Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold872
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: 4866
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Found at i:381 original size:177 final size:177
Alignment explanation
Indices: 134--804 Score: 1155
Period size: 177 Copynumber: 3.8 Consensus size: 177
124 ATTCACCCTC
* * * * * * * ** *
134 TTCGATCTTCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTTAACCTACACCACTACT-A
1 TTCGATCTGCTTCACTACTGTTTAGGGTGACAGAATCTGTAATCTTCAATCAATTCCACTA-TGG
* * * * *
198 CTTAGGGTGATATGACTAATGGCTTAAATTTGCTTCTCCACTGTATTGGGAAAATAAGATTCATC
65 CTTAGGGAGATAGGGCTAATGGCTAAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATC
263 ATATTCGATCTGCTTCTCTACTGTATTAGGAAATTGATATTCATCATA
130 ATATTCGATCTGCTTCTCTACTGTATTAGGAAATTGATATTCATCATA
311 TTCGATCTGCTTCACTACTGTTTAGGGTGACAGAATCTGTAATCTTCAATCAATTCCACTATGGC
1 TTCGATCTGCTTCACTACTGTTTAGGGTGACAGAATCTGTAATCTTCAATCAATTCCACTATGGC
376 TTAGGGAGATAGGGCTAATGGCTAAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCA
66 TTAGGGAGATAGGGCTAATGGCTAAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCA
*
441 TATTCGATCTGCTTCTCTACTGTATTAGGAAATTGATATTCGTCATA
131 TATTCGATCTGCTTCTCTACTGTATTAGGAAATTGATATTCATCATA
488 TTCGATCTGCTTCACTACTGTTTAGGGTGACAGAATCTGTAATCTTCAATCAATTCCACTATGGC
1 TTCGATCTGCTTCACTACTGTTTAGGGTGACAGAATCTGTAATCTTCAATCAATTCCACTATGGC
553 TTAGGGAGATAGGGCTAATGGCTAAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCA
66 TTAGGGAGATAGGGCTAATGGCTAAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCA
618 TATTCGATCTGCTTCTCTACTGTATTAGGAAATTGATATTCATCATA
131 TATTCGATCTGCTTCTCTACTGTATTAGGAAATTGATATTCATCATA
*
665 TTCGATCTGCTTCACTACTATTTAGGGTGACAGAATCTGTAATCTTCAATCAATTCCACTATGGC
1 TTCGATCTGCTTCACTACTGTTTAGGGTGACAGAATCTGTAATCTTCAATCAATTCCACTATGGC
*
730 TTAGGGAGATAGGGCTAATGGCTAAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCA
66 TTAGGGAGATAGGGCTAATGGCTAAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCA
*
795 TCTTCGATCT
131 TATTCGATCT
805 ACTCCAATAC
Statistics
Matches: 473, Mismatches: 20, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
176 1 0.00
177 472 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (177 bp):
TTCGATCTGCTTCACTACTGTTTAGGGTGACAGAATCTGTAATCTTCAATCAATTCCACTATGGC
TTAGGGAGATAGGGCTAATGGCTAAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCA
TATTCGATCTGCTTCTCTACTGTATTAGGAAATTGATATTCATCATA
Found at i:452 original size:45 final size:45
Alignment explanation
Indices: 402--513 Score: 145
Period size: 45 Copynumber: 2.5 Consensus size: 45
392 AATGGCTAAA
*
402 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCATATTCG
1 ATCTGCTTCTCCACTGTATTAGGAAAATAAGATTCATCATATTCG
* * * * *
447 ATCTGCTTCTCTACTGTATTAGGAAATTGATATTCGTCATATTCG
1 ATCTGCTTCTCCACTGTATTAGGAAAATAAGATTCATCATATTCG
* *
492 ATCTGCTTCACTACTGT-TTAGG
1 ATCTGCTTCTCCACTGTATTAGG
514 GTGACAGAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
44 5 0.08
45 55 0.92
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (45 bp):
ATCTGCTTCTCCACTGTATTAGGAAAATAAGATTCATCATATTCG
Found at i:629 original size:45 final size:45
Alignment explanation
Indices: 579--677 Score: 153
