Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold495
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: 208105
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.29
Warning! 20170 characters in sequence are not A, C, G, or T
Found at i:17743 original size:847 final size:847
Alignment explanation
Indices: 16110--17803 Score: 3343
Period size: 847 Copynumber: 2.0 Consensus size: 847
16100 TGATCCCAGT
16110 AGGAGCAACAAGGGCCCCAACTCTAACTGGCCCACCAGATCTAACCTTTTTTCTTAGGCCTCATC
1 AGGAGCAACAAGGGCCCCAACTCTAACTGGCCCACCAGATCTAACCTTTTTTCTTAGGCCTCATC
16175 GCAGAACTCGATGGCTCTAAATCCCTATTATTCTTTCCTCTCTCCTTATCCCAGTTTTGGCGCTC
66 GCAGAACTCGATGGCTCTAAATCCCTATTATTCTTTCCTCTCTCCTTATCCCAGTTTTGGCGCTC
16240 AGCGCGCTTCACCTCCTCGGTGATCTTTGCCTTATCTACCAGTGCTGAAAAGTCACGCTCCCTCT
131 AGCGCGCTTCACCTCCTCGGTGATCTTTGCCTTATCTACCAGTGCTGAAAAGTCACGCTCCCTCT
16305 GCGAAGCTATCAAAACTCTCAAACTATCCTTGAGTCCATCATCGAAGAGGATACAACGCTTATAT
196 GCGAAGCTATCAAAACTCTCAAACTATCCTTGAGTCCATCATCGAAGAGGATACAACGCTTATAT
*
16370 TCGGTCGCCACCATGCCTCGCATATAGCGGCTTAATCTTAGAAACTCGGTATCATACTCGGCCAC
261 TCAGTCGCCACCATGCCTCGCATATAGCGGCTTAATCTTAGAAACTCGGTATCATACTCGGCCAC
16435 TGAATGATCCCCTTACGTGAGATTCAGAAACTCATGTCTTCTAGCGTCAATGTAGCTTGCCCCCA
326 TGAATGATCCCCTTACGTGAGATTCAGAAACTCATGTCTTCTAGCGTCAATGTAGCTTGCCCCCA
16500 CATATTTAACTTGAAAAGCAGGCTTATAGAAATCCCTTCTTAACGGTCAGCCACCATTGGTATGT
391 CATATTTAACTTGAAAAGCAGGCTTATAGAAATCCCTTCTTAACGGTCAGCCACCATTGGTATGT
16565 TTCATCGCGAAGTAAGGAAAAAACCCCTTTCAATTTCTATTCAAGGGTAAAGTCCAGATCGTCTA
456 TTCATCGCGAAGTAAGGAAAAAACCCCTTTCAATTTCTATTCAAGGGTAAAGTCCAGATCGTCTA
16630 CGATTCTTTCCGTGGCCTCCATCCAGTACTCGGCCCCTGGATAGCTCAGCCCCATTGGACCAGAG
521 CGATTCTTTCCGTGGCCTCCATCCAGTACTCGGCCCCTGGATAGCTCAGCCCCATTGGACCAGAG
16695 TTGTTCCGTAACCGACCCTCGGCCCCCAGATCCAGTGTTGGGCCCAACAACCATCTCTAATATCC
586 TTGTTCCGTAACCGACCCTCGGCCCCCAGATCCAGTGTTGGGCCCAACAACCATCTCTAATATCC
16760 TCAGCATAGCCTGGGACAAGGCGTCGTCCACGGCCATGCGATCATGAGACCCAATCTCTGTAGCA
651 TCAGCATAGCCTGGGACAAGGCGTCGTCCACGGCCATGCGATCATGAGACCCAATCTCTGTAGCA
16825 GGTGAAATCGACGTCTCGCTTGTATCCAGATTTGACATGTTGCCTAACGACGAGGACTCAGCTCG
716 GGTGAAATCGACGTCTCGCTTGTATCCAGATTTGACATGTTGCCTAACGACGAGGACTCAGCTCG
16890 AGCCCCTCTACGGCTTCTACCTCGGCCTCTAGTACTCTATCTGCAGATACCTCGTGCACTCATCA
781 AGCCCCTCTACGGCTTCTACCTCGGCCTCTAGTACTCTATCTGCAGATACCTCGTGCACTCATCA
16955 TA
846 TA
16957 AGGAGCAACAAGGGCCCCAACTCTAACTGGCCCACCAGATCTAACCTTTTTTCTTAGGCCTCATC
1 AGGAGCAACAAGGGCCCCAACTCTAACTGGCCCACCAGATCTAACCTTTTTTCTTAGGCCTCATC
17022 GCAGAACTCGATGGCTCTAAATCCCTATTATTCTTTCCTCTCTCCTTATCCCAGTTTTGGCGCTC
66 GCAGAACTCGATGGCTCTAAATCCCTATTATTCTTTCCTCTCTCCTTATCCCAGTTTTGGCGCTC
*
17087 AGCGCGCTTCACCTCCTCGGTGATCTTTGCCTTATCTACCAGTGCTGAAAAGTCACGCTTCCTCT
131 AGCGCGCTTCACCTCCTCGGTGATCTTTGCCTTATCTACCAGTGCTGAAAAGTCACGCTCCCTCT
17152 GCGAAGCTATCAAAACTCTCAAACTATCCTTGAGTCCATCATCGAAGAGGATACAACGCTTATAT
196 GCGAAGCTATCAAAACTCTCAAACTATCCTTGAGTCCATCATCGAAGAGGATACAACGCTTATAT
*
17217 TCAGTCGCCACCATGCCTCGCGTATAGCGGCTTAATCTTAGAAACTCGGTATCATACTCGGCCAC
261 TCAGTCGCCACCATGCCTCGCATATAGCGGCTTAATCTTAGAAACTCGGTATCATACTCGGCCAC
17282 TGAATGATCCCCTTACGTGAGATTCAGAAACTCATGTCTTCTAGCGTCAATGTAGCTTGCCCCCA
326 TGAATGATCCCCTTACGTGAGATTCAGAAACTCATGTCTTCTAGCGTCAATGTAGCTTGCCCCCA
*
17347 CATATTTAACTTGAAAAGCAGGCTTATAGAAATCCCTTCTTAACGGTCAGCCACTATTGGTATGT
391 CATATTTAACTTGAAAAGCAGGCTTATAGAAATCCCTTCTTAACGGTCAGCCACCATTGGTATGT
*
17412 TTCATCGCGAAGTAAGGAAACAACCCCTTTCAATTTCTATTCAAGGGTAAAGTCCAGATCGTCTA
456 TTCATCGCGAAGTAAGGAAAAAACCCCTTTCAATTTCTATTCAAGGGTAAAGTCCAGATCGTCTA
17477 CGATTCTTTCCGTGGCCTCCATCCAGTACTCGGCCCCTGGATAGCTCAGCCCCATTGGACCAGAG
521 CGATTCTTTCCGTGGCCTCCATCCAGTACTCGGCCCCTGGATAGCTCAGCCCCATTGGACCAGAG
17542 TTGTTCCGTAACCGACCCTCGGCCCCCAGATCCAGTGTTGGGCCCAACAACCATCTCTAATATCC
586 TTGTTCCGTAACCGACCCTCGGCCCCCAGATCCAGTGTTGGGCCCAACAACCATCTCTAATATCC
17607 TCAGCATAGCCTGGGACAAGGCGTCGTCCACGGCCATGCGATCATGAGACCCAATCTCTGTAGCA
651 TCAGCATAGCCTGGGACAAGGCGTCGTCCACGGCCATGCGATCATGAGACCCAATCTCTGTAGCA
17672 GGTGAAATCGACGTCTCGCTTGTATCCAGATTTGACATGTTGCCTAACGACGAGGACTCAGCTCG
716 GGTGAAATCGACGTCTCGCTTGTATCCAGATTTGACATGTTGCCTAACGACGAGGACTCAGCTCG
17737 AGCCCCTCTACGGCTTCTACCTCGGCCTCTAGTACTCTATCTGCAGATACCTCGTGCACTCATCA
781 AGCCCCTCTACGGCTTCTACCTCGGCCTCTAGTACTCTATCTGCAGATACCTCGTGCACTCATCA
17802 TA
846 TA
17804 GAATTTGTAG
Statistics
Matches: 842, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
847 842 1.00
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.27
Consensus pattern (847 bp):
AGGAGCAACAAGGGCCCCAACTCTAACTGGCCCACCAGATCTAACCTTTTTTCTTAGGCCTCATC
GCAGAACTCGATGGCTCTAAATCCCTATTATTCTTTCCTCTCTCCTTATCCCAGTTTTGGCGCTC
AGCGCGCTTCACCTCCTCGGTGATCTTTGCCTTATCTACCAGTGCTGAAAAGTCACGCTCCCTCT
GCGAAGCTATCAAAACTCTCAAACTATCCTTGAGTCCATCATCGAAGAGGATACAACGCTTATAT
TCAGTCGCCACCATGCCTCGCATATAGCGGCTTAATCTTAGAAACTCGGTATCATACTCGGCCAC
TGAATGATCCCCTTACGTGAGATTCAGAAACTCATGTCTTCTAGCGTCAATGTAGCTTGCCCCCA
CATATTTAACTTGAAAAGCAGGCTTATAGAAATCCCTTCTTAACGGTCAGCCACCATTGGTATGT
TTCATCGCGAAGTAAGGAAAAAACCCCTTTCAATTTCTATTCAAGGGTAAAGTCCAGATCGTCTA
CGATTCTTTCCGTGGCCTCCATCCAGTACTCGGCCCCTGGATAGCTCAGCCCCATTGGACCAGAG
TTGTTCCGTAACCGACCCTCGGCCCCCAGATCCAGTGTTGGGCCCAACAACCATCTCTAATATCC
TCAGCATAGCCTGGGACAAGGCGTCGTCCACGGCCATGCGATCATGAGACCCAATCTCTGTAGCA
GGTGAAATCGACGTCTCGCTTGTATCCAGATTTGACATGTTGCCTAACGACGAGGACTCAGCTCG
AGCCCCTCTACGGCTTCTACCTCGGCCTCTAGTACTCTATCTGCAGATACCTCGTGCACTCATCA
TA
Found at i:18053 original size:20 final size:20
Alignment explanation
Indices: 18028--18066 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
18018 GCTACTCATA
18028 TTTTTA-AAAACTTATCAGAG
1 TTTTTAGAAAACTTA-CAGAG
*
18048 TTTTTAGAACACTTACAGA
1 TTTTTAGAAAACTTACAGA
18067 ATCGGTGCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (20 bp):
TTTTTAGAAAACTTACAGAG
Found at i:25453 original size:24 final size:22
Alignment explanation
Indices: 25415--25465 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 22
25405 CCGACTATAT
* *
25415 TTTTTTATTTTTTTCTTTCTTTCC
1 TTTTTTATCTCTTTC-TTC-TTCC
25439 TTTTTTATCTCTTTCTTCTTCC
1 TTTTTTATCTCTTTCTTCTTCC
25461 TTTTT
1 TTTTT
25466 CTTTTTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.36
23 3 0.12
24 13 0.52
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTTTATCTCTTTCTTCTTCC
Found at i:25457 original size:27 final size:24
Alignment explanation
Indices: 25415--25480 Score: 62
Period size: 27 Copynumber: 2.6 Consensus size: 24
25405 CCGACTATAT
*
25415 TTTTTTATTTTTTTCTTTCTTTCC
1 TTTTTTATTTTTTTCTTCCTTTCC
*
25439 TTTTTTATCTCTTTCTTCTTCCTTT-T
1 TTTTTTAT-T-TTT-TTCTTCCTTTCC
*
25465 TCTTTTTCTTTTTTTC
1 T-TTTTTATTTTTTTC
25481 AAACCCTAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
24 11 0.31
25 4 0.11
26 5 0.14
27 15 0.43
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTTTTATTTTTTTCTTCCTTTCC
Found at i:25589 original size:25 final size:25
Alignment explanation
Indices: 25560--25614 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
25550 TCTTCCCTCC
* * *
25560 CCCTTCTTTTTTTCTTTTATTCTTT
1 CCCTTATTTTTCTCTTTTATTCTCT
*
25585 CCCTTATTTTTCTCTTTTCTTCTCT
1 CCCTTATTTTTCTCTTTTATTCTCT
25610 CCCTT
1 CCCTT
25615 TCTCTCCAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.04, C:0.31, G:0.00, T:0.65
Consensus pattern (25 bp):
CCCTTATTTTTCTCTTTTATTCTCT
Found at i:26146 original size:29 final size:31
Alignment explanation
Indices: 26095--26157 Score: 94
Period size: 29 Copynumber: 2.1 Consensus size: 31
26085 TAGAGGACGC
* *
26095 AAAACTTTCAAGGTTAAAATGTAATTTTAGG
1 AAAACTTTCAAGGTCAAAATGTAATTTTAAG
26126 AAAA-TTT-AAGGTCAAAATGTAATTTTAAG
1 AAAACTTTCAAGGTCAAAATGTAATTTTAAG
26155 AAA
1 AAA
26158 GTTGAGGGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 23 0.77
30 3 0.10
31 4 0.13
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.33
Consensus pattern (31 bp):
AAAACTTTCAAGGTCAAAATGTAATTTTAAG
Found at i:26173 original size:30 final size:29
Alignment explanation
