGAAAGCCTAATTTCCTTGGGGCAAGGTGCAGCCCACACATTCCCAATCATA
** *
1606400 TTTCTTTCACTTAACCACTAGATG
66 TCCCCTTCACTTAACCACTAGATG
* * * * * *
1606424 GTATTGATGCATCATAAAGCCTGATTTCCTTGGGGCAAGGTGTAGCCCACGCTTTCCTAATCATA
1 GTATTGATGCATCAGAAAGCCTAATTTCCTTGGGGCAAGGTGCAGCCCACACATTCCCAATCATA
* *
1606489 TCCCTTTCACTAAACCACTAGATG
66 TCCCCTTCACTTAACCACTAGATG
* *
1606513 GTATTGATGCATCACAAAGCCTAATTTCCTTGGGGTAAGGTGCAGCCCACACATTCCCAATCATA
1 GTATTGATGCATCAGAAAGCCTAATTTCCTTGGGGCAAGGTGCAGCCCACACATTCCCAATCATA
1606578 T-CCCTTCACTTAACCACTAGATG
66 TCCCCTTCACTTAACCACTAGATG
** * * * *
1606601 GTATTGATGCATC-GCAAAGCCTGGTTTCCTTGGGGCAAGGATATCTCGACCACTCATTCCCAAT
1 GTATTGATGCATCAG-AAAGCCTAATTTCCTTGGGGCAAGG-T-GC-AGCCCACACATTCCCAAT
* *** *
1606665 CATATCCCTTTTTTTTAGCCACTAGATG
62 CATATCCCCTTCACTTAACCACTAGATG
*
1606693 GTATTAATGCATCA
1 GTATTGATGCATCA
1606707 CATGACCACA
Statistics
Matches: 318, Mismatches: 48, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
88 55 0.17
89 184 0.58
90 30 0.09
91 20 0.06
92 29 0.09
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (89 bp):
GTATTGATGCATCAGAAAGCCTAATTTCCTTGGGGCAAGGTGCAGCCCACACATTCCCAATCATA
TCCCCTTCACTTAACCACTAGATG
Found at i:1607113 original size:40 final size:40
Alignment explanation
Indices: 1607066--1607529 Score: 211
Period size: 40 Copynumber: 11.5 Consensus size: 40
1607056 AACCCATTGG
1607066 CTTTATCAGTTTCACCTTGGCTAACCTTTTAATTGGTTGA
1 CTTTATCAGTTTCACCTTGGCTAACCTTTTAATTGGTTGA
* * * ** *
1607106 CTCTATCAGTTTTGC-CCTAGTC-AACCCTTCGAACTT-GTTGG
1 CTTTATCAG-TTT-CACCTTGGCTAA-CCTTTTAA-TTGGTTGA
* * * *
1607147 TTTTATC-GATTTCACCTTGGCCAACCTTTTGATTGATTGA
1 CTTTATCAG-TTTCACCTTGGCTAACCTTTTAATTGGTTGA
* ** * * *
1607187 CTTTATCGGTTTTGCCTTGG-TCAACCTTTTAACCT-ATTGG
1 CTTTATCAGTTTCACCTTGGCT-AACCTTTTAA-TTGGTTGA
*
1607227 CTTTATCAGTTTCACCTTAGCTAACCTTTTAATTGGTTGA
1 CTTTATCAGTTTCACCTTGGCTAACCTTTTAATTGGTTGA
* * *** *
1607267 CTTTATCAGTTTTGC-CCTAGTC-AACCTTTTCTAACCCGTTGG
1 CTTTATCAG-TTT-CACCTTGGCTAACC-TTT-TAATTGGTTGA
** * *
1607309 CTTTATTGGTTTCACCTTGGCCAAGCTTTTAATTGGTTGA
1 CTTTATCAGTTTCACCTTGGCTAACCTTTTAATTGGTTGA
* * ** *
1607349 CTTTATCAATTTCACCCTGG-TCAACCCTTCCAACTT-GTTGG
1 CTTTATCAGTTTCACCTTGGCT-AA-CCTTTTAA-TTGGTTGA
* *
1607390 CTTTATC-GATTTCATGC-TAGC-AACCTTTTAATTGGTTGA
1 CTTTATCAG-TTTCA-CCTTGGCTAACCTTTTAATTGGTTGA
* * * * * * *
1607429 CTTTATCGGTTTCACCCTAG-TCAACCCTTCTAACCT-ATTGG
1 CTTTATCAGTTTCACCTTGGCT-AA-CCTTTTAA-TTGGTTGA
* * * *
1607470 CTTTATCAGTTTCACCCTAGCCAACTTTTTAATTGGTTGA
1 CTTTATCAGTTTCACCTTGGCTAACCTTTTAATTGGTTGA
* * * *
1607510 CTGTATTAGTTACCCCTTGG
1 CTTTATCAGTTTCACCTTGG
1607530 TTAAACCCTT
Statistics
Matches: 312, Mismatches: 79, Indels: 66
0.68 0.17 0.14
Matches are distributed among these distances:
38 3 0.01
39 30 0.10
40 151 0.48
41 103 0.33
42 25 0.08
ACGTcount: A:0.19, C:0.24, G:0.15, T:0.42
Consensus pattern (40 bp):
CTTTATCAGTTTCACCTTGGCTAACCTTTTAATTGGTTGA
Found at i:1607152 original size:81 final size:81
Alignment explanation