Period size: 45 Copynumber: 2.2 Consensus size: 45
569 AATGGCTAAA
*
579 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATCATATTCG
1 ATCTGCTTCTCCACTGTATTAGGAAAATAAGATTCATCATATTCG
* * * *
624 ATCTGCTTCTCTACTGTATTAGGAAATTGATATTCATCATATTCG
1 ATCTGCTTCTCCACTGTATTAGGAAAATAAGATTCATCATATTCG
669 ATCTGCTTC
1 ATCTGCTTC
678 ACTACTATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.39
Consensus pattern (45 bp):
ATCTGCTTCTCCACTGTATTAGGAAAATAAGATTCATCATATTCG
Found at i:683 original size:45 final size:45
Alignment explanation
Indices: 228--336 Score: 157
Period size: 45 Copynumber: 2.4 Consensus size: 45
218 GGCTTAAATT
* *
228 TGCTTCTCCACTGTATTGGGAAAATAAGATTCATCATATTCGATC
1 TGCTTCTCTACTGTATTAGGAAAATAAGATTCATCATATTCGATC
* * *
273 TGCTTCTCTACTGTATTAGGAAATTGATATTCATCATATTCGATC
1 TGCTTCTCTACTGTATTAGGAAAATAAGATTCATCATATTCGATC
*
318 TGCTTCACTACTGT-TTAGG
1 TGCTTCTCTACTGTATTAGG
337 GTGACAGAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 5 0.09
45 53 0.91
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (45 bp):
TGCTTCTCTACTGTATTAGGAAAATAAGATTCATCATATTCGATC
Found at i:760 original size:132 final size:132
Alignment explanation
Indices: 624--4705 Score: 3865
Period size: 132 Copynumber: 30.9 Consensus size: 132
614 ATCATATTCG
* * * * * * * **
624 ATCTGCTTCTCTACTGTATTAGGAAATTGATATTCATCATATTCGATCTGCTTCACTACTATTTA
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTA
* * * * * *
689 GGGTGACAGAATCTGTAATCTTCAATCAATTCCACTA-TGGCTTAGGGAGATAGGGCTAATGGCT
66 GGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT-GCTTAGGGTGATAGGACTAATGGCT
*
753 AAA
130 TAA
* * *
756 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTACTCCAATACTGCTTA
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTA
* * * *
821 GGGTGACAGAATCTGCAATCTTCAACCTAC-CGATCTACTGCTCAGGGAGATTGGACTAATGGCT
66 GGGTGACAGAATCTGCAATCTTCAACCTACTCCA-CTACTGCTTAGGGTGATAGGACTAATGGCT
*
885 CAA
130 TAA
* * * * * * ** *
888 ATCTGCTTCTCCACTATCTTGAGAAGATAAGAATCACCATCTTCAATCCACTCCACTACTGCTTA
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTA
* *
953 GGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTACGGTGATAGTACTAATGGCTT
66 GGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTT
1018 AA
131 AA
* * * * *
1020 ATCTGCTTCTCCACTGTATTGGGAAGATAGGATTGACCATCGTCGATCTAC-TCTACTACTGCTT
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTC-ACTACTGCTT
* * * * *
1084 AGGGTGACAGAATCTGCAATCTTTAACCTACTCCACTACTGCTTTGGGTGATAGCACAAATGGTT
65 AGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCT
1149 TAA
130 TAA
* * * **
1152 ATCTGCTTCTCCACTGTATTGGGAAAATAGGATTCATCATATTTAATCTGCTTCACTACTGCTTA
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTA
* * * * *
1217 GGGTGACAGAATCTGCAATCTTCAATCGACTCCACTACTGGTTAGGGAGATTGGACTAATGGCTT
66 GGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTT
1282 AA
131 AA
* * * *
1284 ATATGCTTC-CCTACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTACTCCACTACTGCTT
1 ATCTGCTTCTCC-ACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTCACTACTGCTT
* * * * * * *
1348 GGGGTGACAGAATCTGCAATCTTCAATCGACTCCACTACTGGTAAGGGAGATTGGACTAATGGCT
65 AGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCT
1413 TAA
130 TAA