Indices: 26104--26173 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
26094 CAAAACTTTC
* * *
26104 AAGGTTAAAATGTAATTTTAGGAAAATTT
1 AAGGTCAAAATGTAATTTTAAGAAAATTG
*
26133 AAGGTCAAAATGTAATTTTAAGAAAGTTG
1 AAGGTCAAAATGTAATTTTAAGAAAATTG
*
26162 AGGGATCAAAAT
1 AAGG-TCAAAAT
26174 TTCGTATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 28 0.80
30 7 0.20
ACGTcount: A:0.46, C:0.03, G:0.20, T:0.31
Consensus pattern (29 bp):
AAGGTCAAAATGTAATTTTAAGAAAATTG
Found at i:31283 original size:404 final size:404
Alignment explanation
Indices: 30534--31341 Score: 1607
Period size: 404 Copynumber: 2.0 Consensus size: 404
30524 GCCCAATTGC
30534 AGGTGACATAATTTTGAATAGGAAGATTTGTAGCTGCTTTGATGGATATGATAGGAGAGATAATG
1 AGGTGACATAATTTTGAATAGGAAGATTTGTAGCTGCTTTGATGGATATGATAGGAGAGATAATG
*
30599 GAAGACTCAGTTCTTCCGGATATGGTATTGGCAGCAGTTCAAGGAAAGCTGTAGAAATGAGCAGG
66 GAAGACCCAGTTCTTCCGGATATGGTATTGGCAGCAGTTCAAGGAAAGCTGTAGAAATGAGCAGG
30664 CCTAGTTCGTCCGTACGGTGACGTTCCACAAAACCGGCAGCTATCAACTTGCCTTTGAGTCCAAA
131 CCTAGTTCGTCCGTACGGTGACGTTCCACAAAACCGGCAGCTATCAACTTGCCTTTGAGTCCAAA
30729 ACGCTGTTACAGGTAGCCTCTTCATAGGAAATGGAGTGGCTCATCAGTTGGAAGCTGATGTTGTT
196 ACGCTGTTACAGGTAGCCTCTTCATAGGAAATGGAGTGGCTCATCAGTTGGAAGCTGATGTTGTT
30794 AACAACATAAAATCTCTTTATTTTGACCGACATATTTCAACATTGAATTATTAGATTCTGTTTTC
261 AACAACATAAAATCTCTTTATTTTGACCGACATATTTCAACATTGAATTATTAGATTCTGTTTTC
30859 AGCTAAAAACAATTTATGCCTTCCTTTATCTCCTCTAGTCTTATATGTGACCATTTTGGAATTTC
326 AGCTAAAAACAATTTATGCCTTCCTTTATCTCCTCTAGTCTTATATGTGACCATTTTGGAATTTC
30924 TGGGAGGCTCCCTT
391 TGGGAGGCTCCCTT
30938 AGGTGACATAATTTTGAATAGGAAGATTTGTAGCTGCTTTGATGGATATGATAGGAGAGATAATG
1 AGGTGACATAATTTTGAATAGGAAGATTTGTAGCTGCTTTGATGGATATGATAGGAGAGATAATG
31003 GAAGACCCAGTTCTTCCGGATATGGTATTGGCAGCAGTTCAAGGAAAGCTGTAGAAATGAGCAGG
66 GAAGACCCAGTTCTTCCGGATATGGTATTGGCAGCAGTTCAAGGAAAGCTGTAGAAATGAGCAGG
31068 CCTAGTTCGTCCGTACGGTGACGTTCCACAAAACCGGCAGCTATCAACTTGCCTTTGAGTCCAAA
131 CCTAGTTCGTCCGTACGGTGACGTTCCACAAAACCGGCAGCTATCAACTTGCCTTTGAGTCCAAA
31133 ACGCTGTTACAGGTAGCCTCTTCATAGGAAATGGAGTGGCTCATCAGTTGGAAGCTGATGTTGTT
196 ACGCTGTTACAGGTAGCCTCTTCATAGGAAATGGAGTGGCTCATCAGTTGGAAGCTGATGTTGTT
31198 AACAACATAAAATCTCTTTATTTTGACCGACATATTTCAACATTGAATTATTAGATTCTGTTTTC
261 AACAACATAAAATCTCTTTATTTTGACCGACATATTTCAACATTGAATTATTAGATTCTGTTTTC
31263 AGCTAAAAACAATTTATGCCTTCCTTTATCTCCTCTAGTCTTATATGTGACCATTTTGGAATTTC
326 AGCTAAAAACAATTTATGCCTTCCTTTATCTCCTCTAGTCTTATATGTGACCATTTTGGAATTTC
31328 TGGGAGGCTCCCTT
391 TGGGAGGCTCCCTT
31342 TGGGGGTAAA
Statistics
Matches: 403, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
404 403 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (404 bp):
AGGTGACATAATTTTGAATAGGAAGATTTGTAGCTGCTTTGATGGATATGATAGGAGAGATAATG
GAAGACCCAGTTCTTCCGGATATGGTATTGGCAGCAGTTCAAGGAAAGCTGTAGAAATGAGCAGG
CCTAGTTCGTCCGTACGGTGACGTTCCACAAAACCGGCAGCTATCAACTTGCCTTTGAGTCCAAA
ACGCTGTTACAGGTAGCCTCTTCATAGGAAATGGAGTGGCTCATCAGTTGGAAGCTGATGTTGTT
AACAACATAAAATCTCTTTATTTTGACCGACATATTTCAACATTGAATTATTAGATTCTGTTTTC
AGCTAAAAACAATTTATGCCTTCCTTTATCTCCTCTAGTCTTATATGTGACCATTTTGGAATTTC
TGGGAGGCTCCCTT
Found at i:33727 original size:2 final size:2
Alignment explanation
Indices: 33720--33749 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
33710 ACTCATTTCT
33720 TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
33750 TTTCTTAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:36301 original size:26 final size:26
Alignment explanation
Indices: 36239--36315 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 26
36229 AGTTTAGCAT
* *
36239 TACTTTTGAAAAGTGCTTTTAAAAAG
1 TACTTTTGAAAAGTGTTTTTAAGAAG
* * *
36265 T-GTTGTGGAAAAGTGTTTTTAAGACG
1 TACTT-TTGAAAAGTGTTTTTAAGAAG
*
36291 TACTTTTGAAAAGTTTTGTTTAAGA
1 TACTTTTGAAAAGTGTT-TTTAAGA
36316 TTTAAGAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
25 2 0.05
26 29 0.73
27 9 0.22
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (26 bp):
TACTTTTGAAAAGTGTTTTTAAGAAG
Found at i:36376 original size:20 final size:18
Alignment explanation
Indices: 36341--36379 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
36331 TTACTGTCAA
36341 AAAATGCTTTTGAGAAAT
1 AAAATGCTTTTGAGAAAT
*
36359 AAAATGTCTATTTTAGAAAT
1 AAAATG-CT-TTTGAGAAAT
36379 A
1 A
36380 GTATTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 2 0.11
20 10 0.56
ACGTcount: A:0.46, C:0.05, G:0.13, T:0.36
Consensus pattern (18 bp):
AAAATGCTTTTGAGAAAT
Found at i:36716 original size:20 final size:21
Alignment explanation
Indices: 36693--36741 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
36683 AACCCATATT
*
36693 AAATATTAACATAACATAG-A
1 AAATATTAACATAACAAAGTA
* *
36713 AAATATAAACCTAACAAAGTA
1 AAATATTAACATAACAAAGTA
36734 AAATATTA
1 AAATATTA
36742 CATGTATTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.61, C:0.10, G:0.04, T:0.24
Consensus pattern (21 bp):
AAATATTAACATAACAAAGTA
Found at i:42503 original size:21 final size:20
Alignment explanation
Indices: 42460--42504 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
42450 GTAGATAGCG
*
42460 AAAACAATCGATTGAAAAGC
1 AAAACAATCAATTGAAAAGC
42480 AAAACAATCAATTGAAACAGC
1 AAAACAATCAATTGAAA-AGC
42501 AAAA
1 AAAA
42505 TAATTGATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.60, C:0.16, G:0.11, T:0.13
Consensus pattern (20 bp):
AAAACAATCAATTGAAAAGC
Found at i:42514 original size:21 final size:20
Alignment explanation
Indices: 42460--42540 Score: 81
Period size: 21 Copynumber: 4.0 Consensus size: 20
42450 GTAGATAGCG
42460 AAAACAATCGATTGAAAAGC
1 AAAACAATCGATTGAAAAGC
*
42480 AAAACAATCAATTGAAACAGC
1 AAAACAATCGATTGAAA-AGC
* * * *
42501 AAAATAATTGATTGTAAAGTG
1 AAAACAATCGATTGAAAAG-C
* *
42522 AAAACAATTGGTTGAAAAG
1 AAAACAATCGATTGAAAAG
42541 AATCATTTCA
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
20 18 0.36
21 32 0.64
ACGTcount: A:0.53, C:0.10, G:0.16, T:0.21
Consensus pattern (20 bp):
AAAACAATCGATTGAAAAGC
Found at i:45199 original size:3 final size:3
Alignment explanation
Indices: 45191--45232 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
45181 GCGTATGTAA
*
45191 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TCT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
45233 AATTCCTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:58051 original size:44 final size:43
Alignment explanation
Indices: 57954--58072 Score: 127
Period size: 44 Copynumber: 2.7 Consensus size: 43
57944 TGAAGAAGCA
*
57954 AATCTTATCTCCCTGAGGTTGCAGTGGAGCATATTGAAGTCAAT
1 AATCTTATCTCCCTGAGGTTGCAGTGGAGCA-ATTAAAGTCAAT
*
57998 AATAC-TATCTCCCTGAGGTTGTAGTGGGGAGC-ATTAAAGT-AAT
1 AAT-CTTATCTCCCTGAGGTTGCAGT--GGAGCAATTAAAGTCAAT
* * *
58041 AGATCTTATCTCTCTGAAGTTGCAGTAGAGCA
1 A-ATCTTATCTCCCTGAGGTTGCAGTGGAGCA
58073 GATCGCATCA
Statistics
Matches: 63, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
42 4 0.06
43 5 0.08
44 48 0.76
45 1 0.02
46 5 0.08
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (43 bp):
AATCTTATCTCCCTGAGGTTGCAGTGGAGCAATTAAAGTCAAT
Found at i:76369 original size:45 final size:48
Alignment explanation
Indices: 76302--76392 Score: 125
Period size: 45 Copynumber: 2.0 Consensus size: 48
76292 TTCTCTGCTT
* * *
76302 AAAACGCCTAAGTCAGCCTAACTTGTAA-AA-AAAGG-TTCAATAGCA
1 AAAACGCCCAAGTCAGCCTAACTCGCAACAATAAAGGATTCAATAGCA
*
76347 AAAACGCCCAAGTCAGCTTAACTCGCAACAATAAAGGATTCAATAG
1 AAAACGCCCAAGTCAGCCTAACTCGCAACAATAAAGGATTCAATAG
76393 AATTCCCTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
45 24 0.62
46 2 0.05
47 5 0.13
48 8 0.21
ACGTcount: A:0.44, C:0.22, G:0.15, T:0.19
Consensus pattern (48 bp):
AAAACGCCCAAGTCAGCCTAACTCGCAACAATAAAGGATTCAATAGCA
Found at i:81769 original size:17 final size:17
Alignment explanation
Indices: 81747--81811 Score: 69
Period size: 17 Copynumber: 3.7 Consensus size: 17
81737 ACATCAAAGG
*
81747 ATACAATTAAAAGCTGT
1 ATACAATTAGAAGCTGT
*
81764 ATACAATTAGAA-CTCT
1 ATACAATTAGAAGCTGT
*
81780 AAGACATAATTAGAAGCTGT
1 -ATAC--AATTAGAAGCTGT