Indices: 1607011--1607520 Score: 571
Period size: 81 Copynumber: 6.3 Consensus size: 81
1607001 AGATATTACT
* ** * *
1607011 TTTTAATTAGTTGACTTTATTGGTTTTGCCCTAGTCAACCCTTTTAACCCATTGGCTTTATCAGT
1 TTTTAATTGGTTGACTTTATCAGTTTTGCCCTAGTCAACCCTTCTAACCTATTGGCTTTATCAGT
* *
1607076 TTCACCTTGGCTAACC
66 TTCACCTTAGCCAACC
* * * * *
1607092 TTTTAATTGGTTGACTCTATCAGTTTTGCCCTAGTCAACCCTTCGAACTTGTTGGTTTTATC-GA
1 TTTTAATTGGTTGACTTTATCAGTTTTGCCCTAGTCAACCCTTCTAACCTATTGGCTTTATCAG-
*
1607156 TTTCACCTTGGCCAACC
65 TTTCACCTTAGCCAACC
* * * * * *
1607173 TTTTGATTGATTGACTTTATCGGTTTTGCCTTGGTCAA-CCTTTTAACCTATTGGCTTTATCAGT
1 TTTTAATTGGTTGACTTTATCAGTTTTGCCCTAGTCAACCCTTCTAACCTATTGGCTTTATCAGT
*
1607237 TTCACCTTAGCTAACC
66 TTCACCTTAGCCAACC
* ** **
1607253 TTTTAATTGGTTGACTTTATCAGTTTTGCCCTAGTCAACCTTTTCTAACCCGTTGGCTTTATTGG
1 TTTTAATTGGTTGACTTTATCAGTTTTGCCCTAGTCAACC-CTTCTAACCTATTGGCTTTATCAG
* *
1607318 TTTCACCTTGGCCAAGC
65 TTTCACCTTAGCCAACC
* ** * * * *
1607335 TTTTAATTGGTTGACTTTATCAATTTCACCCTGGTCAACCCTTCCAACTTGTTGGCTTTATC-GA
1 TTTTAATTGGTTGACTTTATCAGTTTTGCCCTAGTCAACCCTTCTAACCTATTGGCTTTATCAG-
*
1607399 TTTCATGC-TAG-CAACC
65 TTTCA-CCTTAGCCAACC
* **
1607415 TTTTAATTGGTTGACTTTATCGGTTTCACCCTAGTCAACCCTTCTAACCTATTGGCTTTATCAGT
1 TTTTAATTGGTTGACTTTATCAGTTTTGCCCTAGTCAACCCTTCTAACCTATTGGCTTTATCAGT
* *
1607480 TTCACCCTAGCCAACT
66 TTCACCTTAGCCAACC
* *
1607496 TTTTAATTGGTTGACTGTATTAGTT
1 TTTTAATTGGTTGACTTTATCAGTT
1607521 ACCCCTTGGT
Statistics
Matches: 359, Mismatches: 61, Indels: 18
0.82 0.14 0.04
Matches are distributed among these distances:
79 1 0.00
80 136 0.38
81 153 0.43
82 69 0.19
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.43
Consensus pattern (81 bp):
TTTTAATTGGTTGACTTTATCAGTTTTGCCCTAGTCAACCCTTCTAACCTATTGGCTTTATCAGT
TTCACCTTAGCCAACC
Found at i:1607465 original size:243 final size:242
Alignment explanation
Indices: 1607011--1607520 Score: 718
Period size: 243 Copynumber: 2.1 Consensus size: 242
1607001 AGATATTACT
* *
1607011 TTTTAATTAGTTGACTTTATTGGTTTTGCCCTAGTCAACCCTTTTAACCCATTGGCTTTATCAGT
1 TTTTAATTGGTTGACTTTATTAGTTTTGCCCTAGTCAACCCTTTTAACCCATTGGCTTTATCAGT
* * ** *
1607076 TTCACCTTGGCTAACCTTTTAATTGGTTGACTCTATCAGTTTTGCCCTAGTCAACCCTTCGAACT
66 TTCACCTTGGCCAACCTTTTAATTGGTTGACTCTATCAATTTCACCCTAGTCAACCCTTCCAACT
* * * ** * *
1607141 TGTTGGTTTTATCGATTTCACCTTGGCCAACCTTTTGATTGATTGACTTTATCGGTTTTGCCTTG
131 TGTTGGCTTTATCGATTTCACCTTAGCCAACCTTTTAATTGATTGACTTTATCGGTTTCACCCTA
* * *
1607206 GTCAACCTTTTAACCTATTGGCTTTATCAGTTTCACCTTAGCTAACC
196 GTCAACCTTCTAACCTATTGGCTTTATCAGTTTCACCCTAGCCAACC
* * * **
1607253 TTTTAATTGGTTGACTTTATCAGTTTTGCCCTAGTCAACCTTTTCTAACCCGTTGGCTTTATTGG
1 TTTTAATTGGTTGACTTTATTAGTTTTGCCCTAGTCAACCCTTT-TAACCCATTGGCTTTATCAG
* * *
1607318 TTTCACCTTGGCCAAGCTTTTAATTGGTTGACTTTATCAATTTCACCCTGGTCAACCCTTCCAAC
65 TTTCACCTTGGCCAACCTTTTAATTGGTTGACTCTATCAATTTCACCCTAGTCAACCCTTCCAAC
* *
1607383 TTGTTGGCTTTATCGATTTCATGC-TAG-CAACCTTTTAATTGGTTGACTTTATCGGTTTCACCC