* ** * *
1416 ATCTACTTCTCCACTGTATTGAAAAAATAACATTCACCATCTTCGATCTGCATCACTACTAG-TT
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTCACTACT-GCTT
* * * * *
1480 AGGGTGACAGAATCTGTAATCTTCAACCAATTCCACTA-TGGCTTAGGGAGATAGAACTAATGGC
65 AGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT-GCTTAGGGTGATAGGACTAATGGC
1544 TTAA
129 TTAA
* ** * * * *
1548 ATCTACTTCTCCACTGTATTGAAAAAATAACATTCACCATCTTCGATCTACTCCACTACAGCTTA
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTA
* * * *
1613 GGATGACAGAGTCTGCAATCTTCAGCCTATTCCACTACTGCTTAGGGTGATAGGACTAATGGCTT
66 GGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTT
1678 AA
131 AA
* * * * * *
1680 AACTGCTTCTCCACTATATTGGGAAGATAACATTCACCATATTCGATCTGCTCCACTACTGCTTA
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTA
*
1745 GGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATTGGACTAATGGCTT
66 GGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTT
1810 AA
131 AA
* * * * * *
1812 ATCTGCTTCTCCACTATATTGGGAAGATAAGATTCATCATATTCGATCTGCTCCACTACGGCTTA
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTA
* * * * * * *
1877 GGTTGACAAAATCTGGAATCTTCAACCAATTCCAC-AATGGCTTAGGGAGATAGGACTAATGGCT
66 GGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT-GCTTAGGGTGATAGGACTAATGGCT
1941 TAA
130 TAA
* *
1944 ATCTGCTTCTCCACTGTATTGTGAAAATAAGATTCACCATCTTCGATCT-ATTCCAAC-ACTGCT
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTT-C-ACTACTGCT
*
2007 TAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATGGC
64 TAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGC
*
2072 ATAA
129 TTAA
* * * * *
2076 ATCTACTTCTCCACTGTATTGGGAAAATAAGATTCACCAACTTCGATCTACTCCACTACAGCTTA
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTA
*
2141 GGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAAGGTGATAGGACTAATGGCTT
66 GGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTT
2206 AAA
131 -AA
* * * *
2209 TATGCATGCTTCTCCACTATATTGGGAAGATAAGATTCACCATATTCGATCTGCTGCACTACTGC
1 -AT-C-TGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTCACTACTGC
* * *
2274 TTAGGGTGACAGAATCTGGAATCTTCAACCAACTCCACTACTGCTTAGGGTGATATGACTAATGG
63 TTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGG
2339 CTTAA
128 CTTAA
* * *
2344 ATCTGCTTCTCTACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTA
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTA
** * * *
2409 TAGTGACAGAATTTGCAATCTTCAACCAACTCCAGTACTGCTTAGGGTGATAGGACTAATGGCTT
66 GGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTT
2474 AA
131 AA
* * * * *
2476 ATCTGCTTCTCCACTGTATTGGGAAGATAGGATTCCCCATCGTCGATCTGCTCCACTACTGCTTA
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTA
* * * * * * * * * * **
2541 GGGTGATAGGA-CT--AATGGCTTAAATCTGCTTCTCCACTG-TATTGGGAAGATAGGATTCCCC
66 GGGTGACAGAATCTGCAAT--CTTCAACCTACTCCACTACTGCT-TAGGG-TGATAGGA---CTA
* **
2602 AT--CGTCG
124 ATGGCTTAA
* * * * ** * * ** * *
2609 ATCTGCTCCACTACTGCT-TAGGG-TGATAGGACT-A--ATGGCTTAAATCTGCTTCTCCACTG-
1 ATCTGCTTCTCCACTG-TATTGGGAAAATAAGATTCACCAT--CTTCGATCTGCTTCACTACTGC
* * * * * * * * * *
2668 TATTGGGAAGATAGGAT-TCCCCATCGTCGATCTGCTCCACTACTGCTTAGGGTGATAGGACTAA
63 T-TAGGG-TGACAGAATCT-GCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAA
2732 TGGCTTAA
125 TGGCTTAA
* * * * *
2740 ATCTGCTTCTCCACTGTATTGGGAAGATAGGATTCCCCATCGTCGATCTGCTCCACTACTGCTTA
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTA
* * * * * * * * * * **
2805 GGGTGATAGGA-CT--AATGGCTTAAATCTGCTTCTCCACTG-TATTGGGAAGATAGGATTCCCC
66 GGGTGACAGAATCTGCAAT--CTTCAACCTACTCCACTACTGCT-TAGGG-TGATAGGA---CTA
* **
2866 AT--CGTCG
124 ATGGCTTAA
* * * * ** * * ** * * * *
2873 ATCTGCTCCACTACTGCT-TAGGG-TGATAGGACT-A--ATGGCTTAAATCCGCTTCTCCACCG-
1 ATCTGCTTCTCCACTG-TATTGGGAAAATAAGATTCACCAT--CTTCGATCTGCTTCACTACTGC
* ** * * * * * * * * *
2932 TATTGCGAAGATAAGATTC-ACCATCTTCGATCTGCAT-CACTACTGCTTAGGGTGACAGAATCT
63 T-TAG-GGTGA-CAGAATCTGCAATCTTCAACCTAC-TCCACTACTGCTTAGGGTGATAGGA-CT
*
2995 ACAAT--CTTCA
123 --AATGGCTTAA
* * * * * ** * * ** * * *
3005 A-CCGACTCCACTACTGCT-TAGGG-TGATAGGACT-A--ATGGCTTAAATGTGCTTCTCCACTG
1 ATCTG-CTTCTCCACTG-TATTGGGAAAATAAGATTCACCAT--CTTCGATCTGCTTCACTACTG
* * * * * * * * *
3064 -TATTGGGAAGATAGGAT-T-CACCATCGTCGATCTGCTCCACTACTTCTTA-GGTAGATTA-GA
62 CT-TAGGG-TGACAGAATCTGCA--ATCTTCAACCTACTCCACTACTGCTTAGGGT-GA-TAGGA
3124 CTAATGGCTTAA
121 CTAATGGCTTAA
* * * *
3136 ATCTGCTTCTCCACTGTATTGGGAAAGTAAGATTCATCATATTCGATCTGCTTCACTACTGTTTA
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTA
* * * * * * *
3201 CGGTGACAGAATCTGCAATCTTCAACCAATTCCACTA-TGGCTTAAGGTGATAGAACAAATAGCT
66 GGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT-GCTTAGGGTGATAGGACTAATGGCT
3265 TAA
130 TAA
* * * *
3268 ATCTGCTTCTCCACTGTATTGGGAAAGTAAGATTCATCATATTCGATCTGCTTCACTACTGTTTA
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTA
* * * * * * *
3333 CGGTGACAGAATCTGCAATCTTCAACCAATTCCACTA-TGGCTTAAGGTGATAGAACAAATAGCT
66 GGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT-GCTTAGGGTGATAGGACTAATGGCT
3397 TAA
130 TAA
* * *
3400 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCT-ATTCCAATACTACTT
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTT-CACTACTGCTT
* * * * * *
3464 AGTGTGACAGAATCAGCAATATTCAACCTACTCCACTACTGCTTATGGAGATTGGACTAATGGCT
65 AGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCT
*
3529 GAA
130 TAA
* * * * * *
3532 ATCTGCTTCTCCACTATCTTGAGAAGATAAGAATCACCATCTTCGATCCGC-TCAACTACTGCTT
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTC-ACTACTGCTT
** *
3596 AGGGTGACAGAATCTGCAATCTAAAACCTACTCCACTACTGCTTAGGGTGATATGACTAATGGCT
65 AGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCT
3661 TAA
130 TAA
** * * *
3664 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCATTATATTCAATCTGCTTCACTACTGTTTA
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTA
* * * * * *
3729 GGGTGACCGAATCTGTAATCTTCAACCAATTCCACT-GTGGCTTAGGGAGATAGGACTAATGGCT
66 GGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT-GCTTAGGGTGATAGGACTAATGGCT
3793 TAA
130 TAA
* *
3796 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTACTCCAAC-ACTGCTT
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTC-ACTACTGCTT
* * * * ** *
3860 AGGCTGACAGAATCTACAATCTTCAACCTACTGCTCTACTGCTTAGGAAGATTGGACTAATGGCT
65 AGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCT
*
3925 GAA
130 TAA
* * * * * * * * * *
3928 ATATGCTTCTCCACTATCTTGAGAAGATAAGAATGACCATCTTCGACCCGCTCCACTACTGCTTA