81800 ATACAATTAGAA
1 ATACAATTAGAA
81812 CTCTAAGATT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
16 3 0.08
17 22 0.56
19 11 0.28
20 3 0.08
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (17 bp):
ATACAATTAGAAGCTGT
Found at i:81792 original size:19 final size:17
Alignment explanation
Indices: 81766--81819 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
81756 AAAGCTGTAT
81766 ACAATTAGAACTCTAAG
1 ACAATTAGAACTCTAAG
* *
81783 ACATAATTAGAAGCTGT-AT
1 AC--AATTAGAA-CTCTAAG
81802 ACAATTAGAACTCTAAG
1 ACAATTAGAACTCTAAG
81819 A
1 A
81820 TTAAATAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
16 3 0.10
17 12 0.41
19 11 0.38
20 3 0.10
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (17 bp):
ACAATTAGAACTCTAAG
Found at i:81798 original size:36 final size:36
Alignment explanation
Indices: 81751--81819 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
81741 CAAAGGATAC
81751 AATTAAAAGCTGTATACAATTAGAACTCTAAGACAT
1 AATTAAAAGCTGTATACAATTAGAACTCTAAGACAT
*
81787 AATTAGAAGCTGTATACAATTAGAACTCTAAGA
1 AATTAAAAGCTGTATACAATTAGAACTCTAAGA
81820 TTAAATAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (36 bp):
AATTAAAAGCTGTATACAATTAGAACTCTAAGACAT
Found at i:83105 original size:24 final size:24
Alignment explanation
Indices: 83073--83152 Score: 63
Period size: 24 Copynumber: 3.4 Consensus size: 24
83063 TACATAATAC
* **
83073 ATTTAAAATAATAATATTGGATAA
1 ATTTTAAATAATAATATACGATAA
* * *
83097 GTTTTAAATTATAGTATACGATAA
1 ATTTTAAATAATAATATACGATAA
* * *
83121 ATTTTAAATTATGATATATGAT-A
1 ATTTTAAATAATAATATACGATAA
*
83144 ATTTAAAAT
1 ATTTTAAAT
83153 GATAGTTTAT
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 9 0.20
24 36 0.80
ACGTcount: A:0.47, C:0.01, G:0.09, T:0.42
Consensus pattern (24 bp):
ATTTTAAATAATAATATACGATAA
Found at i:83213 original size:23 final size:25
Alignment explanation
Indices: 83161--83219 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 25
83151 ATGATAGTTT
*
83161 ATTAAATATTAAAATAATACTAATG
1 ATTAAATATTAAAACAATACTAATG
**
83186 A-TAAAT-TTAAAACAATGTTAA-G
1 ATTAAATATTAAAACAATACTAATG
83208 ATTAAATATTAA
1 ATTAAATATTAA
83220 CTAGCATTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 2 0.07
23 17 0.59
24 9 0.31
25 1 0.03
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (25 bp):
ATTAAATATTAAAACAATACTAATG
Found at i:84587 original size:16 final size:16
Alignment explanation
Indices: 84563--84616 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
84553 TTTGGTTTGC
* *
84563 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
*
84579 TGTAATGGAATAGATG
1 TGTAATGGAATAGAGG
84595 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
84611 TGTAAT
1 TGTAAT
84617 AACAAATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:84872 original size:56 final size:56
Alignment explanation
Indices: 84812--84918 Score: 144
Period size: 56 Copynumber: 1.9 Consensus size: 56
84802 ATTAATATAA
* *
84812 ATAATTTAATCATATT-TTAACATAATTATTATTAAATATAATTTAATAAAAAATAT
1 ATAATTTAATAAAATTCTTAACATAATTATTATTAAAT-TAATTTAATAAAAAATAT
* * * *
84868 ATAATTTAATAAAATTCTTAATATAATTATTCTTATATTAATTTACTAAAA
1 ATAATTTAATAAAATTCTTAACATAATTATTATTAAATTAATTTAATAAAA
84919 TCATAATATG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
56 26 0.59
57 18 0.41
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.46
Consensus pattern (56 bp):
ATAATTTAATAAAATTCTTAACATAATTATTATTAAATTAATTTAATAAAAAATAT
Found at i:85267 original size:77 final size:77
Alignment explanation
Indices: 85175--85336 Score: 324
Period size: 77 Copynumber: 2.1 Consensus size: 77
85165 ATTTTCTGTC
85175 CACTTTAATAATTGAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
1 CACTTTAATAATTGAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
85240 TTATTGACATAA
66 TTATTGACATAA
85252 CACTTTAATAATTGAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
1 CACTTTAATAATTGAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
85317 TTATTGACATAA
66 TTATTGACATAA
85329 CACTTTAA
1 CACTTTAA
85337 GATTGTCTCA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 85 1.00
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (77 bp):
CACTTTAATAATTGAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
TTATTGACATAA
Found at i:86244 original size:10 final size:10
Alignment explanation
Indices: 86229--86271 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
86219 CTTCTTAGAC
86229 AAATAAACAA
1 AAATAAACAA
86239 AAATAAACAA
1 AAATAAACAA
*
86249 CAATAAACAA
1 AAATAAACAA
*
86259 GAAT-AACAA
1 AAATAAACAA
86268 AAAT
1 AAAT
86272 TGTTTTTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
9 8 0.27
10 22 0.73
ACGTcount: A:0.74, C:0.12, G:0.02, T:0.12
Consensus pattern (10 bp):
AAATAAACAA
Found at i:104855 original size:14 final size:13
Alignment explanation
Indices: 104833--104995 Score: 54
Period size: 13 Copynumber: 12.2 Consensus size: 13
104823 AAGTGTTTTC
*
104833 TTTCTTCAAGTGTT
1 TTTCATCAAGT-TT
104847 TTTCATCAAGTTCT
1 TTTCATCAAGTT-T
104861 TTT-ATCAAGTTT
1 TTTCATCAAGTTT
* *
104873 TTAATTACCAAGGTTTTTT
1 TT--TCATCAA-G---TTT
* *
104892 TTGTTATTAAGT-T
1 TT-TCATCAAGTTT
*
104905 TTGCATCAAGTTCT
1 TTTCATCAAGTT-T
104919 TTT--T-AAGT-T
1 TTTCATCAAGTTT
*
104928 TTTCATCAAGTCT
1 TTTCATCAAGTTT
*
104941 TTTCATAAAG-TT
1 TTTCATCAAGTTT
*
104953 TTCCATCAAGTTT
1 TTTCATCAAGTTT
*
104966 TTAATCATTAAG-TT
1 TT--TCATCAAGTTT
*
104980 TTTCAATTAAGTTT
1 TTTC-ATCAAGTTT
104994 TT
1 TT
104996 ATCTCTTGCA
Statistics
Matches: 115, Mismatches: 15, Indels: 38
0.68 0.09 0.23
Matches are distributed among these distances:
9 4 0.03
11 5 0.04
12 25 0.22
13 32 0.28
14 27 0.23
15 10 0.09
16 1 0.01
17 1 0.01
18 5 0.04
19 5 0.04
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (13 bp):
TTTCATCAAGTTT
Found at i:104924 original size:23 final size:23
Alignment explanation
Indices: 104898--104964 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 23
104888 TTTTTTGTTA
*
104898 TTAAGTTTTGCATCAAGTTCTTT
1 TTAAGTTTTCCATCAAGTTCTTT
*
104921 TTAAGTTTTTCATCAAG-TCTTT
1 TTAAGTTTTCCATCAAGTTCTTT
104943 TCATAAAGTTTTCCATCAAGTT
1 T--T-AAGTTTTCCATCAAGTT
104965 TTTAATCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
22 6 0.16
23 16 0.42
24 1 0.03
25 14 0.37
26 1 0.03
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.49
Consensus pattern (23 bp):
TTAAGTTTTCCATCAAGTTCTTT
Found at i:104990 original size:13 final size:12
Alignment explanation
Indices: 104897--104995 Score: 76
Period size: 13 Copynumber: 7.9 Consensus size: 12
104887 TTTTTTTGTT
*
104897 ATTAAGTTTTGC
1 ATTAAGTTTTTC
*
104909 ATCAAGTTCTTT-
1 ATTAAGTT-TTTC
104921 -TTAAGTTTTTC
1 ATTAAGTTTTTC
*
104932 ATCAAGTCTTTTC
1 ATTAAGT-TTTTC
* *
104945 ATAAAGTTTTCC
1 ATTAAGTTTTTC
*
104957 ATCAAGTTTTTAATC
1 ATTAAG-TTTT--TC
104972 ATTAAGTTTTTC
1 ATTAAGTTTTTC
104984 AATTAAGTTTTT
1 -ATTAAGTTTTT
104996 ATCTCTTGCA
Statistics
Matches: 70, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
10 3 0.04
11 6 0.09
12 23 0.33
13 28 0.40
14 4 0.06
15 6 0.09
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (12 bp):
ATTAAGTTTTTC
Found at i:105450 original size:22 final size:22
Alignment explanation
Indices: 105425--105470 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
105415 TGGTTCCGTC
*
105425 AAGGGAAGTAGTAACCGGATTT
1 AAGGGAAGTAGTAACCAGATTT
*
105447 AAGGGTAGTAGTAACCAGATTT
1 AAGGGAAGTAGTAACCAGATTT
105469 AA
1 AA
105471 ATGTCCCGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.39, C:0.09, G:0.28, T:0.24
Consensus pattern (22 bp):
AAGGGAAGTAGTAACCAGATTT
Found at i:111764 original size:5 final size:5
Alignment explanation
Indices: 111754--111778 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
111744 GAAAACGCAC
111754 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
111779 TATCTTATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:113207 original size:14 final size:13
Alignment explanation