130 TTGTTGGCTTTATCGATTTCA-CCTTAGCCAACCTTTTAATTGATTGACTTTATCGGTTTCACCC
*
1607446 TAGTCAACCCTTCTAACCTATTGGCTTTATCAGTTTCACCCTAGCCAACT
194 TAGTCAA-CCTTCTAACCTATTGGCTTTATCAGTTTCACCCTAGCCAACC
*
1607496 TTTTAATTGGTTGACTGTATTAGTT
1 TTTTAATTGGTTGACTTTATTAGTT
1607521 ACCCCTTGGT
Statistics
Matches: 235, Mismatches: 30, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
242 77 0.33
243 157 0.67
244 1 0.00
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.43
Consensus pattern (242 bp):
TTTTAATTGGTTGACTTTATTAGTTTTGCCCTAGTCAACCCTTTTAACCCATTGGCTTTATCAGT
TTCACCTTGGCCAACCTTTTAATTGGTTGACTCTATCAATTTCACCCTAGTCAACCCTTCCAACT
TGTTGGCTTTATCGATTTCACCTTAGCCAACCTTTTAATTGATTGACTTTATCGGTTTCACCCTA
GTCAACCTTCTAACCTATTGGCTTTATCAGTTTCACCCTAGCCAACC
Found at i:1607628 original size:46 final size:46
Alignment explanation
Indices: 1607506--1607638 Score: 157
Period size: 46 Copynumber: 2.9 Consensus size: 46
1607496 TTTTAATTGG
* * *
1607506 TTGACTGTATTAGTTA-C-CCCTTGGTTAAACCCTTTTCAT-TCTCAT
1 TTGACTGTATCAGTTATCACCC-TGGTTAAACTCTTTTTATCT-TCAT
* *
1607551 TTGACTGTGTCGGTTATCACCCTGGTTAAACTCTTTTTATCTTCAT
1 TTGACTGTATCAGTTATCACCCTGGTTAAACTCTTTTTATCTTCAT
* *
1607597 TTGACTATATCAGTTATCACCCTGGTTAAACT-TTTGTATCTT
1 TTGACTGTATCAGTTATCACCCTGGTTAAACTCTTTTTATCTT
1607639 TGCACGATAT
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
45 22 0.29
46 50 0.66
47 4 0.05
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.45
Consensus pattern (46 bp):
TTGACTGTATCAGTTATCACCCTGGTTAAACTCTTTTTATCTTCAT
Found at i:1607997 original size:42 final size:42
Alignment explanation
Indices: 1607946--1608347 Score: 172
Period size: 42 Copynumber: 9.5 Consensus size: 42
1607936 AGTCCTACTA
* *
1607946 AATCCTTTTATCTTTTGTTAACCTGTC-GATTCAATCTCGATC
1 AATCCTTTTATCTTTTGTT-ACTTGTCAGATTCAATCTCGGTC
* * * *
1607988 AA-CCTTTTTATCTTTTGCTTACCTGTCAGCTT-AGTCTTGGT-
1 AATCC-TTTTATCTTTTG-TTACTTGTCAGATTCAATCTCGGTC
* *
1608029 AATCCTTTTATCTTTTGTTGACTTG-CTGATTCAATCCCGGTC
1 AATCCTTTTATCTTTTGTT-ACTTGTCAGATTCAATCTCGGTC
* * * * *
1608071 AA-CCTTTTTATCCTTTGCTTACTTGTCGGCTT-AGTCTCAGGTA
1 AATCC-TTTTATCTTTTG-TTACTTGTCAGATTCAATCTC-GGTC
1608114 AATCCTTTTATCTTTTGTTGACTTGTC-GATTCAATC-CTGGTC
1 AATCCTTTTATCTTTTGTT-ACTTGTCAGATTCAATCTC-GGTC
*** * * * ** * * * *
1608156 AAAATTTTTATCCTTTTCTTACCTATTGGCTT-AGTCCCAGGTA
1 AATCCTTTTAT-CTTTTGTTACTTGTCAGATTCAATCTC-GGTC
* *
1608199 AATCCTTTAATCTTTTGTTGACTTGTC-GATTCAATCCTAGG-C
1 AATCCTTTTATCTTTTGTT-ACTTGTCAGATTCAAT-CTCGGTC
* * * * * *
1608241 AA-CCTATTTATCCTTTGCTTACCTG-CTGGCTT-AGTCTCGGGTA
1 AATCCT-TTTATCTTTTG-TTACTTGTC-AGATTCAATCTC-GGTC
* **
1608284 AATCATTTTATCTTTTGTTAACTTGTC-GATTCAATCTCACTC
1 AATCCTTTTATCTTTTGTT-ACTTGTCAGATTCAATCTCGGTC
*
1608326 AA-CCTTTTTATCCTTTTCTTAC
1 AATCC-TTTTAT-CTTTTGTTAC
1608348 CTGTTGGCTT
Statistics
Matches: 266, Mismatches: 62, Indels: 64
0.68 0.16 0.16
Matches are distributed among these distances:
40 6 0.02
41 35 0.13
42 120 0.45
43 99 0.37
44 6 0.02
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.46