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTA
3993 GGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTT
66 GGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTT
4058 AA
131 AA
* * * *
4060 ATCTGCTACTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGGTCCACTACTGCTTA
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTA
* * * * * * * *
4125 GGGTG-CCGAAATCTGTAATATTTAACATACACCACTACTGCTTAGGGCGATATGACTAATGGCT
66 GGGTGACAG-AATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCT
4189 TAA
130 TAA
* * * * *
4192 ATCTGCTTCACCACTGTATTGGCAAAATAAGATTCATCATATTCGATCTGCTTCACTACTG-TCA
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTCACTACTGCT-T
* ** * * * * *
4256 AGAGTGACAGAATCTATAATCTTTAACCAATTCTACTA-TGGCTTAGGGAGATAGGACTAATGGC
65 AGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT-GCTTAGGGTGATAGGACTAATGGC
4320 TTAA
129 TTAA
* ** *
4324 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCCATC-AATTCCAATACTGCTT
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTT-CACTACTGCTT
* * *
4388 AGGGTGATAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATTGGACTAATGGCT
65 AGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCT
*
4453 GAA
130 TAA
* * * * * * * *
4456 ATTTGCTTCTCCACTTTCTTGAGAAGATAAGACTCACCATCTTCGATCCGCTCCACTACTGCTTA
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTA
* * *
4521 AGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCATAGGGTGATAGGACTAATGACTT
66 GGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTT
4586 AA
131 AA
* * ** * *
4588 ATCTGCTTCTCCTCTGTATTGCGAGGATAAGATTCACCATATTCGATCTGCATCACTACTGCTTA
1 ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTA
*
4653 GGGTGACAGAATCTGCAATCTTCAA-CTGACTCCACTACTGCATAGGGTGATAG
66 GGGTGACAGAATCTGCAATCTTCAACCT-ACTCCACTACTGCTTAGGGTGATAG
4706 AATCTGCAAT
Statistics
Matches: 3314, Mismatches: 529, Indels: 214
0.82 0.13 0.05
Matches are distributed among these distances:
129 15 0.00
130 8 0.00
131 148 0.04
132 2848 0.86
133 149 0.04
134 14 0.00
135 17 0.01
136 115 0.03
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (132 bp):
ATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTTCACTACTGCTTA
GGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTT
AA
Found at i:1133 original size:44 final size:44
Alignment explanation
Indices: 926--1134 Score: 142
Period size: 44 Copynumber: 4.8 Consensus size: 44
916 AAGAATCACC
926 ATCTTCAATCC-ACTCCACTACTGCTTAGGGTGACAGAATCTGCA
1 ATCTTCAA-CCTACTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * *
970 ATCTTCAACCTACTCCACTACTGCTTACGGTGATAGTA-CT--A
1 ATCTTCAACCTACTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * * * * * * * * *
1011 ATGGCTTAAATCTGCTTCTCCACTG-TATTGGGAAGATAGGAT-TGACC
1 AT--CTTCAACCTACTCCACTACTGCT-TAGGG-TGACAGAATCTG-CA
* * * *
1058 ATCGTCGATCTACTCTACTACTGCTTAGGGTGACAGAATCTGCA
1 ATCTTCAACCTACTCCACTACTGCTTAGGGTGACAGAATCTGCA
* *
1102 ATCTTTAACCTACTCCACTACTGCTTTGGGTGA
1 ATCTTCAACCTACTCCACTACTGCTTAGGGTGA
1135 TAGCACAAAT
Statistics
Matches: 121, Mismatches: 33, Indels: 22
0.69 0.19 0.12
Matches are distributed among these distances:
41 3 0.02
42 1 0.01
43 22 0.18
44 73 0.60
45 19 0.16
46 1 0.01