Indices: 113185--113334 Score: 53
Period size: 13 Copynumber: 11.2 Consensus size: 13
113175 AAGTGTTTTC
*
113185 TTTCTTCAAGTGTT
1 TTTCATCAAGT-TT
113199 TTTCATCAAGTTCT
1 TTTCATCAAGTT-T
113213 TTT-ATCAAGTTT
1 TTTCATCAAGTTT
* *
113225 TTAATTACCAAGGTTTTTT
1 TT--TCATCAA-G---TTT
* *
113244 TTGTTATTAAGT-T
1 TT-TCATCAAGTTT
*
113257 TTGCATCAAGTTCT
1 TTTCATCAAGTT-T
113271 TTT--T-AAGT-T
1 TTTCATCAAGTTT
*
113280 TTTCATCAAGTCT
1 TTTCATCAAGTTT
*
113293 TTTCATAAAG-TT
1 TTTCATCAAGTTT
*
113305 TTCCATCAAGTTT
1 TTTCATCAAGTTT
*
113318 TTAATCATTAAGTTT
1 TT--TCATCAAGTTT
113333 TT
1 TT
113335 CAATTAAGCT
Statistics
Matches: 104, Mismatches: 15, Indels: 33
0.68 0.10 0.22
Matches are distributed among these distances:
9 4 0.04
11 5 0.05
12 23 0.22
13 26 0.25
14 19 0.18
15 15 0.14
16 1 0.01
17 1 0.01
18 5 0.05
19 5 0.05
ACGTcount: A:0.24, C:0.13, G:0.10, T:0.53
Consensus pattern (13 bp):
TTTCATCAAGTTT
Found at i:113276 original size:23 final size:23
Alignment explanation
Indices: 113250--113316 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 23
113240 TTTTTTGTTA
*
113250 TTAAGTTTTGCATCAAGTTCTTT
1 TTAAGTTTTCCATCAAGTTCTTT
*
113273 TTAAGTTTTTCATCAAG-TCTTT
1 TTAAGTTTTCCATCAAGTTCTTT
113295 TCATAAAGTTTTCCATCAAGTT
1 T--T-AAGTTTTCCATCAAGTT
113317 TTTAATCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
22 6 0.16
23 16 0.42
24 1 0.03
25 14 0.37
26 1 0.03
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.49
Consensus pattern (23 bp):
TTAAGTTTTCCATCAAGTTCTTT
Found at i:113317 original size:12 final size:12
Alignment explanation
Indices: 113252--113324 Score: 69
Period size: 12 Copynumber: 6.1 Consensus size: 12
113242 TTTTGTTATT
*
113252 AAGTTTTGCATC
1 AAGTTTTTCATC
*
113264 AAGTTCTTT--TT
1 AAGTT-TTTCATC
113275 AAGTTTTTCATC
1 AAGTTTTTCATC
*
113287 AAGTCTTTTCATA
1 AAGT-TTTTCATC
*
113300 AAGTTTTCCATC
1 AAGTTTTTCATC
*
113312 AAGTTTTTAATC
1 AAGTTTTTCATC
113324 A
1 A
113325 TTAAGTTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
10 3 0.06
11 6 0.12
12 27 0.55
13 13 0.27
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (12 bp):
AAGTTTTTCATC
Found at i:113342 original size:13 final size:12
Alignment explanation
Indices: 113249--113347 Score: 67
Period size: 12 Copynumber: 7.8 Consensus size: 12
113239 TTTTTTTGTT
*
113249 ATTAAGTTTTGC
1 ATTAAGTTTTTC
*
113261 ATCAAGTTCTTT-
1 ATTAAGTT-TTTC
113273 -TTAAGTTTTTC
1 ATTAAGTTTTTC
*
113284 ATCAAGTCTTTTC
1 ATTAAGT-TTTTC
* *
113297 ATAAAGTTTTCC
1 ATTAAGTTTTTC
*
113309 ATCAAGTTTTTAATC
1 ATTAAG-TTTT--TC
113324 ATTAAGTTTTTC
1 ATTAAGTTTTTC
113336 AATTAAGCTTTT
1 -ATTAAG-TTTT
113348 ATCCCTTGCA
Statistics
Matches: 69, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
10 3 0.04
11 6 0.09
12 23 0.33
13 23 0.33
14 8 0.12
15 6 0.09
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.51
Consensus pattern (12 bp):
ATTAAGTTTTTC
Found at i:113852 original size:36 final size:37
Alignment explanation
Indices: 113781--113852 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 37
113771 TTATTTAACT
* **
113781 GCATTTTATTATTTTATTTTCAGCTTTTACTTTTTAC
1 GCATTTTATTATTTTATTTTCAGCTTTCAAATTTTAC
*
113818 GCATTTTATT-TATTTA-TTTCAGGTTTCAAATTTTA
1 GCATTTTATTAT-TTTATTTTCAGCTTTCAAATTTTA
113853 TCCCCCCGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
36 16 0.53
37 14 0.47
ACGTcount: A:0.22, C:0.11, G:0.07, T:0.60
Consensus pattern (37 bp):
GCATTTTATTATTTTATTTTCAGCTTTCAAATTTTAC
Found at i:125240 original size:41 final size:41
Alignment explanation
Indices: 125182--125508 Score: 550
Period size: 41 Copynumber: 8.0 Consensus size: 41
125172 NNNNNNNNNN
125182 CCTGCTAGGCTTATAGCCTGATTCAGTTCACCGACACTTAG
1 CCTGCTAGGCTTATAGCCTGATTCAGTTCACCGACACTTAG
*
125223 TCTGCTAGGCTTATAGCCTGATTCAGTTCACCGACACTTAG
1 CCTGCTAGGCTTATAGCCTGATTCAGTTCACCGACACTTAG
* * *
125264 TCTGCTAGGCTTATAGCCTGATTCAATTCA-CTAGCACTTCA-
1 CCTGCTAGGCTTATAGCCTGATTCAGTTCACCGA-CACTT-AG
125305 CCTGCTAGGCTTATAGCCTGATTCAGTTCACCGACACTTAG
1 CCTGCTAGGCTTATAGCCTGATTCAGTTCACCGACACTTAG
*
125346 CCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAG
1 CCTGCTAGGCTTATAGCCTGATTCAGTTCACCGACACTTAG
*
125387 CCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAG
1 CCTGCTAGGCTTATAGCCTGATTCAGTTCACCGACACTTAG
*
125428 CCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAG
1 CCTGCTAGGCTTATAGCCTGATTCAGTTCACCGACACTTAG
*
125469 CCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTA
1 CCTGCTAGGCTTATAGCCTGATTCAGTTCACCGACACTTA
125509 ATCTGATTGG
Statistics
Matches: 275, Mismatches: 7, Indels: 8
0.95 0.02 0.03
Matches are distributed among these distances:
40 3 0.01
41 269 0.98
42 3 0.01
ACGTcount: A:0.21, C:0.29, G:0.20, T:0.30
Consensus pattern (41 bp):
CCTGCTAGGCTTATAGCCTGATTCAGTTCACCGACACTTAG
Found at i:144686 original size:42 final size:42
Alignment explanation
Indices: 144625--144754 Score: 181
Period size: 42 Copynumber: 3.1 Consensus size: 42
144615 CACAGATGCA
* * *
144625 CATAAGTGCTAAACAGAAACCCATAAGGGTTGAA-TGGAAGCT
1 CATAAGAGCTAAACGGAAACCCATAAGGGTTAAACT-GAAGCT
*
144667 CATAAGAGCTGAACGGAAACCCATAAGGGTTAAACTGAAGCT
1 CATAAGAGCTAAACGGAAACCCATAAGGGTTAAACTGAAGCT
* * *
144709 CAAAAGAGCTTAACGGAAACCCATAAGGGTTAAACTGAAACT
1 CATAAGAGCTAAACGGAAACCCATAAGGGTTAAACTGAAGCT
144751 CATA
1 CATA
144755 TGAGTTAACA
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
42 78 0.99
43 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (42 bp):
CATAAGAGCTAAACGGAAACCCATAAGGGTTAAACTGAAGCT
Found at i:144748 original size:21 final size:21
Alignment explanation
Indices: 144625--144754 Score: 84
Period size: 21 Copynumber: 6.2 Consensus size: 21
144615 CACAGATGCA
* * *
144625 CATAAGTGCTAAACAGAAACC
1 CATAAGGGTTAAACTGAAACC
* * *
144646 CATAAGGGTTGAA-TGGAAGCT
1 CATAAGGGTTAAACT-GAAACC
* * * *
144667 CATAAGAGCTGAACGGAAACC
1 CATAAGGGTTAAACTGAAACC
* *
144688 CATAAGGGTTAAACTGAAGCT
1 CATAAGGGTTAAACTGAAACC
* * *
144709 CAAAAGAGCTT-AACGGAAACC
1 CATAAG-GGTTAAACTGAAACC
*
144730 CATAAGGGTTAAACTGAAACT
1 CATAAGGGTTAAACTGAAACC
144751 CATA
1 CATA
144755 TGAGTTAACA
Statistics
Matches: 79, Mismatches: 26, Indels: 8
0.70 0.23 0.07
Matches are distributed among these distances:
20 3 0.04
21 73 0.92
22 3 0.04
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (21 bp):
CATAAGGGTTAAACTGAAACC
Found at i:144761 original size:21 final size:20
Alignment explanation
Indices: 144665--144771 Score: 79
Period size: 21 Copynumber: 5.2 Consensus size: 20
144655 TGAATGGAAG
* *
144665 CTCATAAGAGCTGAACGGAAA
1 CTCATAAGAG-TTAACTGAAA
* * *
144686 CCCATAAGGGTTAAACTGAAG
1 CTCATAAGAGTT-AACTGAAA
* *
144707 CTCAAAAGAGCTTAACGGAAA
1 CTCATAAGAG-TTAACTGAAA
* *
144728 CCCATAAGGGTTAAACTGAAA
1 CTCATAAGAGTT-AACTGAAA
* *
144749 CTCATATGAGTTAACAGAAA
1 CTCATAAGAGTTAACTGAAA
144769 CTC
1 CTC
144772 GTGAGAGCTA
Statistics
Matches: 65, Mismatches: 18, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
20 13 0.20
21 50 0.77
22 2 0.03
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.19
Consensus pattern (20 bp):
CTCATAAGAGTTAACTGAAA
Found at i:146701 original size:43 final size:43
Alignment explanation
Indices: 146653--146871 Score: 267
Period size: 43 Copynumber: 5.1 Consensus size: 43
146643 GTTTTTAGAA
* *
146653 ACAAACACCGCTATAGAACAAGACATTTAGCGGCGCTTTTCCC
1 ACAAACGCCGCTATAGAACAAGACCTTTAGCGGCGCTTTTCCC
* * *
146696 ACAAACGCCACTATAGAACAAGACCTTTAACGGCGCTTTTCAC
1 ACAAACGCCGCTATAGAACAAGACCTTTAGCGGCGCTTTTCCC
* *
146739 TCAAACGCCGCTATAGAACAAGACCTTTAGCGGCACTTTTCCC
1 ACAAACGCCGCTATAGAACAAGACCTTTAGCGGCGCTTTTCCC
* * * * * * *
146782 ACAAACGCCGCTAAAGATCATGACTTTTAACGGCACTTTTACC
1 ACAAACGCCGCTATAGAACAAGACCTTTAGCGGCGCTTTTCCC
** * * *
146825 ACAAACGCCGCTATAGGTCATGACTTTTAGCGGTGCTTTTCCC
1 ACAAACGCCGCTATAGAACAAGACCTTTAGCGGCGCTTTTCCC
146868 ACAA
1 ACAA
146872 TCATGACTTT
Statistics
Matches: 153, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 153 1.00