Consensus pattern (42 bp):
AATCCTTTTATCTTTTGTTACTTGTCAGATTCAATCTCGGTC
Found at i:1608147 original size:85 final size:85
Alignment explanation
Indices: 1607701--1608516 Score: 653
Period size: 85 Copynumber: 9.9 Consensus size: 85
1607691 AGTTAAGTCT
* * * *
1607701 TTTTATCCTTTGTTGACTTGTTGATTCAATCTTGGTCAACC-TTTTCTCCTTTG-TCTACCTGTC
1 TTTTATCTTTTGTTGACTTGTCGATTCAATCTCGGTCAACCTTTTTATCCTTTGCT-TACCTGTC
* * *
1607764 GACTTAGTC-CTAAGTAAATCT
65 GGCTTAGTCTC-AGGTAAATCC
* * * * *
1607785 TTTTATCCTTTGATT---TT-T-GATTTAGTCTCGGTCAACTTCTTTTATCCTTTGTTTACCTGT
1 TTTTATCTTTTG-TTGACTTGTCGATTCAATCTCGGTCAACCT-TTTTATCCTTTGCTTACCTGT
** **
1607845 CAACTTAGTCTTGGGTAAAT-C
64 CGGCTTAGTCTCAGGTAAATCC
* * * * * * * *
1607866 TTCTTAT-TCTTTATTAACTT-TCGATTTAGTCTCGATCAACTTCTTTTATCCTTTGTTTACTTG
1 TT-TTATCT-TTTGTTGACTTGTCGATTCAATCTCGGTCAACCT-TTTTATCCTTTGCTTACCTG
** *
1607929 TTAGCTTAGTC-CTA-CTAAATCC
63 TCGGCTTAGTCTC-AGGTAAATCC
* * * * *
1607951 TTTTATCTTTTGTTAACCTGTCGATTCAATCTCGATCAACCTTTTTATCTTTTGCTTACCTGTCA
1 TTTTATCTTTTGTTGACTTGTCGATTCAATCTCGGTCAACCTTTTTATCCTTTGCTTACCTGTCG
*
1608016 GCTTAGTCT-TGGT-AATCC
66 GCTTAGTCTCAGGTAAATCC
* *
1608034 TTTTATCTTTTGTTGACTTG-CTGATTCAATCCCGGTCAACCTTTTTATCCTTTGCTTACTTGTC
1 TTTTATCTTTTGTTGACTTGTC-GATTCAATCTCGGTCAACCTTTTTATCCTTTGCTTACCTGTC
1608098 GGCTTAGTCTCAGGTAAATCC
65 GGCTTAGTCTCAGGTAAATCC
** * * *
1608119 TTTTATCTTTTGTTGACTTGTCGATTCAATC-CTGGTCAAAATTTTTATCCTTTTCTTACCTATT
1 TTTTATCTTTTGTTGACTTGTCGATTCAATCTC-GGTCAACCTTTTTATCCTTTGCTTACCTGTC
*
1608183 GGCTTAGTCCCAGGTAAATCC
65 GGCTTAGTCTCAGGTAAATCC
* * *
1608204 TTTAATCTTTTGTTGACTTGTCGATTCAATCCTAGG-CAACCTATTTATCCTTTGCTTACCTG-C
1 TTTTATCTTTTGTTGACTTGTCGATTCAAT-CTCGGTCAACCTTTTTATCCTTTGCTTACCTGTC
* *
1608267 TGGCTTAGTCTCGGGTAAATCA
65 -GGCTTAGTCTCAGGTAAATCC
* ** * *
1608289 TTTTATCTTTTGTTAACTTGTCGATTCAATCTCACTCAACCTTTTTATCCTTTTCTTACCTGTTG
1 TTTTATCTTTTGTTGACTTGTCGATTCAATCTCGGTCAACCTTTTTATCCTTTGCTTACCTGTCG
* *
1608354 GCTTAGTCACGGGT---T--
66 GCTTAGTCTCAGGTAAATCC
* * * * * * * *
1608369 TGTTAAC--CTGTTGA--T-TCAATCTCGA--TC----AACCATTTTATCCTTTGCATACCTGTT
1 TTTTATCTTTTGTTGACTTGTCGAT-TCAATCTCGGTCAACCTTTTTATCCTTTGCTTACCTGTC
* * *
1608423 GACTTAGTCCCGGGTAAATCC
65 GGCTTAGTCTCAGGTAAATCC
*
1608444 TTTTATCTTTTGTTGATTTGTCGATTCAATC-CTGGTCAACCTTTTTATCC-TTGCTTACCTGTC
1 TTTTATCTTTTGTTGACTTGTCGATTCAATCTC-GGTCAACCTTTTTATCCTTTGCTTACCTGTC
*
1608507 AGCTTAGTCT
65 GGCTTAGTCT
1608517 TGTGTAAGTT
Statistics
Matches: 600, Mismatches: 87, Indels: 90
0.77 0.11 0.12
Matches are distributed among these distances:
70 37 0.06
73 1 0.00
74 2 0.00
75 9 0.01
76 4 0.01
77 6 0.01
78 5 0.01
79 4 0.01
80 25 0.04
81 5 0.01
82 44 0.07
83 71 0.12
84 85 0.14
85 298 0.50
86 4 0.01
ACGTcount: A:0.18, C:0.22, G:0.13, T:0.46
Consensus pattern (85 bp):
TTTTATCTTTTGTTGACTTGTCGATTCAATCTCGGTCAACCTTTTTATCCTTTGCTTACCTGTCG
GCTTAGTCTCAGGTAAATCC
Found at i:1608410 original size:70 final size:70
Alignment explanation