47 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (44 bp):
ATCTTCAACCTACTCCACTACTGCTTAGGGTGACAGAATCTGCA
Found at i:2545 original size:88 final size:88
Alignment explanation
Indices: 2438--2986 Score: 1019
Period size: 88 Copynumber: 6.2 Consensus size: 88
2428 CTTCAACCAA
*
2438 CTCCAGTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
2503 TAGGATTCCCCATCGTCGATCTG
66 TAGGATTCCCCATCGTCGATCTG
2526 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
2591 TAGGATTCCCCATCGTCGATCTG
66 TAGGATTCCCCATCGTCGATCTG
2614 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
2679 TAGGATTCCCCATCGTCGATCTG
66 TAGGATTCCCCATCGTCGATCTG
2702 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
2767 TAGGATTCCCCATCGTCGATCTG
66 TAGGATTCCCCATCGTCGATCTG
2790 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
2855 TAGGATTCCCCATCGTCGATCTG
66 TAGGATTCCCCATCGTCGATCTG
* * *
2878 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCCGCTTCTCCACCGTATTGCGAAGA
1 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
* * *
2943 TAAGATTCACCATCTTCGATCTG
66 TAGGATTCCCCATCGTCGATCTG
2966 CAT-CACTACTGCTTAGGGTGA
1 C-TCCACTACTGCTTAGGGTGA
2987 CAGAATCTAC
Statistics
Matches: 453, Mismatches: 7, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
88 452 1.00
89 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.30
Consensus pattern (88 bp):
CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
TAGGATTCCCCATCGTCGATCTG
Found at i:3025 original size:220 final size:219
Alignment explanation
Indices: 2790--3338 Score: 791
Period size: 220 Copynumber: 2.5 Consensus size: 219
2780 CGTCGATCTG
2790 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
*
2855 TAGGATTCCCCATCGTCGATCTGCTCCACTACTGCTTAGGGTGA-TAGGACTAATGGCTTAAATC
66 TAGGATTCACCATCGTCGATCTGCTCCACTACTGCTTA-GGTGATTA-GACTAATGGCTTAAATC
* *
2919 CGCTTCTCCACCGTATTGCG-AAGATAAGATTCACCATCTTCGATCTGCATCACTACTGCTTAGG
129 CGCTTCTCCACCGTATTGCGAAAG-TAAGATTCACCATATTCGATCTGCATCACTACTGCTTACG
*
2983 GTGACAGAATCTACAATCTTCAACCGA
193 GTGACAGAATCTACAATCTTCAACCAA
*
3010 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATGTGCTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
* *
3075 TAGGATTCACCATCGTCGATCTGCTCCACTACTTCTTAGGTAGATTAGACTAATGGCTTAAATCT
66 TAGGATTCACCATCGTCGATCTGCTCCACTACTGCTTAGGT-GATTAGACTAATGGCTTAAATCC
* * * * *
3140 GCTTCTCCACTGTATTGGGAAAGTAAGATTCATCATATTCGATCTGCTTCACTACTGTTTACGGT
130 GCTTCTCCACCGTATTGCGAAAGTAAGATTCACCATATTCGATCTGCATCACTACTGCTTACGGT
*
3205 GACAGAATCTGCAATCTTCAACCAA
195 GACAGAATCTACAATCTTCAACCAA
* * * * *
3230 TTCCACTA-TGGCTTAAGGTGATAGAACAAATAGCTTAAATCTGCTTCTCCACTGTATTGGGAA-
1 CTCCACTACT-GCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAG
* * ** * *
3293 AGTAAGATTCATCATATTCGATCTGCTTCACTACTGTTTACGGTGA
65 A-TAGGATTCACCATCGTCGATCTGCTCCACTACTGCTTA-GGTGA
3339 CAGAATCTGC
Statistics
Matches: 297, Mismatches: 26, Indels: 12
0.89 0.08 0.04
Matches are distributed among these distances:
219 5 0.02
220 284 0.96
221 8 0.03
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (219 bp):
CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
TAGGATTCACCATCGTCGATCTGCTCCACTACTGCTTAGGTGATTAGACTAATGGCTTAAATCCG