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.24
Consensus pattern (43 bp):
ACAAACGCCGCTATAGAACAAGACCTTTAGCGGCGCTTTTCCC
Found at i:146892 original size:71 final size:73
Alignment explanation
Indices: 146798--146942 Score: 276
Period size: 71 Copynumber: 2.0 Consensus size: 73
146788 GCCGCTAAAG
146798 ATCATGACTTTTAACGGCACTTTTACCACAAACGCCGCTATAGGTCATGACTTTTAGCGGTGCTT
1 ATCATGACTTTTAACGGCACTTTTACCACAAACGCCGCTATAGGTCATGACTTTTAGCGGTGCTT
146863 TTCCCACA
66 TTCCCACA
146871 ATCATGAC-TTT-ACGGCACTTTTACCACAAACGCCGCTATAGGTCATGACTTTTAGCGGTGCTT
1 ATCATGACTTTTAACGGCACTTTTACCACAAACGCCGCTATAGGTCATGACTTTTAGCGGTGCTT
146934 TTCCCACA
66 TTCCCACA
146942 A
1 A
146943 ACGCCGCTAA
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
71 61 0.85
72 3 0.04
73 8 0.11
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (73 bp):
ATCATGACTTTTAACGGCACTTTTACCACAAACGCCGCTATAGGTCATGACTTTTAGCGGTGCTT
TTCCCACA
Found at i:146898 original size:28 final size:30
Alignment explanation
Indices: 146842--146899 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 30
146832 CCGCTATAGG
** *
146842 TCATGACTTTTAGCGGTGCTTTTCCCACAA
1 TCATGACTTTTAGCGGCACTTTTACCACAA
146872 TCATGAC-TTTA-CGGCACTTTTACCACAA
1 TCATGACTTTTAGCGGCACTTTTACCACAA
146900 ACGCCGCTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 14 0.56
29 4 0.16
30 7 0.28
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.34
Consensus pattern (30 bp):
TCATGACTTTTAGCGGCACTTTTACCACAA
Found at i:146919 original size:41 final size:43
Alignment explanation
Indices: 146872--146951 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
146862 TTTCCCACAA
146872 TCATGAC-TTTA-CGGCACTTTTACCACAAACGCCGCTATAGG
1 TCATGACTTTTAGCGGCACTTTTACCACAAACGCCGCTATAGG
** *
146913 TCATGACTTTTAGCGGTGCTTTTCCCACAAACGCCGCTA
1 TCATGACTTTTAGCGGCACTTTTACCACAAACGCCGCTA
146952 AAAACATATC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 7 0.21
42 4 0.12
43 23 0.68
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (43 bp):
TCATGACTTTTAGCGGCACTTTTACCACAAACGCCGCTATAGG
Found at i:152195 original size:114 final size:114
Alignment explanation
Indices: 151942--152277 Score: 494
Period size: 114 Copynumber: 2.9 Consensus size: 114
151932 GGTGTCGTTG
* * *
151942 GGCTTAGGTTTTTTGCGGCGCTTTCTAAAAAACGCCGCTAAAAGCCCTGAGCATTAGTGACGCTT
1 GGCTTAGGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCT-AAAGCCCTGAGCATTAGCGGCGCTT
** * *
152007 TATTAAAAAACGCCGCTAAATCCCTGAAAGCTCACAAAACGGTGTCATTTT
65 CCTT-AAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCATTTT
* * *
152058 GGCTTAGGTTTTTTGCGGTGCTTTCTCAAAAACGCAGCTAAAGCCCTAAGCATTAGCGGCGCTTC
1 GGCTTAGGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTC
* * * * *
152123 CTTTAAAATGCCACTAAATCCCCAAAATCTCACAAAACGGCGT-AGTTTT
66 CTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCA-TTTT
*
152172 GGCTTAGGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGTGCTTC
1 GGCTTAGGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTC
152237 CTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGC
66 CTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGC
152278 TAAATCCCCG
Statistics
Matches: 195, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
113 1 0.01
114 134 0.69
115 24 0.12
116 36 0.18
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (114 bp):
GGCTTAGGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTC
CTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCATTTT
Found at i:152281 original size:27 final size:27
Alignment explanation
Indices: 152249--152303 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
152239 TAAAAACGCC
152249 GCTAAATCCCCGAAAGCTCACAAAACG
1 GCTAAATCCCCGAAAGCTCACAAAACG
152276 GCTAAATCCCCGAAAGCTCACAAAACG
1 GCTAAATCCCCGAAAGCTCACAAAACG
152303 G
1 G
152304 TGTCTTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.40, C:0.33, G:0.16, T:0.11
Consensus pattern (27 bp):
GCTAAATCCCCGAAAGCTCACAAAACG
Found at i:162488 original size:22 final size:22
Alignment explanation
Indices: 162463--162504 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
162453 AAATAGTAAG
* *
162463 AAAATAACAAGAAAATAGCAGT
1 AAAACAACAAAAAAATAGCAGT
*
162485 AAAACAATAAAAAAATAGCA
1 AAAACAACAAAAAAATAGCA
162505 TATTTTTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.69, C:0.10, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAACAACAAAAAAATAGCAGT
Found at i:163154 original size:28 final size:28
Alignment explanation
Indices: 163095--163165 Score: 119
Period size: 28 Copynumber: 2.6 Consensus size: 28
163085 AAAAATAAAA
163095 ATTTACCAAAATAT-TACAATTTTTTTT
1 ATTTACCAAAATATATACAATTTTTTTT
163122 ATTTACCAAAATATATA-AACTTTTTTTT
1 ATTTACCAAAATATATACAA-TTTTTTTT
163150 ATTTACCAAAATATAT
1 ATTTACCAAAATATAT
163166 CAAAAAAACC
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 16 0.38
28 26 0.62
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (28 bp):
ATTTACCAAAATATATACAATTTTTTTT
Found at i:163263 original size:27 final size:27
Alignment explanation
Indices: 163224--163299 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
163214 TACTGGTCAC
*
163224 GCCAATGGAATTGGCGACACCAATGGT
1 GCCAATGCAATTGGCGACACCAATGGT
* *
163251 GCCAATGCCATTGGCGGCACCAATGGT
1 GCCAATGCAATTGGCGACACCAATGGT
* *
163278 GCC-ATACTAATTGGCGGCACCA
1 GCCAATGC-AATTGGCGACACCA
163300 CTCGTATTAC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 3 0.07
27 40 0.93
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (27 bp):
GCCAATGCAATTGGCGACACCAATGGT
Found at i:163468 original size:19 final size:21
Alignment explanation
Indices: 163430--163468 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
163420 AATAATTGAT
*
163430 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
163451 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
163469 TTGTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:163544 original size:3 final size:3
Alignment explanation
Indices: 163538--163563 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
163528 ATTATTATTA
163538 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
163564 AGTATGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:163744 original size:62 final size:62
Alignment explanation
Indices: 163674--163843 Score: 331
Period size: 62 Copynumber: 2.7 Consensus size: 62
163664 GAAAATAAAC
163674 TTCATAGTATAAATTTAATAATTTTAGTGTGTATTATTTTGAGTATAAAATTATTAATATTA
1 TTCATAGTATAAATTTAATAATTTTAGTGTGTATTATTTTGAGTATAAAATTATTAATATTA
163736 TTCATAGTATAAATTTAATAATTTTAGTGTGTATTATTTTGAGTATAAAATTATTAATATTA
1 TTCATAGTATAAATTTAATAATTTTAGTGTGTATTATTTTGAGTATAAAATTATTAATATTA
*
163798 TTCATAGTATAAATTTAATAATTTTAGTGTGTATTATTTTGTGTAT
1 TTCATAGTATAAATTTAATAATTTTAGTGTGTATTATTTTGAGTAT
163844 TATTTTGAGT
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 107 1.00
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (62 bp):
TTCATAGTATAAATTTAATAATTTTAGTGTGTATTATTTTGAGTATAAAATTATTAATATTA
Found at i:163842 original size:12 final size:12
Alignment explanation
Indices: 163825--163861 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
163815 ATAATTTTAG
163825 TGTGTATTATTT
1 TGTGTATTATTT
163837 TGTGTATTATTT
1 TGTGTATTATTT
* *
163849 TGAGTATAATTT
1 TGTGTATTATTT
163861 T
1 T
163862 TTTTAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (12 bp):
TGTGTATTATTT
Found at i:169958 original size:19 final size:19
Alignment explanation
Indices: 169923--169960 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
169913 TTTAAACACA
169923 CAAATATTACAAAAAAATT
1 CAAATATTACAAAAAAATT
*
169942 CAAAT-TTATAAATAAAATT
1 CAAATATTACAAA-AAAATT
169961 ACCTTTTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (19 bp):
CAAATATTACAAAAAAATT
Found at i:170011 original size:16 final size:15
Alignment explanation
Indices: 169996--170044 Score: 53
Period size: 18 Copynumber: 3.0 Consensus size: 15
169986 TCCCTCTTCT
169996 TCTTCTTCTTTTTTC
1 TCTTCTTCTTTTTTC