Indices: 1608297--1608437 Score: 203
Period size: 70 Copynumber: 2.0 Consensus size: 70
1608287 CATTTTATCT
* * * * *
1608297 TTTGTTAACTTGTCGATTCAATCTCACTCAACCTTTTTATCCTTTTCTTACCTGTTGGCTTAGTC
1 TTTGTTAACCTGTCGATTCAATCTCACTCAACCATTTTATCCTTTGCATACCTGTTGACTTAGTC
1608362 ACGGG
66 ACGGG
*
1608367 TTTGTTAACCTGTTGATTCAATCTCGA-TCAACCATTTTATCCTTTGCATACCTGTTGACTTAGT
1 TTTGTTAACCTGTCGATTCAATCTC-ACTCAACCATTTTATCCTTTGCATACCTGTTGACTTAGT
*
1608431 CCCGGG
65 CACGGG
1608437 T
1 T
1608438 AAATCCTTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
70 62 0.98
71 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.43
Consensus pattern (70 bp):
TTTGTTAACCTGTCGATTCAATCTCACTCAACCATTTTATCCTTTGCATACCTGTTGACTTAGTC
ACGGG
Found at i:1609935 original size:168 final size:165
Alignment explanation
Indices: 1609537--1609994 Score: 479
Period size: 168 Copynumber: 2.8 Consensus size: 165
1609527 TTTTGGTGTA
* * * * *
1609537 ATTTTCTCAAGTTTTTAA-TTTCAAAATTCTTTAAATATCATCATTTAATTACCATGAA-ATCAG
1 ATTTTCACTAGTTTATAATTTTCAAAATTCATCAAATATCATCATTTAATT--CAT-AATATCAG
* * * * * *
1609600 TTTT-AAAAATTTCCTTT-TATTTTATGAGTTATTGA--TTTTCATTAGAATT-TCTCTTATTTC
63 TTTTAAAAAATTT-ATTTAT-TTTTATGAGTTTTTCATTTTTTCCTTAAAATTCTCT-TTTTTTC
* * *
1609660 CAAAATATAAAGTTTTCTTCTCTATAAATTTTTTTGGGAGG
125 CAAAATACAAAGTTTTCTTCTCTATAAATGTTTTTGAGAGG
* *
1609701 ATTTTCACTAGTTTATAATTTTTAAAATTCATCAAATATCATCATTTAACTCTTATTAA-ATCAG
1 ATTTTCACTAGTTTATAATTTTCAAAATTCATCAAATATCATCATTTAA-T-TCA-TAATATCAG
*
1609765 TTTTAAAAAATTTATTTATTTTTATGAGTTTTTTATTTTTTCCTTAAAATTCTCTTTTTTTCCAA
63 TTTTAAAAAATTTATTTATTTTTATGAGTTTTTCATTTTTTCCTTAAAATTCTCTTTTTTTCCAA
** * *
1609830 AATACGGAGTTTTTTGTACTCTGTAAATGTTTTTGAG-GG
128 AATACAAAGTTTTCT-T-CTCTATAAATGTTTTTGAGAGG
* *
1609869 ATTTTTC-TTAGTTTATAATTTTCAAAATTCATCAAATATCATTATTTAATTCATAATCAGTCAG
1 A-TTTTCACTAGTTTATAATTTTCAAAATTCATCAAATATCATCATTTAATTCATAAT-A-TCAG
* *
1609933 TTTTAAAAAATTTATTTATTTTTATGAGCTTTTCATTTTTTCCTTGAAAA-TCTCTTGTTTTC
63 TTTTAAAAAATTTATTTATTTTTATGAGTTTTTCATTTTTTCCTT-AAAATTCTCTTTTTTTC
1609995 AAAGAATTGA
Statistics
Matches: 251, Mismatches: 27, Indels: 28
0.82 0.09 0.09
Matches are distributed among these distances:
164 15 0.06
165 59 0.24
166 13 0.05
167 35 0.14
168 104 0.41
169 25 0.10
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.51
Consensus pattern (165 bp):
ATTTTCACTAGTTTATAATTTTCAAAATTCATCAAATATCATCATTTAATTCATAATATCAGTTT
TAAAAAATTTATTTATTTTTATGAGTTTTTCATTTTTTCCTTAAAATTCTCTTTTTTTCCAAAAT
ACAAAGTTTTCTTCTCTATAAATGTTTTTGAGAGG
Found at i:1612140 original size:118 final size:118
Alignment explanation
Indices: 1612012--1612232 Score: 291
Period size: 118 Copynumber: 1.9 Consensus size: 118
1612002 ATACCTATAG
* * * * **
1612012 GGGCATTTTTGTAATTTTACTAGAA-CTAAGTCCTAGTTTGTCACTGGGTTGCTTCTATGCCGAG
1 GGGCATTTTTGTAATTTTACTAAAATC-AAGTCCTAATTTGTCACTAGATCACTTCTATGCCGAG
1612076 GGTACGTATTAGGCATAGGTTCACTTTTCTTTTTGAAGTTTTTTATACCCATTA
65 GGTACGTATTAGGCATAGGTTCACTTTTCTTTTTGAAGTTTTTTATACCCATTA