CTTCTCCACCGTATTGCGAAAGTAAGATTCACCATATTCGATCTGCATCACTACTGCTTACGGTG
ACAGAATCTACAATCTTCAACCAA
Found at i:3159 original size:88 final size:88
Alignment explanation
Indices: 3010--3206 Score: 265
Period size: 88 Copynumber: 2.2 Consensus size: 88
3000 CTTCAACCGA
*
3010 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATGTGCTTCTCCACTGTATTGGG-AAG
1 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAG
* *
3074 ATAGGATTCACCATCGTCGATCTG
66 -TAAGATTCACCATAGTCGATCTG
*
3098 CTCCACTACTTCTTA-GGTAGATTA-GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAA
1 CTCCACTACTGCTTAGGGT-GA-TAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAA
* *
3161 AGTAAGATTCATCATATTCGATCTG
64 AGTAAGATTCACCATAGTCGATCTG
* * *
3186 CTTCACTACTGTTTACGGTGA
1 CTCCACTACTGCTTAGGGTGA
3207 CAGAATCTGC
Statistics
Matches: 96, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
87 3 0.03
88 85 0.89
89 8 0.08
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (88 bp):
CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAAG
TAAGATTCACCATAGTCGATCTG
Found at i:4708 original size:44 final size:44
Alignment explanation
Indices: 4641--4749 Score: 166
Period size: 44 Copynumber: 2.5 Consensus size: 44
4631 CGATCTGCAT
*
4641 CACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAA-CTGACTC
1 CACTACTGCTTAGGGTGATAGAATCTGCAATCTTCAACCT-ACTC
* *
4685 CACTACTGCATAGGGTGATAGAATCTGCAATCTTTAACCTACTC
1 CACTACTGCTTAGGGTGATAGAATCTGCAATCTTCAACCTACTC
*
4729 CACTACTGCTTTGGGTGATAG
1 CACTACTGCTTAGGGTGATAG
4750 GACTAATGGC
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
44 57 0.97
45 2 0.03
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (44 bp):
CACTACTGCTTAGGGTGATAGAATCTGCAATCTTCAACCTACTC
Found at i:4730 original size:176 final size:176
Alignment explanation
Indices: 4506--4866 Score: 526
Period size: 176 Copynumber: 2.1 Consensus size: 176
4496 CTTCGATCCG
*
4506 CTCCACTACTGCTTAAGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCATAGGGTGA
1 CTCCACTACTGCATAAGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCATAGGGTGA
* * ** *
4571 TAGGACTAATGACTTAAATCTGCTTCTCCTCTGTATTGCGAGGATAAGATTCACCA-TATTCGAT
66 TAGGACTAATGACTTAAATCTACTTCTCCACTGTATTGCGAAAATAAGATTCACCATTATTAG-T
* *
4635 CTGCATCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACTGA
130 CTGCATCACTACTGCTTAGGATGACAGAATCTGCAATCTTCAACCGA
* * * * *
4682 CTCCACTACTGCATAGGGTGATAGAATCTGCAATCTTTAACCTACTCCACTACTGCTTTGGGTGA
1 CTCCACTACTGCATAAGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCATAGGGTGA
* * ** *
4747 TAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTGGGAAAATAAGATTCGTCATTCTTAGTC
66 TAGGACTAATGACTTAAATCTACTTCTCCACTGTATTGCGAAAATAAGATTCACCATTATTAGTC
* *
4812 TTCTTCACTACTGCTTAGGATGACAGAATCTGCAATCTTCAACCGA
131 TGCATCACTACTGCTTAGGATGACAGAATCTGCAATCTTCAACCGA
4858 CTCCACTAC
1 CTCCACTAC
Statistics
Matches: 164, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
176 160 0.98
177 4 0.02
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (176 bp):
CTCCACTACTGCATAAGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCATAGGGTGA
TAGGACTAATGACTTAAATCTACTTCTCCACTGTATTGCGAAAATAAGATTCACCATTATTAGTC
TGCATCACTACTGCTTAGGATGACAGAATCTGCAATCTTCAACCGA
Done.