170011 TCTTTCTTTCCTTTTTTC
1 TC-TTC-TT-CTTTTTTC
*
170029 TCTTCTCCTTTCTTTC
1 TCTTCTTCTTT-TTTC
170045 CTTTTTTCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 6 0.21
16 8 0.28
17 5 0.17
18 10 0.34
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (15 bp):
TCTTCTTCTTTTTTC
Found at i:170020 original size:4 final size:4
Alignment explanation
Indices: 170001--170112 Score: 88
Period size: 4 Copynumber: 27.0 Consensus size: 4
169991 CTTCTTCTTC
* *
170001 TTCT TTTT TCTCT TTCT TTCCT TT-T TTCT CTTC- TCCT TTCT TTCCT
1 TTCT TTCT T-TCT TTCT TT-CT TTCT TTCT -TTCT TTCT TTCT TT-CT
* *
170047 TT-T TTCT CTTC- TCCT TTCCT TTCT TTCT TTCCT CTCCT TTCT TTCT
1 TTCT TTCT -TTCT TTCT TT-CT TTCT TTCT TT-CT -TTCT TTCT TTCT
170093 TTCT TTCT TTCT TTCT TTCT
1 TTCT TTCT TTCT TTCT TTCT
170113 ACCCCCACCA
Statistics
Matches: 88, Mismatches: 8, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
3 10 0.11
4 52 0.59
5 25 0.28
6 1 0.01
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
TTCT
Found at i:170033 original size:33 final size:31
Alignment explanation
Indices: 169973--170111 Score: 105
Period size: 30 Copynumber: 4.5 Consensus size: 31
169963 CTTTTTCCCT
* *
169973 TTTTTTCCTTTCTTCCCTCTTCTTCTTCTTC
1 TTTTTTCCTTTCTTTCCTCTTCTTCTTCTCC
* *
170004 TTTTTTCTCTTTCTTTCCTTTTTTCTCTTCTCC
1 TTTTTTC-CTTTCTTTCCTCTTCT-TCTTCTCC
*
170037 TTTCTTTCCTTT-TTT-CTCTTCTCCTT-TCC
1 TTT-TTTCCTTTCTTTCCTCTTCTTCTTCTCC
*
170066 TTTCTTT-CTTTCCTCTCCT-TTCTTTCTT-T-C
1 TTT-TTTCCTTT-CTTTCCTCTTC-TTCTTCTCC
170096 TTTCTTT-CTTTCTTTC
1 TTT-TTTCCTTTCTTTC
170112 TACCCCCACC
Statistics
Matches: 91, Mismatches: 10, Indels: 16
0.78 0.09 0.14
Matches are distributed among these distances:
28 4 0.04
29 14 0.15
30 20 0.22
31 19 0.21
32 16 0.18
33 14 0.15
34 4 0.04
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (31 bp):
TTTTTTCCTTTCTTTCCTCTTCTTCTTCTCC
Found at i:170043 original size:24 final size:24
Alignment explanation
Indices: 170008--170111 Score: 125
Period size: 24 Copynumber: 4.6 Consensus size: 24
169998 TTCTTCTTTT
170008 TTCT-CTTTCTTTCCTTTTTTCTC
1 TTCTCCTTTCTTTCCTTTTTTCTC
170031 TTCTCCTTTCTTTCCTTTTTTCTC
1 TTCTCCTTTCTTTCCTTTTTTCTC
170055 TTCTCCTTTCCTTT-CTTTCTTTC-C
1 TTCTCCTTT-CTTTCCTTT-TTTCTC
*
170079 -TCTCCTTTCTTT-CTTTCTT-TC
1 TTCTCCTTTCTTTCCTTTTTTCTC
170100 TT-T-CTTTCTTTC
1 TTCTCCTTTCTTTC
170112 TACCCCCACC
Statistics
Matches: 74, Mismatches: 1, Indels: 14
0.83 0.01 0.16
Matches are distributed among these distances:
20 8 0.11
21 4 0.05
22 9 0.12
23 12 0.16
24 33 0.45
25 8 0.11
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (24 bp):
TTCTCCTTTCTTTCCTTTTTTCTC
Found at i:170083 original size:47 final size:45
Alignment explanation
Indices: 170001--170112 Score: 139
Period size: 42 Copynumber: 2.6 Consensus size: 45
169991 CTTCTTCTTC
*
170001 TTCTTTTTTCTCTT-TCTTTCCTTT-TTTC--TCTTCTCCTTTCT
1 TTCTTTTTTCTCTTCTCTTTCCTTTCTTTCTTTCCTCTCCTTTCT
170042 TTCCTTTTTTCTCTTCTCCTTTCCTTTCTTTCTTTCCTCTCCTTTCT
1 TT-CTTTTTTCTCTTCT-CTTTCCTTTCTTTCTTTCCTCTCCTTTCT
*
170089 TTCTTTCTT-TCTT-TCTTT-CTTTCT
1 TTCTTTTTTCTCTTCTCTTTCCTTTCT
170113 ACCCCCACCA
Statistics
Matches: 63, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
41 2 0.03
42 18 0.29
43 5 0.08
44 10 0.16
45 8 0.13
46 6 0.10
47 14 0.22
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (45 bp):
TTCTTTTTTCTCTTCTCTTTCCTTTCTTTCTTTCCTCTCCTTTCT
Found at i:170190 original size:18 final size:18
Alignment explanation
Indices: 170167--170210 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
170157 TGGCATTGGC
170167 ACCATTGGTGCCGCCAAT
1 ACCATTGGTGCCGCCAAT
170185 ACCATTGGTGCCGCCAAT
1 ACCATTGGTGCCGCCAAT
170203 ACCATTGG
1 ACCATTGG
170211 CGTGACTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.23
Consensus pattern (18 bp):
ACCATTGGTGCCGCCAAT
Found at i:170294 original size:28 final size:28
Alignment explanation
Indices: 170263--170337 Score: 107
Period size: 28 Copynumber: 2.7 Consensus size: 28
170253 GTTTTGTTTT
*
170263 TTTATACATTTTGGTAAATAAAAAAAAG
1 TTTATATATTTTGGTAAATAAAAAAAAG
* *
170291 TTTATATGTTTTGGTAAATAAAAAAGAG
1 TTTATATATTTTGGTAAATAAAAAAAAG
170319 TTGTA-ATATTTTGGTAAAT
1 TT-TATATATTTTGGTAAAT
170338 TTTTATTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 40 0.95
29 2 0.05
ACGTcount: A:0.43, C:0.01, G:0.15, T:0.41
Consensus pattern (28 bp):
TTTATATATTTTGGTAAATAAAAAAAAG
Found at i:179372 original size:27 final size:27
Alignment explanation
Indices: 179334--179469 Score: 236
Period size: 27 Copynumber: 5.0 Consensus size: 27
179324 TAGTATTGGC
179334 GCCTATCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
179361 GCCTATTTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
179388 GCCTATCTAGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
179415 GCCTATTTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
179442 GCCTATCTAGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
179469 G
1 G
179470 TCATACTGAA
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 102 1.00
ACGTcount: A:0.16, C:0.21, G:0.40, T:0.24
Consensus pattern (27 bp):
GCCTATCTGGGAGGCGCCAATGGTGGT
Found at i:179483 original size:27 final size:27
Alignment explanation
Indices: 179334--179490 Score: 203
Period size: 27 Copynumber: 5.8 Consensus size: 27
179324 TAGTATTGGC
*
179334 GCCTATCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGAGAGGCGCCAATGGTGGT
* *
179361 GCCTATTTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGAGAGGCGCCAATGGTGGT
179388 GCCTATCT-AGGAGGCGCCAATGGTGGT
1 GCCTATCTGA-GAGGCGCCAATGGTGGT
* *
179415 GCCTATTTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGAGAGGCGCCAATGGTGGT
179442 GCCTATCT-AGGAGGCGCCAATGGTGGT
1 GCCTATCTGA-GAGGCGCCAATGGTGGT
* *
179469 GTC-ATACTGAAAGGCGCCAATG
1 GCCTAT-CTGAGAGGCGCCAATG
179491 CTATGATTTT
Statistics
Matches: 116, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.02
27 113 0.97
28 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.38, T:0.23
Consensus pattern (27 bp):
GCCTATCTGAGAGGCGCCAATGGTGGT
Found at i:179484 original size:81 final size:81
Alignment explanation
Indices: 179334--179490 Score: 237
Period size: 81 Copynumber: 1.9 Consensus size: 81
179324 TAGTATTGGC
* * * *
179334 GCCTATCTGGGAGGCGCCAATGGTGGTGCCTATTTGGGAGGCGCCAATGGTGGTGCCTATCTAGG
1 GCCTATCTGGGAGGCGCCAATGGTGGTGCCTATCTAGGAGGCGCCAATGGTGGTGCATATCTAGA
179399 AGGCGCCAATGGTGGT
66 AGGCGCCAATGGTGGT
*
179415 GCCTATTTGGGAGGCGCCAATGGTGGTGCCTATCTAGGAGGCGCCAATGGTGGTGTCATA-CT-G
1 GCCTATCTGGGAGGCGCCAATGGTGGTGCCTATCTAGGAGGCGCCAATGGTGGTG-CATATCTAG
179478 AAAGGCGCCAATG
65 -AAGGCGCCAATG
179491 CTATGATTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
80 1 0.01
81 65 0.94
82 3 0.04
ACGTcount: A:0.18, C:0.21, G:0.38, T:0.23
Consensus pattern (81 bp):
GCCTATCTGGGAGGCGCCAATGGTGGTGCCTATCTAGGAGGCGCCAATGGTGGTGCATATCTAGA
AGGCGCCAATGGTGGT
Found at i:179490 original size:54 final size:54
Alignment explanation
Indices: 179334--179469 Score: 263
Period size: 54 Copynumber: 2.5 Consensus size: 54
179324 TAGTATTGGC
*
179334 GCCTATCTGGGAGGCGCCAATGGTGGTGCCTATTTGGGAGGCGCCAATGGTGGT
1 GCCTATCTAGGAGGCGCCAATGGTGGTGCCTATTTGGGAGGCGCCAATGGTGGT
179388 GCCTATCTAGGAGGCGCCAATGGTGGTGCCTATTTGGGAGGCGCCAATGGTGGT
1 GCCTATCTAGGAGGCGCCAATGGTGGTGCCTATTTGGGAGGCGCCAATGGTGGT
179442 GCCTATCTAGGAGGCGCCAATGGTGGTG
1 GCCTATCTAGGAGGCGCCAATGGTGGTG
179470 TCATACTGAA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 81 1.00
ACGTcount: A:0.16, C:0.21, G:0.40, T:0.24
Consensus pattern (54 bp):
GCCTATCTAGGAGGCGCCAATGGTGGTGCCTATTTGGGAGGCGCCAATGGTGGT
Found at i:179594 original size:18 final size:20
Alignment explanation
Indices: 179552--179598 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
179542 GAAACGGAAG
179552 AAAGAAGAAGGAAGGAAGCA
1 AAAGAAGAAGGAAGGAAGCA
* *
179572 GAAGAA-AA-GAAGGAAGGA
1 AAAGAAGAAGGAAGGAAGCA
179590 AAAGAAGAA
1 AAAGAAGAA
179599 AAAAATTAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 14 0.61