* ** * * *
1612130 GGGCTTTTTTGTAATTTTTTTAAAATCGAGTCTTAATTTGTCACTAGATCACTTCTATGTCGAGG
1 GGGCATTTTTGTAATTTTACTAAAATCAAGTCCTAATTTGTCACTAGATCACTTCTATGCCGAGG
* * *
1612195 GTACGTATTAGGCGTATGTTCACTTTTCTTTTTTAAGT
66 GTACGTATTAGGCATAGGTTCACTTTTCTTTTTGAAGT
1612233 CCTTTAGGGT
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
118 86 0.99
119 1 0.01
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.44
Consensus pattern (118 bp):
GGGCATTTTTGTAATTTTACTAAAATCAAGTCCTAATTTGTCACTAGATCACTTCTATGCCGAGG
GTACGTATTAGGCATAGGTTCACTTTTCTTTTTGAAGTTTTTTATACCCATTA
Found at i:1612952 original size:150 final size:150
Alignment explanation
Indices: 1612630--1612930 Score: 374
Period size: 150 Copynumber: 2.0 Consensus size: 150
1612620 TTCTACGCTG
** * * * *
1612630 AAGGTATGAATTAGGAATAGGATCGTTTTTACTTTTTCAAGTCCTCTAGGATCACCAGGTACTTC
1 AAGGTATGAATTAGGAGCAGGTTTGTCTTTACTTTTTCAAGTCCTCTAGGATCACCAGGCACTTC
* *
1612695 TAAATCGATGGTAGACCTTAGAGACCTTTTAGCCTTTTTCCCCAAAACCTAATCTTATATAACTA
66 TAAATCGATAGTAGACCTTAGAGACCTTTTAGCCTTTTTCCCCAAAACCTAATCTCATATAACTA
*
1612760 CTAGGTCCGCTTGTATGCTA
131 CCAGGTCCGCTTGTATGCTA
* * *
1612780 AAGGTATGAATTAGGAGCAGGTTTGTCTTTACTTTTTCAAGTTCTCTGGGATCACCGGGCACTTC
1 AAGGTATGAATTAGGAGCAGGTTTGTCTTTACTTTTTCAAGTCCTCTAGGATCACCAGGCACTTC
* * * * * *
1612845 TAAGTCGATAGTAGACCTTAGGGACATTTTTAGCAC-TTTTCCCCGAAACCTAGTCTCGTGA-AA
66 TAAATCGATAGTAGACCTTAGAGAC-CTTTTAGC-CTTTTTCCCCAAAACCTAATCTCAT-ATAA
* *
1612908 CTACCGGGT-CGCTTTTATGCTA
128 CTACCAGGTCCGCTTGTATGCTA
1612930 A
1 A
1612931 GGGTGTGCCT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
150 91 0.71
151 35 0.27
152 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (150 bp):
AAGGTATGAATTAGGAGCAGGTTTGTCTTTACTTTTTCAAGTCCTCTAGGATCACCAGGCACTTC
TAAATCGATAGTAGACCTTAGAGACCTTTTAGCCTTTTTCCCCAAAACCTAATCTCATATAACTA
CCAGGTCCGCTTGTATGCTA
Found at i:1614411 original size:24 final size:27
Alignment explanation
Indices: 1614360--1614411 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1614350 AAGCATGATT
*
1614360 AAAATCAAGGAATAATCATATTTTATA
1 AAAATCAAAGAATAATCATATTTTATA
1614387 AAAATCAAAGAAT-AT-A-ATTTTATA
1 AAAATCAAAGAATAATCATATTTTATA
1614411 A
1 A
1614412 TTTTTTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 9 0.38
25 1 0.04
26 2 0.08
27 12 0.50
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.33
Consensus pattern (27 bp):
AAAATCAAAGAATAATCATATTTTATA
Found at i:1614735 original size:15 final size:15
Alignment explanation
Indices: 1614715--1614743 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1614705 TGGATCAATG
1614715 ATAACTTTAAGGATC
1 ATAACTTTAAGGATC
1614730 ATAACTTTAAGGAT
1 ATAACTTTAAGGAT
1614744 GAAAACCTAC
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:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (15 bp):
ATAACTTTAAGGATC
Found at i:1617154 original size:3 final size:3
Alignment explanation
Indices: 1617135--1617185 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
1617125 TGAAACTTAT
*
1617135 TTA TTA TT- TTA CT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1617181 TTA TT
1 TTA TT
1617186 CTCAAAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 3 0.07
3 41 0.93
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1618076 original size:19 final size:19
Alignment explanation
Indices: 1618052--1618090 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1618042 TTTATTTTAT
1618052 TTTTTCTCTT-TTTTCTTTC
1 TTTTTCT-TTCTTTTCTTTC
*
1618071 TTTTTCTTTCTTTTTTTTC
1 TTTTTCTTTCTTTTCTTTC
1618090 T
1 T
1618091 CTCTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTCTTTCTTTTCTTTC
Found at i:1618086 original size:23 final size:23
Alignment explanation
Indices: 1618054--1618098 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1618044 TATTTTATTT
*
1618054 TTTCTCTTTTTTCTTTCTTTTTC
1 TTTCTCTTTTTTCTCTCTTTTTC
*
1618077 TTTCTTTTTTTTCTCTCTTTTT
1 TTTCTCTTTTTTCTCTCTTTTT
1618099 TTCCAAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTCTCTTTTTTCTCTCTTTTTC
Found at i:1618087 original size:13 final size:13
Alignment explanation
Indices: 1618063--1618100 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
1618053 TTTTCTCTTT
1618063 TTTCTTTCTTTTTC
1 TTTCTTT-TTTTTC
1618077 TTTCTTTTTTTTC
1 TTTCTTTTTTTTC
*
1618090 TCTCTTTTTTT
1 TTTCTTTTTTT
1618101 CCAAGTTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 16 0.70
14 7 0.30
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTCTTTTTTTTC
Found at i:1618098 original size:10 final size:10
Alignment explanation
Indices: 1618052--1618090 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
1618042 TTTATTTTAT
*
1618052 TTTTTCTCT-
1 TTTTTCTTTC
1618061 TTTTTCTTTC
1 TTTTTCTTTC
1618071 TTTTTCTTTC
1 TTTTTCTTTC
1618081 TTTTT-TTTC
1 TTTTTCTTTC
1618090 T
1 T
1618091 CTCTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
9 13 0.46
10 15 0.54
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:1619190 original size:165 final size:164
Alignment explanation
Indices: 1618672--1619173 Score: 543
Period size: 164 Copynumber: 3.1 Consensus size: 164
1618662 AGATGTATTA
* * * * * ** * *
1618672 TAAAAATTTTAAACCAA-AGAAAATCCCTTCGAAAACATTTATGGGATGGAAAATTCAGTTTTTT
1 TAAAAATTTCAAACCAAGA-AAAATCCCCT-GAAAACCTTTATAGAATAAAAAACTCAATTTTTT
* * * * * ** * *
1618736 GAAAGTA-AGGTATTTCAA-GAAAA-AATGAAAAACTCATGAAAAGAAATGAAAATTTCAAAACT
64 GAAAATAGA-GAATTTCAAGGAAAAGAAT-AAAAAATGATGAAAATAAATGAATTTTTGAAAATT
* *
1618798 GATTTAATATGAATTAAATGATCATATTTTATGAATAT
127 GATTTAATATGAATTAAATAATCATATTTAATGAATAT
* *
1618836 TCAAAATTTCAAACCAAGAAAAAT-CCCTCAAAACCTTTATAGAATAAAAAACTCAATTTTTTGA
1 TAAAAATTTCAAACCAAGAAAAATCCCCTGAAAACCTTTATAGAATAAAAAACTCAATTTTTTGA
* *
1618900 AAATAAGGGAATTTCAAGGAAAAGAATAAAAAATGATGAAAATGAATGAATTTTTGAAAATTGAT
66 AAAT-AGAGAATTTCAAGGAAAAGAATAAAAAATGATGAAAATAAATGAATTTTTGAAAATTGAT
* *
1618965 TTAATATGAATTAAATAATCATATTTGATGAATAA
130 TTAATATGAATTAAATAATCATATTTAATGAATAT
* * **