19 4 0.17
20 5 0.22
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (20 bp):
AAAGAAGAAGGAAGGAAGCA
Found at i:179601 original size:22 final size:23
Alignment explanation
Indices: 179548--179601 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
179538 TACAGAAACG
*
179548 GAAGAAAGAAGAAGGAAGGAAGCA
1 GAAGAAA-AAGAAGGAAGGAAGAA
179572 GAAG-AAAAGAAGGAAGGAA-AA
1 GAAGAAAAAGAAGGAAGGAAGAA
179593 GAAGAAAAA
1 GAAGAAAAA
179602 AATTAGGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.18
22 17 0.61
23 2 0.07
24 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (23 bp):
GAAGAAAAAGAAGGAAGGAAGAA
Found at i:184196 original size:38 final size:38
Alignment explanation
Indices: 184154--184273 Score: 213
Period size: 38 Copynumber: 3.2 Consensus size: 38
184144 NNNNNNNNNN
*
184154 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATGAAATGATTTTTAATTTTT
*
184192 TTATAATTAAACTTTTAATGAAATGATTTTTAGTTTTT
1 TTATAATTAAACTTTTAATGAAATGATTTTTAATTTTT
*
184230 TTATAATTAAACTTTTAATGAAATAATTTTTAATTTTT
1 TTATAATTAAACTTTTAATGAAATGATTTTTAATTTTT
184268 TTATAA
1 TTATAA
184274 ACTTTATGTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 78 1.00
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATGAAATGATTTTTAATTTTT
Found at i:184383 original size:60 final size:59
Alignment explanation
Indices: 184307--184427 Score: 154
Period size: 60 Copynumber: 2.0 Consensus size: 59
184297 ATACTAAACT
* * * *
184307 AAACACAACAACTTATAGCTTAATCCTAAATTACCAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACCAA-AAATT-AATTATAAAATAATTAC
* * *
184367 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAATTAATTATAAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACCAAAAATTAATTATAAAATAATTAC
184426 AA
1 AA
184428 TATTCATACA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 4 0.08
59 17 0.32
60 32 0.60
ACGTcount: A:0.54, C:0.15, G:0.01, T:0.31
Consensus pattern (59 bp):
AAACACAAAAACTTATAACATAATCCTAAATTACCAAAAATTAATTATAAAATAATTAC
Found at i:184427 original size:21 final size:22
Alignment explanation
Indices: 184403--184449 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
184393 TAAATTACTA
*
184403 ACAATTAATT-ATA-AAATAATT
1 ACAATT-ATTCATACAAAAAATT
184424 ACAA-TATTCATACAAAAAATT
1 ACAATTATTCATACAAAAAATT
184445 ACAAT
1 ACAAT
184450 ATTACAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 3 0.14
20 4 0.18
21 15 0.68
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (22 bp):
ACAATTATTCATACAAAAAATT
Found at i:184495 original size:19 final size:19
Alignment explanation
Indices: 184489--184727 Score: 126
Period size: 19 Copynumber: 12.5 Consensus size: 19
184479 CATACAAAAT
*
184489 TACAATATTACAATATTCA
1 TACAAAATTACAATATTCA
*
184508 TACAAAAAATTGCAATATTCA
1 TAC--AAAATTACAATATTCA
* *
184529 TATAAAATTATAATA-T--
1 TACAAAATTACAATATTCA
*
184545 TACAATATT-C-ATA--CA
1 TACAAAATTACAATATTCA
*
184560 -AAAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
184578 TACAAAATTACAA-ATTCA
1 TACAAAATTACAATATTCA
184596 TACAAAAAATTACAATATTCA
1 TAC--AAAATTACAATATTCA
* *
184617 TACAAAA-TACTA-ATGCA
1 TACAAAATTACAATATTCA
* *
184634 -AAATTATAAATACAAATTTAATT-A
1 TACA--A-AATTAC-AA--T-ATTCA
* *
184658 TAAAATAATTATAATATTCA
1 TACAA-AATTACAATATTCA
*
184678 TAAAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
*
184697 TACAAAAAAATTAGAATATTCA
1 TAC---AAAATTACAATATTCA
184719 TACAAAATT
1 TACAAAATT
184728 CTAATCCAAA
Statistics
Matches: 173, Mismatches: 21, Indels: 52
0.70 0.09 0.21
Matches are distributed among these distances:
14 9 0.05
15 1 0.01
16 12 0.07
17 4 0.02
18 16 0.09
19 54 0.31
20 20 0.12
21 25 0.14
22 20 0.12
23 6 0.03
24 1 0.01
25 5 0.03
ACGTcount: A:0.55, C:0.11, G:0.01, T:0.32
Consensus pattern (19 bp):
TACAAAATTACAATATTCA
Found at i:184526 original size:29 final size:27
Alignment explanation
Indices: 184468--184590 Score: 133
Period size: 27 Copynumber: 5.0 Consensus size: 27
184458 ATATCTCGAC
*
184468 ATTATAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
184495 ATTACAATATTCATAC--AA--A-AA-
1 ATTACAATATTCATACAAAATTACAAT
* * *
184516 ATTGCAATATTCATATAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
184543 ATTACAATATTCATAC-AAA--A-AA-
1 ATTACAATATTCATACAAAATTACAAT
184565 ATTACAATATTCATACAAAATTACAA
1 ATTACAATATTCATACAAAATTACAA
184591 ATTCATACAA
Statistics
Matches: 81, Mismatches: 5, Indels: 21
0.76 0.05 0.20
Matches are distributed among these distances:
21 14 0.17
22 18 0.22
23 8 0.10
24 1 0.01
25 4 0.05
26 7 0.09
27 29 0.36
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.33
Consensus pattern (27 bp):
ATTACAATATTCATACAAAATTACAAT
Found at i:184544 original size:48 final size:49
Alignment explanation
Indices: 184415--184590 Score: 220
Period size: 48 Copynumber: 3.7 Consensus size: 49
184405 AATTAATTAT
*
184415 AAAATAATTACAATATTCATACAAAAAATTACAATATTACAATATATC-T-C
1 AAAAAAATTACAATATTCATAC--AAAATTACAATATTACAATAT-TCATAC
* * *
184465 ---GACATTATAATATTCATACAAAATTACAATATTACAATATTCATAC
1 AAAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
* * *
184511 -AAAAAATTGCAATATTCATATAAAATTATAATATTACAATATTCATAC
1 AAAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
184559 AAAAAAATTACAATATTCATACAAAATTACAA
1 AAAAAAATTACAATATTCATACAAAATTACAA
184591 ATTCATACAA
Statistics
Matches: 108, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
44 2 0.02
45 22 0.20
46 1 0.01
47 15 0.14
48 40 0.37
49 28 0.26
ACGTcount: A:0.53, C:0.13, G:0.01, T:0.32
Consensus pattern (49 bp):
AAAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
Found at i:184612 original size:39 final size:41
Alignment explanation
Indices: 184543--184624 Score: 150
Period size: 39 Copynumber: 2.0 Consensus size: 41
184533 AAATTATAAT
184543 ATTACAATATTCATACAAAAAAATTACAATATTCATACAAA
1 ATTACAATATTCATACAAAAAAATTACAATATTCATACAAA
184584 ATTACAA-ATTCATAC-AAAAAATTACAATATTCATACAAA
1 ATTACAATATTCATACAAAAAAATTACAATATTCATACAAA
184623 AT
1 AT
184625 ACTAATGCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 26 0.63
40 8 0.20
41 7 0.17
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (41 bp):
ATTACAATATTCATACAAAAAAATTACAATATTCATACAAA
Found at i:184704 original size:22 final size:22
Alignment explanation
Indices: 184659--184725 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 22
184649 ATTTAATTAT
* *
184659 AAAATAATTATAATATTCAT--
1 AAAAAAATTACAATATTCATAC
184679 -AAAAAATTACAATATTCATAC
1 AAAAAAATTACAATATTCATAC
*
184700 AAAAAAATTAGAATATTCATAC
1 AAAAAAATTACAATATTCATAC
184722 AAAA
1 AAAA
184726 TTCTAATCCA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
19 17 0.41
22 24 0.59
ACGTcount: A:0.60, C:0.09, G:0.01, T:0.30
Consensus pattern (22 bp):
AAAAAAATTACAATATTCATAC
Found at i:184770 original size:102 final size:100
Alignment explanation
Indices: 184559--184761 Score: 273
Period size: 102 Copynumber: 2.0 Consensus size: 100
184549 ATATTCATAC
* * *
184559 AAAAAAATTACAATATTCATACAAAATTACAAATTCATACAAAAAATTACAATATTCATACAAAA
1 AAAATAATTATAATATTCATAAAAAATTACAAATTCATACAAAAAATTACAATATTCATACAAAA
* * * *
184624 TACTAATGCAAAATTATAAATACAAATTTAATTAT
66 TACTAATGCAAAACTATAAACACAAATATAATAAT
*
184659 AAAATAATTATAATATTCATAAAAAATTACAATATTCATACAAAAAAATTAGAATATTCATACAA
1 AAAATAATTATAATATTCATAAAAAATTACAA-ATTCATAC-AAAAAATTACAATATTCATACAA
* *
184724 AATTCTAAT-CCAAACTATAAACACTAAATATAGATAAT
64 AATACTAATGCAAAACTATAAACAC-AAATATA-ATAAT
184762 TTATAATTAA
Statistics
Matches: 89, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
100 29 0.33
101 20 0.22
102 36 0.40
103 4 0.04
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (100 bp):
AAAATAATTATAATATTCATAAAAAATTACAAATTCATACAAAAAATTACAATATTCATACAAAA
TACTAATGCAAAACTATAAACACAAATATAATAAT
Found at i:184922 original size:17 final size:16
Alignment explanation
Indices: 184885--184924 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
184875 TTCTTTCTTT