1619000 CAAAAATTTCAAACCAAGAAAAATCCCCTGAAAACCTTTATGGAATAAAAAAACTTGATTTTTTG
1 TAAAAATTTCAAACCAAGAAAAATCCCCTGAAAACCTTTATAGAAT-AAAAAACTCAATTTTTT-
* *
1619065 GAAAAT-GAGAATTTCAAGGAAAA-AA-AGAAAAATGAATGAACATAAATGCATTTTTGAAAATT
64 GAAAATAGAGAATTTCAAGGAAAAGAATA-AAAAATG-ATGAAAATAAATGAATTTTTGAAAATT
* * * *
1619127 TATTTAACATGAATTAAATAATAATATTTAATGAATTT
127 GATTTAATATGAATTAAATAATCATATTTAATGAATAT
1619165 TAAAAATTT
1 TAAAAATTT
1619174 TGGATCAATG
Statistics
Matches: 286, Mismatches: 42, Indels: 19
0.82 0.12 0.05
Matches are distributed among these distances:
162 31 0.11
163 13 0.05
164 118 0.41
165 103 0.36
166 15 0.05
167 6 0.02
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (164 bp):
TAAAAATTTCAAACCAAGAAAAATCCCCTGAAAACCTTTATAGAATAAAAAACTCAATTTTTTGA
AAATAGAGAATTTCAAGGAAAAGAATAAAAAATGATGAAAATAAATGAATTTTTGAAAATTGATT
TAATATGAATTAAATAATCATATTTAATGAATAT
Found at i:1637291 original size:21 final size:20
Alignment explanation
Indices: 1637267--1637305 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1637257 ATACTAAAAG
1637267 ATTTTAGAAA-AATCTTTTAGT
1 ATTTTA-AAATAAT-TTTTAGT
1637288 ATTTTAAAATAATTTTTA
1 ATTTTAAAATAATTTTTA
1637306 AACATGCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (20 bp):
ATTTTAAAATAATTTTTAGT
Found at i:1644160 original size:19 final size:20
Alignment explanation
Indices: 1644136--1644189 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
1644126 AGGGCAGTTT
1644136 TGTATCGATACAAAACT-TA
1 TGTATCGATACAAAACTGTA
** *
1644155 TGTATCGATACATTTACTGTT
1 TGTATCGATACA-AAACTGTA
1644176 TGTATCGATACAAA
1 TGTATCGATACAAA
1644190 TTGTAAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 12 0.43
20 3 0.11
21 13 0.46
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTATCGATACAAAACTGTA
Found at i:1644181 original size:21 final size:19
Alignment explanation
Indices: 1644133--1644189 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1644123 TGCAGGGCAG
1644133 TTTTGTATCGATACAAAAC
1 TTTTGTATCGATACAAAAC
* **
1644152 TTATGTATCGATACATTTAC
1 TTTTGTATCGATACA-AAAC
1644172 TGTTTGTATCGATACAAA
1 T-TTTGTATCGATACAAA
1644190 TTGTAAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 14 0.47
20 3 0.10
21 13 0.43
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (19 bp):
TTTTGTATCGATACAAAAC
Found at i:1646990 original size:13 final size:13
Alignment explanation
Indices: 1646972--1646997 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1646962 AATTTTTTTG
1646972 TGTATCGATACAT
1 TGTATCGATACAT
1646985 TGTATCGATACAT
1 TGTATCGATACAT
1646998 GCTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1647296 original size:21 final size:21
Alignment explanation
Indices: 1647267--1647311 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1647257 AAGTTTTCAT
*
1647267 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1647287 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1647309 TTT
1 TTT
1647312 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Done.