184885 CTTCTC-CTTCTTCTC
1 CTTCTCTCTTCTTCTC
184900 C-T-TCTCTTCTTCTC
1 CTTCTCTCTTCTTCTC
184914 CTTTCTCTCTT
1 C-TTCTCTCTT
184925 TTTTTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
13 2 0.10
14 11 0.52
15 1 0.05
16 1 0.05
17 6 0.29
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.57
Consensus pattern (16 bp):
CTTCTCTCTTCTTCTC
Found at i:184924 original size:14 final size:14
Alignment explanation
Indices: 184885--184921 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
184875 TTCTTTCTTT
184885 CTTCTCCTTCTTCTC
1 CTTCT-CTTCTTCTC
184900 CTTCTCTTCTTCTC
1 CTTCTCTTCTTCTC
184914 CTTTCTCT
1 C-TTCTCT
184922 CTTTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (14 bp):
CTTCTCTTCTTCTC
Found at i:185113 original size:27 final size:27
Alignment explanation
Indices: 185051--185116 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
185041 GCAGAGGACA
*
185051 CCATTGGCACCTCTCCATGAGGCTCCT
1 CCATTGGCGCCTCTCCATGAGGCTCCT
* *
185078 TCATTGGCGCCTCTGCATGAGGCTCCT
1 CCATTGGCGCCTCTCCATGAGGCTCCT
185105 CCATTGGCGCCT
1 CCATTGGCGCCT
185117 ACTAGACAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.12, C:0.38, G:0.23, T:0.27
Consensus pattern (27 bp):
CCATTGGCGCCTCTCCATGAGGCTCCT
Found at i:186741 original size:21 final size:20
Alignment explanation
Indices: 186711--186749 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
186701 GAGGAGAATG
*
186711 GAACAAAAAAGAAAGTTAAAA
1 GAACAAAAAA-AAAATTAAAA
*
186732 GAACATAAAAAAAATTAA
1 GAACAAAAAAAAAATTAA
186750 GTTGCTCAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.72, C:0.05, G:0.10, T:0.13
Consensus pattern (20 bp):
GAACAAAAAAAAAATTAAAA
Found at i:188274 original size:2 final size:2
Alignment explanation
Indices: 188267--188293 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
188257 TTGTTTCCTT
188267 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
188294 TATTTTACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:188428 original size:84 final size:85
Alignment explanation
Indices: 188277--188437 Score: 197
Period size: 84 Copynumber: 1.9 Consensus size: 85
188267 TATATATATA
** **
188277 TATATATATATATATATTATTTTACTATATTCTACTGAACACTCGTCATCACTTTAACTTTGGTT
1 TATATATATATATATATTATTTTACTATATTCTACTGAACACTCGTCATCACCCTAACTTTACTT
188342 GTGG-GATCTAAAAACTTTTT
66 GTGGAG-TCTAAAAACTTTTT
* *
188362 TATATATATAT-TTTATTATTTTATTATA-TCTTA-TAGAACACTCGTCATCACCCTAA-TCTTA
1 TATATATATATATATATTATTTTACTATATTC-TACT-GAACACTCGTCATCACCCTAACT-TTA
188423 CTTGTGGAGTCTAAA
63 CTTGTGGAGTCTAAA
188438 CATTCCACTC
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
83 4 0.06
84 50 0.76
85 12 0.18
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.45
Consensus pattern (85 bp):
TATATATATATATATATTATTTTACTATATTCTACTGAACACTCGTCATCACCCTAACTTTACTT
GTGGAGTCTAAAAACTTTTT
Found at i:189164 original size:16 final size:16
Alignment explanation
Indices: 189131--189160 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
189121 TGTGTCTCAT
189131 TTCTTTTATATATTTA
1 TTCTTTTATATATTTA
189147 TTCTTTTA-ATATTT
1 TTCTTTTATATATTT
189161 TATTATACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTTTTATATATTTA
Found at i:189558 original size:16 final size:16
Alignment explanation
Indices: 189537--189579 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
189527 ATTATTTTAA
189537 TTGGTCACTCAACATT
1 TTGGTCACTCAACATT
**
189553 TTGGTCACT-TTCATT
1 TTGGTCACTCAACATT
*
189568 TTGGTCAATCAA
1 TTGGTCACTCAA
189580 TTTTTTTTTA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (16 bp):
TTGGTCACTCAACATT
Found at i:190609 original size:2 final size:2
Alignment explanation
Indices: 190602--190640 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
190592 CCAGAACTTA
190602 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
190641 CAACTAATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:191155 original size:40 final size:39
Alignment explanation
Indices: 191100--191233 Score: 120
Period size: 40 Copynumber: 3.5 Consensus size: 39
191090 AAAAGGTTGC
*
191100 GCCCAGCGCTAGTTGGATTA-ACCGACAATAATAATTGTGA
1 GCCCAGCTCTAGTTGGA-TAGACCGA-AATAATAATTGTGA
* *
191140 GCCCAGCTCTAGTTGGATAGACC-AAA-AAT-ATTTTCA
1 GCCCAGCTCTAGTTGGATAGACCGAAATAATAATTGTGA
* *
191176 -CCCAG-TGCTAGTCGGATATG-CCGATGATAATAATTGTGA
1 GCCCAGCT-CTAGTTGGATA-GACCGA-AATAATAATTGTGA
*
191215 GCCTAGCTCTAGTTGGATA
1 GCCCAGCTCTAGTTGGATA
191234 AACTAACGGT
Statistics
Matches: 76, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
34 1 0.01
35 17 0.22
36 7 0.09
37 4 0.05
38 5 0.07
39 8 0.11
40 33 0.43
41 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (39 bp):
GCCCAGCTCTAGTTGGATAGACCGAAATAATAATTGTGA
Found at i:191255 original size:75 final size:76
Alignment explanation
Indices: 191096--191277 Score: 210
Period size: 75 Copynumber: 2.4 Consensus size: 76
191086 ACAGAAAAGG
* *
191096 TTGCGCCCAGCGCTAGTTGGAT-TAACCGACAATAATAATTGTGAGCCCAGCTCTAGTTGGATAG
1 TTGCGCCCAGCGCTAGTCGGATATAACCGACAATAATAATTGTGAGCCCAGCTCTAGTTGGATAA
191160 ACCAAAAATAT
66 ACCAAAAATAT
* * * * ** *
191171 TTTCACCCAGTGCTAGTCGGATAT-GCCGATGATAATAATTGTGAGCCTAGCTCTAGTTGGATAA
1 TTGCGCCCAGCGCTAGTCGGATATAACCGACAATAATAATTGTGAGCCCAGCTCTAGTTGGATAA
* ***
191235 ACTAACGGTGA-
66 ACCAAAAAT-AT
191246 TTGCGCCCAGCGCTAGTCGGATA-AACCGACAA
1 TTGCGCCCAGCGCTAGTCGGATATAACCGACAA
191278 ATGTGTGCCC
Statistics
Matches: 85, Mismatches: 19, Indels: 6
0.77 0.17 0.05
Matches are distributed among these distances:
75 83 0.98
76 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (76 bp):
TTGCGCCCAGCGCTAGTCGGATATAACCGACAATAATAATTGTGAGCCCAGCTCTAGTTGGATAA
ACCAAAAATAT
Found at i:197744 original size:41 final size:35
Alignment explanation
Indices: 197699--197789 Score: 103
Period size: 35 Copynumber: 2.4 Consensus size: 35
197689 TATGAATGCA
197699 TTTTAATTTTAATATTTTGAATTTCTATGAATTTTTTATAT
1 TTTTAATTTTAA-ATTTTG-ATTT-TAT--ATTTTTTAT-T
*
197740 TTTTAATTTT-AATTTTGATTTTATTTTTTTTATT
1 TTTTAATTTTAAATTTTGATTTTATATTTTTTATT
197774 TTTATAATTTTAAATT
1 TTT-TAATTTTAAATT
197790 ATTTGTTAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
34 4 0.09
35 15 0.32
36 4 0.09
37 3 0.06
38 4 0.09
39 6 0.13
40 1 0.02
41 10 0.21
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.68
Consensus pattern (35 bp):
TTTTAATTTTAAATTTTGATTTTATATTTTTTATT
Found at i:198255 original size:13 final size:13
Alignment explanation
Indices: 198237--198276 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
198227 GTTGACAATC
198237 TATTTGTAACTAA
1 TATTTGTAACTAA
198250 TATTTGTAACTAA
1 TATTTGTAACTAA
*
198263 CT-TTTGTAATTAA
1 -TATTTGTAACTAA
198276 T
1 T
198277 TAGGCCGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 1 0.04
13 23 0.92
14 1 0.04
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.50
Consensus pattern (13 bp):
TATTTGTAACTAA
Found at i:198680 original size:34 final size:37
Alignment explanation
Indices: 198613--198684 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 37
198603 GATCATAACT
198613 TACATAAATACATATCATAACTTACATAACTTACATAA
1 TACATAAATACATATCATAAC-TACATAACTTACATAA
*
198651 TACATAAATATATATCAT-A-T-CATAACTTACATAA
1 TACATAAATACATATCATAACTACATAACTTACATAA
198685 AACTTTGGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
34 14 0.42
35 1 0.03
37 1 0.03
38 17 0.52
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (37 bp):
TACATAAATACATATCATAACTACATAACTTACATAA
Found at i:201226 original size:22 final size:21
Alignment explanation
Indices: 201180--201226 Score: 51
Period size: 22 Copynumber: 2.1 Consensus size: 21
201170 ATAATATAGA
*
201180 TTTAATAAATGCAGAAAAATCT
1 TTTAATAAATGAAGAAAAA-CT
201202 TTTAATAAATAGAAAGAAAAA-T
1 TTTAATAAAT-G-AAGAAAAACT
201224 TTT
1 TTT
201227 GAATTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 14 0.64
23 1 0.05
24 7 0.32
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.34
Consensus pattern (21 bp):
TTTAATAAATGAAGAAAAACT
Done.